Current Developments in Biotechnology and Bioengineering: Filamentous Fungi Biorefinery 0323918727, 9780323918725

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Current Developments in Biotechnology and Bioengineering

Series Editor: Professor Ashok Pandey Centre for Innovation and Translational Research CSIR-Indian Institute of Toxicology Research Lucknow, India & Sustainability Cluster School of Engineering University of Petroleum and Energy Studies Dehradun, India

Current Developments in Biotechnology and Bioengineering

Filamentous Fungi Biorefinery

Edited by Mohammad J. Taherzadeh Swedish Centre for Resource Recovery, University of Bora˚s, Bora˚s, Sweden

Jorge A. Ferreira Swedish Centre for Resource Recovery, University of Bora˚s, Bora˚s, Sweden

Ashok Pandey Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, India

Elsevier Radarweg 29, PO Box 211, 1000 AE Amsterdam, Netherlands The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States Copyright © 2023 Elsevier Inc. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions. This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein). Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary. Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility. To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein. ISBN: 978-0-323-91872-5 For information on all Elsevier publications visit our website at https://www.elsevier.com/books-and-journals

Publisher: Susan Dennis Editorial Project Manager: Helena Beauchamp Production Project Manager: Kiruthika Govindaraju Cover Designer: Matthew Limbert Typeset by STRAIVE, India

Contributors Ruchi Agrawal The Energy and Resources Institute, TERI Gram, Gwal Pahari, Haryana, India Hamid Amiri Department of Biotechnology, Faculty of Biological Science and Technology; Environmental Research Institute, University of Isfahan, Isfahan, Iran K. Amulya Bioengineering and Environmental Sciences, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology, Hyderabad, India Elisabet Aranda Institute of Water Research; Department of Microbiology, University of Granada, Granada, Spain Mohammadtaghi Asadollahzadeh Swedish Centre for Resource Recovery, University of Bora˚s, Bora˚s, Sweden Aparna Banerjee Centro de investigacio´n en Estudios Avanzados del Maule (CIEAM), Vicerrectorı´a de Investigacio´n Y Posgrado, Universidad Cato´lica del Maule, Talca, Chile Parameswaran Binod Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, India Kamalpreet Kaur Brar Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, ON; Industrial Waste Technology Center, Abitibi Temiscamingue, QC, Canada € lru Bulkan Swedish Centre for Resource Recovery, University of Bora˚s, Bora˚s, Gu Sweden Gustavo Cabrera-Barjas Universidad de Concepcio´n, Unidad de Desarrollo Tecnolo´gico (UDT), Coronel, Chile Marta Cebria´n AZTI, Food Research, Basque Research and Technology Alliance (BRTA), Parque Tecnolo´gico de Bizkaia, Derio, Bizkaia, Spain Chiu-Wen Chen Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan

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Eduardo Coelho CEB—Centre of Biological Engineering, University of Minho, Braga, Portugal ´ ngeles de Paz Institute of Water Research, University of Granada, Granada, Gabriela A Spain dric Delattre Universite  Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Ce Pascal, Clermont-Ferrand; Institut Universitaire de France (IUF), Paris, France Ratih Dewanti-Hariyadi Department of Food Science and Technology, IPB University, Bogor, Indonesia Lucı´lia Domingues CEB—Centre of Biological Engineering, University of Minho, Braga, Portugal Cheng-Di Dong Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan  Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal Dubessay Universite Pascal, Clermont-Ferrand, France  Chemistry and Biotechnology of Natural Products (CHEMBIOPRO), Laurent Dufosse University of Reunion Island, ESIROI Food Science, Saint-Denis Cedex 9, Reunion Island, France Jorge A. Ferreira Swedish Centre for Resource Recovery, University of Bora˚s, Bora˚s, Sweden Shakuntala Ghorai Department of Microbiology, Raidighi College, Raidighi, India Daniel G. Gomes CEB—Centre of Biological Engineering, University of Minho, Braga, Portugal Sharareh Harirchi Swedish Centre for Resource Recovery, University of Bora˚s, Bora˚s, Sweden; Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran Jone Ibarruri AZTI, Food Research, Basque Research and Technology Alliance (BRTA), Parque Tecnolo´gico de Bizkaia, Derio, Bizkaia, Spain Sajjad Karimi Swedish Centre for Resource Recovery, University of Bora˚s, Bora˚s, Sweden Vinod Kumar School of Water, Energy, and Environment, Cranfield University, Cranfield, United Kingdom Patrik Roland Lennartsson Swedish Centre for Resource Recovery, University of Bora˚s, Bora˚s, Sweden Hanifah Nuryani Lioe Department of Food Science and Technology, IPB University, Bogor, Indonesia

Contributors

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Sara Magdouli Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, ON; Industrial Waste Technology Center, Abitibi Temiscamingue, QC, Canada Manikharda Department of Food and Agricultural Product Technology, Universitas Gadjah Mada, Yogyakarta, Indonesia  Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Philippe Michaud Universite Pascal, Clermont-Ferrand, France Marzieh Mohammadi Swedish Centre for Resource Recovery, University of Bora˚s, Bora˚s, Sweden Rafael Leo´n Morcillo Institute of Water Research, University of Granada, Granada, Spain Soumya Mukherjee University of Toledo, Toledo, OH, United States Vivek Narisetty School of Water, Energy, and Environment, Cranfield University, Cranfield, United Kingdom Seyyed Vahid Niknezhad Burn and Wound Healing Research Center; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran Ashok Pandey Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow; Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, India Mohsen Parchami Swedish Centre for Resource Recovery, University of Bora˚s, Bora˚s, Sweden Anil Kumar Patel Department of Marine Environmental Engineering; Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan  Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Guillaume Pierre Universite Pascal, Clermont-Ferrand, France Endang Sutriswati Rahayu Department of Food and Agricultural Product Technology, Universitas Gadjah Mada, Yogyakarta, Indonesia G. Renuka Department of Microbiology, Pingle Government Degree College for Women, Warangal, India Saddys Rodriguez-Llamazares Centro de Investigacio´n de Polı´meros Avanzados (CIPA), Edificio Laboratorio CIPA, Concepcio´n, Chile Neda Rousta Swedish Centre for Resource Recovery, University of Bora˚s, Bora˚s, Sweden

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Taner Sar Swedish Centre for Resource Recovery, University of Bora˚s, Bora˚s, Sweden Behzad Satari Department of Food Technology, College of Aburaihan, University of Tehran, Tehran, Iran Ulises Conejo Saucedo Institute of Water Research, University of Granada, Granada, Spain Zohresadat Shahryari Swedish Centre for Resource Recovery, University of Bora˚s, Bora˚s, Sweden; Avidzyme Company, Shiraz, Iran Pooja Sharma Environmental Research Institute, National University of Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore, Singapore Rui Silva CEB—Centre of Biological Engineering, University of Minho, Braga, Portugal Raveendran Sindhu Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, India Reeta Rani Singhania Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan Mohammad J. Taherzadeh Swedish Centre for Resource Recovery, University of Bora˚s, Bora˚s, Sweden  A. Teixeira CEB—Centre of Biological Engineering, University of Minho, Braga, Jose Portugal Sunita Varjani Gujarat Pollution Control Board, Gandhinagar, Gujarat, India S. Venkata Mohan Bioengineering and Environmental Sciences, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology, Hyderabad, India Rachma Wikandari Department of Food and Agricultural Product Technology, Universitas Gadjah Mada, Yogyakarta, Indonesia Akram Zamani Swedish Centre for Resource Recovery, University of Bora˚s, Bora˚s, Sweden

Preface Advances in Filamentous Fungi Biorefinery is a book in the Elsevier series on Current Developments in Biotechnology and Bioengineering (Editor-in-Chief: Ashok Pandey). This book explores various fundamental and industrial aspects of filamentous fungi for the manufacture of different products used in our society. Fungi are part of the ecosystem, and the world would look totally different without them. Most people know only mushrooms and their fruiting bodies as fungi. However, the main fungal biomass is their filaments, which can have many applications. Filamentous fungi can grow on a large variety of materials that contain carbohydrates, proteins, fats, etc., by degrading the macromolecules and then assimilating the monomers to grow and produce various enzymes and metabolites. This means that there are a large number of substrates on which to grow fungi, from agricultural and forest residuals to industrial residuals and products, to household wastes and wastewaters. Depending on the ecosystem and the environmental or cultivation conditions, fungi can grow in various morphologies, and many fungal strains are dimorphic, meaning that they can grow both like yeast and filaments. In addition, they can grow in various environmental conditions, such as aerobic or anaerobic. They adapt their enzyme machinery as required to these conditions, producing a variety of metabolites that are necessary for the fungi to grow. As fungi grow on a large number of substrates, they can produce various extracellular enzymes such as hydrolytic enzymes to degrade biopolymers. Therefore, fungi are an industrial source of enzyme production. Ultimately, we should not forget that the only goal of fungi is to grow. However, in certain conditions they can produce, for example, enzymes and/or various metabolites, which can be used as products. Bearing in mind the single goal of fungi, one of their major products is always fungal biomass or mycelium. This biomass normally contains protein, fat, and other biopolymers such as chitosan or beta-glucan in its cell wall, and a variety of bioactive compounds. As a result, the biomass of many filamentous fungi can be a good source for food and feed. Some of these fungi, particularly among the zygomycetes and ascomycetes, are edible and can be used for different food preparations such as tempeh, oncom, and koji. However, there is also an interest nowadays in developing new food and feed such as fish feed from fungi as an environmentally friendly and healthy alternative to meat, chicken, or even soy-based vegetarian products, for example. However, as some fungi produce mycotoxins, the fungal strain and the process conditions should be chosen carefully in order to avoid any risks to humans or animals. The aim of this book is to explore comprehensively the advances in using filamentous fungi as the core of industrial biorefinery. The book provides a thorough overview and xvii

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understanding of fungal biology, biotechnology, and ecosystems, and covers a variety of industrial products that can be developed from fungi. The contents of this book are organized in 18 chapters to cover: (a) the fungal ecosystem, biology, and biotechnology; (b) the fungal growth and process in solid state and submerged fermentation, particular aspects of bioreactors, and sampling, preservation, and process monitoring; (c) mycotoxins as an important aspect to choose the fungal strains for processes; (d) products of biorefinery that the fungi including food, feed, organic acids, alcohols, bioactive pigmented compounds, and antibiotics; and (e) fungi in novel processes. We are grateful to the authors for compiling the pertinent information in their chapters, which we believe will be a valuable resource for both the scientific community and readers in general. We are also grateful to the expert reviewers for their useful comments and scientific insights, which helped shape the book’s organization and which improved the scientific discussions and overall quality of the chapters. The Editors (Mohammad J. Taherzadeh and Jorge A. Ferreira) acknowledge support from the €xtverket) through a European Swedish Agency for Economic and Regional Growth (Tillva Regional Development Fund “Ways2Tastes.” Finally, our sincere thanks go to the staff at Elsevier, including Dr. Kostas Marinakis (former Senior Book Acquisition Editor), Dr. Katie Hammon (Senior Book Acquisition Editor), and Bernadine A. Miralles (Editorial Project Manager), and the entire Elsevier production team for their support in publishing this book. Editors Mohammad J. Taherzadeh Jorge A. Ferreira Ashok Pandey

1 World of fungi and fungal ecosystems Gabriela A´ngeles de Paza, Ulises Conejo Saucedoa, Rafael Leo´n Morcilloa,#, and Elisabet Arandaa,b b

a INSTITUTE OF WATER RESEARCH, UNIVERSITY O F GRANADA, GR ANADA, SPAIN DEPARTMENT OF MICROBIOLOGY, UNIVERSITY O F GRANADA, GR ANADA, SPAIN

1. Introduction Fungi, belonging to Eukarya, are highly diverse and less explored. They are cosmopolitan and play important ecological roles as saprotrophs, mutualists, symbionts, parasites, or hyperparasites. Advances in molecular phylogeny have allowed to clarify the complex relationships of anamorphic fungi (fungi imperfecti) and to place some of them outside the fungi. Exiting progress have been made in developing fungi for modern and postmodern biotechnology, such as obtaining enzymes, alcohols, organic acids, pharmaceuticals, or recombinant deoxyribonucleic acid (DNA). Filamentous fungi and yeasts are extensively used as efficient cell factories in the production of bioactive substances and metabolites or for native or heterologous protein expression. This is due to their metabolic diversity, secretion efficiency, high-production capacity, and capability of carrying out post-translational protein modifications. The commercial exploitation of fungi has been reported for multiple industrial sectors, such as those involved in the production of antibiotics, simple organic compounds (citric acids), fungicides or food and beverages.

2. Fungal morphology Fungi can colonize new places by growing as a system of branching tubes, known as hyphae, whose aggregates form the mycelium (filamentous fungi). Mycelium can be found in the substrates where the fungi growth or belowground and play an important role in obtaining nutrients for growth and development. The hyphae are characterized by the presence or absence of septa, cross-walls that are distinctive among different taxonomic groups. They are absent in Oomycota and Zygomycota, known as coenocytic hyphae (koinos ¼ shared, kytos ¼ a hollow vessel). The presence of septa is a common feature of Basidiomycota and Ascomycota, in which the exchange of cytoplasm or organelles is ensured by septal # Current affiliation: Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM), CSICUMA, Campus de Teatinos, Ma´laga, Spain.

Current Developments in Biotechnology and Bioengineering. https://doi.org/10.1016/B978-0-323-91872-5.00010-7 Copyright © 2023 Elsevier Inc. All rights reserved.

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FIG. 1 Septum types in fungal hyphae.

pores. These pores can be simple or dolipores, pores with a distinctive morphology that have a barrel-shaped swelling that surrounds the central pore (Fig. 1). Under senescence processes, differentiation or simply under mechanical breaking off, different organelles act as septal pore plugs, preventing the detrimental effect of trauma senescence or permitting differentiation processes. They include Woronin bodies, hexagonal crystals, elongated crystalline bodies, nuclei, mitochondria, or de novo deposition of plugging material (Markham, 1994). The septum represents a specialized structure for cell division. Not all fungi grow as hyphae; some occur as yeasts (yeast-like fungi). They usually grow on surfaces where penetration is not required (such as the digestive tract). Such fungi have attracted the attention of biotechnologists because they grow rapidly and can easily be manipulated. Other fungi can switch between yeast-like fungi and filamentous fungi; they are known as dimorphic fungi and include some pathogens such as the plant pathogen Ustilago maydis or the human pathogen Candida albicans. This attribute is highly important as a model of differentiation in eukaryotic organisms (Bossche et al., 1993). Dimorphism is a common treat in pathogenic fungi (animals and plants pathogen) and usually is regulated by different factors such as temperature, glucose, pH, nitrogen source, carbon dioxide levels, chelating agents, transition metals and inoculum size or initial cell density (Romano, 1966). However, a number of fungi with unknown pathogenic activity have important industrial applications such as the production of chitosan, chitin from Saccharomyces, bioremediation process by Yarrowia, ethanol or enzyme production (Doiphode et al., 2009). This fact is of special interest in industry, since (i) it is possible to overcome the operational problems generated during hyphal growth in bioreactors, (ii) morphology could be an indicator of biotechnological process (enzymes secretion or proliferation vs penetration), or (iii) can be an advantage for biocontrol formulations (Doiphode et al., 2009). From a point of view of biotechnology, the morphology of fungi has an important implication since the adaptation of the cultivation system must be optimized.

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Filamentous fungi can growth as disperse mycelial or pellets, depending on the mechanical conditions of the cultivation. Industrial cultivation processes with fungi have been optimized over decades to increase productivity (Walker and White, 2017). The fungal cell wall is a dynamic and complex structure and usually based on glucans and chitin (Ruiz-Herrera, 1991). However, the chemical composition varies among different taxonomic groups, with implications for biotechnological processes since different enzymatic activities occur in the cell wall. The balance between wall synthesis and lysis could influence hyphal morphology and cell growth, with impacts on the retention of chemical compounds through bio-adsorption processes, enabling the successful industrial fermentation of filamentous fungi. In addition, some components of the cell wall, such as chitosan and chitin are considered high-value products for their use in biomedicine, agriculture, paper making, food industry, and textile industry that can be easily extracted using different technologies (Nwe et al., 2011; Table 1).

2.1 General aspects of reproduction Fungi can reproduce sexually or asexually (vegetative reproduction). These two reproduction modes differ according to the fungal morphology and taxonomic group (yeast, filamentous, or dimorphic fungi) (Hawker, 2016). In yeasts, the most frequent mode of vegetative reproduction is budding, which has been studied in detail for Saccharomyces cerevisiae. This mode can be multilateral, bipolar, unipolar, or monopolar budding. However, fission by forming a septum can also occur in yeasts such as Schizosaccharomyces pombe (host for heterologous expression). This fission can be binary or a bud fission, in which a cross-wall at the base of the bud separates both cells. Ballistoconidiogenesis is a specific vegetative reproduction in species such as Bullera (β-galactosidase) or Sporobolomyces (carotenoids and fatty acids). Pseudomycelia are typical in dimorphic species in which a single filament is produced when cells fail to separate after budding or fission (Walker and White, 2017). In filamentous fungi, such as basidiomycetes, this vegetative reproduction can occur by fragmentation of the hyphae; in some ascomycetes, the formation of mitotic spores has been observed. Sexual reproduction is a complex mechanism and differs according to the taxonomic groups; it involves the formation of a meiotic spore by planogametic copulation, gametangial contact, gametangial copulation, spermatization, and somatogamia. Table 1 Percentages of dry weight of the total cell wall fraction of the main components (chitin, cellulose, glucans, protein, and lipids) in different groups of fungi. Group

Chitin

Cellulose

Glucans

Protein

Lipids

Oomycota Chytridiomycota Zygomycota Ascomycota Basidiomycota

0 58 9 1–39 5–33

25 0 0 0 0

65 16 44 29–60 50–81

4 10 6 7–13 2–10

2 n/a 8 6–8 n/a

n/a (Data not available). Data adapted from Ruiz-Herrera, J., Ortiz-Castellanos, L., 2019. Cell wall glucans of fungi. A review. Cell Surf. 5, 100022.

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2.2 Fungal nutrition Filamentous fungi and yeasts are chemo-organotroph microorganisms with relatively simple nutritional needs. Fungi are heterotrophic organisms since they lack photosynthetic pigments. Most fungi are aerobes, but we can find representatives of obligate anaerobes (Neocallimastix) or facultative anaerobes (Blastocladia). In aerobic respiration, the terminal electron acceptor is oxygen; however, based on oxygen availability, we can find obligate fermentative or facultative fermentative fungi, including Crabtree-positive (Saccharomyces cerevisiae), Crabtree-negative (Candida utilis), non-fermentative (Phycomyces, Rhodotorula rubra) or obligate aerobes (most fungi) (Walker and White, 2017).

2.2.1 Nutrient uptake Filamentous fungi and few yeast species obtain their nutrients via extracellular enzymes; they absorb smaller molecules produced after extracellular digestion. These enzymes can be wall-bound-enzymes or may diffuse externally into the environment, depending on the lifestyle of the fungus (Section 3). Nutrient distribution through the hyphae might occur by passive (diffusion-driven) or active translocation (metabolically driven) through the protoplasm (Olsson and Gray, 1998; Persson et al., 2000). In both cases, nutrient translocation allows filamentous fungi to growth in habitats where the spatial distribution of nutrients and minerals is irregular and variable, including environments with low nutrient concentrations or polluted areas, by exploiting the resources available in other parts of the mycelium (Boswell et al., 2002). The enzymatic system in fungi depends on the taxonomic group. Some ecophysiological artificial groups have been established based on the capability to produce enzymes. These groups include the former ligninolytic fungi because of their ability to secrete a set of enzymes involved in the degradation of lignin. These enzymes play a significant role in biotechnology since they can be used in biorefineries. They include lipases produced by some yeasts (Candida, Yarrowia lipolytica), hydrolytic enzymes such as glycoside hydrolases (GHs), polysaccharide lyases (PLs), glycosyltransferases (GTFs), carbohydrate esterases (CEs), lytic polysaccharide monooxygenases (LPMOs), non-catalytic carbohydrate-binding modules (CBMs) and enzymes with “auxiliary activities,” including all enzymes involved in lignocellulosic conversion such as laccases, peroxidases, manganese peroxidase, lignin peroxidases, versatile peroxidases, DyP-type peroxidases (Levasseur et al., 2013). These enzymes are classified in the CAZymes database, which describes the families of structurally related catalytic and CBMs of enzymes that degrade, modify, or create glycosidic bonds (http://www.cazy. org/). These enzymes are important in biotechnology, particularly in biorefineries, for the deconstruction of plant biomass into simple sugars to obtain fermentation-based products and for the recovery of value-added compounds (Contesini et al., 2021).

3. Lifestyles of fungi Fungi, as heterotrophic eukaryotic microorganisms and efficient producers of enzymes, can live in different habitats and on different organic substrates. In general terms, fungi

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are either saprophytic—they feed on nutrients from organic, non-living matter in the surrounding environment-, symbiotic—they share a mutually beneficial relationship with another organism-, parasitic—they feed off a living host that may survive (biotrophs) or die (necrotrophs)- or hyperparasitic—they live at the expense of another parasites. Saprotrophic fungi are important for the recycling of nutrients, especially phosphate minerals and carbon incorporated in wood and other plant tissues. Their role as decomposers of organic matter is fundamental, since together with bacteria, they prevent the accumulation of organic matter, ensure the distribution of nutrients and play a crucial role in the global carbon cycle in terrestrial and aquatic ecosystems (Kjøller and Struwe, 2002; Cebrian, 2004; Moore et al., 2004). Besides, filamentous fungi play other significant roles in natural ecosystems. For instance, in terrestrial systems, fungi maintain the soil structure due to their filamentous branching growth and participate in the transformation of rocks and minerals (Gadd, 2008), incorporating new elements into the ecosystem that may be used by other organisms. In addition to the important role in natural processes, and as stated before, the decomposition of organic matter by fungi represents an important trait for biotechnological purposes due to the potential use of individual microbial strains or enzymes for the use of renewable resources, such as plant biomass. In general terms, saprotrophic basidiomycetes can degrade plant litter and wood more rapidly than other fungi because of their high capacity to decompose lignin and other plant polymers, allowing them to spread rapidly in the environment (Osono and Takeda, 2002; Martı´nez et al., 2005; Baldrian, 2008). Nevertheless, litter and wood decomposition is a successive process, of which basidiomycetes and ascomycetes govern different phases (Osono, 2007; Vo
r´ısˇkova´ and Baldrian, 2013). This capacity has been widely used in at industrial scale in various applications because of the oxidation of phenolic and non-phenolic lignin-derived compounds. Few examples are fungal laccases, ligninolytic enzymes which degrade complex recalcitrant lignin polymers and are widely used in the food industry (Minussi et al., 2002; MayoloDeloisa et al., 2020), in cosmetic, pharmaceutical, and medical applications (Golz-Berner et al., 2004; Niedermeyer et al., 2005; Hu et al., 2011; Ueda et al., 2012; Sun et al., 2014), in the paper and textile industry (Bourbonnais et al., 1995; Ozyurt and Atacag, 2003; Rodrı´guez Couto and Toca Herrera, 2006; Virk et al., 2012) or in the nano-biotechnology (Li et al., 2017; Kumari et al., 2018). Apart from industrial applications, the potential capacity of saprophytic fungal intra- and extracellular enzymes to degrade/transform complex polymers, such as lignin, is used in the biodegradation of organic xenobiotic pollutants. Among them, oxidoreductases represent the most important group of enzymes used in xenobiotic bioremediation transformations, including peroxidases, laccases, and oxygenases, and can catalyze oxidative coupling reactions using oxidizing agents to support the reactions (Sharma et al., 2018; Baker et al., 2019). These enzymes are produced by a wide diversity of fungi, which are some of the most extensively fungi used to detoxify xenobiotic compounds; they belong to the basidiomycetes group called “white rot fungi” and include the genera Trametes, Pleurotus, and Phanerochaete spp. (Aust, 1995; Pointing, 2001; Baldrian, 2003; Asif et al., 2017), but also ascomycetes genera such as Aspergillus or Penicillium (Aranda, 2016; Aranda et al., 2017).

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Pathogenic and parasitic fungi virtually attack all groups of organisms, including bacteria, other fungi, plants, and animals, including humans. According to their nutritional relationship with the host, parasitic fungi can be divided into biotrophic parasites, which obtain their sustenance directly from living cells, and necrotrophic parasites, which first destroy the parasitized cell and then absorb its nutrients. Besides, fungi might be facultative parasites, which are capable of growing and developing on dead organic matter and artificial culture media, or obligate parasites, which can only obtain food from living protoplasm and, therefore, cannot be cultured in non-living media (Brian, 1967; Lewis, 1973) Fungi possess the broadest host range spectrum of any group of pathogens. For instance, the filamentous ascomycetous fungus Fusarium oxysporum causes vascular wilt on many different plant species (Pietro et al., 2003), but it is also responsible for causing life-threatening disseminated infections in immunocompromised humans (Boutati and Anaissie, 1997). Nonetheless, there are many examples of fungal pathogens that infect only one host (Shivas and Hyde, 1997; Zhou and Hyde, 2001), highlighting the high host specificity of diseases produced by certain fungal infections. To explain this dual aspect of fungal infection specificity, the pathogenic strains of parasitic fungi are divided into formae speciales, defining the existence of different subgroups within species based on their host specificity (Armstrong and Armstrong, 1981; Anikster, 1984). In terms of agriculture, the estimated crop losses due to fungal diseases would be sufficient to feed approximately 600 million people a year (Fisher et al., 2012). To colonize plants, fungi secrete hydrolytic enzymes, including cutinases, cellulases, pectinases and proteases that degrade these polymers and permit fungal entrance through the external plant structural barriers. These enzymes are also required for the saprophytic lifestyle of fungi. As mentioned above, some fungi are facultative parasites and may attack plant roots from a saprophytic base in the soil through the mycelium, progressively causing the death of the host and thereafter living as saprophytes (Zhou and Hyde, 2001). Some fungi have developed other mechanisms to colonize plant hosts, such as via specialized penetration organs, called appressoria, or via penetrating through wounds or natural openings, such as stomata (Knogge, 1996). Fungal pathogens are responsible for numerous diseases in humans and for the extinction of amphibian and mammal populations (Brown et al., 2012; Fisher et al., 2012). For example, Batrachochytrium dendrobatidis, an aquatic chytrid fungus that attacks the skin of over 500 species of amphibians, and Geomyces destructans, a ascomycete fungus that attacks numerous bat species, seriously threaten the survival of these animals and might lead to the decline in the populations of other species (Colo´n-Gaud et al., 2009; Fisher et al., 2009; Lorch et al., 2011). For humans, fungal infections are rarely life-threatening; however, superficial fungal infections of the skin, hair and nails are common worldwide and affect approximately one-quarter of the human population (Schwartz, 2004). Airborne pathogenic fungi can also cause different respiratory diseases and also be lethal in immunocompromised patients (Mendell et al., 2011). The infection process is, generally, similar to that in plants. However, and contrary to plant infections, appressoria have not been described for

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animal-pathogenic fungi, except for a few similarly shaped structures formed by Candida albicans (Kriznik et al., 2005). Instead to appressoria, in animals, fungal pathogens use other mechanisms, such as the binding of specific receptors that facilitate the endocytosis € rnberger of host cells and, therefore, their entrance into the living tissue (Woods, 2003; Nu et al., 2004). Nonetheless, and similar to fungal infections in plants and other fungal lifestyles such as saprophytes, this process may also be mediated by lytic enzymes, such as proteases, that degrade the surface of the host cells and permit fungal penetration into the € rnberger et al., 2004; Schaller et al., 2005). living host (Nu A special type of parasitic fungi is represented by hyperparasites, fungi that live at the expense of another parasite, which is highly common among fungi ( Jeffries and Young, 1994). Hyperparasitism is often used in agriculture for plant protection as an alternative to chemical treatments (Brozˇova´, 2004). A classic example is Trichoderma harzianum, a fungus extensively used as biological agent against a wide range of fungal parasites. Nonetheless, it is estimated that 90% of all fungi used in plant protection products belong to the genus Trichoderma (Benı´tez et al., 2004). Fungi may also live as mutualistic symbionts, associating with other organisms with benefits for both parties. Remarkable examples of these symbioses are mycorrhizae and lichens. Mycorrhizae are the symbiotic association of soil fungi with the roots of vascular plants. Generally, fungi colonize plant roots and provide nutrients and water, which are captured from the soil through the external hyphal network, whereas plants supply organic molecules derived from photosynthesis, such as sugars or fatty acids, to the obligate biotrophic fungi (Harrison, 1999; Keymer et al., 2017). This represents a universal symbiosis, not only because almost all plant species are susceptible to form the symbiosis, but also because such symbioses can be established in the majority of terrestrial ecosystems, even under highly adverse conditions (Mosse et al., 1981). Moreover, this symbiosis contributes to global carbon cycles as plant hosts divert up to 20% of photosynthates to the host fungi (Smith and Read, 2010). There are three different types of mycorrhizae: endomycorrhizae, ectomycorrhizae, and ectendomycorrhizae. Endomycorrhizae are characterized by the presence of hyphae inside the cells of the root cortex. It is estimated that at least 90% of all known vascular plants, (about 300,000 species), form this type of mycorrhizae. On the other hand, in the ectomycorrhizae symbiosis, the hyphae of the fungus do not penetrate the cells of the cortex of the roots and form a dense hyphal sheath, known as the mantle, surrounding the root surface. It is believed that at least 3% of vascular plants develop this type of mycorrhizae, including almost all species of the most important forest tree genera. Finally, the ectendomycorrhizae present characteristics of both endo- and ectomycorrhizae, namely a mantle surrounding the plant roots and fungal hyphae that penetrate the root cells (Smith and Read, 2010). Mycorrhizal symbiosis plays an essential role in the establishment and functioning of terrestrial ecosystems, being involved in natural processes such as nutrient cycling and, in part, in the structure and dynamics of populations and plant communities (Newman, 1988; Klironomos et al., 2011). In terms of agriculture, mycorrhizae improve the

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Current Developments in Biotechnology and Bioengineering

productive capacity of poor soils, such as those affected by desertification, salinization, and wind erosion, because of the fungal capacity to obtain and translocate nutrients and water to the host plants (George, 2000). In addition, the symbiosis enhances soil aggregation and structure (Miller and Jastrow, 2000) and contributes to defence against diverse plant pathogens (Elsen et al., 2001; Azco´n-Aguilar et al., 2002; Garcı´a-Garrido and Ocampo, 2002) and abiotic stresses, such as drought or salinity (Ruiz-Lozano et al., 1996; Ruiz-Lozano, 2003). Another form of symbiotic association of fungi is represented by lichens, which are composite organisms composed of algae or cyanobacteria, called photobionts, living among filaments of a fungus, the so-called mycobiont. The algae, as an autotrophic organism, provides the fungus with organic compounds and oxygen derived from its photosynthetic activity, whereas the fungus, as a heterotroph, supplies the algae with carbon dioxide, minerals and water, since contrary to plants, lichens lack vascular organs to directly control their water homeostasis (Proctor and Tuba, 2002; Lutzoni and Miadlikowska, 2009). Most of the lichenized fungal species (98% approximately) belong to the phylum Ascomycota, whereas only few orders are in the phylum Basidiomycota and mitosporic fungi (Hawksworth et al., 1996). Although some lichens inhabit partially shaded areas and forests (Neitlich and McCune, 1997), most lichens often live in highly exposed places under intense light intensities, such as deserts or arctic and alpine ecosystems. For this reason, the mycobiont normally produces secondary colored compounds, called lichen compounds, that strongly absorb UV-B radiation and prevent damage to the algae’s photosynthetic apparatus (Fahselt, 1994). These compounds are a source of structurally diverse groups of natural products, with a wide range of biological activities including antibiotic, analgesic, and antipyretic activities (Yousuf et al., 2014) and have traditionally been used in the cosmetic and dye industry as well as in food and natural remedies (Oksanen, 2006). In nature, lichens are important as early-stage primary succession organisms. For instance, they are the pioneers in the colonization of rocky habitats and, after dying, their organic matter might be used by other organisms (Lutzoni and Miadlikowska, 2009; Muggia et al., 2016). As poikilohydric organisms, their water status passively follows the atmospheric humidity (Nash, 1996), and they can tolerate irregular and extended periods of severe desiccation. This allows them to colonize habits that cannot be colonized by most plants. Despite this, many lichens also grow as epiphytes on plants, mainly on the trunks and branches of trees. However, they are not parasites or pathogens since they do not consume or infect the holding plant (Ellis, 2012). In addition, lichens adsorb and are sensitive to heavy metals and pollutants (Garty, 2001), making them perfect environmental indicators.

4. Taxonomy of fungi Understanding how fungi have adapted to so many ecosystems, the way in which they have evolved, but above all, taxonomic classification, has not been an easy task. Fungi, after plants and animals, are one of the most diverse and dominant groups in almost

Chapter 1 • World of fungi and fungal ecosystems

9

all ecosystems. It is estimated that there are between 1.5 and 5.1 million species. However, a new estimation of the number of fungi ranges between 500,000 and almost 10 million € cking, 2017), although only almost 10% have been identified so far (Hawksworth and Lu (Blackwell, 2011; Hibbett et al., 2016) In the middle of the 18th century, the scientist Carl von Linnaeus implemented a binomial system to classify living beings (Systema naturae). This system is based on the classification of organisms according to their morphological characteristics and phenotypic traits. Fungi were considered as part of the plant kingdom (Linnaeus, 1767). Some years after, Whittaker classified the fungi as an independent group, which he called “true fungi” (Eumycota) (Whittaker, 1969). Then, different taxonomic classifications continued until the middle of the 19th century. Advances in the classification of fungi have always gone hand in hand with the development of new technologies, such as electron microscopy, new biochemical, and physiological analysis methods, the study of secondary metabolites, cell wall composition and fatty acid composition, as well as molecular technologies, among others (Guarro et al., 1999). In the last two decades, the development of PCR techniques and, later, genome sequencing, has significantly contributed to the advance in fungal taxonomy. This promoted rapid changes, and therefore, different proposals for the reclassification of fungi have been made, tripling the number of phyla from 4 to more than 12. However, less than 5% of the identified species have been taxonomically classified ( James et al., 2020). Nextgeneration sequencing tools have allowed fungal genome sequencing, transcriptomes, and mitochondrial genomes that provided relevant information for phylogenetic studies in fungi. Additionally, specific regions of ribosomal RNA (rRNA), such as internal transcribed spacers (ITSs), large subunit (LSU), small subunit (SSU) and intergenic spacer of rDNA, as well as various markers including translation elongation factor 1 (TEF1), glycerol-3-phosphate dehydrogenase (GAPDH), histones (H3, H4), calmodulin gene, RNA polymerase II largest subunit (RPB1) genes and mitochondrial genes (cytochrome c oxidase I and ATPase subunit 6), have played an important role in the development of the fungal taxonomy (Zhang et al., 2017). The organization of such information (genomes) by the scientific community has required different efforts. On the one hand, the Y1000 + project aims to sequence the genomes of 1000 yeast species (https://y1000plus.wei.wisc.edu), and on the other hand, the 1000 Fungal Genomes project (http://1000.fungalgenomes.org/home) has the objective of sequencing 1000 fungal genomes. The database UNITE is a recent database that concentrates the sequences of the ITS ribosomal region of fungi included in the International Nucleotide Sequence Database (http://www.insdc.org/). This database resulted from the collaboration of researchers and taxonomic specialists who collected and deposited fungal sequences, specifically with the purpose of building a database that registers, analyses, and shares this information with the scientific community (Ko˜ljalg et al., 2020). In the last 14 years, the taxonomy of fungi has been under major changes. The kingdom of fungi, proposed by Hibbett et al. (2007), includes one subkingdom (Dikaria) and seven

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Current Developments in Biotechnology and Bioengineering

FIG. 2 Fungal classification proposed by Hibbett et al. (2007).

phyla: Blastocladiomycota, Glomeromycota, Chytridiomycota, Neocallimastigomycota, Microsporidia, Ascomycota, and Basidiomycota; four subphyla, namely Entomophthoromycotina, Kickxellomycotina, Mucoromycotina, Zoopagomycotina, and a total of 31 classes (Hibbett et al., 2007)(Fig. 2). Over the last few years, different approaches, reclassifications, and updates on fungal taxonomy have been made (Gryganskyi et al., 2012; Hyde et al., 2013; Slippers et al., 2013; Phookamsak et al., 2014; Ariyawansa et al., blova´ et al., 2015; Li et al., 2016; Spatafora et al., 2016; Marin-Felix et al., 2017, 2019; Re 2018; Voglmayr et al., 2019; Mitchell et al., 2021). Tedersoo et al. (2018) described and proposed an updated classification for the fungal kingdom based on divergence time and phylogenies of particular taxa. Under this point of view, nine subkingdoms have been proposed (1Rozellomyceta, 2Aphelidiomyceta, 3Blastocladiomyceta, 4Chytridiomyceta, 5Olpidiomyceta, 6Basidiobolomyceta, 7Zoopagomyceta, 8Mucoromyceta and 9Dikarya); each subkingdoms divides into one or more phyla (18 phyla-1Rozellomycota, 2Aphelidiomycota, 3Blastocladiomycota, 4Chytridiomycota, 4 Monoblepharomycota, 4Neocallimastigomycota, 5Olpidiomycota, 6Basidiobolomycota, 7 Entomophthoromycota, 7Kickxellomycota, 7Zoopagomycota, 8Mucoromycota, 8Mortierellomycota, 8Calcarisporiellomycota, 8Glomeromycota, 9Entorrhizomycota, 9Basidiomycota, and 9Ascomycota). Additionally, each phylum divides into one or more subphyla

Chapter 1 • World of fungi and fungal ecosystems

11

FIG. 3 Fungal classification proposed by Tedersoo et al. (2018).

(20 subphyla—1Rozellomycotina, 2Aphelidiomycotina, 3Blastocladiomycotina, 4Chytridiomycotina, 4Monoblepharomycotina, 4Neocallimastigomycotina, 5Olpidiomycotina, 6Basidiobolomycotina, 7Entomophthoromycotina, 7Kickxellomycotina, 7Zoopagomycotina, 8 Mucoromycotina, 8Mortierellomycotina, 8Calcarisporiellomycotina, 8Glomeromycotina, 9 Entorrhizomycotina, 9Agaricomycotina, 9Pucciniomycotina, 9Ustilaginomycotina, 9Wallemiomycotina, 9Pezizomycotina, 9Taphrinomycotina, 9Saccharomycotina), and 76 classes are included (Fig. 3). An alternative classification was proposed by Naranjo-Ortiz and Gabaldo´n (2019), based on nine main lines: Opisthosporidia, Neocallimastigomycota, Blastocladiomycota, Chytridiomycota, Mucoromycota, Glomeromycota, Zoopagomycota, Ascomycota, and Basidiomycota. The main differences with respect to other proposals can be found in the incorporation of Opisthosporidia. This group incorporates three lineages: Rozellidea, Aphelidea, and Microsporidia. In turn, the group of Chytridiomycota was divided into three classes: Monoblepharidomycetes, Hyaloraphidiomycetes, and Chytridiomycetes, whereas Mucoromycota includes the two subphyla Mucoromycotina and Mortierellomycotina. Additionally, Basidiomycota comprised Pucciniomycotina, Ustilagomycotina, Agaricomycotina, Wallemiomycotina, and Bartheletiomycetes. Finally, Ascomycota contains three main clades: Taphrinomycotina, Saccharomycotina, and Pezizomycotina. Most recently, the classification of fungi proposed by Wijayawardene et al. (2020) has coincided, for many clades, with the proposal of Tedersoo et al. (2018). The subkingdom taxonomic rank was removed, and 16 phyla were recognized: Rozellomycota,

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Current Developments in Biotechnology and Bioengineering

Blastocladiomycota, Aphelidiomycota, Monoblepharomycota, Neocallimastigomycota, Chytridiomycota, Caulochytriomycota, Basidiobolomycota, Olpidiomycota, Entomophthoromycota, Glomeromycota, Zoopagomycota, Mortierellomycota, Mucoromycota, Calcarisporiellomycota, and three higher fungi (Dikarya-Entorrhizomycota, Basidiomycota, Ascomycota). In this study, only four subphyla were proposed (Mucoromycota Mortierellomycota, Entomophthoromycota, and Calcarisporiellomycota); in the case of Dycaria (Ascomycota and Basidiomycota), seven subphyla are described (Fig. 4). Some changes and additions have also been described, including the creation of the phylum Rozellomycota which contains the classes Rudimicrosporea and Microsporidea. The order Metchnikovellida was moved to the class Rudimicrosporea, and the most significant changes occurred in the phyla Ascomycota and Basidiomycota; the class Bartheletiomycetes, which was included in the phylum Basidiomycota, was changed to the subphylum Agaricomycotina. Moreover, Agaricomycetes, Dacrymycetes, Tremellomycetes and Bartheletiomycetes were grouped together. From the class Collemopsidiomycetes, the subphylum Pezizomycotina was eliminated, and new classes were included (Candelariomycetes and Xylobotryomycetes). The order Collemopsidiales was moved to the class Dothideomycetes. In the class Geminibasidiomycetes, the subphylum Wallemiomycotina was excluded, and only the class Wallemiomycetes remained.

FIG. 4 Fungal classification proposed by Wijayawardene et al. (2020).

Chapter 1 • World of fungi and fungal ecosystems

13

Despite these efforts, there are large numbers of genera, orders and families that have not yet been classified. Only in the phyla Ascomycota and Basidiomycota, remain not assigned families for 876 genera (Wijayawardene et al., 2018). According to a compilation from the Royal Botanic Gardens, in the last 10 years, 350 new families have been described, including Pucciniaceae with 5000 species, Mycosphaerellaceae with 6400 species, Cortinariaceae and Agaricaceae consisting of 3000 species. On the other hand, about 30% of the new incorporations are basidiomycetes, whereas 68% are ascomycetes. Until now, the continuous contribution of different groups of researchers, which has resulted in the growth of databases, and the development of new technologies and molecular tools have helped to establish a universal classification for fungi. The organization of this enormous amount of information through taxonomy allows to correlate the different styles of life as well as the structural, genetic, and metabolic characteristics, which, as mentioned here, are used to classify fungi. This taxonomic panorama allows us to show the great diversity of species that exist on earth, study their evolution and, in some cases, take advantage of certain metabolic functions that can be applied in different industrial processes; most of the fungi used belong to the phyla Ascomycota and Basidiomycota. These fungi play an important role in the production of various products or intermediates in the generation of bioethanol (fungi from the subphyla Agaricomycotina, Pezizomycotina, and Mucoromycotina), biodiesel (fungi from the subphyla Pezizomycotina, Ustilaginomycotina, and Saccharomycotina), biogas (fungi from the subphyla Mucoromycotina, Agaricomycotina, Pucciniomycotina, Pezizomycotina, Saccharomycotina), the pre-treatment of lignocellulosic biomass (fungi from the subphyla Basidiomycotina and class Agaricomycetes), applications in the pulp and paper industry (Agaricomycotina, Pezizomycotina), xylitol production (Saccharomycotina), and lactic acid production (Mucoromycotina, Saccharomycotina), among others (Kumari et al., 2018).

5. Fungal diversity An increasing number of studies are addressing fungal diversity. The total richness and diversity of fungal taxa across the studies published mainly involve Ascomycota (56.8% of the taxa) and Basidiomycota (36.7% of the taxa), with a total fungal diversity of around 6.28 million taxa. These studios represent a conservative estimate of global fungal species richness (Baldrian et al., 2021). In the largest study of fungal diversity, around 45,000 operational taxonomic units (OTUs) were recovered from 365 sites worldwide, using 1.4 million ITS sequences (Tedersoo et al., 2014). One-third of the total OTUs showed 97% of similarity compared with others reported in public databases; thereby, 30,000 new and different OTUs have been detected. These results greatly contributed to the discovery of new fungal species. The subkingdom Dikarya (Ascomycetes and Basidiomycetes) contains most of the fungal diversity on earth in terms of described species, but is small compared to the size of the total fungal kingdom. Recently, more taxa have been described, such as Cryptomycota

14

Current Developments in Biotechnology and Bioengineering

(Jones et al., 2011; Lara et al., 2010), a chytrid group, Archaeorhizomycetes and other soil ascomycete groups (Porter et al., 2008; Rosling et al., 2003; Schadt and Rosling, 2015). Furthermore, around 150 genera have been estimated as being a part of the fungal group called Microsporidia, with 1200–1300 species (Lee et al., 2009); the actual figures are presumably higher than the figures for the host diversity. However, molecular diversity studies have not been detailed enough to elucidate this information (Krebes et al., 2010; McClymont, et al., 2005). Those approximations have been made possible due to DNA sequencing and the widespread use of the formal fungal barcode Nuclear ribosomal Internal Transcribed Spacer ITS 1–2. It is recognized as the official molecular marker of choice for the exploration of fungal diversity in environmental samples (Ko˜ljalg et al., 2013) and counts with a vast and up-to-date database, which is necessary for data analysis (Schoch et al., 2012). Nevertheless, it cannot differentiate between all groups and cryptic species. Therefore, identification and diversity analysis of fungi is still greatly challenging (De Filippis et al., 2017). Moreover, the relationships between fungal diversity and their environments have not been completely described, which is also the case for the processes and mechanisms involved (Branco, 2019). As a consequence, two disciplines have been recognized to understand the relationship between fungal diversity and their environment, community ecology, and population genetics (Branco, 2019). Community ecology studies focus on the species level, addressing both ecological and biological questions, with a high level of accuracy and reliability. In contrast, population genetics studies have determined species assemblies and ranges, comprehending fungal intra-specific variation, dispersion, and establishment and including the identification of key traits influencing fitness (Mittelbach and Schemske, 2015). Cryptic species are biological entities that have already been named and described; however, they are morphologically different, and molecular studies are needed to elucidate, detect and enumerate these differences at the alpha diversity level (Bickford et al., 2007; Horton and Bruns, 2001; Rapp e and Giovannoni, 2003; Sogin et al., 2006). These studies highlight their diversity potential, proposing the measurement by genetic distances to know how hyper-diverse they are and to determine their species-level differences in many multicellular groups. Although novel molecular tools and new methods of identification have been used over the years, fungal diversity is barely known. This is mainly due the species with different morphological and ecological features (Hawksworth, 2004).

6. Fungal ecosystems As mentioned above, fungi are highly diverse and constitute a major portion of various ecosystems in terms of biomass, genetic diversification, and total biosphere DNA (Bajpai et al., 2019). Their distribution is extraordinarily diverse and shows biogeographical patterns depending upon local and global factors, such as climate, latitude, dispersal limitation, and evolutionary relationships (Bajpai et al., 2019). In terms of diversity, the

Chapter 1 • World of fungi and fungal ecosystems

15

highest alpha diversity of fungi has been found in soils and terrestrial environments, mainly in plant shoots, plant roots, and deadwood (Baldrian et al., 2021). These associations with plants lead us to infer that fungi play a dominant role in terrestrial environments.

6.1 Terrestrial ecosystems Fungi in terrestrial habitats exhibit different preferences related to the edaphic condition, with a higher diversity in tropical ecosystems. Fungal endemicity is especially strong in such regions. Nevertheless, this distribution depends on the group of the fungi and their features; for instance, ectomycorrhizal fungi and other classes are most diverse in temperate or boreal ecosystems. In general, several taxa show a cosmopolitan distribution throughout habitats (Tedersoo et al., 2014). Sequencing studies have been performed in different terrestrial environments, revealing several numbers of novel sequences clustered conservatively. For example, in forest soil, fungal diversity showed around 830 OTUs that were not matched to any fungal taxon previously described when blasted against NCBI (http://www.ncbi.nlm.nih.gov/) or e et al. (2009). This analysis resulted in an estimated diverUNITE (http://unite.ut.ee/) Bue sity of 2240 (71.5%) by using Chao1, a non-parametric richness tool. The authors also compared the sequences with a curated database of robustly identified sequences and found that 11% of the total sequences, excluding all “uncultured fungi,” remained unclase et al., 2009). sified and a further 20% belonged to the unclassified Dikarya (Bue Fungal diversity in forest soil is highly associated with plants. Their symbiosis plays an important role in vegetation dynamics. Moreover, strong relation and similarities in fungal alpha and beta diversity studies (Hooper et al., 2000; Wardle et al., 2004; Gilbert and Webb, 2007) have been reported since Hawksworth and Mound (1991) estimated around 1.5 M of fungal species only in this habitat. Mycorrhizal and saprotrophic fungi are usually the primary regulators of plant-soil feedbacks across a range of temperate grassland plant species; the most abundant families are Paraglomeraceae, Glomeraceae, and Acaulosporaceae, whereas the most abundant genera of saprotrophic fungi are Mortierella and Clavaria (Semchenko et al., 2018).

6.2 Aquatic ecosystems Aquatic ecosystems comprise the largest portion of the biosphere and include both freshwater and marine ecosystems. Numerous studies in different aquatic habitats have indicated that fungi are abundant eukaryotes in aquatic ecosystems (Grossart et al., 2019; Money, 2016). They can reach relative abundances of >50% in freshwater and about >1% in saline habitats (Comeau et al., 2016; Monchy et al., 2011). However, these results can be extremely variable and depend on the respective habitat and its environmental settings. The predominant fungi in aquatic habitats are mostly determined by cultivation methods. This, coupled with temporal dynamics, spatial connectivity, and vectors such

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Current Developments in Biotechnology and Bioengineering

as migration, can represent a huge limitation when studying aquatic fungal diversity, interactions, and distribution (Grossart et al., 2019). Nevertheless, advances in sequencing technologies have revealed novel fungal biodiversity and new approaches for the understanding of fungal phylogeny, lineages, and evolution (Hyde et al., 2021; Richards et al., 2015; Wurzbacher et al., 2019). Despite those limitations, many different aquatic fungi have been reported, such as species of the genera Aspergillus, Penicillium, Cladosporium, Aureobasidium, Cryptococcus, Malassezia, Candida, and Rhodotorula (Lo´pez-Garcı´a et al., 2007; Edgcomb et al., 2011; Jones et al., 2014). In marine habitats, 1901 species have been reported (2012). The dominant species on the surface belong to the groups Ascomycetes and Basidiomycetes, whereas yeasts and some other filamentous forms have been found in the deepest regions (Bass et al., 2007; Tisthammer et al., 2016). As mentioned before, fungi play multiple roles, engaging with all members of the aquatic community. Their interactions highlight them as important drivers of many ecosystem functions (Deveau et al., 2018). Marine fungi are especially adept at living on or inside other living organisms such as algae, corals, sponges, and even other fungi. Regarding such interactions, we can find multiple fungal groups such as Basidiomycota, Ascomycota, Zigomycota, Chytridiomycota, and Cryptomycota (Corsaro et al., 2018). The most studied groups are Chrytridiomycota and Cryptomycota, early diverging lineages that may not have a terrestrial ancestor, unlike the majority of marine fungi (Grossart et al., 2019). However, there is still a huge gap in terms of ecological and interaction studies of fungi and higher organisms, requiring further analyses of these roles. Numerous studies have already been carried out in freshwater habitats. In such environments, we can find different fungi belonging to the phyla Aphelidiomycota, Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Monoblepharomycota, Mortierellomycota, and Rozellomycota (Wijayawardene et al., 2020). Different species of Phycomycetes, Hiphomycetes and some zoosporic fungi belong to the genus Chytridium, Tetracladium, Cercospora, and Ophioceras were also reported (Chauvet et al., 2016; Wijayawardene et al., 2020). Mangrove fungi are strongly related to the geochemical cycles in the water. Mangrove forests share several kinds of fungi with other aquatic environments, and recent studies have reported about 850 taxa, including yeasts and lower mangrove fungi found exclusively in mangrove environments (Devadatha et al., 2021).

6.3 Extremophile environments New and hardly explored habitats are rich in fungal diversity. Those extremophile fungi have developed several mechanisms, involving enzyme production, that allow them to grow and reproduce in such harsh conditions. These enzyme systems are potential candidates for the isolation of new bioactive compounds with unusual but highly useful structures (Cha´vez et al., 2015). This has resulted in an increase in studies on extremophile fungi. The phyla Ascomycota, Basidiomycota, and a few traditional Zygomycota are the major fungi in Antarctic habitats. However, the endemism in Antarctic fungi can largely

Chapter 1 • World of fungi and fungal ecosystems

17

be ascribed to the classes Eurotiomycetes and Dothideomycetes. These fungi have developed several mechanisms, involving the production of rock-mineralizing enzymes. As a consequence, they can adapt to and colonize these extreme environments, showing a high tolerance to UV radiation, extreme temperatures, and drought. Moreover, they also show competitive advantages over other fungal groups (Treseder and Lennon, 2015). In this sense, Antarctic fungi appear to possess novel or unusual metabolic pathways, with a potential for biotechnological applications. Habitats with high temperatures have been extensively studied, and most of the resident fungi are limited primarily by water stress, carbon limitation, high salinity, and UV irradiation. However, some fungi display specific adaptations that enable them to survive in spite of these conditions ( Jones et al., 2018). This fact is of main concern for biotechnological applications since thermotolerant enzymes are desirable for various industrial processes. Although sampling in such regions is difficult, numerous studies have been performed, greatly contributing to a deeper knowledge about extremophile fungi under extremely arid and saline conditions (Fuentes et al., 2020). Yungay halities, for instance, showed a high diversity and number of species of Penicillium and Aspergillus. Also, in the Atacama Desert, numerous melanized fungi and Neucatenulostroma species have been reported, isolated from the hyper-arid core in this region, approximately 45 km south of Yungay and the Pacific coast (Culka et al., 2017). The yeasts Rhodosporidium toruloides, Exophiala sp., Cryptococcus friedmannii, and Holtermanniella watticus are great examples of the versatility of fungi and can survive and thrive in volcanoes. They are resistant to UVC, UVB, and UVC radiation, high NaCl concentrations, and extremely high temperature (Pulschen et al., 2015), making them promising model organisms for astrobiological studies (Ametrano et al., 2019). Deep-sea environments are characterized by the absence of sunlight irradiation and remain among the least explored regions of the earth. They are extreme environments because of large temperature fluctuations, with predominantly low temperatures (occasionally extremely high, >400°C near hydrothermal vents) and high hydrostatic pressure (up to 110 MPa). Deep-sea environmental gene libraries suggest that fungi are rare and non-diverse in high-pressure marine environments, in contrast to surface environments (Bass et al., 2007). Phylogenetic analyses have suggested the novel phylogenetic affiliation of a group of predominant deep-sea phylotypes within the phylum Ascomycota. Some of the amplified sequences were identified as common terrestrial fungal species, but the majority were novel sequences. Another novel phylotype is the phylum Chytridiomycota, with Rozella spp. as the closest related organism (Nagano et al., 2010). Yeast forms have also been reported to be the dominant fungi in some oceans, especially in depths from 1500 to 4000 m (Bass et al., 2007). In terms of evolution, the fungal diversity detected suggests that deep-sea environments are habitats hosting previously unexplored fungi and represent ancient ecosystems, thereby providing key insights into the early evolution of fungi and their ecological and physiological significance (Nagano et al., 2010).

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Current Developments in Biotechnology and Bioengineering

The discovered and isolation of anaerobic fungi (AF) in 1975 played an important role in general knowledge of fungi kingdom, being of the first isolation reports of fungi that not need oxygen to survive (Orpin, 1975). From then on, different AF has been isolated, identified mainly in gut ecosystems, and represent a key source of novel enzymes. These enzymes are related with degradation, fermentation, and bioaugmentation activity; became the most efficient source of plant fibber digestion enzymes (Morgavi et al., 2015). In general, some of the AF isolated belongs to the phylum Neocallimastigomycota. However, this phylum is understudied due to the limited information of full genomes, hard crop conditions, and the lack of genetics toolset to manipulate them. Nevertheless, loads of scientists have been doing the best effort to take advantage of AF potential as a enzymatic resource, especially those in which biomass degradation are related (Hooker et al., 2019). Recently, all of these efforts are reflected in the enhancement of biogas production by AF and algal biomass, producing 41% more methane (Sevcan et al., 2017). Furthermore, co-cultures of AF and methanogens improve biogas production and represent a decrease in the final cost of the process (Vinzelj et al., 2020).

7. Applications of fungi in biorefineries Lignocellulose represents the largest reservoir of carbon in nature, them, the bioconversion of renewable lignocellulosic biomass has become mandatory to face global warming and shortage of fossil fuels. The aforementioned metabolic and ecophysiological diversity of fungi makes them a valuable tool for their use in biorefineries. They or a cocktail of their enzymes as well as the use of genetically modified fungi can be used for biopre-treatment of lignocelluloses, to remove lignin and solubilize hemicellulose, making cellulose more accessible to hydrolytic enzymes (Camarero et al., 2014). In this context, filamentous fungi have the ability to extracellularly produce a large variety of nonspecific and specific enzymes capable of breaking down lignin, cellulose, and hemicellulose. In recent years, the development of techniques such as genome sequencing, transcriptomics, and proteomics have revealed the presence of enzymes of great interest for this industry, among which are xylanases, LPMOs, or endoglucanases. This capacity makes them microorganisms of special interest for their use in biotechnological processes such as the production of bioethanol from lignocellulosic materials. In addition, the new technologies of genome editing by CRISPR-Cas9 appears to be a novel tool in the design of fungal genomes to edit certain desired traits, such as tolerance to inhibitors, better tolerance to biofuels, thermotolerance, consumption of substrates, silenced, and targeted the competitive mechanisms and modification of strategic enzymes using in biofuel production (Javed et al., 2019). Genetic manipulation in the yeast genome through CRISPR-Cas9 (gene insertions and mutations) has demonstrated an important advance in the production of fatty acids as a precursor of biofuels (Ullah et al., 2021).

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8. Conclusions and perspectives This chapter summarizes the main aspects of the physiological diversity of fungi related with applications in biotechnology. Understanding the basic aspects of fungal physiology and distribution is crucial when exploiting these microorganisms in biorefineries. The diversity of fungi allows specific uses for different purposes, since a combination of adaptation to different conditions and specific biotechnological treatments in some species make them a suitable option for biotechnological application. However, one of the main bottlenecks in fungal application is the lack of databases with annotated genomes, restricting industrial applications since proteomics, metabolomics, and transcriptomics represent important tools for industrial and biotechnological development. Thus, further studies are necessary to obtain an integrated biotechnological application of fungi.

References Ametrano, C.G., Grewe, F., Crous, P.W., Goodwin, S.B., Liang, C., Selbmann, L., Lumbsch, H.T., Leavitt, S.D., Muggia, L., 2019. Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota). IMA Fungus 10 (1), 19. Anikster, Y., 1984. The formae speciales. In: The Cereal Rusts. vol. 1. Academic Press, pp. 115–130. Aranda, E., 2016. Promising approaches towards biotransformation of polycyclic aromatic hydrocarbons with Ascomycota fungi. Curr. Opin. Biotechnol. 38, 1–8. Aranda, E., Godoy, P., Reina, R., Badia-Fabregat, M., Rosell, M., Marco-Urrea, E., Garcı´a-Romera, I., 2017. Isolation of Ascomycota fungi with capability to transform PAHs: insights into the biodegradation mechanisms of Penicillium oxalicum. Int. Biodeterior. Biodegrad. 122, 141–150. Ariyawansa, H.A., Hyde, K.D., Jayasiri, S.C., Buyck, B., Chethana, K.W.T., Dai, D.Q., Dai, Y.C., € cking, R., Ghobad-Nejhad, M., Niskanen, T., Thambugala, K.Daranagama, D.A., Jayawardena, R.S., Lu M., Voigt, K., Zhao, R.L., Li, G.-J., Doilom, M., Boonmee, S., Yang, Z.L., Cai, Q., Cui, Y.-Y., Bahkali, A.H., Chen, J., Cui, B.K., Chen, J.J., Dayarathne, M.C., Dissanayake, A.J., Ekanayaka, A.H., Hashimoto, A., Hongsanan, S., Jones, E.B.G., Larsson, E., Li, W.J., Li, Q.-R., Liu, J.K., Luo, Z.L., Maharachchikumbura, S.S.N., Mapook, A., McKenzie, E.H.C., Norphanphoun, C., Konta, S., Pang, K.L., Perera, R.H., Phookamsak, R., Phukhamsakda, C., Pinruan, U., Randrianjohany, E., Singtripop, C., Tanaka, K., Tian, C.M., Tibpromma, S., Abdel-Wahab, M.A., Wanasinghe, D.N., Wijayawardene, N.N., Zhang, J.F., Zhang, H., Abdel-Aziz, F.A., Wedin, M., Westberg, M., Ammirati, J.F., Bulgakov, T.S., Lima, D.X., Callaghan, T.M., Callac, P., Chang, C.-H., Coca, L.F., Dal-Forno, M., Dollhofer, V., Fliegerova´, K., Greiner, K., Griffith, G.W., Ho, H.-M., Hofstetter, V., Jeewon, R., Kang, J.C., Wen, T.-C., Kirk, P.M., € vuori, I., Lawrey, J.D., Xing, J., Li, H., Liu, Z.Y., Liu, X.Z., Liimatainen, K., Lumbsch, H.T., Kyto Matsumura, M., Moncada, B., Nuankaew, S., Parnmen, S., de Azevedo Santiago, A.L.C.M., Sommai, S., Song, Y., de Souza, C.A.F., de Souza-Motta, C.M., Su, H.Y., Suetrong, S., Wang, Y., Wei, blova´, M., Fournier, J., Camporesi, E., Luangsa-ard, J.J., S.-F., Wen, T.C., Yuan, H.S., Zhou, L.W., Re Tasanathai, K., Khonsanit, A., Thanakitpipattana, D., Somrithipol, S., Diederich, P., Millanes, A.M., Common, R.S., Stadler, M., Yan, J.Y., Li, X., Lee, H.W., Nguyen, T.T.T., Lee, H.B., Battistin, E., Marsico, O., Vizzini, A., Vila, J., Ercole, E., Eberhardt, U., Simonini, G., Wen, H.-A., Chen, X.-H., Miettinen, O., Spirin, V., Hernawati, 2015. Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa. Fungal Divers. 75 (1), 27–274. Armstrong, G.M., Armstrong, J.K., 1981. Formae speciales and races of Fusarium oxysporum causing wilt diseases. In: Nelson, P.E., Toussoun, T.A., Cook, R.J. (Eds.), Fusarium: Diseases, Biology, and Taxonomy. The Pennsylvania State University Press, Pensilvania, USA, pp. 391–399. Asif, M.B., Hai, F.I., Singh, L., Price, W.E., Nghiem, L.D., 2017. Degradation of pharmaceuticals and personal care products by white-rot fungi—a critical review. Curr. Pollut. Rep. 3 (2), 88–103.

20

Current Developments in Biotechnology and Bioengineering

Aust, S.D., 1995. Mechanisms of degradation by white rot fungi. Environ Health Perspect 103 (Suppl. 5), 59–61. Azco´n-Aguilar, C., Jaizme-Vega, M.C., Calvet, C., 2002. The contribution of arbuscular mycorrhizal fungi to € epp, H., Barea, J.M., Haselwandter, K. the control of soil-borne plant pathogens. In: Gianinazzi, S., Schu €user Basel, Basel, pp. (Eds.), Mycorrhizal Technology in Agriculture: From Genes to Bioproducts. Birkha 187–197. Bajpai, A., Rawat, S., Johri, B.N., 2019. Fungal diversity: global perspective and ecosystem dynamics. In: Satyanarayana, T., Johri, B.N., Das, S.K. (Eds.), Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications: Volume 1. Microbial Diversity in Normal & Extreme Environments. Springer Singapore, Singapore, pp. 83–113. Baker, P., Tiroumalechetty, A., Mohan, R., 2019. Fungal enzymes for bioremediation of xenobiotic compounds. In: Yadav, A.N., Singh, S., Mishra, S., Gupta, A. (Eds.), Recent Advancement in White Biotechnology Through Fungi: Volume 3: Perspective for Sustainable Environments. Springer International Publishing, Cham, pp. 463–489. Baldrian, P., 2003. Interactions of heavy metals with white-rot fungi. Enzym. Microb. Technol. 32 (1), 78–91. Baldrian, P., 2008. In: Boddy, L., Frankland, J.C., van West, P. (Eds.), Enzymes of Saprotrophic Basidiomycetes. British Mycological Society Symposia Series, vol. 28. Academic Press, Amsterdam, pp. 19–41. Baldrian, P., Veˇtrovsky´, T., Lepinay, C., Kohout, P., 2021. High-throughput sequencing view on the magnitude of global fungal diversity. Fungal Divers. 114, 539–547. Bass, D., Howe, A., Brown, N., Barton, H., Demidova, M., Michelle, H., Li, L., Sanders, H., Watkinson, S.C., Willcock, S., Richards, T.A., 2007. Yeast forms dominate fungal diversity in the deep oceans. Proc. Biol. Sci. 274 (1629), 3069–3077. Benı´tez, T., Rinco´n, A.M., Limo´n, M.C., Codon, A.C., 2004. Biocontrol mechanisms of Trichoderma strains. Int. Microbiol. 7 (4), 249–260. Bickford, D., Lohman, D.J., Sodhi, N.S., Ng, P.K.L., Meier, R., Winker, K., Ingram, K.K., Das, I., 2007. Cryptic species as a window on diversity and conservation. Trends Ecol. Evol. 22 (3), 148–155. Blackwell, M., 2011. The Fungi: 1, 2, 3… 5.1 million species? Am. J. Bot. 98 (3), 426–438. Bossche, H.V., Odds, F.C., Kerridge, D., 1993. Dimorphic Fungi in Biology and Medicine. Springer. Boswell, G.P., Jacobs, H., Davidson, F.A., Gadd, G.M., Ritz, K., 2002. Functional consequences of nutrient translocation in mycelial fungi. J. Theor. Biol. 217 (4), 459–477. https://doi.org/10.1006/jtbi.2002.3048. Bourbonnais, R., Paice, M.G., Reid, I.D., Lanthier, P., Yaguchi, M., 1995. Lignin oxidation by laccase isozymes from Trametes versicolor and role of the mediator 2,20 -azinobis(3-ethylbenzthiazoline-6-sulfonate) in kraft lignin depolymerization. Appl. Environ. Microbiol. 61 (5), 1876. Boutati, E.I., Anaissie, E.J., 1997. Fusarium, a significant emerging pathogen in patients with hematologic malignancy: ten years’ experience at a cancer center and implications for management. Blood 90 (3), 999–1008. Branco, S., 2019. Fungal diversity from communities to genes. Fungal Biol. Rev. 33 (3), 225–237. Brian, P.W., 1967. The Leeuwenhoek Lecture, 1966. Obligate parasitism in fungi. Proc. R. Soc. Lond. B Biol. Sci. 168 (1011), 101–118. Brown, G.D., Denning, D.W., Gow, N.A., Levitz, S.M., Netea, M.G., White, T.C., 2012. Hidden killers: human fungal infections. Sci. Transl. Med. 4 (165), 165rv113. Brozˇova´, J., 2004. Mycoparasitic fungi Trichoderma spp. in plant protection—review. Plant Prot. Sci. 40 (2), 63. e, M., Reich, M., Murat, C., Morin, E., Nilsson, R.H., Uroz, S., Martin, F., 2009. 454 Pyrosequencing anaBue lyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol. 184 (2), 449–456. Camarero, S., Martı´nez, M.J., Martı´nez, A.T., 2014. Understanding lignin biodegradation for the improved utilization of plant biomass in modern biorefineries. Biofuels Bioprod. Biorefin. 8 (5), 615–625.

Chapter 1 • World of fungi and fungal ecosystems

21

Cebrian, J., 2004. Role of first-order consumers in ecosystem carbon flow. Ecol. Lett. 7 (3), 232–240. €rlocher, F., 2016. Beyond the water column: aquatic Chauvet, E., Cornut, J., Sridhar, K.R., Selosse, M.-A., Ba hyphomycetes outside their preferred habitat. Fungal Ecol. 19, 112–127. Cha´vez, R., Fierro, F., Garcı´a-Rico, R.O., Vaca, I., 2015. Filamentous fungi from extreme environments as a promising source of novel bioactive secondary metabolites. Front. Microbiol. 6 (903). Colo´n-Gaud, C., Whiles, M.R., Kilham, S.S., Lips, K.R., Pringle, C.M., Connelly, S., Peterson, S.D., 2009. Assessing ecological responses to catastrophic amphibian declines: patterns of macroinvertebrate production and food web structure in upland Panamanian streams. Limnol. Oceanogr. 54 (1), 331–343. Comeau, A.M., Vincent, W.F., Bernier, L., Lovejoy, C., 2016. Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats. Sci. Rep. 6 (1), 30120. Contesini, F.J., Frandsen, R.J.N., Damasio, A., 2021. CAZymes in biorefinery: from genes to application. Front. Bioeng. Biotechnol. 9, 86. € hsler, M., Wylezich, C., Venditti, D., Walochnik, J., Michel, R., 2018. New insights from Corsaro, D., Ko molecular phylogenetics of amoebophagous fungi (Zoopagomycota, Zoopagales). Parasitol. Res. 117 (1), 157–167. Culka, A., Jehli
cka, J., Ascaso,, C., Artieda,, O., Casero, C.M., Wierzchos, J., 2017. Raman microspectrometric study of pigments in melanized fungi from the hyperarid Atacama desert gypsum crust. J. Raman Spectrosc. 48 (11), 1487–1493. De Filippis, F., Laiola, M., Blaiotta, G., Ercolini, D., 2017. Different amplicon targets for sequencing-based studies of fungal diversity. Appl. Environ. Microbiol. 83 (17). Devadatha, B., Jones, E.B.G., Pang, K.L., Abdel-Wahab, M.A., Hyde, K.D., Sakayaroj, J., Bahkali, A.H., Calabon, M.S., Sarma, V.V., Sutreong, S., Zhang, S.N., 2021. Occurrence and geographical distribution of mangrove fungi. Fungal Divers. 106 (1), 137–227. , V., Labb Deveau, A., Bonito, G., Uehling, J., Paoletti, M., Becker, M., Bindschedler, S., Hacquard, S., Herve e, J., Lastovetsky, O.A., Mieszkin, S., Millet, L.J., Vajna, B., Junier, P., Bonfante, P., Krom, B.P., Olsson, S., van Elsas, J.D., Wick, L.Y., 2018. Bacterial-fungal interactions: ecology, mechanisms and challenges. FEMS Microbiol. Rev. 42 (3), 335–352. Doiphode, N., Joshi, C., Ghormade, V., Deshpande, M.V., 2009. Biotechnological applications of dimorphic yeasts. In: Yeast Biotechnology: Diversity and Applications. Springer, Dordrecht, pp. 635–650. Edgcomb, V.P., Beaudoin, D., Gast, R., Biddle, J.F., Teske, A., 2011. Marine subsurface eukaryotes: the fungal majority. Environ. Microbiol. 13 (1), 172–183. Ellis, C.J., 2012. Lichen epiphyte diversity: a species, community and trait-based review. Perspect. Plant Ecol. Evol. Syst. 14 (2), 131–152. Elsen, A., Declerck, S., De Waele, D., 2001. Effects of Glomus intraradices on the reproduction of the burrowing nematode (Radopholus similis) in dixenic culture. Mycorrhiza 11 (1), 49–51. Fahselt, D., 1994. Review Article Secondary Biochemistry of Lichens. Symbiosis. Fisher, M.C., Garner, T.W.J., Walker, S.F., 2009. Global emergence of batrachochytrium dendrobatidis and amphibian chytridiomycosis in space, time, and host. Annu. Rev. Microbiol. 63 (1), 291–310. Fisher, M.C., Henk, D.A., Briggs, C.J., Brownstein, J.S., Madoff, L.C., McCraw, S.L., Gurr, S.J., 2012. Emerging fungal threats to animal, plant and ecosystem health. Nature 484 (7393), 186–194. Fuentes, A., Herrera, H., Charles, T.C., Arriagada, C., 2020. Fungal and bacterial microbiome associated with the rhizosphere of native plants from the Atacama Desert. Microorganisms 8 (2), 209. Gadd, G., 2008. Fungi and their role in the biosphere. In: Jørgensen, S.E., Fath, B.D. (Eds.), Encyclopedia of Ecology. Elsevier, Oxford, pp. 1709–1717. Garcı´a-Garrido, J.M., Ocampo, J.A., 2002. Regulation of the plant defence response in arbuscular mycorrhizal symbiosis. J. Exp. Bot. 53 (373), 1377–1386.

22

Current Developments in Biotechnology and Bioengineering

Garty, J., 2001. Biomonitoring atmospheric heavy metals with lichens: theory and application. Crit. Rev. Plant Sci. 20 (4), 309–371. George, E., 2000. Nutrient uptake. In: Kapulnik, Y., Douds, D. (Eds.), Arbuscular Mycorrhizas: Physiology and Function. vol. 1. Kluwer, Springer Netherlands, Dordrecht, pp. 307–343. Gilbert, G.S., Webb, C.O., 2007. Phylogenetic signal in plant pathogen–host range. Proc. Natl. Acad. Sci. USA 104 (12), 4979–4983. Golz-Berner, K., Walzel, B., Zastrow, L., Doucet, O., 2004. Cosmetic or dermatological preparation with skin-lightening proteins. WO2004017931A1. Grossart, H.-P., Van den Wyngaert, S., Kagami, M., Wurzbacher, C., Cunliffe, M., Rojas-Jimenez, K., 2019. Fungi in aquatic ecosystems. Nat. Rev. Microbiol. 17 (6), 339–354. Gryganskyi, A.P., Humber, R.A., Smith, M.E., Miadlikovska, J., Wu, S., Voigt, K., Walther, G., Anishchenko, I.M., Vilgalys, R., 2012. Molecular phylogeny of the Entomophthoromycota. Mol. Phylogenet. Evol. 65 (2), 682–694. , J., Stchigel, A.M., 1999. Developments in fungal taxonomy. Clin. Microbiol. Rev. 12 (3), Guarro, J., Gene 454–500. Harrison, M.J., 1999. Molecular and cellular aspects of the arbuscular mycorrhizal symbiosis. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50 (1), 361–389. Hawker, L.E., 2016. The Physiology of Reproduction in Fungi. Cambridge University Press. Hawksworth, D.L., 2004. Fungal diversity and its implications for genetic resource collections. Stud. Mycol. 50, 9–17. Hawksworth, D.L., Kirk, P.M., Sutton, B.C., Pegler, D.N., 1996. Ainsworth & Bisby’s dictionary of the fungi. Rev. Inst. Med. Trop. Sao Paulo 38 (4), 272. € cking, R., 2017. Fungal diversity revisited: 2.2 to 3.8 million species. Microbiol. Spectr. Hawksworth, D.L., Lu 5 (4). https://doi.org/10.1128/microbiolspec.FUNK-0052-2016. Hawksworth, D.L., Mound, L.A., 1991. Biodiversity databases: the crucial significance of collections. In: Hawksworth, D.L. (Ed.), Biodiversity of Microorganisms and Invertebrates and Its Role in Sustainable Agriculture. CAB International, Wallingford, UK, pp. 17–29. € Hibbett, D., Abarenkov, K., Ko˜ljalg,, U., Opik,, M., Chai, B., Wang, Q., Crous, P., Robert, V., Helgason, T., Geiser, D.M., et al., 2016. Sequence-based classification and identification of Fungi. Mycologia 108, 1049–1068. Hibbett, D.S., Binder, M., Bischoff, J.F., Blackwell, M., Cannon, P.F., Eriksson, O.E., Huhndorf, S., James, T., € cking, R., Thorsten Lumbsch, H., Lutzoni, F., Matheny, P.B., McLaughlin, D.J., Powell, M.J., Kirk, P.M., Lu Redhead, S., Schoch, C.L., Spatafora, J.W., Stalpers, J.A., Vilgalys, R., Aime, M.C., Aptroot, A., Bauer, R., Begerow, D., Benny, G.L., Castlebury, L.A., Crous, P.W., Dai, Y.-C., Gams, W., Geiser, D.M., Griffith, G.W., Gueidan, C., Hawksworth, D.L., Hestmark, G., Hosaka, K., Humber, R.A., Hyde, K.D., Ironside, J.E., Ko˜ljalg, U., Kurtzman, C.P., Larsson, K.-H., Lichtwardt, R., Longcore, J., Mia˛dlikowska, J., Miller, A., Moncalvo, J.-M., Mozley-Standridge, S., Oberwinkler, F., Parmasto, E., Reeb, V., Rogers, J.D., Roux, C., € ßler, A., Sugiyama, J., Thorn, R.G., Tibell, L., Untereiner, W.A., Ryvarden, L., Sampaio, J.P., Schu Walker, C., Wang, Z., Weir, A., Weiss, M., White, M.M., Winka, K., Yao, Y.-J., Zhang, N., 2007. A higher-level phylogenetic classification of the Fungi. Mycol. Res. 111 (5), 509–547. Hooker, C.A., Lee, K.Z., Solomon, K.V., 2019. Leveraging anaerobic fungi for biotechnology. Curr. Opin. Biotechnol. 59, 103–110. Hooper, D.U., Bignell, D.E., Brown, V.K., Brussard, L., Dangerfield, J.M., Wall, D.H., Wardle, D.A., Coleman, D.C., Giller, K.E., Lavelle, P., Van Der Putten, W.H., De Ruiter, P.C., Rusek, J., Silver, W.L., Tiedje, J.M., Wolters, V., 2000. Interactions between aboveground and belowground biodiversity in terrestrial ecosystems: patterns, mechanisms, and feedbacks: we assess the evidence for correlation between aboveground and belowground diversity and conclude that a variety of mechanisms could lead to positive, negative, or no relationship—depending on the strength and type of interactions among species. Bioscience 50 (12), 1049–1061.

Chapter 1 • World of fungi and fungal ecosystems

23

Horton, T.R., Bruns, T.D., 2001. The molecular revolution in ectomycorrhizal ecology: peeking into the black-box. Mol. Ecol. 10 (8), 1855–1871. Hu, D.D., Zhang, R.Y., Zhang, G.Q., Wang, H.X., Ng, T.B., 2011. A laccase with antiproliferative activity against tumor cells from an edible mushroom, white common Agrocybe cylindracea. Phytomedicine 18 (5), 374–379. Hyde, K.D., Jones, E.B.G., Liu, J.-K., Ariyawansa, H., Boehm, E., Boonmee, S., Braun, U., Chomnunti, P., Crous, P.W., Dai, D.-Q., Diederich, P., Dissanayake, A., Doilom, M., Doveri, F., Hongsanan, S., € cking, R., Monkai, J., Muggia, L., Nelsen, M.P., Pang, Jayawardena, R., Lawrey, J.D., Li, Y.-M., Liu, Y.-X., Lu K.-L., Phookamsak, R., Senanayake, I.C., Shearer, C.A., Suetrong, S., Tanaka, K., Thambugala, K.M., Wijayawardene, N.N., Wikee, S., Wu, H.-X., Zhang, Y., Aguirre-Hudson, B., Alias, S.A., Aptroot, A., Bahkali, A.H., Bezerra, J.L., Bhat, D.J., Camporesi, E., Chukeatirote, E., Gueidan, C., Hawksworth, D.L., Hirayama, K., De Hoog, S., Kang, J.-C., Knudsen, K., Li, W.-J., Li, X.-H., Liu, Z.-Y., Mapook, A., McKenzie, E.H.C., Miller, A.N., Mortimer, P.E., Phillips, A.J.L., Raja, H.A., Scheuer, C., Schumm, F., Taylor, J.E., Tian, Q., Tibpromma, S., Wanasinghe, D.N., Wang, Y., Xu, J.-C., Yacharoen, S., Yan, J.-Y., Zhang, M., 2013. Families of Dothideomycetes. Fungal Divers. 63 (1), 1–313. Hyde, K.D., Bao, D.-F., Hongsanan, S., Chethana, K.W.T., Yang, J., Suwannarach, N., 2021. Evolution of freshwater Diaporthomycetidae (Sordariomycetes) provides evidence for five new orders and six new families. Fungal Divers. 107 (1), 71–105. James, T.Y., Stajich, J.E., Hittinger, C.T., Rokas, A., 2020. Toward a fully resolved fungal tree of life. Annu. Rev. Microbiol. 74 (1), 291–313. Javed, F., Aslam, M., Rashid, N., Shamair, Z., Khan, A.L., Yasin, M., Fazal, T., et al., 2019. Microalgae-based biofuels, resource recovery and wastewater treatment: a pathway towards sustainable biorefinery. Fuel 255, 115826. Jeffries, P., Young, T.W., 1994. Interfungal Parasitic Relationships. Cab International. Jones, M.D.M., Forn, I., Gadelha, C., Egan, M.J., Bass, D., Massana, R., Richards, T.A., et al., 2011. Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474, 200–203. Jones, E.G., Hyde, K.D., Pang, K.-L., 2014. Freshwater Fungi: And Fungal-like Organisms. Walter de Gruyter GmbH & Co KG. Jones, D.L., Olivera-Ardid, S., Klumpp, E., Knief, C., Hill, P.W., Lehndorff, E., Bol, R., 2018. Moisture activation and carbon use efficiency of soil microbial communities along an aridity gradient in the Atacama Desert. Soil Biol. Biochem. 117, 68–71. Keymer, A., Pimprikar, P., Wewer, V., Huber, C., Brands, M., Bucerius, S.L., Delaux, P.-M., Klingl, V., € penack-Lahaye, E.V., Wang, T.L., Eisenreich, W., Do €rmann, P., Parniske, M., Gutjahr, C., 2017. Lipid Ro transfer from plants to arbuscular mycorrhiza fungi. elife 6, e29107. Kjøller, A.H., Struwe, S., 2002. Fungal communities, succession, enzymes, and decomposition. In: Enzymes in the Environment: Activity, Ecology and Applications. vol. 1. Marcel Dekker, Inc., New York, Basel, pp. 267–284. Klironomos, J., Zobel, M., Tibbett, M., Stock, W.D., Rillig, M.C., Parrent, J.L., Moora, M., Koch, A.M., Facelli, J.M., Facelli, E., Dickie, I.A., Bever, J.D., 2011. Forces that structure plant communities: quantifying the importance of the mycorrhizal symbiosis. New Phytol. 189 (2), 366–370. Knogge, W., 1996. Fungal infection of plants. Plant Cell 8 (10), 1711–1722. Ko˜ljalg, U., Nilsson, R.H., Abarenkov, K., Tedersoo, L., Taylor, A.F.S., Bahram, M., Bates, S.T., Bruns, T.D., ˜ as, M., Bengtsson-Palme, J., Callaghan, T.M., Douglas, B., Drenkhan, T., Eberhardt, U., Duen € cking, Grebenc, T., Griffith, G.W., Hartmann, M., Kirk, P.M., Kohout, P., Larsson, E., Lindahl, B.D., Lu R., Martı´n, M.P., Matheny, P.B., Nguyen, N.H., Niskanen, T., Oja, J., Peay, K.G., Peintner, U., € ßler, A., Scott, J.A., Sene s, C., Smith, M.E., Suija, A., Peterson, M., Po˜ldmaa, K., Saag, L., Saar, I., Schu Taylor, D.L., Telleria, M.T., Weiss, M., Larsson, K.-H., 2013. Towards a unified paradigm for sequence-based identification of fungi. Mol. Ecol. 22 (21), 5271–5277.

24

Current Developments in Biotechnology and Bioengineering

Ko˜ljalg, U., Nilsson, H.R., Schigel, D., Tedersoo, L., Larsson, K.-H., May, T.W., Taylor, A.F.S., Jeppesen, T.S., Frøslev, T.G., Lindahl, B.D., Po˜ldmaa, K., Saar, I., Suija, A., Savchenko, A., Yatsiuk, I., Adojaan, K., € ho € nen, R., Zirk, A., Abarenkov, K., 2020. The taxon hypothesis paradigmIvanov, F., Piirmann, T., Po on the unambiguous detection and communication of taxa. Microorganisms 8 (12), 1910. Krebes, L., Blank, M., Frankowski, J., Bastrop,, R., 2010. Molecular characterisation of the Microsporidia of the amphipod Gammarus duebeni across its natural range revealed hidden diversity, wide-ranging prevalence and potential for co-evolution. Infect. Genet. Evol. 10, 1027–1038. Kriznik, A., Bouillot, M., Coulon, J., Gaboriaud, F., 2005. Morphological specificity of yeast and filamentous Candida albicans forms on surface properties. C. R. Biol. 328 (10), 928–935. Kumari, A., Kishor, N., Guptasarma, P., 2018. Characterization of a mildly alkalophilic and thermostable recombinant Thermus thermophilus laccase with applications in decolourization of dyes. Biotechnol. Lett. 40 (2), 285–295. Lara, E., Moreira, D., Lo´pez-Garcı´a, P., 2010. The environmental clade LKM11 and Rozella form the deepest branching clade of fungi. Protist 161 (1), 116–121. Lee, S.C., Weiss, L.M., Heitman, J., et al., 2009. Generation of genetic diversity in microsporidia via sexual reproduction and horizontal gene transfer. Commun. Integr. Biol. 2 (5), 414–417. https://doi.org/ 10.4161/cib.2.5.8846. Levasseur, A., Drula, E., Lombard, V., Coutinho, P.M., Henrissat, B., 2013. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol. Biofuels 6 (1), 1–14. Lewis, D.H., 1973. Concepts in fungal nutrition and the origin of biotrophy. Biol. Rev. 48 (2), 261–277. Li, G.J., Hyde, K.D., Zhao, R.L., Hongsanan, S., Abdel-Aziz, F.A., Abdel-Wahab, M.A., Alvarado, P., AlvesSilva, G., Ammirati, J.F., Ariyawansa, H.A., Baghela, A., Bahkali, A.H., Beug, M., Bhat, D.J., Bojantchev, D., Boonpratuang, T., Bulgakov, T.S., Camporesi, E., Boro, M.C., Ceska, O., Chakraborty, D., Chen, J.J., Chethana, K.W.T., Chomnunti, P., Consiglio, G., Cui, B.K., Dai, D.Q., Dai, Y.C., Daranagama, D.A., Das, K., Dayarathne, M.C., De Crop, E., De Oliveira, R.J.V., de Souza, C.A.F., de Souza, J.I., Dentinger, B.T.M., Dissanayake, A.J., Doilom, M., Drechsler-Santos, E.R., Ghobad-Nejhad, M., Gilmore, S.P., Go´es-Neto, A., Gorczak, M., Haitjema, C.H., Hapuarachchi, K.K., Hashimoto, A., He, M.Q., Henske, J.K., Hirayama, K., Iribarren, M.J., Jayasiri, S.C., Jayawardena, R.S., Jeon, S.J., ^ nimo, G.H., Jesus, A.L., Jones, E.B.G., Kang, J.C., Karunarathna, S.C., Kirk, P.M., Konta, S., Jero Kuhnert, E., Langer, E., Lee, H.S., Lee, H.B., Li, W.J., Li, X.H., Liimatainen, K., Lima, D.X., Lin, C.G., Liu, J.€ cking, R., Lumbsch, H.T., Lumyong, S., Lean˜o, E.M., K., Liu, X.Z., Liu, Z.Y., Luangsa-ard, J.J., Lu Marano, A.V., Matsumura, M., McKenzie, E.H.C., Mongkolsamrit, S., Mortimer, P.E., Nguyen, T.T.T., Niskanen, T., Norphanphoun, C., O’Malley, M.A., Parnmen, S., Pawłowska, J., Perera, R.H., Phookamsak, R., Phukhamsakda, C., Pires-Zottarelli, C.L.A., Rasp e, O., Reck, M.A., Rocha, S.C.O., de Santiago, A.L.C.M.A., Senanayake, I.C., Setti, L., Shang, Q.J., Singh, S.K., Sir, E.B., Solomon, K.V., Song, J., Srikitikulchai, P., Stadler, M., Suetrong, S., Takahashi, H., Takahashi, T., Tanaka, K., Tang, L.P., Thambugala, K.M., Thanakitpipattana, D., Theodorou, M.K., Thongbai, B., Thummarukcharoen, T., Tian, Q., Tibpromma, S., Verbeken, A., Vizzini, A., Vlasa´k, J., Voigt, K., Wanasinghe, D.N., Wang, Y., Weerakoon, G., Wen, H.A., Wen, T.C., Wijayawardene, N.N., Wongkanoun, S., Wrzosek, M., Xiao, Y.P., Xu, J.C., Yan, J.Y., Yang, J., Da Yang, S., Hu, Y., Zhang, J.F., Zhao, J., Zhou, L.W., Persˇoh, D., Phillips, A.J.L., Maharachchikumbura, S.S.N., 2016. Fungal diversity notes 253–366: taxonomic and phylogenetic contributions to fungal taxa. Fungal Divers. 78 (1), 1–237. Li, F., Li, Z., Zeng, C., Hu, Y., 2017. Laccase-assisted rapid synthesis of colloidal gold nanoparticles for the catalytic reduction of 4-nitrophenol. J. Braz. Chem. Soc. 28, 960–966. Linnaeus, C., 1767. Systema naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Ed. 12. 1., Regnum Animale. 1 & 2. Laurentii Salvii, Holmiae [Stockholm]. Lo´pez-Garcı´a, P., Vereshchaka, A., Moreira, D., 2007. Eukaryotic diversity associated with carbonates and fluid-seawater interface in Lost City hydrothermal field. Environ. Microbiol. 9 (2), 546–554.

Chapter 1 • World of fungi and fungal ecosystems

25

Lorch, J.M., Meteyer, C.U., Behr, M.J., Boyles, J.G., Cryan, P.M., Hicks, A.C., Ballmann, A.E., Coleman, J.T., Redell, D.N., Reeder, D.M., Blehert, D.S., 2011. Experimental infection of bats with Geomyces destructans causes white-nose syndrome. Nature 480 (7377), 376–378. Lutzoni, F., Miadlikowska, J., 2009. Lichens. Curr. Biol. 19 (13), R502–R503. Marin-Felix, Y., Groenewald, J.Z., Cai, L., Chen, Q., Marincowitz, S., Barnes, I., Bensch, K., Braun, U., Camporesi, E., Damm, U., de Beer, Z.W., Dissanayake, A., Edwards, J., Giraldo, A., Herna´ndez-Restrepo, M., Hyde, K.D., Jayawardena, R.S., Lombard, L., Luangsa-ard, J., McTaggart, A.R., Rossman, A.Y., Sandoval-Denis, M., Shen, M., Shivas, R.G., Tan, Y.P., van der Linde, E.J., Wingfield, M.J., Wood, A.R., Zhang, J.Q., Zhang, Y., Crous, P.W., 2017. Genera of phytopathogenic fungi: GOPHY 1. Stud. Mycol. 86, 99–216. Marin-Felix, Y., Herna´ndez-Restrepo, M., Wingfield, M.J., Akulov, A., Carnegie, A.J., Cheewangkoon, R., Gramaje, D., Groenewald, J.Z., Guarnaccia, V., Halleen, F., Lombard, L., Luangsa-ard, J., Marincowitz, S., Moslemi, A., Mostert, L., Quaedvlieg, W., Schumacher, R.K., Spies, C.F.J., Thangavel, R., Taylor, P.W.J., Wilson, A.M., Wingfield, B.D., Wood, A.R., Crous, P.W., 2019. Genera of phytopathogenic fungi: GOPHY 2. Stud. Mycol. 92, 47–133. Markham, P., 1994. Occlusions of septal pores in filamentous fungi. Mycol. Res. 98 (10), 1089–1106. n, F., Martı´nez, M.J., ˜ as, F.J., Ferreira, P., Camarero, S., Guille Martı´nez, A.T., Speranza, M., Ruiz-Duen rrez, A., del Rı´o, J.C., 2005. Biodegradation of lignocellulosics: microbial, chemical, and enzyGutie matic aspects of the fungal attack of lignin. Int. Microbiol. 8 (3), 195–204. Mayolo-Deloisa, K., Gonza´lez-Gonza´lez, M., Rito-Palomares, M., 2020. Laccases in food industry: bioprocessing, potential industrial and biotechnological applications. Front. Bioeng. Biotechnol. 8 (222). McClymont,, H.E, Dunn, A.M., Terry, R.S., Rollinson, D., Littlewood, D.T.J., Smith, J.E., et al., 2005. Molecular data suggest that microsporidian parasites in freshwater snails are diverse. Int. J. Parasitol. 35, 1071–1078. Mendell, M.J., Mirer, A.G., Cheung, K., Tong, M., Douwes, J., 2011. Respiratory and allergic health effects of dampness, mold, and dampness-related agents: a review of the epidemiologic evidence. Environ. Health Perspect. 119 (6), 748–756. Miller, R., Jastrow, J., 2000. Mycorrhizal fungi influence soil structure. In: Kapulnik, Y., Douds, D.D. (Eds.), Arbuscular Mycorrhizas: Physiology and Function. Springer, Dordrecht, pp. 3–18. Minussi, R.C., Pastore, G.M., Dura´n, N., 2002. Potential applications of laccase in the food industry. Trends Food Sci. Technol. 13 (6–7), 205–216. Mitchell, J.K., Garrido-Benavent, I., Quijada, L., Pfister, D.H., 2021. Sareomycetes: more diverse than meets the eye. IMA Fungus 12 (1), 6. Mittelbach, G.G., Schemske, D.W., 2015. Ecological and evolutionary perspectives on community assembly. Trends Ecol. Evol. 30 (5), 241–247. Monchy, S., Sanciu, G., Jobard, M., Rasconi, S., Gerphagnon, M., Chab e, M., Cian, A., Meloni, D., Niquil, N., Christaki, U., Viscogliosi, E., Sime-Ngando, T., 2011. Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing. Environ. Microbiol. 13 (6), 1433–1453. Money, N.P., 2016. Fungal diversity. In: Watkinson, S.C., Boddy, L., Money, N.P. (Eds.), The Fungi, third ed. Academic Press, Boston, pp. 1–36 (Chapter 1). Moore, J.C., Berlow, E.L., Coleman, D.C., de Ruiter, P.C., Dong, Q., Hastings, A., Johnson, N.C., McCann, K.S., Melville, K., Morin, P.J., Nadelhoffer, K., Rosemond, A.D., Post, D.M., Sabo, J.L., Scow, K.M., Vanni, M.J., Wall, D.H., 2004. Detritus, trophic dynamics and biodiversity. Ecol. Lett. 7 (7), 584–600. Morgavi, D.P., Rathahao-Paris, E., Popova, M., Boccard, J., Nielsen, K.F., Boudra, H., 2015. Rumen microbial communities influence metabolic phenotypes in lambs. Front. Microbiol. 6, 1060. https://doi.org/ 10.3389/fmicb.2015.01060.

26

Current Developments in Biotechnology and Bioengineering

Mosse, B., Stribley, D.P., LeTacon, F., 1981. Ecology of mycorrhizae and mycorrhizal fungi. In: Alexander, M. (Ed.), Advances in Microbial Ecology. Springer US, Boston, MA, pp. 137–210. Muggia, L., Fleischhacker, A., Kopun, T., Grube, M., 2016. Extremotolerant fungi from alpine rock lichens and their phylogenetic relationships. Fungal Divers. 76, 119–142. Nagano, Y., Nagahama, T., Hatada, Y., Nunoura, T., Takami, H., Miyazaki, J., Takai, K., Horikoshi, K., 2010. Fungal diversity in deep-sea sediments—the presence of novel fungal groups. Fungal Ecol. 3 (4), 316–325. Naranjo-Ortiz, M.A., Gabaldo´n, T., 2019. Fungal evolution: diversity, taxonomy and phylogeny of the Fungi. Biol. Rev. 94 (6), 2101–2137. Nash, T.H., 1996. Lichen Biology. Cambridge University Press. Neitlich, P.N., McCune, B., 1997. Hotspots of epiphytic lichen diversity in two young managed forests. Conserv. Biol. 11 (1), 172–182. Newman, E.I., 1988. Mycorrhizal links between plants: their functioning and ecological significance. In: Begon, M., Fitter, A.H., Ford, E.D., Macfadyen, A. (Eds.), Advances in Ecological Research. vol. 18. Academic Press, pp. 243–270. Niedermeyer, T.H.J., Mikolasch, A., Lalk, M., 2005. Nuclear amination catalyzed by fungal laccases: reaction products of p-hydroquinones and primary aromatic amines. J. Org. Chem. 70 (6), 2002–2008. € rnberger, T., Brunner, F., Kemmerling, B., Piater, L., 2004. Innate immunity in plants and animals: strikNu ing similarities and obvious differences. Immunol. Rev. 198 (1), 249–266. Nwe, N., Furuike, T., Tamura, H., 2011. Production, properties and applications of fungal cell wall polysaccharides: chitosan and glucan. In: Jayakumar, R., Prabaharan, M., Muzzarelli, R. (Eds.), Chitosan for Biomaterials II. Advances in Polymer Science. vol. 244. Springer, Berlin, Heidelberg. Oksanen, I., 2006. Ecological and biotechnological aspects of lichens. Appl. Microbiol. Biotechnol. 73 (4), 723–734. Olsson, S., Gray, S.N., 1998. Patterns and dynamics of 32P-phosphate and labelled 2-aminoisobutyric acid (14C-AIB) translocation in intact basidiomycete mycelia. FEMS Microbiol. Ecol. 26 (2), 109–120. Orpin, C.G., 1975. Studies on the rumen flagellate Neocallimastix frontalis. J. Gen. Microbiol. 91, 249–262. Osono, T., 2007. Ecology of ligninolytic fungi associated with leaf litter decomposition. Ecol. Res. 22 (6), 955–974. Osono, T., Takeda, H., 2002. Comparison of litter decomposing ability among diverse fungi in a cool temperate deciduous forest in Japan. Mycologia 94 (3), 421–427. Ozyurt, M., Atacag, H., 2003. Biodegradation of azo dyes: a review. Fresenius Environ. Bull. 12, 1294–1302. Persson, C., Olsson, S., Jansson, H.-B., 2000. Growth of Arthrobotrys superba from a birch wood resource base into soil determined by radioactive tracing. FEMS Microbiol. Ecol. 31 (1), 47–51. Phookamsak, R., Liu, J.-K., McKenzie, E.H.C., Manamgoda, D.S., Ariyawansa, H., Thambugala, K.M., Dai, D.-Q., Camporesi, E., Chukeatirote, E., Wijayawardene, N.N., Bahkali, A.H., Mortimer, P.E., Xu, J.-C., Hyde, K.D., 2014. Revision of Phaeosphaeriaceae. Fungal Divers. 68 (1), 159–238. Pietro, A.D., Madrid, M.P., Caracuel, Z., Delgado-Jarana, J., Roncero, M.I.G., 2003. Fusarium oxysporum: exploring the molecular arsenal of a vascular wilt fungus. Mol. Plant Pathol. 4 (5), 315–325. Pointing, S., 2001. Feasibility of bioremediation by white-rot fungi. Appl. Microbiol. Biotechnol. 57 (1), 20–33. Porter, T.M., Schadt, C.W., Rizvi, L., Martin, A.P., Schmidt, S.K., Scott-Denton, L., Vilgalys, R., Moncalvo, J.M., 2008. Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life. Mol. Phylogenet. Evol. 46 (2), 635–644. Proctor, M.C.F., Tuba, Z., 2002. Poikilohydry and homoihydry: antithesis or spectrum of possibilities? New Phytol. 156 (3), 327–349.

Chapter 1 • World of fungi and fungal ecosystems

27

Pulschen, A.A., Rodrigues, F., Duarte, R.T., Araujo, G.G., Santiago, I.F., Paulino-Lima, I.G., Rosa, C.A., Kato, M.J., Pellizari, V.H., Galante, D., 2015. UV-resistant yeasts isolated from a high-altitude volcanic area on the Atacama Desert as eukaryotic models for astrobiology. Microbiology 4 (4), 574–588. , M.S., Giovannoni, S.J., 2003. The uncultured microbial majority. Annu. Rev. Microbiol. 57, 369–394. Rappe blova´, M., Miller, A.N., R Re eblova´, K., Sˇteˇpa´nek, V., 2018. Phylogenetic classification and generic delineation of Calyptosphaeria gen. nov., Lentomitella, Spadicoides and Torrentispora (Sordariomycetes). Stud. Mycol. 89, 1–62. , F., del Campo, J., Romac, S., Jones, M.D.M., Maguire, F., Dunthorn, M., Richards, T.A., Leonard, G., Mahe De Vargas, C., Massana, R., Chambouvet, A., 2015. Molecular diversity and distribution of marine fungi across 130 European environmental samples. Proc. R. Soc. B Biol. Sci. 282 (1819), 20152243. Rodrı´guez Couto, S., Toca Herrera, J.L., 2006. Industrial and biotechnological applications of laccases: a review. Biotechnol. Adv. 24 (5), 500–513. Romano, A., 1966. Dimorphism. In: Ainsworth, G.C., Sussman, A.S. (Eds.), The Fungi. vol. 2. Academic Press, New York, pp. 181–209. Rosling, A., Landeweert, R., Lindahl, B., Larsson, K.H., Kuyper, T., Taylor, A., Finlay, R.J.N.P., et al., 2003. Vertical distribution of ectomycorrhizal fungal taxa in a podzol soil profile. New Phytol. 159 (3), 775–783. Ruiz-Herrera, J., 1991. Fungal Cell Wall: Structure, Synthesis, and Assembly. CRC Press. Ruiz-Lozano, J.M., 2003. Arbuscular mycorrhizal symbiosis and alleviation of osmotic stress. New perspectives for molecular studies. Mycorrhiza 13 (6), 309–317. Ruiz-Lozano, J.M., Azco´n, R., Go´mez, M., 1996. Alleviation of salt stress by arbuscular-mycorrhizal Glomus species in Lactuca sativa plants. Physiol. Plant. 98 (4), 767–772. Schadt, C.W., Rosling, A., 2015. Comment on “Global diversity and geography of soil fungi”. Science 348 (6242). Schaller, M., Borelli, C., Korting, H.C., Hube, B., 2005. Hydrolytic enzymes as virulence factors of Candida albicans. Mycoses 48 (6), 365–377. Schoch, C.L., Seifert, K.A., Huhndorf, S., Robert, V., Spouge, J.L., Levesque, C.A., Chen, W., 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc. Natl. Acad. Sci. 109 (16), 6241–6246. Schwartz, R.A., 2004. Superficial fungal infections. Lancet 364 (9440), 1173–1182. Semchenko, M., Leff, J.W., Lozano, Y.M., Saar, S., Davison, J., Wilkinson, A., Jackson, B.G., Pritchard, W.J., De Long, J.R., Oakley, S., Mason, K.E., Ostle, N.J., Baggs, E.M., Johnson, D., Fierer, N., Bardgett, R.D., 2018. Fungal diversity regulates plant-soil feedbacks in temperate grassland. Sci. Adv. 4 (11). Sevcan, A., Yildirim, E., Ince, O., Ince, B., 2017. Rumen anaerobic fungi create new opportunities for enhanced methane production from microalgae biomass. Algal Res. 23, 150–160. Sharma, B., Dangi, A.K., Shukla, P., 2018. Contemporary enzyme based technologies for bioremediation: a review. J. Environ. Manag. 210, 10–22. Shivas, R., Hyde, K., 1997. Biodiversity of plant pathogenic fungi in the tropics. In: Biodiversity of Tropical Microfungi. Hong Kong University Press, pp. 47–56. Slippers, B., Boissin, E., Phillips, A.J.L., Groenewald, J.Z., Lombard, L., Wingfield, M.J., Postma, A., Burgess, T., Crous, P.W., 2013. Phylogenetic lineages in the Botryosphaeriales: a systematic and evolutionary framework. Stud. Mycol. 76 (1), 31–49. Smith, S.E., Read, D.J., 2010. Mycorrhizal symbiosis. Academic Press. Sogin, M.L., Morrison, H.G., Huber, J.A., Welch, D.M., Huse, S.M., Neal, P.R., Arrieta, J.M., Herndl, G.J., 2006. Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc. Natl. Acad. Sci. U. S. A. 103 (32), 12115–12120.

28

Current Developments in Biotechnology and Bioengineering

Spatafora, J.W., Chang, Y., Benny, G.L., Lazarus, K., Smith, M.E., Berbee, M.L., Bonito, G., Corradi, N., Grigoriev, I., Gryganskyi, A., James, T.Y., O’Donnell, K., Roberson, R.W., Taylor, T.N., Uehling, J., Vilgalys, R., White, M.M., Stajich, J.E., 2016. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108 (5), 1028–1046. Sun, J., Chen, Q.-J., Zhu, M.-J., Wang, H.-X., Zhang, G.-Q., 2014. An extracellular laccase with antiproliferative activity from the sanghuang mushroom Inonotus baumii. J. Mol. Catal. B Enzym. 99, 20–25. Tedersoo, L., Bahram, M., Po˜lme, S., Ko˜ljalg, U., Yorou, N.S., Wijesundera, R., Ruiz, L.V., Vasco-Palacios, A.M., Thu, P.Q., Suija, A., Smith, M.E., Sharp, C., Saluveer, E., Saitta, A., Rosas, M., Riit, T., €rtel, Ratkowsky, D., Pritsch, K., Po˜ldmaa, K., Piepenbring, M., Phosri, C., Peterson, M., Parts, K., Pa K., Otsing, E., Nouhra, E., Njouonkou, A.L., Nilsson, R.H., Morgado, L.N., Mayor, J., May, T.W., Majuakim, L., Lodge, D.J., Lee, S.S., Larsson, K.-H., Kohout, P., Hosaka, K., Hiiesalu, I., Henkel, T.W., Harend, H., Guo, L.-d., Greslebin, A., Grelet, G., Geml, J., Gates, G., Dunstan, W., Dunk, C., Drenkhan, R., Dearnaley, J., De Kesel, A., Dang, T., Chen, X., Buegger, F., Brearley, F.Q., Bonito, G., Anslan, S., Abell, S., Abarenkov, K., 2014. Global diversity and geography of soil fungi. Science 346 (6213), 1256688. €ring, M., Schigel, D., May, T., Ryberg, M., Tedersoo, L., Sa´nchez-Ramı´rez, S., Ko˜ljalg, U., Bahram, M., Do Abarenkov, K., 2018. High-level classification of the fungi and a tool for evolutionary ecological analyses. Fungal Divers. 90 (1), 135–159. Tisthammer, K.H., Cobian, G.M., Amend, A.S., 2016. Global biogeography of marine fungi is shaped by the environment. Fungal Ecol. 19, 39–46. Treseder, K.K., Lennon, J.T., 2015. Fungal traits that drive ecosystem dynamics on land. Microbiol. Mol. Biol. Rev. 79 (2), 243–262. https://doi.org/10.1128/MMBR.00001-15. Ueda, M., Shintani, K., Nakanishi-Anjyuin, A., Nakazawa, M., Kusuda, M., Nakatani, F., Kawaguchi, T., Tsujiyama, S.-i., Kawanishi, M., Yagi, T., Miyatake, K., 2012. A protein from Pleurotus eryngii var. tuoliensis C.J. Mou with strong removal activity against the natural steroid hormone, estriol: purification, characterization, and identification as a laccase. Enzym. Microb. Technol. 51 (6), 402–407. Ullah, N., Shahzad, K., Wang, M., 2021. The role of metabolic engineering technologies for the production of fatty acids in yeast. Biology 10, 632. https://doi.org/10.3390/biology10070632. Vinzelj, J., Joshi, A., Insam, H., Podmirseg, S.M., 2020. Employing anaerobic fungi bioga´s production: challenges & opportunities. Bioresour. Technol. 300, 122687. Virk, A.P., Sharma, P., Capalash, N., 2012. Use of laccase in pulp and paper industry. Biotechnol. Prog. 28 (1), 21–32. Voglmayr, H., Fournier, J., Jaklitsch, W.M., 2019. Two new classes of Ascomycota: Xylobotryomycetes and Candelariomycetes. Persoonia 42, 36–49. Vo
r´ısˇkova´, J., Baldrian, P., 2013. Fungal community on decomposing leaf litter undergoes rapid successional changes. ISME J. 7 (3), 477–486. Walker, G.M., White, N.A., 2017. Introduction to fungal physiology. In: Fungi: Biology and Applications. John Wiley & Sons, pp. 1–35. € la €, H., van der Putten, W.H., Wall, D.H., 2004. Ecological Wardle, D.A., Bardgett, R.D., Klironomos, J.N., Seta linkages between aboveground and belowground biota. Science 304 (5677), 1629–1633. Whittaker, R.H., 1969. New concepts of kingdoms of organisms. Science 163 (3863), 150–160. Wijayawardene, N.N., Hyde, K.D., Lumbsch, H.T., Liu, J.K., Maharachchikumbura, S.S.N., Ekanayaka, A.H., Tian, Q., Phookamsak, R., 2018. Outline of ascomycota: 2017. Fungal Divers. 88 (1), 167–263. Wijayawardene, N., Hyde, K., Al-Ani, L., Tedersoo, L., Haelewaters, D., Rajeshkumar, K.C., Zhao, R.-L., Aptroot, A., Saxena, R., Tokarev, Y., Dai, D.-Q., Letcher, P., Stephenson, S., Dolatabadi, S., Lumbsch, T., Maharachchikumbura, S., Issi, I.V., Madrid, H., 2020. Outline of fungi and fungus-like taxa. Mycosphere 11, 1160–1456.

Chapter 1 • World of fungi and fungal ecosystems

29

Woods, J.P., 2003. Knocking on the right door and making a comfortable home: Histoplasma capsulatum intracellular pathogenesis. Curr. Opin. Microbiol. 6 (4), 327–331. Wurzbacher, C., Larsson, E., Bengtsson-Palme, J., Van den Wyngaert, S., Svantesson, S., Kristiansson, E., Kagami, M., Nilsson, R.H., 2019. Introducing ribosomal tandem repeat barcoding for fungi. Mol. Ecol. Resour. 19 (1), 118–127. Yousuf, S., Choudhary, M.I., Atta-ur, R., 2014. Lichens: chemistry and biological activities. In: Atta-ur, R. (Ed.), Studies in Natural Products Chemistry. vol. 43. Elsevier, pp. 223–259 (Chapter 7). Zhang, N., Luo, J., Bhattacharya, D., 2017. Advances in fungal phylogenomics and their impact on fungal systematics. In: Townsend, J.P., Wang, Z. (Eds.), Advances in Genetics. vol. 100. Academic Press, pp. 309–328 (Chapter Eight). Zhou, D., Hyde, K.D., 2001. Host-specificity, host-exclusivity, and host-recurrence in saprobic fungi*. *Paper presented at the Asian mycological congress 2000 (AMC 2000) incorporating the 2nd AsiaPacific mycological congress on biodiversity and biotechnology, and held at the University of Hong Kong on 9-13 July 2000. Mycol. Res. 105 (12), 1449–1457.

2 Fungal biotechnology Mohammadtaghi Asadollahzadeh, Marzieh Mohammadi, and Patrik Roland Lennartsson ˚ S , SW EDEN SWE DISH C ENTRE FOR RE SOUR CE R ECOVE RY, UNIVERS ITY O F BORA˚ S, BOR A

1. Introduction As described in the first chapter of this book, filamentous fungi can be found almost everywhere on the planet where they fulfill a number of different ecological roles. Considering this vast diversity and that they are all heterotrophs, it should come as no surprise that filamentous fungi are able to both degrade and produce a plethora of different compounds. Fungal biotechnology is about exploiting these properties to produce whichever product is to be made, usually in a biorefinery, which is the topic for this book. Thus, this chapter will give an overview of the entire field with detailed descriptions in later chapters. In this chapter, we first provide an overview of the more technical aspects of fungal cultivations (Fungal cultivation and requirements followed by Fungal biorefineries) and then focus more on what can generally be produced by the different groups of fungi (Fungal metabolites and Fungal biomass). As the astute reader is probably already well aware of, biotechnological processes can both be considered as very simplistic, since ethanol fermentation has been carried out for thousands of years, and as highly complicated requiring very sophisticated control and state-of-the-art technology. This is also true for fungal biotechnology using filamentous fungi, which is what will be discussed here (by definition, yeast is also fungi but will not be included in this discussion). Fermentation with filamentous fungi ranges from small-scale fermented foods such as tempeh or beverages such as sake that have been produced using filamentous fungi for centuries, to fully industrial scale processes using the latest technology. The latter also includes the optimized traditional processes. A major part of the issue of complicated processes is the number of different factors (see Fig. 1 for a very brief overview) each with a very large number of different possibilities that interact with each other. Plenty of general trends can be found between different fungal species. For example, a metabolite that is produced under oxygen limited conditions for one species most likely requires oxygen limited conditions for another species, assuming the other species can produce the metabolite at all. However, general trends are not always true for all cases, and in some areas, identical conditions may lead to opposite reactions. For example, a few years ago Nyman et al. (2013) investigated pellet formation and found that addition

Current Developments in Biotechnology and Bioengineering. https://doi.org/10.1016/B978-0-323-91872-5.00006-5 Copyright © 2023 Elsevier Inc. All rights reserved.

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FIG. 1 A brief overview of fungal biotechnology and the main process conditions to consider and which process outputs can generally be considered.

of solids to the liquid medium decreased the likelihood of pellet formation for the investigated species, which was in direct contradiction to what was reported for most other species. Although fungal biotechnology brings a number of interesting possibilities, it also has special requirements or issues to deal with. Compared with yeast- or bacterial-based biotechnology, chief of these special requirements for fungal biotechnology is most likely caused by the filamentous growth of the fungi. These microscopic filaments can cause the fungi to attach to surfaces, entangle with each other, and influence the entire medium rheology. Thus, the filamentous growth always must be considered as it can influence the entirety of the process. This should be remembered as the rest of this chapter is read as well as the entire book.

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2. Fungal cultivation and requirements Fungi are known as decomposers but also as parasites of animals and plants, which can grow in almost all habitats and ecosystems on earth including soil, water, and vegetal environments. They thrive under very different environmental conditions and have variety of growth requirements like nutrients, pH, oxygen, osmotic conditions, and temperature (Chambergo and Valencia, 2016; Blackwell, 2011; Sugiharto, 2019). Under natural conditions of the environment, each microorganism usually adapt to the habitats most suitable for their needs. However, in the laboratory and industrial environments, a culture medium and reactor (or fermenter) must meet these requirements. The range of requirements depends on different factors and detailed investigations are needed to establish the most suitable chemical and physical requirements for fungal growth.

2.1 Fungal cultivation medium A substance on which a microorganism is grown on in the laboratory or industrial environment is called a medium and the microorganism growing on it, a culture. Culture medium contain all required components for growing and producing any primary or secondary products the cell has been designed to generate (Ikechi-Nwogu and Elenwo, 2012; Harvey and McNeil, 2008). A wide range of medium are used for growing fungi because of their diversity and numerous metabolic pathways. There are three general types of fungal culture medium based on chemical composition: natural, semisynthetic, or synthetic. Natural media are composed of various natural materials that are usually of plant or animal origin. The exact chemical composition is not known in natural medium but they are usually easy to prepare. Natural medium are used for many biotechnological processes because they are usually relatively cheap and available (Harvey and McNeil, 2008; Basu et al., 2015). Semi-synthetic medium are based on both natural ingredients and defined components. Potato dextrose agar (PDA), oatmeal agar (OMA), corn meal agar (CMA), yeast extract dextrose agar (YEDA), and peptone dextrose agar (PDA) are examples ( Jong and Birmingham, 2001). Synthetic media, on the other hand, contain ingredients of known composition and each component and its concentration are controlled. Synthetic medium are usually quite simple and also useful in research and laboratory works where experimental accuracy is paramount and data interpretation needs to be clear. Industrialists have not tended to use this kind of medium in fermentation processes because they are generally not cost effective at a large-scale (Harvey and McNeil, 2008; Jong and Birmingham, 2001). Medium used in bioprocessing can also be classified based on consistency (liquid or broth, semisolid and solid) and application or function (all-purpose medium, selective/differential medium, enrichment medium, and reducing medium) (Chauhan and Jindal, 2020).

2.1.1 Growth chemical requirements Despite the variety of medium in the type and combination of nutrients, the general composition of a medium remains the same with carbon source, nitrogen source, vitamins,

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and minerals (Chauhan and Jindal, 2020; Sood et al., 2011). Such essential nutrients can be divided into two categories: macronutrients, which are needed in large amounts, and micronutrients, which are needed in trace or small amounts. Macronutrients comprise sources of carbon, nitrogen, oxygen, hydrogen, sulfur, phosphorus, potassium, and magnesium; and micronutrients include trace elements like calcium, copper, iron, manganese, cobalt, molybdenum, and zinc (Chauhan and Jindal, 2020; Walker and White, 2017). The trace elements are generally part of enzymes and cofactors as well as help to maintain protein structure. These elements may not be necessary when natural or semi-synthetic medium are utilized. However, they must be added to pure synthetic medium or a medium in which a cell has an absolute requirement for a particular element or elements (Harvey and McNeil, 2008; Basu et al., 2015). Macronutrients usually help maintain the cell structure and metabolism. The physiological role of each macronutrients and their working concentration id presented in Table 1. A wide range of materials are used as carbon sources in culture media and the one chosen should both be appropriate to the microorganism and cost-effective (Harvey and McNeil, 2008). Sugars/carbohydrates are universally acceptable for fungal growth, and can range from simple monosaccharides like glucose to polysaccharides like starch and cellulose. In recent years, lignocellulosic materials have become more established as potential carbon sources due to their availability and low raw material cost. Following the carbon source, the nitrogen source is generally the next most plentiful substance in the cultivation medium (Kampen, 2014). Most industrially used microorganisms are able to use both inorganic and organic nitrogen sources. Inorganic nitrogen sources are generally NH3, NH4 + , NO3
, and NO2
. Components such as yeast extract, peptone, and whey are organic nitrogen sources and contain certain growth factors like amino acids or vitamins (Clarke, 2013; Stanbury et al., 2017a). Table 1 Physiological functions of macro-nutrients and their required concentration (Harvey and McNeil, 2008; Chauhan and Jindal, 2020; Kampen, 2014).

Element

Physiological function

Carbon Nitrogen Hydrogen Oxygen

Constituent of organic cell materials and energy source Constituent of proteins, nucleic acids, and coenzymes Constituent of cellular water and organic cell materials Constituent of cellular water and organic materials, as O2 electron acceptor in respiration of aerobes Constituent of amino acid (cysteine, cysteine, and methionine), some vitamins, e.g., biotin, as well as some coenzymes as CoA and cocarboxylase Constituent of phospholipids, coenzymes, and nucleic acids and the generation of energy (ATP, ADP) Principal intracellular cation and cofactor for the activity of certain enzymes This often acts as a cofactor for the activity of many enzymes, can play a significant role in membrane structure and function

Sulfur Phosphorus Potassium Magnesium

Required concentration (mol/L) > 10
2 10
3 – – 10
4 10
3–10
4 10
3–10
4 10
3–10
4

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In addition to the carbon and nitrogen sources, carbon to nitrogen (C:N) ratio play an important role in fungal growth, sporulation, and production of mycelia. The C:N ratios required by a number of fungi have been reported in literature. The C:N ratios in semisynthetic media are closer to reality, assuming that “reality” is approximately equal to the C:N ratio of soil materials or about 9:1 or 12:1. In this range, the medium is appropriate for growth and for some synthesis of nitrogen containing by-products (Cooke, 1968). Sometimes, the culture medium should be supplemented with certain components such as growth factors, chelating agents, buffers, precursors, inhibitors, inducers, and antifoams to provide all requirements for optimum growth and to control some of the problems in the fermentation process.

2.1.2 Design and preparation of culture medium A successful fermentation process needs a proper medium design. Factors such as cost, availability of substrates, reliability of substrate supply, handling, storage, ease of preparation (and storage), and transportation of components make medium design complicated. Therefore, substantial research must be put into obtaining all the information needed to optimize the medium (Harvey and McNeil, 2008). In general, medium are designed based on the following simplified equation (oxygen is only present in aerobic bioprocesses): C + N + O2 + other nutrients ! biomass + productðsÞ + CO2 + H2 O + Heat

In this equation, it is important to calculate the minimal quantities of nutrients which will be needed to produce a specific (and maximum) amount of biomass and required product yields. The medium should generally be designed to: • • • • • • • •

Produce the maximum yield of product Produce the maximum concentration of biomass Obtain the maximum rate of product formation Minimize the yield of undesirable products Be of consistent quality and available throughout the year Cause minimal problems during medium sterilization Allow for easy aeration, agitation, downstream processing, waste treatment, etc. Be able to scale-up (Sood et al., 2011; Stanbury et al., 2017a)

After the medium design and identification of its constituents, it is time to prepare it. The medium preparation is not just a scientific work but it requires detailed monitoring and planning. It is also important to find an appropriate preservation method and use the constituents optimally. When the culture medium has been made, it still (most often) has to be sterilized because of microbial contamination from air, receptacle or glassware, hands, etc. Although, all components present in the medium are usually sterilized together, some components like vitamins are sterilized separately in order to prevent losses (Harvey and McNeil, 2008).

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2.2 Fungal fermentation process 2.2.1 Inoculum preparation The population of microorganisms or cells that are introduced in the fermentation medium or any other suitable medium is the inoculum. The inoculum preparation and optimization are carried out before the fermentation process starts. During the first stage of inoculum development, the inoculum as spores or hyphae (mycelia) is taken from the working stock culture and transferred to a suitable culture medium to initiate the fungal growth. Growth at this stage is influenced by the adaptation of inoculum to the new environment, inoculum size, inoculum morphology, and inoculum transfer strategy that further influences the final product (Sood et al., 2011; Harvey and McNeil, 2008). The inoculum performance can be improved by various modifications including DNA recombination, radiation, and chemical addition (Sood et al., 2011). The inoculum transfer to the next cultivation stage can be done as spore suspension, mycelia disc, mycelia suspension, and pre-inoculated substrates. Among these, spore inoculum is used in most fermentation processes due to far more “propagules” compared to vegetative inoculum. In addition, this approach is easier to operate aseptically and it may be applied on a large scale. Nevertheless, vegetative inoculum is well suited to solid substrate fermentation as their penetrating hyphal habit facilitates the colonization of solid substrates (Stanbury et al., 2017b). The inoculum can be polluted by the contamination of an undesirable organism or undesirable organisms, which can result in lower productivity or even complete fermentation failure. Therefore, various sterilization methods and offline and online monitoring methods are applied to detect and prevent contamination (Sood et al., 2011).

2.2.2 Types of fermentation processes Fermentation is controlled cultivation of microorganisms like fungi for conversion of renewable feedstock into useful products. There are two common fermentation techniques called submerged fermentation (SmF) and solid-state fermentation (SSF) systems that are applied to produce biomass and metabolites by amplifying their production from a laboratory to large scale (Moslamy, 2019). Both systems have their own benefits and drawbacks, and choosing the appropriate technique is crucial for achieving the best performance from the microorganisms during the fermentation process and recovery of the products. SSF is the cultivation of microorganisms on the surface and at the interior of a solid € lker et al., matrix, in the absence or near absence of free water (Soccol et al., 2017; Ho 2004). SSF is one of the oldest biotechnological processes known and traditional fermented foods like koji, tapai, tempe, soy sauce, annatto, miso, etc. have been produced by this € lker et al., 2004; Nigam et al., 2003). In process, especially in Asia, for many centuries (Ho recent years, SSF has gained attention from the academic and industrial sectors because of its potential for producing industrially important products such as animal feeds, bioethanol, and various enzymes (Soccol et al., 2017; Nigam et al., 2003). In addition,

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SSF is currently the best method of collecting fungal spores by aerial hyphae. The morphological, functional, and biochemical properties of spores produced in SSF differ distinctly from those obtained in SmF. It was found that more spores are obtained if a combination of SmF (for biomass production in a first step) and SSF (for subsequent spore production) € lker et al., 2004). is utilized (Ho The mycelial modes of growth and neutral physiological capabilities of filamentous fungi have made them a dominant microorganism in SSF processes. Considerable amounts of enzymes and other metabolites are synthesized by filamentous fungi in this condition (Soccol et al., 2017). The typical advantages of SSF processes include lower capital and operating costs, low energy requirements, simple and low-cost medium, lesser wastewater production, less effort in down-stream processing and stirring, less susceptible to bacterial contamination and substrate inhibition, better oxygen circulation, and higher productivity (Stanbury et al., 2017a; Mandal and Banerjee, 2019; Robinson et al., 2001). On the other hand, wild-type strains of fungi tend to perform better in SSF conditions than genetically modified fungi (Robinson et al., 2001). In spite of the advantages mentioned, there are also several disadvantages of SSF, which have discouraged the use of this technique for industrial production. The main drawbacks are difficulties of scale-up, low mixing efficiency, difficult control of process parameters (pH, heat, moisture, nutrient conditions, etc.), problems with heat build-up, higher impurity of the product, increased product recovery costs, relatively slow growth rate of microorganisms, and the process being limited to € lker et al., microorganisms that can survive and thrive in low moisture conditions (Ho 2004; Couto and Sanroma´n, 2006). The fungal growth and product formation take place in a vessel referred to as the bioreactor that is considered as the heart of all bioprocess operations. The bioreactor provides a well-monitored system to meet the needs of the biological reaction system so that a high yield of the bioproduct is achieved. The bioreactors in SSF have been classified into four categories based on the operation modes that are used: (1) reactors without forced aeration and mixing/agitation of the solid substrate (e.g., tray bioreactor), (2) reactors without mixing/agitation but with forced aeration (e.g., packed-bed bioreactor), (3) reactors with mixing/agitation but without forced aeration (e.g., rotating-drum and stirred-drum bioreactors), and (4) reactors with mixing/agitation and forced aeration (e.g., fluidized-bed, rocking-drum, and stirred-aerated bioreactors) (Ge et al., 2017; Zhong, 2011). Some versions are illustrated in Fig. 2. SmF involves inoculation of the microbial culture as a suspension in a liquid medium in which various nutrients are either dissolved or suspended as particulate solids in many commercial medium. These days, most of the commercial products including enzymes and secondary metabolites are produced through the SmF processes due to its advantages (Kapoor et al., 2016). The SmF possesses considerable advantages including ease of scale-up and automation, shorter required fermentation time, ease of product purification, and better control of the physical-chemical variables of the process. However, the major disadvantages

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Current Developments in Biotechnology and Bioengineering

FIG. 2 Schematic of bioreactors for SSF: tray bioreactor, packed-bed bioreactor, rotating-drum bioreactor, stirred packed bed bioreactor.

associated with the SmF processes as compared to the SSF are lower productivity, high production cost, and complexity of medium, more effluent generation, complex fermentation equipment, large reactors needed, and risk of contamination (Kapoor et al., 2016; de Carvalho, 2016). There are three major fermentation modes in SmF processes, i.e., batch, fed-batch, and continuous cultivation (they exist for SSF processes as well), which can be operated either aerobic or anaerobic conditions. The development and optimization of the SmF processes involve understanding the three modes of fermenter operation so that the one best suited to the process can be determined (Kapoor et al., 2016; Macauley-Patrick and Finn, 2008). Batch fermentation is considered as the simplest mode of cultivation systems, as it is operated in a closed vessel where all of the nutrients required for the organism’s growth and product formation are added to the vessel, mostly under aseptic conditions, at the beginning of the fermentation process. Indeed, no extra feeding is used during the process; all is done as one batch. During batch fermentation, four typical phases can normally be observed: lag phase, exponential phase, stationary phase, and declination phase (Fig. 3). Fed-batch fermentation is a semi-open system in which one or more nutrients continuously or intermittently are introduced into the bioreactor after the start of cultivation, or from a certain point during the batch process and optimum concentrations of required nutrients are maintained by such intermittent feeding. Intracellular products of cell cultures that are stored within the cells are often produced by fed-batch cultures. In a continuous culture, the microorganisms are continuously fed with fresh medium and the nutrients consumed by the cells are removed from the system at the same rate. Therefore, factors such as culture volume, biomass or cell number, product and substrate concentrations, as well as the physical parameters of the system such as pH, temperature, and dissolved oxygen will be kept constant throughout the fermentation. This balanced growth is a very attractive tool in studies on growth and production kinetics or cell physiology (Zhong, 2011; Kapoor et al., 2016; Macauley-Patrick and Finn, 2008). Several types of bioreactors including stirred tank, airlift, bubble column, membrane, packed-bed, and fluidized-bed bioreactors, which are designed for the SmF processes.

Chapter 2 • Fungal biotechnology

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FIG. 3 The four phases seen in batch cultivation: lag phase during which the fungi get acclimatized, exponential phase during which exponential growth occurs, stationary phase during which no net change in biomass concentration happens, and declination phase during which the biomass concentration decreases.

Novel bioreactors are constantly being developed for special applications and new forms of biocatalysts. In stirred tank reactors, mechanical devices like impellers and baffles provide efficient mixing and bubble dispersion, which allow for a good control of pH, temperature, airflow, and dissolved oxygen. This technique requires a relatively high input of energy per unit volume. Unlike stirred tank reactors, aeration, and mixing in bubble column and airlift reactors are achieved by air or gas sparging without mechanical devices. The patterns of liquid flow in airlift reactors differ from those in bubble column reactors. Packedbed reactors are operated with immobilized or particulate biocatalysts. The reactor consists of a tube, usually vertical, packed with catalyst particles. After medium feeding at either the top or bottom of the column, a continuous liquid phase between the particles is formed. This bioreactor considered as a promising tool for tissue engineering applications that support various cell lines for long incubation periods due to the immobilization of cells within matrices. In fluidized-bed bioreactors, biocatalysts such as enzymes or microbial cells are used to complete a variety of multiphase of chemical reactions. Despite the complexity of fluidized-bed bioreactors, it has been using in many industrial applications. When packed-beds are operated in upflow mode with catalyst beads of appropriate size and density, the bed expands at high liquid flow rates due to upward motion of the particles. This is the basis for operation of fluidized-bed reactors as illustrated in Fig. 4. Because particles in fluidized-beds are in constant motion, clogging of the bed and flow channeling are avoided so that air can be introduced directly into the column. This reactor can be used in waste treatment with sand or similar material supporting mixed microbial populations and vinegar production by flocculating organisms (Zhong, 2011; Doran, 2013; Moslamy, 2019).

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FIG. 4 Schematic of bioreactors for SmF: stirred tank bioreactor, bubble column bioreactor, airlift bioreactor, packedbed bioreactor, and fluidized-bed bioreactor.

2.3 Effects of process variables on growth and product formation Factors influencing the performance of a cultivation (or fermentation) process can be categorized into physical, chemical, or biological. The physical and chemical factors define the environment of microorganism, while the biological factors describe its behavior (Fazenda et al., 2008). The medium composition including type and concentration of nutrients affect fungal growth, metabolite production, and morphological differentiation. An evaluation was carried out on the cultivation of Aspergillus niger, Aspergillus flavus, Penicillium chrysogenum, Aspergillus terreus, Aspergillus glaucus, Fusarium oxysporium, and Rhizopus stolonifer on potato dextrose, soybean dextrose, sawdust sucrose, ofor (Detarium macrocarpum, a tree growing in Africa) sucrose, and groundnut dextrose broth. From the results

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obtained, soybean dextrose broth performed better than other broths for the growth of the fungi evaluated probably because it contains more vitamins and minerals vital to fungal growth. Groundnut dextrose broth was the second best medium, probably due to higher nutritional content, including the presence of cystine, thiamine (vitamin B1), riboflavin (vitamin B2), niacin (vitamin B3), pantothenic acid (vitamin B5), and folate (vitamin B9) (Ikechi-Nwogu and Elenwo, 2012). The comparison of nine agro-industrial and forestry by-products including (i) nut (almond and walnut 1:1 w:w) shells, (ii) beech sawdust, (iii) corn cobs, (iv) grape marc plus cotton gin trash (1:1, w:w), (v) olive mill by-products (leaves plus two-phase olive mill waste 1:1, w:w), (vi) extracted olive press-cake, (vii) pine needles, (viii) date palm leaves, and (ix) wheat straw fermented by Agrocybe cylindracea and Pleurotus ostreatus in SSF showed that grape marc waste plus cotton gin trash was the best performing medium for both fungi followed by olive mill by-products and pine needles for the former and latter species, respectively. Substrate composition had a marked effect on most cultivation parameters (Koutrotsios et al., 2014). Singh et al. (2020) found that glucose and sucrose when used as a carbon source resulted in higher biomass concentration of Pleurotus eryngii in comparison to other carbon sources. In addition, nitrogen sources favorable for the mycelial growth were observed to be yeast extract and peptone. The effect of physical factors including temperature, pH, oxygen concentration or oxygen transfer, aeration, and agitation rates on fungi performance and its productivity has been investigated by many researchers. This is discussed below. Although fungi can survive in a range of temperatures, but small variations in temperature can greatly reduce the productivity. The temperature range usually reported for fungal growth is 10–35 °C, with a few species capable of growth below or above this range (phsycrophillic to thermophilic). Increasing temperature generally results in higher metabolic rates, but decreases the solubility of dissolved oxygen in the medium (Fazenda et al., 2008). The optimal temperature for mycelium growth of oyster mushroom Pleurotus ostreatus and Pleurotus cystidiosus was 28 °C (Hoa and Wang, 2015). As Singh et al. (2020) reported, the initial pH of the medium did not influence the mycelial biomass concentration whereas the shaking frequency (i.e., mixing) and temperature variation had a positive influence on the mycelial biomass concentration. All microorganisms have an optimal pH at which they grow the best. Alteration of this pH value leads to undesirable growth. Most fungi are acidophilic and grow well between pH 4 and 6, but some species can grow in more acidic or alkaline conditions (around pH 3 or pH 8, respectively). Sar et al. (2020) found that changing the initial pH (6.1–6.5) to 5.0 had a negative influence on the amount of biomass produced from the edible filamentous fungus Rhizopus oryzae cultivated on fish industry side streams while medium supplementation had no influence. The maximum xylanase activity has been found to differ considerably dependant on the species producing it. In Aspergillus fischeri optimum pH was between pH 6 and 10, whereas the optimal pH for xylanase production by strains of Aspergillus fumigatus was pH 5 or less and maximal xylanase production by Aspergillus fumigatus occurred below pH 3.5. Moreover, a cultivation pH of up to 7.5 favored xylanase production by a Thermomyces lanuginosus and Aspergillus

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oryzae (Chipeta et al., 2008). A low initial pH of the medium (below 2.0) was necessary for increased yields in the citric acid fermentation by Aspergillus niger whereas the optimal pH for maximum gluconic acid production by Aspergillus niger was 6.5. Increasing the pH to 4.5 during the production phase reduced the final yield of citric acid by up to 80% (Papagianni, 2019). Oxygen transfer and maintaining a suitable oxygen concentration in the culture broth are always a concern in aerobic fermentation systems. When the supply of oxygen is limited, both cell growth and product formation can be severely affected (Zhong, 2011). Increased dissolved oxygen (DO) concentrations resulted in increased citric acid yield from Aspergillus niger fermentation, while even a short interruption in aeration had detrimental effects on the yield as it rerouted metabolism toward biomass formation (Papagianni, 2019). In SmF, aeration and agitation provide two related functions: (i) to supply dissolving oxygen needed by the growing hyphae, and (ii) to homogenize mycelial mass, nutrients and products within the culture broth. However, the shear forces created by agitation may damage cell structure, lead to morphological changes, and cause variations in growth rate and product formation. Therefore, the optimum agitation rate represents a balance between achieving adequate oxygen transfer into the medium and shear stress, both of which increase with increasing agitation rate (Zhong, 2011; Fazenda et al., 2008). It is widely accepted that inoculum concentration and age exert a major influence on the fungal fermentation profile. In fact, the amount, type (spore vs vegetative), age, and viability of the inoculum all may affect morphological state of the cells, especially in pellet production and the type of pellets produced (Fazenda et al., 2008).

3. Fungal biorefineries Fungal biorefineries are multi-output systems that convert biological feedstocks into a spectrum of high added value products, and are able to reduce the contamination of the environment. These systems have been the subject of a growing interest for the biorefinery concept because they represent a rich source of enzymes, organic acids, pigments, vitamins, volatile compounds, antibiotics, and other substances of relevance to the pharmaceutical, food, feed, agricultural, textile, pulp and paper, chemical, and biotechnological industries (Fig. 5). The most attractive group for fungal biorefineries are the so-called filamentous fungi, such as those belonging to the Ascomycetes, Basidiomycetes, and Zygomycetes groups. Filamentous fungi have some inherent important characteristics such as being able to produce a remarkable wealth of commercially interesting metabolites, a welldemonstrated growth ability on a broad substrate range, and well-developed methodology for genetic modification, which makes them great contributions within a wide range of industrial sectors (Chroumpi et al., 2020; Ferreira et al., 2013, 2016).

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FIG. 5 Industries profiting from the metabolic capacities of fungi.

3.1 Fungal biorefinery-based industries 3.1.1 Agriculture The importance of fungi in the agriculture industry can be considered from different aspects. One of the cost-effective and eco-friendly means for solubilizing insoluble phosphorous (P) in soils is to use phosphate-solubilizing fungi, especially plant growthpromoting fungal strains. Furthermore, fungi are among one of the novel and potential sources of biological control agents. Thus, these helps to increase the availability of phosphorous for plants and could be potent and promising alternatives to synthetic pesticides and chemical fertilizers, and such beneficial microorganisms are perfect candidates for sustainable agricultural production (Challa et al., 2019; Vyas and Bansal, 2018; Kaur and Sudhakara Reddy, 2017). Fungi belonging to the order Hypocreales are used to control

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Current Developments in Biotechnology and Bioengineering

pests (insects or phytopathogens). The biopesticides available in the market capable of controlling insects include Beauveria bassiana, Nomuraea rileyi, Metarhizium anisopliae, and Paecilomyces fumosoroseus (mitosporic or asexual or conidiogenous entomopathogenic fungi), whereas phytopathogens are inhibited using biocontrol agent Trichoderma viride (Challa et al., 2019). Fungi play a fascinating role in the composting processes, degrading recalcitrant compounds during composting, remediating soils contaminated by pollutants, stabilizing organic matter while releasing nutrients and essential elements that are beneficial for plant growth and fertility. Acremonium, Alternaria, Aspergillus, Chaetomium, Cladosporium, Emericella, Fusarium, Geotrichum, Mortierella, Mucor, Penicillium, Pseudallescheria, Scopulariopsis, and Trichoderma are the fungi most isolated from compost. Some fungi including Absidia, Aspergillus, Chaetomium, Coprinus, Mucor, Paecilomyces, Penicillium, Rhizomucor, Scytalidium, and Thermomyces can grow at elevated temperatures (>65 °C) and are isolated from thermophilic compost phases (Wright et al., 2016).

3.1.2 Food and feed Fungi have long been known to play a significant role in the food and feed industry. Fungi are used as a direct source of food (mushrooms and truffles as the edible fungi), processed food (bread, cheese and other bakery products), fermented foods (alcohols, beverages), fodder, etc. They can also be used to produce protein biomass such as single-cell protein € ttner et al., 2020; Challa et al., 2019; Ghorai et al., 2009). (SCP) (Hu The fungi and fungal biomass as food and feed are very nutritive as they are good source of protein, essential and nonessential amino acids, dietary fiber and vitamins, almost low in fat, free of cholesterol, and easy to digest. Thus, such beneficial properties, diet consciousness and increasing health awareness has increased the fungal food utilization on a global basis over the past few years. Particularly, the people who are vegetarian have resorted to eating mushrooms or processed foods, dietary supplements, and beverages of fungal origin (Devi et al., 2020; Kour et al., 2019; Ghorai et al., 2009). Quorn® mycoprotein is a commercial form of SCP created from filamentous fungus Fusarium venenatum. It is popular since it has many similar characteristics with meat, e.g., texture and appearance, and effectively competes with meat alternatives like soy and pea on € ttner et al., 2020; Challa et al., 2019; Kour et al., 2019). health grounds (Hu In addition, a number of ingredients used during food processing such as acidulants, enzymes, flavors, vitamins, colorants (pigments), and polyunsaturated fatty acids (PUFAs) are obtained from fungi through industrial fermentation (Copetti, 2019). Organic acids as acidulant and also as flavoring agents, buffers, preservatives, and technology adjuvants are widely used in modern food processing (Copetti, 2019). Filamentous fungi are considered as excellent sources of food-grade pigments. Some pigments commercially produced by filamentous fungi are Monascus pigments, natural red from Penicillium oxalicum, riboflavin from Ashbya gossypii, lycopene, and β-carotene from Blakeslea trispora (Challa et al., 2019; Copetti, 2019; Ghorai et al., 2009). Enzymes are used in the food industry for many different applications including production of dairy, meat, cereal, beverage,

Chapter 2 • Fungal biotechnology

45

bakery and confectionery products, development and enhancement aroma, color, appearance, texture and flavor as well as improving quality of the final product while decreasing processing time and production costs (Copetti, 2019; Kour et al., 2019). Moreover, fungi, especially filamentous fungi, produce edible oils rich in PUFAs for dietary supplements and infant nutrition applications (Coradini et al., 2015).

3.1.3 Pharmaceutical Among microorganisms, fungi have significant ability to protect against a number of pathogenic bacteria and fungi due to the bioactive agents that they naturally produce as secondary metabolites. Penicillin was the first and the best-known discovery, which proved to inhibit the growth of Gram-positive bacteria (Devi et al., 2020; Gholami-Shabani et al., 2019). Several effective antibiotics and drugs with antifungal, nematocidal, antiprotozoal, antibacterial, antiplasmodial, and antiviral properties, as well as anti-inflammatory inhibitors, anti-tuberculosis and anticancer drugs, agonists or antagonists at adrenergic, dopaminergic, and serotonergic receptors, and hypercholesterolemia treatment agents are being produced using fungi (Devi et al., 2020; Chambergo and Valencia, 2016). For this, some human diseases are treated by fungi. For example, Agaricus campestris is used against sinusitis, inflammation, and tuberculosis. Laricifomes officinalis can be used for treating diarrhea and night sweating. Daedaleopsis flavida helps in the reduction of bilirubin and biliviridin and is very effective for the treatment of jaundice. The treatment of chronic gastritis, early tumors, and ulcers is done using Inonotus obliquus. Alkaloid secreted from Aspergillus, Penicillium, Pestalotiopsis, and Chromocleista is a β-carboline group containing secondary metabolites having antimicrobial, anti-HIV, and antiparasitic activities (Devi et al., 2020). Lovastatin as a cholesterol lowering drug is produced by a diverse range of filamentous fungi like Aspergillus sp., Aspergillus terreus, Monascus sp., Phoma sp., Gymnoascus umbrinus, Penicillium brevicompactum, Penicillium citrinum (Saberi et al., 2020; Chambergo and Valencia, 2016). The utilization of filamentous fungal enzymes is also growing in pharma industry, particularly ones that catalyze bio-oxidations. This includes oxidative functionalization of steroidal building blocks, and could be used to mimic reactions that take place in the human liver. Furthermore, transaminases, imine reductases, keto reductases, and lipases are the most relevant enabling enzyme classes for pharma research and development applications (Meyer et al., 2016). Some fungal metabolites such as xylitol and pigments are used as non-carcinogenic sweetener and coloring agents in pharmaceutical industry, respectively. Xylitol is also recommended in cases such as lipid metabolism disorder and respiratory infections, for the prevention of osteoporosis as well as for persons suffering with kidney and parental lesions. Pigments can be exploited for the treatment of cancer, diabetes, and other infectious diseases because of anticancer, antidiabetic, and antimicrobial properties. They are also proved to be efficient antioxidants and could be applied to bring down the level of free radicals. Fungal pigments also work as antibacterial, antifungal, and antiprotozoal (Dhiman and Mukherjee, 2018; Tirumale and Wani, 2018).

46

Current Developments in Biotechnology and Bioengineering

3.1.4 Pulp and paper Biotechnology has attracted growing attention in the pulp and paper industry in the last decade, since biotechnology provides tools to increase both the quality and the supply of feedstocks for pulp and paper, reduce manufacturing costs, and create novel high-value products (Bajpai, 2018). The various approaches to the usage of fungi to remove undesirable components of wood, pulp, and wastewater have been developed in the pulp and paper industry. White-rot fungi have a high selectivity for delignification, which can reduce cellulose loss to make fungal pre-treatment practical for biopulping (Chowdhary et al., 2018). Moreover, fungi have been used for removal and detoxification of extractives from wood to reduce pitch related problems to satisfactory level (Bajpai, 2018). Among the biological methods tried so far, fungal treatment technology using white-rot fungi appears to be the most promising for decolorization and detoxification of pulp and paper mill wastewaters especially bleach effluents (Bajpai, 2018). In addition, the number of applications of enzymes of fungal origin in pulp and paper manufacturing has steadily increased during recent years, and several have reached or are approaching commercial reality. These include enzyme-aided bleaching with xylanases, direct delignification with oxidative enzymes, deinking and fiber modification with cellulase-hemicellulase mixture, refining with cellulases, pitch reduction/removal with lipases, stickies control with esterases, freeness (or drainage) enhancement with cellulases rrez et al., 2011). and hemicellulases as well as enzymatic slime control (Bajpai, 2018; Gutie The use of fungi and their enzymes in different parts of the pulp and paper industry has demonstrated environmental, economic, and technical benefits due to reduction of energy and chemicals consumption as well as improvement of final product (or paper) quality.

3.1.5 Textile Textile industries use a large amount of synthetic dyes (pigments) during their manufacture process as these dyes are widely available at a reasonable price and produce a broad spectrum of colors, but they may cause skin allergy and other negative effects to human body as well as release toxic substances into the environment. The use of natural or microbial pigments with their better biodegradability and higher compatibility with the environment and human body coupled with fungal bioremediation of textile effluents have been proven to overcome these problems (Tirumale and Wani, 2018; Mukherjee et al., 2017). Filamentous fungi produce amazing pigments like carotenoids, melanins, flavins, phenazines, quinones, and monascins from different chemical classes (Venil et al., 2020). Bioremediation of synthetic dyes in textile waste effluents by fungi has been demonstrated to be more efficient, cost-effective, and environmentally friendly compared with other techniques. White-rot fungi such as Phanerochaete chrysosporium, Trametes versicolor, Pleurotus ostreatus, Pycnoporus sanguineus, Irpex flavus, Phellinus gilvus have shown a strong ability to degrade a wide range of synthetic dyes with different structures (Munck et al., 2018; Ma et al., 2014).

Chapter 2 • Fungal biotechnology

47

Fabric from fungi is an attractive innovation in the textile industry as it can be antimicrobial, biodegradable, comfortable to wear, durable, eco-friendly, fire-resistant, flexible, non-toxic, skin-friendly, strong, suitable for sensitive skin, waterproof, and mended easily. Possibly, it could also be used to substitute animal leather and suede and be used for accessories, bags, and shoes (Challa et al., 2019). Bio-fabrication of renewable fibers from cell wall of zygomycetes fungus Rhizopus delemar cultivated on bread waste as a novel resource for production of sustainable textiles was investigated by Svensson et al. (2021).

3.1.6 Biotechnological industries for biofuels, biochemical, and biomaterial production The need to reduce fossil fuel dependence in the chemical and petrochemical industries due to their high prices and environmental concerns has led to the emergence of sustainable bio-based alternatives. In this regard, the proportion of bio-based products produced by biotechnology such as biofuels, biochemical, and biomaterials, particularly those obtained from fungi, has been increasing during recent years (Chambergo and Valencia, 2016). Many companies such as AB Enzymes, BASF, Bayer, Chr. Hansen, Dyadic International, DSM, DuPont, Kerry Group, Marlow Foods, Novozymes, Puratos, Syngenta, and Roal Oy are global leaders in using fungi for bulk manufacturing of organic acids, proteins, enzymes, and secondary metabolites, e.g., antibiotics (Meyer et al., 2020). The following are given an illustration of some bio-based products. Fungi can be a good source of biofuels and are explored globally for generation of various biofuels such as bioethanol, biodiesel, biogas, and so on. Filamentous fungi have attracted a lot of research interest due to their ability to produce a variety of lignocellulolytic enzymes and ferment both hexoses and pentoses to ethanol ( Joseph and Wang, 2018). Microbial lipids from oleaginous fungi, due to their plant-like oil composition, are now being studied to produce biodiesel in a sustainable and economical manner (Coradini et al., 2015). Anaerobic fungi have a great potential in the production of biogas from lignocellulosic waste due to the combination of their highly effective ability to hydrolyse lignocellulose (Saye et al., 2021; Chowdhary et al., 2018). Moreover, the fermentative production of novel biofuels such as butanol and isobutanol using fungi and yeast is being developed to overcome disadvantages of the common biofuels like ethanol and biodiesel (Coradini et al., 2015). Organic acids, which can be used as food additives, cosmetic ingredients, and chemical intermediates for the production of biodegradable polymers, are often produced by fila€ ttner et al., 2020). At present, citric acid and gluconic acid produced mentous fungi (Hu with the filamentous fungus Aspergillus niger are the two biggest commercial fungal products in terms of production volume (Troiano et al., 2020). Fungi are also capable of producing some innovative products. For example, they are excellent candidates to explore new eco-friendly methods for inorganic nanoparticles (NPs) production either intra- or extracellularly. Iron oxide NPs and gold NPs are two examples. The unique catalytic, optical, electronic, and photochemical properties of the NPs contribute toward a wide range of applications in the field of applied and basic research (Mahanty et al., 2019; Va´go´ et al., 2016). Mycelium-based composites, e.g.,

48

Current Developments in Biotechnology and Bioengineering

mycelium board biocomposites and mycelium/straw biocomposites, are a relatively new and environmentally sustainable class of materials that can replace petroleum-based products such as synthetic plastics (e.g., polystyrene) or other foams as well as natural materials such as cork and wood. They can be used in various applications such as automobile, aerospace, packaging and building industries, and sports instruments (Rafiee € sten, 2019). et al., 2021; Soh et al., 2020; Wo

3.2 Adding value to organic wastes through fungi Carbon-rich wastes are interesting raw materials for biorefineries, due to their high abundance and relatively low price. Indeed, there are vast amounts from different types of the wastes of industrial, agricultural and municipal origin that have little use but can be converted to higher value products. The production of valuable components from organic wastes, and the simultaneous elimination of the organic load are key steps toward mitigating economic and environmental hurdles (Chan et al., 2018). Among methods used for transformation of organic wastes into value-added components, the biochemical (or biotechnological) pathway has become an important research focus. There are many instances where fungi have been used for the conversion of various organic wastes into diverse value-added products. In fact, fungal bioconversion, through fermentative processes, has been revealed to be an eco-friendly and beneficial biotechnological approach for either the reutilization or the valorization of these wastes. Ethanol and fungal biomass production from waste or by-product streams generated in current industrial plants (e.g., the pulp and paper industry, the food industry, firstgeneration biofuel production plants) by using filamentous fungi have been investigated by several researchers (Asadollahzadeh et al., 2018; Mahboubi et al., 2017a,b; Ba´tori et al., 2015; Ferreira et al., 2012, 2014). Gmoser et al. (2020) produced new protein-enriched products using the edible filamentous fungi Neurospora intermedia and Rhizopus oryzae from stale bread and brewers spent grain. In the study of Souza Filho et al. (2018), a veganmycoprotein concentrate from pea-industry by-product using edible fungal strains of Ascomycota (Aspergillus oryzae, Fusarium venenatum, Monascus purpureus, Neurospora intermedia) and Zygomycota (Rhizopus oryzae) was obtained. Valorization of thin stillage, bakery waste, and food processing industry by-products (apple, pomegranate, black carrot, and red beet pulps) as nutrient sources for the fermentative production of biocolorant (pigment) by filamentous fungi has been developed (Gmoser et al., 2019; Bezirhan Arikan et al., 2020; Haque et al., 2016). Muniraj et al. (2015) showed the production of microbial lipids and γ-linolenic acid by Aspergillus flavus and Mucor rouxii (indicus), with potato processing wastewater as nutrient source. In addition, a variety of enzymes were produced from a number of organic wastes inoculated with filamentous fungi.

3.3 Strategies to improve investment and productivity in fungal biorefineries Fungal biorefinery operations may be made cost-competitive with petrochemical processes through a number of steps. Cheaper feedstocks, potentially lignocellulosic, and

Chapter 2 • Fungal biotechnology

49

food processing residues can be used. Complete valorization of biomass can be carried out, including integration of multiple revenue streams and bioconversion steps. Furthermore, two or more distinct microorganisms can be used in the same culture to obtain a synergistic effect, and genetic engineering can be attempted (Troiano et al., 2020). The production of further value-added products, besides the main product, from by-products or waste-streams generated in already established industrial processes like dairy, paper and pulp, oil, fruit, sugar producing industries, and first-generation ethanol plants can lead to energy and cost savings as well as an increase in revenue (Ferreira et al., 2018). For example, in a starch-based ethanol facility, the thin stillage waste stream has been investigated for valorization into animal feed and additional ethanol using various filamentous fungi. Moreover, lignin extracted from the pre-treatment step when lignocellulosic feedstocks are used, can be used for purposes other than heat such as production of carbon fibers, resin, biocomposites, etc. Integration of first- and second-generation ethanol is an attractive way to reduce the investment costs and risks compared to a standalone second-generation process. This reduces a major part of the investment of necessary downstream infrastructure, as it is already available. Thus, in total the feasibility of commercial-scale second-generation bioethanol plants is potentially increased (Ferreira et al., 2018; Lennartsson et al., 2014). It is suggested that simplification of the biomass conversion process and consolidation of the three main steps of enzyme production, substrate hydrolysis, and fermentation into a single step, referred to as consolidated bioprocessing (CBP), can serve as a successful strategy to reduce capital and processing costs and enhance process efficiencies (Troiano et al., 2020; Salehi Jouzani and Taherzadeh, 2015). CBP has been discussed as one of the most promising fermentation approaches for bioethanol production from lignocellulosic biomass and has attracted international interest in recent years. In addition to ethanol, several additional compounds can potentially be produced through CBP by fungi and yeasts. The capability of filamentous fungi in deconstructing lignocellulosic biomass makes them potential components in CBP (Ali et al., 2016). Co-cultivation, which consists of two or more fungal partners or a fungus (fungi) with another microorganism such as a bacterium (bacteria) in the same culture, would be a potential strategy to decrease the number of steps involved in biorefining. The use of fungal co-cultures potentially also helps increase production yield, decrease operational costs, and avoid downstream processing costs (Troiano et al., 2020; Sperandio and Ferreira € sten, 2019). Pietrzak and Kawa-Rygielska (2019) found that a co-culture of Filho, 2019; Wo edible filamentous fungi (Aspergillus oryzae and Rhizopus oligosporus) with fodder yeast Candida utilis for backset water treatment was effective in improving the core production stage in an ethanol-production plant. The yield of biotechnological products can be much less when naturally available microorganisms are used. The modification of genetic structure of microorganisms is reported to increase their productivity. Genetic modifications in microorganisms can be prompted by various methods such as improvement of a classical strain by mutation and selection or by the use of recombinant DNA technology (Sood et al., 2011). Classical examples of successful strain improvement used in the industry can be found in the

50

Current Developments in Biotechnology and Bioengineering

production of antibiotics and significantly increased titres, e.g., penicillin titres have been increased by more than a factor 1000 (Kavanagh, 2011).

4. Fungal metabolites Filamentous fungi are good producers of metabolites such as organic acid and ethanol, but also value-added products such as enzymes and pigments (Karimi et al., 2018). Traditionally, filamentous fungi have been classified to contain four groups (for a more recent classification, see Chapter 3 of this book): Ascomycota, Zygomycota, Basidiomycota, and Chytridiomycota (Ferreira et al., 2013). For biotechnological applications, the first three have been found to be of interest thus far. The following section aims to give an overview of the bulk chemicals that potentially could be produced by these fungi.

4.1 Ascomycetes Filamentous ascomycetes are, and have been, considered of interest to produce metabolites such as organic acids (citric, gluconic, and itaconic acid) and ethanol because of their enzymatic capabilities (Ferreira et al., 2016). Neurospora spp. and Fusarium spp. are mostly used in research for ethanol production and Aspergillus spp. are best known for the production of organic acids such as citric, gluconic, and itaconic acid (Karimi et al., 2018; Ferreira et al., 2016). Among the organic acids, especially production of citric acid is of interest due to a projected continuous growth in demand (Ferreira et al., 2016).

4.1.1 Ethanol A lot of the research interest for bioethanol production using filamentous fungi has been focused on converting lignocellulosic materials, which in general is limited by the high enzyme costs. In the 1980s, a few species such as Neurospora crassa and Fusarium oxysporum were reported as useful microbial catalysts for ethanol production directly from cellulose without the need of any external enzyme (Christakopoulos et al., 1989; Salehi Jouzani and Taherzadeh, 2015). Furthermore, the ability to produce ethanol from xylose is another advantage of utilizing filamentous fungi such as ascomycetes (Ferreira et al., 2015). In the case of Fusarium oxysporum it has been considered as a biocatalyst for conversion of brewer’s spent grain (BG), a by-product from breweries (Xiros and Christakopoulos, 2009). Fusarium oxysporum has also been investigated to produce ethanol directly from wheat straw (Panagiotou et al., 2005, 2011). Apparently, a glucose transporter belonging to Fusarium oxysporum was found to be interesting enough that it led to an investigation on its own (Ali et al., 2013). As mentioned earlier, Neurospora crassa is the most interesting microbial source for ethanol production among the Neurospora genus (Ferreira et al., 2016). For example, it has been considered for ethanol production using SSF of brewer’s spent grains (Xiros et al., 2008) and of sweet sorghum bagasse (Dogaris et al., 2012). A close relative, Neurospora intermedia, has also been considered for ethanol production from various by-products such as thin stillage (Ferreira et al., 2014, 2015) and wheat bran (Nair et al., 2015).

Chapter 2 • Fungal biotechnology

51

4.1.2 Citric acid Citric acid (C6H8O7) is a weak organic acid and an intermediate of the tricarboxylic acid cycle. It is mainly used in the food (ca 70%) and pharmaceutical industry (ca 12%) (Singh Dhillon et al., 2011; Soccol et al., 2006; Sawant et al., 2018). Similar to bioethanol, the low price of citric acid makes low cost substrates such as orange processing waste and apple pomace very interesting (Dhillon et al., 2013; Singh Dhillon et al., 2011). Nowadays, Aspergillus niger is used for the production of citric acid and is being further developed for production from various novel substrates (Barrington et al., 2009; Angumeenal and Venkappayya, 2005; Wang et al., 2017). Both SSF and SmF seem to be of interest.

4.1.3 Gluconic acid Gluconic acid (C6H12O7) is an organic acid used a bulk chemical in many industries such as food, feed, pharmaceutical, paper, textile, and construction. It is derived from glucose through dehydrogenation catalyzed by glucose oxidase (Ferreira et al., 2016). Once again, Aspergillus niger is the most studied (Mukhopadhyay et al., 2005; Ikeda et al., 2006; Sharma et al., 2008). Up to now, various parameters such as type of carbon and nitrogen source, oxygen transport, and mode of cultivation (submerged or SSF) have been investigated to optimize the gluconic acid production from Aspergillus niger (Singh and Kumar, 2007; Ferreira et al., 2016). More recently, the thermostability of the glucose oxidase from Aspergillus niger has been investigated to produce gluconic acid more efficiently (Mu et al., 2019).

4.1.4 Itaconic acid Itaconic acid (C5H6O4) is an unsaturated dicarboxylic acid with considerable interest to use as a building block chemical, including as a co-monomer in the production of plastics and resins (Li et al., 2012). Itaconic acid is currently produced by fermentation of glucose or molasses by Aspergillus itaconicus and Aspergillus terreus (Blumhoff et al., 2013; Okabe et al., 2009). However, itaconic acid production by Aspergillus terreus is lower than its precursor citric acid: >80 g/L compared to >200 g/L (Ferreira et al., 2016; Zhao et al., 2018). Therefore, production of itaconic acid by Aspergillus niger using some genetic modification have been investigated (Li et al., 2012; Blumhoff et al., 2013; van der Straat et al., 2014). Various parameters for itaconic acid production such as type of substrate, oxygen source, € chs (2013) and and cultivation methodology have been reviewed by Klement and Bu Bafana and Pandey (2018). Furthermore, the medium components needed for production of itaconic acid has been investigated and the results showed similarity to that of citric acid production medium (Li et al., 2012).

4.2 Zygomycetes In zygomycetes, the final glycolysis product (pyruvate) can be directed to different pathways and can produce several value-added products based on the strain and cultivation medium type (Ferreira et al., 2013). Several species of zygomycetes are able to consume pentoses to produce ethanol (Omidvar et al., 2016). Some species can produce organic acids, such as Rhizopus sp. that have been used for production of fumaric and lactic acid (Zhang et al., 2007; Roa Engel et al., 2008).

52

Current Developments in Biotechnology and Bioengineering

4.2.1 Ethanol Ethanol is a well-studied metabolite produced during the fermentation process of zygomycetes (Mohammadi et al., 2012; Omidvar et al., 2016). Theoretically, 0.51 kg ethanol can be produced per kg of sugar monomer. However, several factors such as cultivation conditions such as nutrient concentration, oxygen supply, temperature and pH, and genetic stability influence the ethanol yield (Mohammadi et al., 2013; Aditiya et al., 2016). In a screening experiment, Millati et al. (2005) found ethanol yields in the range of 0.37–0.43 g/g glucose from different zygomycete species while Wikandari et al. (2012) reported yields in the range of 0.26–0.41 g/g. Anaerobic fermentation of Mucor indicus resulted in yields up to 0.46 g/g (Sues et al., 2005). These values represent the types of yields that can be expected, however, far from all zygomycetes are able to produce ethanol.

4.2.2 Lactic acid Lactic acid (C3H6O3) is the most abundant organic acid in nature and almost 2,000,000 metric tons were estimated from industrial production in 2020, of which ca 90% is derived from fermentation processes (Yuwa-amornpitak and Chookietwatana, 2018). L(+)-lactic acid and D(
)-lactic acid are two isomers of lactic acid. L(+)-lactic acid is preferred in food, pharmaceutical, textile, cosmetic, and chemical industries (Ferreira et al., 2013). A significant amount of research has been performed about using Rhizopus strains to produce L-lactic acid instead of lactic acid bacteria (Zhang et al., 2007; Ahmad et al., 2020; Ferreira et al., 2013). Research on lactic acid production by zygomycetes is still an active research area, and some of the later findings are summarized in Table 2. Very briefly, the research seems to be most focused on using different species and strain to produce L-lactic acid from different sources, which most often are wastes or residues of some kind.

Table 2

Recent investigations on the production of L-lactic acid by Rhizopus strains.

Microorganism

Medium/substrate

Yield (g/g) or concentration (g/L)

References

Rhizopus microsporus (DMKU 33) Rhizopus oryzae (3.819) Rhizopus oryzae (NLX-M-1) Rhizopus oryzae (MTCC5384) Rhizopus microsporus (LTH23) Rhizopus oryzae (NRRL 395) Rhizopus oryzae (NRRL-395)

Liquefied cassava starch

0.93 (g/g)

Trakarnpaiboon et al. (2017)

Sophora flavescens residues

47 (g/L)

Ma et al. (2020)

Xylo-oligosaccharides (XOS) manufacturing waste Paper sludge (PS)

0.60 (g/g)

Zhang et al. (2015)

27 (g/L)

Dhandapani et al. (2019)

Cabbage glycerol media

4.0 (g/L)

Solid pineapple waste (SPW)

0.10 (g/g)

Yuwa-amornpitak and Chookietwatana (2018) Zain et al. (2021)

Wheat wastewater

5.7 (g/L)

€ c¸eri et al. (2021) Go

Chapter 2 • Fungal biotechnology

53

Specifically worth mentioning is that lactic acid fermentation by zygomycetes have carried out in 5 m3 bioreactor scale (Matsumoto and Furuta, 2018), and should thus be considered to be in the pilot scale.

4.2.3 Fumaric acid Fumaric acid (C4H4O4) is a non-toxic naturally occurring organic acid that can be produced chemically from maleic anhydride (produced from butane). However, the price of maleic anhydride as a petroleum derivative is increasing due to the rising petroleum prices (Sebastian et al., 2019a) and the environmental side effects of using fossil-based resources should be considered as well. However, fumaric acid is among the top 10 chemicals that could be produced by fermentation on industrial scale (Roa Engel et al., 2008). Fumaric acid is used in the food and pharmaceutical sectors, and has potential in the production of biodegradable polymers (Ferreira et al., 2013). Fungi in general could be considered for fumaric acid production (Sebastian et al., 2019a). In particular, the zygomycete Rhizopus oryzae has potential as a main producer as it has small nutritional demands for growth and fumaric acid production (Xin Li, 2020). With glucose as a carbon source, yields up to 0.70 g/g has been reported (Ferreira et al., 2013). Conversion of lignocellulosic biomasses has also been investigated for fumaric acid production, but the studies are infrequent and the yields are considerably lower with reported values of 0.35 and 0.43 g/g (Xu et al., 2010; Deng and Aita, 2018). A promising characteristic is that fumaric acid production has been reported to be successful without pH control, with pH values as low as 3.6 (Roa Engel et al., 2011).

4.3 Basidiomycetes Basidomycetes, or more specifically those classified as white-rot fungi, have been found to produce ethanol. However, the number of publications are rather limited, probably due to the general slow growth of basidiomycetes.

4.3.1 Ethanol One of the fungi worth mentioning is Trametes versicolor since it is able to directly convert hexose sugars, xylose, and untreated lignocellulosic biomass to ethanol. It can thus be suitable for fermentation of xylan-containing lignocellulosic biomass (Okamoto et al., 2014). Flammulina velutipes is a well-known basidiomycete mushroom in the food industry. It is also able to produce ethanol from glucose, mannose, sucrose, fructose, maltose, and cellobiose, but not galactose and pentose sugars. Furthermore, the fermentation time is long (6 days or even more) (Salehi Jouzani and Taherzadeh, 2015). Interestingly, ethanol yields of up to 0.36 g/g cellulose has been achieved from bagasse for this fungus (Maehara et al., 2013), which is quite high. Phlebia sp. MG 60, originally isolated from driftwood, has also been considered for ethanol production. It is interesting in the regard that it is able to utilize xylose, and convert lignocellulosic material with rather high yields, reaching 0.42 g/g from kraft pulp (Kamei et al., 2012, 2014; Khuong et al., 2014a,b).

54

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Other basidiomycetes that have been investigated include Peniophora cinerea, Trametes suaveolens, Lenzites betulinus (Okamoto et al., 2014; Im et al., 2016), but no noteworthy properties were discovered. Interestingly, Pleurotus ostreatus and Agaricus blazei, both normally used for mushroom production, have been found to be able to produce wines with 12.2% and 8% ethanol, respectively (Okamura et al., 2001). This is far higher than what is normally achieved by filamentous fungi that quite often seems to be limited by their ethanol tolerance.

4.4 Pigments and enzymes Filamentous fungi are known to produce various secondary metabolites that can be used for biotechnological purposes such as food, drug development, and cosmetics. Pigments including carotenoids, melanins, and flavins are among the important secondary metabolites from fungi due to their biological properties, e.g., antibacterial and antifungal (Nirlane da Costa Souza et al., 2016). Among the ascomycetes, Monascus spp. have been important sources for pigment production (Ferreira et al., 2016). The major pigments consist of yellow (monascin and ankaflavin), orange (monascorubrin and rubropunctatin), and red componds (monascorubramine and rubropunctamine). Other examples of pigments, e.g., yellow in the form of emodin and physcion, and red in the form of erythroglaucin, rubrocristin, and catenarin, are produced by some strains of Aspergillus spp. (Caro et al., 2015). As previously mentioned, filamentous fungi produce enzymes as well (Karimi et al., 2018). Zygomycetes fungi can produce a great diversity of hydrolytic enzymes including amylases, cellulases, xylanases, proteases, and lipases (Ferreira et al., 2013). Among the ascomycetes especially Aspergillus and Trichoderma spp. are very well known for industrial production of enzymes, including cellulases (Ferreira et al., 2016). Basidiomycetes are especially interesting for their ability to produce enzymes that degrade lignin and a potential source of cellulases (Kozhevnikova et al., 2017).

5. Fungal biomass Fungal biomass is rich in proteins and has a good composition of amino acids. The lipid content, with different fatty acids, and vitamin content is also worth mentioning. This makes fungal biomass a suitable source for animal feed (Karimi et al., 2018) and potentially human food. Furthermore, whenever the main product is ethanol, organic acid, or enzymes, filamentous biomass is also produced, which has a good potential to act as an addition valuable by-product. Compared with yeast, filamentous fungi also have the advantage that it can easily be separated from a liquid medium, only requiring a sieve like separator (Ferreira et al., 2016).

5.1 Ascomycetes 5.1.1 Human food Filamentous fungi, especially ascomycetes, are currently used in the production of human food. Especially Neurospora, Aspergillus, Monascus, and Fusarium are important in food

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applications containing species that are classified as Generally Recognized as Safe (GRAS) (Ferreira et al., 2016). Oncom, a traditional fermented food in Indonesia, is produced using Neurospora intermedia and is known to have a relatively high protein content (Shurtleff and Aoyagi, 1985). In Europe, Fusarium venenatum was investigated as a potential source to easily produce a palatable microbial source of protein from glucose or starch-based media for human consumption by the company Rank Hovis McDougall (O’Donnell et al., 1998; Wiebe, 2002). It resulted in Fusarium venenatum being commercially produced from a synthetic medium based on glucose, ammonium, and biotin, and is sold under the trade name “Quorn” (Wiebe, 2004). Another dish is red rice, which is produced using Monascus purpureus, and has known anti-hypertensive effects (Seraman et al., 2010). Aspergillus oryzae is well known in the production of koji among other things (Shurtleff and Aoyagi, 2012). Ascomycetes are also being investigated for more novel food products. For instance, Aspergillus oryzae, Fusarium venenatum, Monascus purpureus, and Neurospora intermedia have been investigated to convert by-products from the pea industry (Souza Filho et al., 2018). Neurospora intermedia has also been considered for conversion of leftover bread (Gmoser et al., 2020). These fungi grow fast and produce high amounts of protein-rich biomass. The total protein content increased from 16.5% to 21.1% in the final product. Minerals (Cu, Fe, Zn) vitamin E, and vitamin D2 all increased in concentration in comparison with untreated bread. The increase in mineral content can be attributed to a decrease in the total mass. One potential application of the fermented product is as a fungi burger patty, although the bitterness chewiness could still be improved. Many more examples can be found in the literature, and most seems to focus on using ascomycete strains that are already used for food production due to the safety of the final product and legal reasons.

5.1.2 Animal feed Protein rich fungal biomass seems like a good alternative to current soybean-based animal feed, especially if the fungal biomass is produced from by-product/waste stream. Other than protein content, amino acid composition, fatty acid content and composition, antioxidants, and pigments make fungal biomass a good choice for application as animal feed (Karimi et al., 2018). A major focus has been on ascomycetes, including Neurospora intermedia that has been extensively investigated to utilize by-products from bioethanol production (Ferreira et al., 2016) with the advantage that a co-product is ethanol. Aspergillus oryzae has also found research interest (Batori et al., 2015).

5.2 Zygomycetes Zygomycetes biomass contains considerable amounts of proteins, lipids, chitin, and chitosan (Ferreira et al., 2013). Zygomycetes isolated from different foods have been investigated to be considered for human consumption or animal feed (Lennartsson, 2012). Furthermore, the fungal biomass of zygomycetes can be used for heavy metal removal,

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as a source of chitosan, and superabsorbents production (Mohammadi et al., 2012; Ruholahi et al., 2016). Thus, the biomass of zygomycetes is investigated for human food, animal feed, and chitosan production.

5.2.1 Food and feed applications Commonly, zygomycetes contain about 40–50% protein and has thus become of interest for feed and food applications (Mohammadi et al., 2013; Karimi et al., 2018), since protein content is quite often crucial. The protein content of fungal biomass depends on the fungal species, harvesting, dewatering, drying methods, and cultivation medium and its composition such as nitrogen concentration (Karimi et al., 2018; Ferreira et al., 2013). Furthermore, many zygomycetes are classified as GRAS, which could reduce the amount of testing needed to be accepted for food production on large scale. One good example are the zygomycetes used in the production of tempeh, a traditional Indonesian food from fermented soybean by zygomycetes (Nout et al., 2007). The pleasant smell and taste, and easy separation of the zygomycetes biomass from the medium are other advantages of these fungi for feed and food purposes (Lennartsson, 2012). However, similar to other fungi, zygomycetes contain nucleic acids in levels that could limit their application in feed and food fields (Ferreira et al., 2013). This could be solved by treating the fungal biomass, or use the fungi for feed for animals that produce high levels of active uricase to metabolize nucleic acids without any health risk, such as salmonids (Karimi et al., 2018). Thus, it is not surprising that the research in the field has been focused on Rhizopus species related to tempeh fermentation. Examples include Rhizopus cultivation on paper pulp wastewater, e.g., spent sulfite liquor, to replace fishmeal in fish feed (Wikandari et al., 2012; Edebo, 2008), and Rhizopus cultivation on potato protein liquor (PPL), a side stream from the potato starch industry, for animal feed (Souza Filho et al., 2017). More examples can be found in the literature, but in general the research is not that well developed.

5.2.2 Chitosan The high amount of chitosan in the zygomycetes cell walls is one of the remarkable properties of these fungi with many potential applications (Ferreira et al., 2013; Abo Elsoud and El Kady, 2019). Chitosan is a linear polysaccharide containing randomly distributed glucosamine and N-acetyl glucosamine monomers. Chitosan is used in a variety of applications such as medicine, food, and chemical industry (Sathiyaseelan et al., 2017; Batista et al., 2018; Darwesh et al., 2018; Hamedi et al., 2018). Chitosan is often produced by chemical deacetylation of chitin from shellfish wastes. The zygomycetes cell wall is an alternative source of chitosan, which would require milder conditions to isolate (Mohammadi et al., 2012; Sebastian et al., 2019b). Mucor indicus is one of the zygomycetes species that have been investigated as a potential source of chitosan, since it can also produce ethanol (Mohammadi et al., 2013). The fungus is dimorphic (i.e., can grow as both yeast and filaments) and the amount of chitosan in the cell wall differ from one morphology to another. According to the research, 0.46 (g/g cell wall) of chitosan could be achieved when Mucor indicus grows

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as filaments, which is reduced to 0.23 (g/g cell wall) for yeast-like morphology (Mohammadi et al., 2012). Rhizopus oryzae has also been considered as a source of chitosan, as the fungus can be used for lactic and fumaric acid production (Liao et al., 2008; Liu et al., 2008).

5.3 Basidiomycetes In the case of basidiomycetes much of the focus has been on the mushrooms, which is slightly off topic and will thus only be discussed briefly. Generally, they are considered to have potential in various biotechnological applications such as production of food, dietary supplements and pharmaceutical substances (Asatiani et al., 2010). Antioxidant, immunostimulatory, antibacterial, and hypocholesterolemic properties are among the health-promoting properties of edible mushrooms (Bederska-Łojewska et al., 2017). Basidiomycetes also find potential applications due to their health benefits in other applications than direct human use. For example, many mushrooms such as Lentinula edodes, Agaricus bisporus, Agaricus blazei, Hericium caput-medusae, Pleurotus ostreatus, Pleurotus eryngii, Fomitella fraxinea, Flammulina velutipes, Ganoderma lucidum, Cordyceps inensis, and Cordyceps militaris could be used to improve poultry performance and health (Bederska-Łojewska et al., 2017).

6. Conclusions and perspectives Filamentous fungi have been used by humans for centuries and only recently have we started to fully unlock their potential. This ranges from materials, bulk chemicals, feed and food, enzymes, and pharmaceuticals (including antibiotics). Undoubtedly, there are many more potential applications that we have not even considered yet. Many fungi are also quite modest in their demands for nutrients, which makes industrial applications easier and potentially more profitable. However, there are also unique challenges in using filamentous for SmF, which is the most popular form of industrial cultivation by far, which potentially limits direct utilization of fungi. Considering the ever increasing arsenal of genetic tools, the question thus rises if filamentous fungi will be used for production of novel products, or if only their genes will be used after insertion into yeasts or Escherichia coli. Only time will truly be able to answer this question.

References Abo Elsoud, M.M., El Kady, E.M., 2019. Current trends in fungal biosynthesis of chitin and chitosan. Bull. Natl. Res. Cent. 43, 59. Aditiya, H.B., Mahlia, T.M.I., Chong, W.T., Nur, H., Sebayang, A.H., 2016. Second generation bioethanol production: a critical review. Renew. Sustain. Energy Rev. 66, 631–653. Ahmad, A., Banat, F., Taher, H., 2020. A review on the lactic acid fermentation from low-cost renewable materials: recent developments and challenges. Environ. Technol. Innov. 20, 101138.

58

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Ali, S.S., Nugent, B., Mullins, E., Doohan, F.M., 2013. Insights from the fungus Fusarium oxysporum point to high affinity glucose transporters as targets for enhancing ethanol production from lignocellulose. PLoS One 8, e54701. Ali, S.S., Nugent, B., Mullins, E., Doohan, F.M., 2016. Fungal-mediated consolidated bioprocessing: the potential of Fusarium oxysporum for the lignocellulosic ethanol industry. AMB Express 6, 13. Angumeenal, A., Venkappayya, D., 2005. Artrocarpus heterophyllus—a potential substrate for citric acid biosynthesis using Aspergillus niger. LWT Food Sci. Technol. 38, 89–93. Asadollahzadeh, M., Ghasemian, A., Saraeian, A., Resalati, H., Taherzadeh, M.J., 2018. Production of fungal biomass protein by filamentous fungi cultivation on liquid waste streams from pulping process. Bioresources 13 (3), 5013–5031. Asatiani, M.D., Elisashvili, V., Songulashvili, G., Reznick, A.Z., Wasser, S.P., 2010. Higher Basidiomycetes €vics, G. (Eds.), Progress in Mycology. Springer mushrooms as a source of antioxidants. In: Rai, M., Ko Netherlands, Dordrecht. Bafana, R., Pandey, R.A., 2018. New approaches for itaconic acid production: bottlenecks and possible remedies. Crit. Rev. Biotechnol. 38, 68–82. Bajpai, P., 2018. Introduction. In: Biotechnology for Pulp and Paper Processing. Springer Singapore, Singapore. Barrington, S., Kim, J.S., Wang, L., Kim, J.-W., 2009. Optimization of citric acid production by Aspergillus niger NRRL 567 grown in a column bioreactor. Korean J. Chem. Eng. 26, 422–427. Basu, S., Bose, C., Ojha, N., Das, N., Pal, M., Khurana, S., 2015. Evolution of bacterial and fungal growth media. Bioinformation 11, 182–184. Batista, A.C.D.L., Souza Neto, F.E.D., Paiva, W.D.S., 2018. Review of fungal chitosan: past, present and perspectives in Brazil. Polı´meros 28, 275–283. Batori, V., Ferreira, J.A., Taherzadeh, M.J., Lennartsson, P.R., 2015. Ethanol and protein form ethanol plant by-products using edible fungi Neurospora intermedia and Aspergillus oryzae. Biomed. Res. Int. 2015, 1–10. Ba´tori, V., Ferreira, J.A., Taherzadeh, M.J., Lennartsson, P.R., 2015. Ethanol and protein from ethanol plant by-products using edible fungi Neurospora intermedia and Aspergillus oryzae. Biomed. Res. Int. 2015, 176371.  ska, B., 2017. The use of Basidiomycota mushrooms in Bederska-Łojewska, D., S´wia˛tkiewicz, S., Muszyn poultry nutrition—a review. Anim. Feed Sci. Technol. 230, 59–69. , L., Dizge, N., 2020. Production of bio-based pigments from Bezirhan Arikan, E., Canli, O., Caro, Y., Dufosse food processing industry by-products (apple, pomegranate, black carrot, red beet pulps) using Aspergillus carbonarius. J. Fungi 6, 240. Blackwell, M., 2011. The fungi: 1, 2, 3 … 5.1 million species? Am. J. Bot. 98, 426–438. Blumhoff, M.L., Steiger, M.G., Mattanovich, D., Sauer, M., 2013. Targeting enzymes to the right compartment: metabolic engineering for itaconic acid production by Aspergillus niger. Metab. Eng. 19, 26–32. , L., 2015. Pigments and colorants from filCaro, Y., Venkatachalam, M., Lebeau, J., Fouillaud, M., Dufosse rillon, J.M., Ramawat, K.G. (Eds.), Fungal Metabolites. Springer, Berlin. amentous fungi. In: Me Challa, S., Dutta, T., Neelapu, N.R.R., Yadav, A.N., Singh, S., Mishra, S., Gupta, A., 2019. Fungal white biotechnology applications for food security: opportunities and challenges. In: Recent Advancement in White Biotechnology Through Fungi: Volume 2: Perspective for Value-Added Products and Environments. Springer International Publishing, Cham. Chambergo, F.S., Valencia, E.Y., 2016. Fungal biodiversity to biotechnology. Appl. Microbiol. Biotechnol. 100, 2567–2577.

Chapter 2 • Fungal biotechnology

59

Chan, L.G., Cohen, J.L., Bell, J.M.L.N.D.M., 2018. Conversion of agricultural streams and food-processing by-products to value-added compounds using filamentous fungi. Annu. Rev. Food Sci. Technol. 9, 503–523. Chauhan, A., Jindal, T., 2020. Microbiological culture media: types, role and composition. In: Microbiological Methods for Environment, Food and Pharmaceutical Analysis. Springer International Publishing, Cham. Chipeta, Z.A., Du Preez, J.C., Christopher, L., 2008. Effect of cultivation pH and agitation rate on growth and xylanase production by Aspergillus oryzae in spent sulphite liquor. J. Ind. Microbiol. Biotechnol. 35, 587–594. Chowdhary, K., Prasad, U., Sharma, S., 2018. Role of fungi in biorefinery: a perspective. In: Kumar, S., Dheeran, P., Taherzadeh, M., Khanal, S. (Eds.), Fungal Biorefineries. Springer International Publishing, Cham. Christakopoulos, P., Macris, B.J., Kekos, D., 1989. Direct fermentation of cellulose to ethanol by Fusarium oxysporum. Enzym. Microb. Technol. 11, 236–239. €kela €, M.R., De Vries, R.P., 2020. Engineering of primary carbon metabolism in filamenChroumpi, T., Ma tous fungi. Biotechnol. Adv. 43, 107551. Clarke, K.G., 2013. Microbiology. In: Clarke, K.G. (Ed.), Bioprocess Engineering. Woodhead Publishing (Chapter 2). Cooke, W.B., 1968. Carbon/nitrogen relationships of fungus culture media. Mycopathologia 34, 305–316. Copetti, M.V., 2019. Fungi as industrial producers of food ingredients. Curr. Opin. Food Sci. 25, 52–56.  Coradini, A.L.V., Anschau, A., Vidotti, A.D.S., Reis, E.M., Da Cunha Abreu Xavier, M., Coelho, R.S., Franco, T.T., 2015. Microorganism for bioconversion of sugar hydrolysates into lipids. In: Kamm, B. (Ed.), Microorganisms in Biorefineries. Springer Berlin Heidelberg, Berlin, Heidelberg. ´ ., 2006. Application of solid-state fermentation to food industry—a review. Couto, S.R., Sanroma´n, M.A J. Food Eng. 76, 291–302. Darwesh, O.M., Sultan, Y.Y., Seif, M.M., Marrez, D.A., 2018. Bio-evaluation of crustacean and fungal nanochitosan for applying as food ingredient. Toxicol. Rep. 5, 348–356. De Carvalho, C.C.C.R., 2016. Fungi in fermentation and biotransformation systems. In: Li, D.-W. (Ed.), Biology of Microfungi. Springer International Publishing, Cham. Deng, F., Aita, G.M., 2018. Fumaric acid production by Rhizopus oryzae ATCC® 20344™ from lignocellulosic syrup. BioEnergy Res. 11, 330–340. Devi, R., Kaur, T., Guleria, G., Rana, K.L., Kour, D., Yadav, N., Yadav, A.N., Saxena, A.K., 2020. Fungal secondary metabolites and their biotechnological applications for human health. In: Rastegari, A.A., Yadav, A.N., Yadav, N. (Eds.), New and Future Developments in Microbial Biotechnology and Bioengineering. Elsevier (Chapter 9). Dhandapani, B., Vishnu, D., Murshid, S., Prasath A, R., Muruganandh, R., Prasanth, D., Sekar, S., Senthilkumar, K., 2019. Production of lactic acid from industrial waste paper sludge using Rhizopus oryzae MTCC5384 by simultaneous saccharification and fermentation. Chem. Eng. Commun. 1–9. Dhillon, G.S., Brar, S.K., Kaur, S., Verma, M., 2013. Bioproduction and extraction optimization of citric acid from Aspergillus niger by rotating drum type solid-state bioreactor. Ind. Crop. Prod. 41, 78–84. Dhiman, S., Mukherjee, G., 2018. Recent advances and industrial applications of microbial xylanases: a review. In: Gehlot, P., Singh, J. (Eds.), Fungi and Their Role in Sustainable Development: Current Perspectives. Springer Singapore, Singapore. Dogaris, I., Gkounta, O., Mamma, D., Kekos, D., 2012. Bioconversion of dilute-acid pretreated sorghum bagasse to ethanol by Neurospora crassa. Appl. Microbiol. Biotechnol. 95, 541–550.

60

Current Developments in Biotechnology and Bioengineering

Doran, P.M., 2013. Reactor engineering. In: Doran, P.M. (Ed.), Bioprocess Engineering Principle, second ed. Academic Press, London (Chapter 14). Edebo, L., 2008. Zygomycetes for Fish Feed. U.S. Patent: US20090136617A1. Fazenda, M.L., Seviour, R., Mcneil, B., Harvey, L.M., 2008. Submerged culture fermentation of “Higher Fungi”: the macrofungi. In: Advances in Applied Microbiology. Academic Press. Ferreira, J.A., Lennartsson, P.R., Niklasson, C., Lundin, M., Edebo, L., Taherzadeh, M.J., 2012. Spent sulphite liquor for cultivation of an edible Rhizopus sp. Bioresources 7, 173–188. Ferreira, J.A., Lennartsson, P.R., Edebo, L., Taherzadeh, M.J., 2013. Zygomycetes-based biorefinery: present status and future prospects. Bioresour. Technol. 135, 523–532. Ferreira, J.A., Lennartsson, P.R., Taherzadeh, M.J., 2014. Production of ethanol and biomass from thin stillage using food-grade Zygomycetes and Ascomycetes filamentous fungi. Energies 7, 3872–3885. Ferreira, J.A., Lennartsson, P.R., Taherzadeh, M.J., 2015. Production of ethanol and biomass from thin stillage by Neurospora intermedia: a pilot study for process diversification. Eng. Life Sci. 15, 751–759. Ferreira, J.A., Mahboubi, A., Lennartsson, P.R., Taherzadeh, M.J., 2016. Waste biorefineries using filamentous ascomycetes fungi: present status and future prospects. Bioresour. Technol. 215, 334–345. Ferreira, J.A., Brancoli, P., Agnihotri, S., Bolton, K., Taherzadeh, M.J., 2018. A review of integration strategies of lignocelluloses and other wastes in 1st generation bioethanol processes. Process Biochem. 75, 173–186. Ge, X., Vasco-Correa, J., Li, Y., 2017. Solid-state fermentation bioreactors and fundamentals. In: ´ ., Du, G., Pandey, A. (Eds.), Current Developments in Biotechnology Larroche, C., Sanroma´n, M.A and Bioengineering. Elsevier (Chapter 13). Gholami-Shabani, M., Shams-Ghahfarokhi, M., Razzaghi-Abyaneh, M., 2019. Natural product synthesis by fungi: recent trends and future prospects. In: Yadav, A.N., Singh, S., Mishra, S., Gupta, A. (Eds.), Recent Advancement in White Biotechnology Through Fungi: Volume 2: Perspective for Value-Added Products and Environments. Springer International Publishing, Cham. Ghorai, S., Banik, S.P., Verma, D., Chowdhury, S., Mukherjee, S., Khowala, S., 2009. Fungal biotechnology in food and feed processing. Food Res. Int. 42, 577–587. Gmoser, R., Ferreira, J.A., Taherzadeh, M.J., Lennartsson, P.R., 2019. Post-treatment of fungal biomass to enhance pigment production. Appl. Biochem. Biotechnol. 189, 160–174. Gmoser, R., Fristedt, R., Larsson, K., Undeland, I., Taherzadeh, M.J., Lennartsson, P.R., 2020. From stale bread and brewers spent grain to a new food source using edible filamentous fungi. Bioengineered 11, 582–598. _ A., Alma, M.H., Gezginc, Y., Karaougul, E., 2021. The effect of some parameters on the production € Goc¸erI, _ €tc¸u € Imam of L(+) lactic acid using wheat wastewater by Rhizopus oryzae NRRL-395. Kahramannaras¸ Su  Univ. Doga Bilim. Derg. 24, 293–298. ´ .T., 2011. Fungi and their enzymes for pitch control in the pulp and Gutierrez, A., Del Rı´o, J.C., Martı´nez, A paper industry. In: Hofrichter, M. (Ed.), Industrial Applications. Springer Berlin Heidelberg, Berlin, Heidelberg. Hamedi, H., Moradi, S., Hudson, S.M., Tonelli, A.E., 2018. Chitosan based hydrogels and their applications for drug delivery in wound dressings: a review. Carbohydr. Polym. 199, 445–460. Haque, M.A., Kachrimanidou, V., Koutinas, A., Lin, C.S.K., 2016. Valorization of bakery waste for biocolorant and enzyme production by Monascus purpureus. J. Biotechnol. 231, 55–64. Harvey, L.M., McNeil, B., 2008. The design and preparation of media for bioprocesses. In: McNeil, B., Harvey, L.M. (Eds.), Practical Fermentation Technology. John Wiley & Sons, Ltd. Hoa, H.T., Wang, C.-L., 2015. The effects of temperature and nutritional conditions on mycelium growth of two oyster mushrooms (Pleurotus ostreatus and Pleurotus cystidiosus). Mycobiology 43, 14–23.

Chapter 2 • Fungal biotechnology

61

€ lker, U., Ho € fer, M., Lenz, J., 2004. Biotechnological advantages of laboratory-scale solid-state fermenHo tation with fungi. Appl. Microbiol. Biotechnol. 64, 175–186. € ttner, S., Johansson, A., Gonc¸alves Teixeira, P., Achterberg, P., Nair, R.B., 2020. Recent advances in the Hu intellectual property landscape of filamentous fungi. Fungal Biol. Biotechnol. 7, 16. Ikechi-Nwogu, C.G., Elenwo, E.N., 2012. Comparative evaluation of growth media for the cultivation of fungal cultures. J. Plant Pathol. Microbiol. 3, 1000139. Ikeda, Y., Park, E.Y., Okuda, N., 2006. Bioconversion of waste office paper to gluconic acid in a turbine blade reactor by the filamentous fungus Aspergillus niger. Bioresour. Technol. 97, 1030–1035. Im, K.H., Nguyen, T.K., Choi, J., Lee, T.S., 2016. Ethanol production from various sugars and cellulosic biomass by white rot fungus Lenzites betulinus. Mycobiology 44, 48–53. Jong, S.-C., Birmingham, J.M., 2001. Cultivation and preservation of fungi in culture. In: Mclaughlin, D.J., Mclaughlin, E.G., Lemke, P.A. (Eds.), Systematics and Evolution. Springer Berlin Heidelberg, Berlin, Heidelberg. Joseph, G., Wang, L., 2018. Production of biofuels from biomass by fungi. In: Kumar, S., Dheeran, P., Taherzadeh, M., Khanal, S. (Eds.), Fungal Biorefineries. Springer International Publishing, Cham. Kamei, I., Hirota, Y., Mori, T., Hirai, H., Meguro, S., Kondo, R., 2012. Direct ethanol production from cellulosic materials by the hypersaline-tolerant white-rot fungus Phlebia sp. MG-60. Bioresour. Technol. 112, 137–142. Kamei, I., Hirota, Y., Meguro, S., 2014. Direct fungal production of ethanol from high-solids pulps by the ethanol-fermenting white-rot fungus Phlebiasp. MG-60. Bioresources 9, 5114–5124. Kampen, W.H., 2014. Nutritional requirements in fermentation processes. In: Vogel, H.C., Todaro, C.M. (Eds.), Fermentation and Biochemical Engineering Handbook, third ed. William Andrew Publishing, Boston (Chapter 4). Kapoor, M., Panwar, D., Kaira, G.S., 2016. Bioprocesses for enzyme production using agro-industrial wastes: technical challenges and commercialization potential. In: Dhillon, G.S., Kaur, S. (Eds.), Agro-Industrial Wastes as Feedstock for Enzyme Production. Academic Press, San Diego (Chapter 3). Karimi, S., Mahboobi Soofiani, N., Mahboubi, A., Taherzadeh, M.J., 2018. Use of organic wastes and industrial by-products to produce filamentous fungi with potential as aqua-feed ingredients. Sustainability 10, 3296. Kaur, G., Sudhakara Reddy, M., 2017. Role of phosphate-solubilizing fungi in sustainable agriculture. In: Satyanarayana, T., Deshmukh, S.K., Johri, B.N. (Eds.), Developments in Fungal Biology and Applied Mycology. Springer Singapore, Singapore. Kavanagh, K., 2011. Fungal fermentations systems and products. In: Kavanagh, K. (Ed.), Fungi: Biology and Applications, second ed. Jon Wiley & Sons Incorporated. Khuong, L.D., Kondo, R., De Leon, R., Kim Anh, T., Shimizu, K., Kamei, I., 2014a. Bioethanol production from alkaline-pretreated sugarcane bagasse by consolidated bioprocessing using Phlebia sp. MG-60. Int. Biodeterior. Biodegradation 88, 62–68. Khuong, L.D., Kondo, R., Leon, R.D., Anh, T.K., Meguro, S., Shimizu, K., Kamei, I., 2014b. Effect of chemical factors on integrated fungal fermentation of sugarcane bagasse for ethanol production by a white-rot fungus, Phlebia sp. MG-60. Bioresour. Technol. 167, 33–40. € chs, J., 2013. Itaconic acid—a biotechnological process in change. Bioresour. Technol. 135, Klement, T., Bu 422–431. Kour, D., Rana, K.L., Yadav, N., Yadav, A.N., Singh, J., Rastegari, A.A., Saxena, A.K., 2019. Agriculturally and industrially important fungi: current developments and potential biotechnological applications. In: Yadav, A.N., Singh, S., Mishra, S., Gupta, A. (Eds.), Recent Advancement in White Biotechnology Through Fungi: Volume 2: Perspective for Value-Added Products and Environments. Springer International Publishing, Cham.

62

Current Developments in Biotechnology and Bioengineering

Koutrotsios, G., Mountzouris, K.C., Chatzipavlidis, I., Zervakis, G.I., 2014. Bioconversion of lignocellulosic residues by Agrocybe cylindracea and Pleurotus ostreatus mushroom fungi—assessment of their effect on the final product and spent substrate properties. Food Chem. 161, 127–135. Kozhevnikova, E.Y., Petrova, D.A., Novikov, A.A., Shnyreva, A.V., Barkov, A.V., Vinokurov, V.A., 2017. Prospects for the use of new basidiomycete strains for the direct conversion of lignocellulose into ethanol. Appl. Biochem. Microbiol. 53, 557–561. Lennartsson, P.R., 2012. Zygomycetes and Cellulose Residuals: Hydrolysis, Cultivation and Applications. Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg. Lennartsson, P.R., Erlandsson, P., Taherzadeh, M.J., 2014. Integration of the first and second generation bioethanol processes and the importance of by-products. Bioresour. Technol. 165, 3–8. Li, A., Pfelzer, N., Zuijderwijk, R., Punt, P., 2012. Enhanced itaconic acid production in Aspergillus niger using genetic modification and medium optimization. BMC Biotechnol. 12, 57. Liao, W., Liu, Y., Frear, C., Chen, S., 2008. Co-production of fumaric acid and chitin from a nitrogen-rich lignocellulosic material—dairy manure—using a pelletized filamentous fungus Rhizopus oryzae ATCC 20344. Bioresour. Technol. 99, 5859–5866. Liu, Y., Liao, W., Chen, S., 2008. Co-production of lactic acid and chitin using a pelletized filamentous fungus Rhizopus oryzae cultured on cull potatoes and glucose. J. Appl. Microbiol. 105, 1521–1528. Ma, L., Zhuo, R., Liu, H., Yu, D., Jiang, M., Zhang, X., Yang, Y., 2014. Efficient decolorization and detoxification of the sulfonated azo dye Reactive Orange 16 and simulated textile wastewater containing Reactive Orange 16 by the white-rot fungus Ganoderma sp. En3 isolated from the forest of Tzu-chin Mountain in China. Biochem. Eng. J. 82, 1–9. Ma, X., Gao, M., Yin, Z., Zhu, W., Liu, S., Wang, Q., 2020. Lactic acid and animal feeds production from Sophora flavescens residues by Rhizopus oryzae fermentation. Process Biochem. 92, 401–408. Macauley-Patrick, S., Finn, B., 2008. Modes of fermenter operation. In: Practical Fermentation Technology. John Wiley & Sons, Ltd. Maehara, T., Ichinose, H., Furukawa, T., Ogasawara, W., Takabatake, K., Kaneko, S., 2013. Ethanol production from high cellulose concentration by the basidiomycete fungus Flammulina velutipes. Fungal Biol. 117, 220–226. Mahanty, S., Bakshi, M., Ghosh, S., Chatterjee, S., Bhattacharyya, S., Das, P., Das, S., Chaudhuri, P., 2019. Green synthesis of iron oxide nanoparticles mediated by filamentous fungi isolated from Sundarban mangrove ecosystem, India. BioNanoScience 9, 637–651. Mahboubi, A., Ferreira, J., Taherzadeh, M., Lennartsson, P., 2017a. Production of fungal biomass for feed, fatty acids, and glycerol by Aspergillus oryzae from fat-rich dairy substrates. Fermentation 3, 48. Mahboubi, A., Ferreira, J.A., Taherzadeh, M.J., Lennartsson, P.R., 2017b. Value-added products from dairy waste using edible fungi. Waste Manag. 59. Mandal, S., Banerjee, D., 2019. Proteases from endophytic fungi with potential industrial applications. In: Yadav, A.N., Mishra, S., Singh, S., Gupta, A. (Eds.), Recent Advancement in White Biotechnology Through Fungi: Volume 1: Diversity and Enzymes Perspectives. Springer International Publishing, Cham. Matsumoto, M., Furuta, H., 2018. In situ extractive fermentation of lactic acid by Rhizopus oryzae in an airlift bioreactor. Chem. Biochem. Eng. Q. 32, 275–280. Meyer, V., Andersen, M.R., Brakhage, A.A., Braus, G.H., Caddick, M.X., Cairns, T.C., De Vries, R.P., ˜ alva, M.A., Haarmann, T., Hansen, K., Hertz-Fowler, C., Krappmann, S., Mortensen, U.H., Pen Ram, A.F.J., Head, R.M., 2016. Current challenges of research on filamentous fungi in relation to human welfare and a sustainable bio-economy: a white paper. Fungal Biol. Biotechnol. 3, 6. Meyer, V., Basenko, E.Y., Benz, J.P., Braus, G.H., Caddick, M.X., Csukai, M., De Vries, R.P., Endy, D., Frisvad, J.C., Gunde-Cimerman, N., Haarmann, T., Hadar, Y., Hansen, K., Johnson, R.I., Keller, N.P., Krasˇevec, N., Mortensen, U.H., Perez, R., Ram, A.F.J., Record, E., Ross, P., Shapaval, V., Steiniger, C., Van Den Brink, H.,

Chapter 2 • Fungal biotechnology

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€ sten, H.A.B., 2020. Growing a circular economy with fungal biotechnolVan Munster, J., Yarden, O., Wo ogy: a white paper. Fungal Biol. Biotechnol. 7, 5. Millati, R., Edebo, L., Taherzadeh, M.J., 2005. Performance of Rhizopus, Rhizomucor, and Mucor in ethanol production from glucose, xylose, and wood hydrolyzates. Enzym. Microb. Technol. 36, 294–300. Mohammadi, M., Zamani, A., Karimi, K., 2012. Determination of glucosamine in fungal cell walls by highperformance liquid chromatography (HPLC). J. Agric. Food Chem. 60, 10511–10515. Mohammadi, M., Zamani, A., Karimi, K., 2013. Effect of phosphate on glucosamine production by ethanolic fungus Mucor indicus. Appl. Biochem. Biotechnol. 171, 1465–1472. Moslamy, S.J.E., 2019. Application of fed-batch fermentation modes for industrial bioprocess development of microbial behaviour. Ann. Biotechnol. Bioeng. 1, 1001. Mu, Q., Cui, Y., Tian, Y.E., Hu, M., Tao, Y., Wu, B., 2019. Thermostability improvement of the glucose oxidase from Aspergillus niger for efficient gluconic acid production via computational design. Int. J. Biol. Macromol. 136, 1060–1068. Mukherjee, G., Mishra, T., Deshmukh, S.K., 2017. Fungal pigments: an overview. In: Satyanarayana, T., Deshmukh, S.K., Johri, B.N. (Eds.), Developments in Fungal Biology and Applied Mycology. Springer Singapore, Singapore. Mukhopadhyay, R., Chatterjee, S., Chatterjee, B.P., Banerjee, P.C., Guha, A.K., 2005. Production of gluconic acid from whey by free and immobilized Aspergillus niger. Int. Dairy J. 15, 299–303. €ßle, S., Chen, S.H., Ting, A.S.Y., 2018. Biofilm formation of filamentous fungi Munck, C., Thierry, E., Gra Coriolopsis sp. on simple muslin cloth to enhance removal of triphenylmethane dyes. J. Environ. Manag. 214, 261–266. Muniraj, I.K., Xiao, L., Liu, H., Zhan, X., 2015. Utilisation of potato processing wastewater for microbial lipids and γ-linolenic acid production by oleaginous fungi. J. Sci. Food Agric. 95, 3084–3090. Nair, R.B., Lundin, M., Brandberg, T., Lennartsson, P.R., Taherzadeh, M.J., 2015. Dilute phosphoric acid pretreatment of wheat bran for enzymatic hydrolysis and subsequent ethanol production by edible fungi Neurospora intermedia. Ind. Crop. Prod. 69, 314–323. Nigam, P., Robinson, T., Singh, D., 2003. Solid-state fermentation: an overview. In: Arora, D.K. (Ed.), Handbook of Fungal Biology. CRC Press, Boca Raton. Nirlane Da Costa Souza, P., Luiza Bim Grigoletto, T., Alberto Beraldo De Moraes, L., Abreu, L.M., Henrique Souza Guimara˜es, L., Santos, C., Ribeiro Galva˜o, L., Gomes Cardoso, P., 2016. Production and chemical characterization of pigments in filamentous fungi. Microbiology 162, 12–22. Nout, M.J.R., Sarkar, P.K., Beuchat, L.R., 2007. Indigenous fermented foods. In: Food Microbiology: Fundamentals and Frontiers, third ed. American Society of Microbiology, Washington, DC. Nyman, J., Lacintra, M.G., Westman, J.O., Berglin, M., Lundin, M., Lennartsson, P.R., Taherzadeh, M.J., 2013. Pellet formation of zygomycetes and immobilization of yeast. New Biotechnol. 30, 516–522. O’Donnell, K., Cigelnik, E., Casper, H.H., 1998. Molecular phylogenetic, morphological, and mycotoxin data support reidentification of the quorn mycoprotein fungus as Fusarium venenatum. Fungal Genet. Biol. 23, 57–67. Okabe, M., Lies, D., Kanamasa, S., Park, E.Y., 2009. Biotechnological production of itaconic acid and its biosynthesis in Aspergillus terreus. Appl. Microbiol. Biotechnol. 84, 597–606. Okamoto, K., Uchii, A., Kanawaku, R., Yanase, H., 2014. Bioconversion of xylose, hexoses and biomass to ethanol by a new isolate of the white rot basidiomycete Trametes versicolor. Springerplus 3, 121. Okamura, T., Ogata, T., Minamimoto, N., Takeno, T., Noda, H., Fukuda, S., Ohsugi, M., 2001. Characteristics of wine produced by mushroom fermentation. Biosci. Biotechnol. Biochem. 65, 1596–1600. Omidvar, M., Karimi, K., Mohammadi, M., 2016. Enhanced ethanol and glucosamine production from rice husk by NAOH pretreatment and fermentation by fungus Mucor hiemalis. Biofuel Res. J. 3, 475–481.

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Panagiotou, G., Christakopoulos, P., Olsson, L., 2005. Simultaneous saccharification and fermentation of cellulose by Fusarium oxysporum F3—growth characteristics and metabolite profiling. Enzym. Microb. Technol. 36, 693–699. Panagiotou, G., Topakas, E., Moukouli, M., Christakopoulos, P., Olsson, L., 2011. Studying the ability of Fusarium oxysporum and recombinant Saccharomyces cerevisiae to efficiently cooperate in decomposition and ethanolic fermentation of wheat straw. Biomass Bioenergy 35, 3727–3732. Papagianni, M., 2019. 1.07—Organic acids. In: Moo-Young, M. (Ed.), Comprehensive Biotechnology, third ed. Pergamon, Oxford. Pietrzak, W., Kawa-Rygielska, J., 2019. Backset valorization in dry-grind ethanol process by co-culture of edible filamentous fungi and fodder yeast. J. Clean. Prod. 220, 376–385. Rafiee, K., Kaur, G., Brar, S.K., 2021. Fungal biocomposites: how process engineering affects composition and properties? Bioresour. Technol. Rep. 14, 100692. Roa Engel, C., Straathof, A., Zijlmans, T., Van Gulik, W., Van Der Wielen, L., 2008. Fumaric acid production by fermentation. Appl. Microbiol. Biotechnol. 78, 379–389. Roa Engel, C.A., Van Gulik, W.M., Marang, L., Van Der Wielen, L.A.M., Straathof, A.J.J., 2011. Development of a low pH fermentation strategy for fumaric acid production by Rhizopus oryzae. Enzym. Microb. Technol. 48, 39–47. Robinson, T., Singh, D., Nigam, P., 2001. Solid-state fermentation: a promising microbial technology for secondary metabolite production. Appl. Microbiol. Biotechnol. 55, 284–289. Ruholahi, F., Mohammadi, M., Karimi, K., Zamani, A., 2016. Nickel biosorption by fungal chitosan from Mucor indicus. J. Chitin Chitosan Sci. 4, 69–73. Saberi, A., Jalili, H., Nikfarjam, A., Koohsorkhi, J., Jarmoshti, J., Bizukojc, M., 2020. Monitoring of Aspergillus terreus morphology for the lovastatin production in submerge culture by impedimetry. Biochem. Eng. J. 159, 107615. Salehi Jouzani, G., Taherzadeh, M.J., 2015. Advances in consolidated bioprocessing systems for bioethanol and butanol production from biomass: a comprehensive review. Biofuel Res. J. 2, 152–195. Sar, T., Ferreira, J.A., Taherzadeh, M.J., 2020. Bioprocessing strategies to increase the protein fraction of Rhizopus oryzae biomass using fish industry sidestreams. Waste Manag. 113, 261–269. Sathiyaseelan, A., Shajahan, A., Kalaichelvan, P.T., Kaviyarasan, V., 2017. Fungal chitosan based nanocomposites sponges—an alternative medicine for wound dressing. Int. J. Biol. Macromol. 104, 1905–1915. Sawant, O., Mahale, S., Ramchandran, V., Nagaraj, G., Bankar, A., 2018. Fungal citric acid production using waste materials: a mini-review. J. Microbiol. Biotechnol. Food Sci. 8, 821–828. Saye, L.M.G., Navaratna, T.A., Chong, J.P.J., O’Malley, M.A., Theodorou, M.K., Reilly, M., 2021. The anaerobic fungi: challenges and opportunities for industrial lignocellulosic biofuel production. Microorganisms 9, 694. Sebastian, J., Hegde, K., Kumar, P., Rouissi, T., Brar, S.K., 2019a. Bioproduction of fumaric acid: an insight into microbial strain improvement strategies. Crit. Rev. Biotechnol. 39, 817–834. Sebastian, J., Rouissi, T., Brar, S.K., Hegde, K., Verma, M., 2019b. Microwave-assisted extraction of chitosan from Rhizopus oryzae NRRL 1526 biomass. Carbohydr. Polym. 219, 431–440. Seraman, S., Rajendran, A., Thangavelu, V., 2010. Statistical optimization of anticholesterolemic drug lovastatin production by the red mold Monascus purpureus. Food Bioprod. Process. 88, 266–276. Sharma, A., Vivekanand, V., Singh, R.P., 2008. Solid-state fermentation for gluconic acid production from sugarcane molasses by Aspergillus niger ARNU-4 employing tea waste as the novel solid support. Bioresour. Technol. 99, 3444–3450. Shurtleff, W., Aoyagi, A., 1985. History of Tempeh: A Fermented Soyfood From Indonesia. Soyfoods Center, Lafayette, CA, USA.

Chapter 2 • Fungal biotechnology

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Shurtleff, W., Aoyagi, A., 2012. History of Koji—Grains and/or Soybeans Enrobed With a Mold Culture (300 BCE to 2012). Soyinfo Center, Lafayette, CA, USA. Singh Dhillon, G., Kaur Brar, S., Verma, M., Tyagi, R.D., 2011. Recent advances in citric acid bio-production and recovery. Food Bioprocess Technol. 4, 505–529. Singh, O.V., Kumar, R., 2007. Biotechnological production of gluconic acid: future implications. Appl. Microbiol. Biotechnol. 75, 713–722. Singh, U., Gautam, A., Singha, T.K., Tiwari, A., Tiwari, P., Sahai, V., Sharma, S., 2020. Mass production of Pleurotus eryngii mycelia under submerged culture conditions with improved minerals and vitamin D2. LWT 131, 109665. Soccol, C., Vandenberghe, L., Rodrigues, C., Pandey, A., 2006. New perspectives for citric acid production and application. Food Technol. Biotechnol. 44, 141–149. Soccol, C.R., Costa, E.S.F.D., Letti, L.A.J., Karp, S.G., Woiciechowski, A.L., Vandenberghe, L.P.D.S., 2017. Recent developments and innovations in solid state fermentation. Biotechnol. Res. Innov. 1, 52–71. Soh, E., Chew, Z.Y., Saeidi, N., Javadian, A., Hebel, D., Le Ferrand, H., 2020. Development of an extrudable paste to build mycelium-bound composites. Mater. Des. 195, 109058. Sood, S., Singhal, R., Bhat, S., Kumar, A., 2011. 2.19—Inoculum preparation. In: Moo-Young, M. (Ed.), Comprehensive Biotechnology, third ed. Pergamon, Oxford. Souza Filho, P.F., Zamani, A., Taherzadeh, M.J., 2017. Production of edible fungi from potato protein liquor (PPL) in airlift bioreactor. Fermentation 3, 12. Souza Filho, P.F., Nair, R.B., Andersson, D., Lennartsson, P.R., Taherzadeh, M.J., 2018. Vegan-mycoprotein concentrate from pea-processing industry byproduct using edible filamentous fungi. Fungal Biol. Biotechnol. 5, 5. Sperandio, G.B., Ferreira Filho, E.X., 2019. Fungal co-cultures in the lignocellulosic biorefinery context: a review. Int. Biodeterior. Biodegradation 142, 109–123. Stanbury, P.F., Whitaker, A., Hall, S.J., 2017a. Media for industrial fermentations. In: Stanbury, P.F., Whitaker, A., Hall, S.J. (Eds.), Principles of Fermentation Technology, third ed. ButterworthHeinemann, Oxford (Chapter 4). Stanbury, P.F., Whitaker, A., Hall, S.J., 2017b. Culture preservation and inoculum development. In: Stanbury, P.F., Whitaker, A., Hall, S.J. (Eds.), Principles of Fermentation Technology, third ed. Butterworth-Heinemann, Oxford (Chapter 6). Sues, A., Millati, R., Edebo, L., Taherzadeh, M.J., 2005. Ethanol production from hexoses, pentoses, and dilute-acid hydrolyzate by Mucor indicus. FEMS Yeast Res. 5, 669–676. Sugiharto, S., 2019. A review of filamentous fungi in broiler production. Ann. Agric. Sci. 64, 1–8. Svensson, S.E., Ferreira, J.A., Hakkarainen, M., Adolfsson, K.H., Zamani, A., 2021. Fungal textiles: wet spinning of fungal microfibers to produce monofilament yarns. Sustain. Mater. Technol. 28, e00256. Tirumale, S., Wani, N.A., 2018. Biopigments: fungal pigments. In: Gehlot, P., Singh, J. (Eds.), Fungi and Their Role in Sustainable Development: Current Perspectives. Springer Singapore, Singapore. Trakarnpaiboon, S., Srisuk, N., Piyachomkwan, K., Yang, S.-T., Kitpreechavanich, V., 2017. l-Lactic acid production from liquefied cassava starch by thermotolerant Rhizopus microsporus: characterization and optimization. Process Biochem. 63, 26–34. Troiano, D., Orsat, V., Dumont, M.J., 2020. Status of filamentous fungi in integrated biorefineries. Renew. Sustain. Energy Rev. 117, 109472. cz, B., Lagzi, I., 2016. One-step green synthesis of gold Va´go´, A., Szakacs, G., Sa´fra´n, G., Horvath, R., Pe nanoparticles by mesophilic filamentous fungi. Chem. Phys. Lett. 645, 1–4.

66

Current Developments in Biotechnology and Bioengineering

Van Der Straat, L., Vernooij, M., Lammers, M., Van Den Berg, W., Schonewille, T., Cordewener, J., Van Der Meer, I., Koops, A., De Graaff, L.H., 2014. Expression of the Aspergillus terreus itaconic acid biosynthesis cluster in Aspergillus niger. Microb. Cell Factories 13, 11. , L., Renuka Devi, P., Veera Ravi, A., 2020. Fungal pigments: potential Venil, C.K., Velmurugan, P., Dufosse coloring compounds for wide ranging applications in textile dyeing. J. Fungi 6, 68. Vyas, P., Bansal, A., 2018. Fungal endophytes: role in sustainable agriculture. In: Gehlot, P., Singh, J. (Eds.), Fungi and Their Role in Sustainable Development: Current Perspectives. Springer Singapore, Singapore. Walker, G.M., White, N.A., 2017. Introduction to fungal physiology. In: Fungi. John Wiley & Sons, Ltd. Wang, B., Li, H., Zhu, L., Tan, F., Li, Y., Zhang, L., Ding, Z., Shi, G., 2017. High-efficient production of citric acid by Aspergillus niger from high concentration of substrate based on the staged-addition glucoamylase strategy. Bioprocess Biosyst. Eng. 40, 891–899. Wiebe, M., 2002. Myco-protein from Fusarium venenatum: a well-established product for human consumption. Appl. Microbiol. Biotechnol. 58, 421–427. Wiebe, M.G., 2004. QuornTM myco-protein—overview of a successful fungal product. Mycologist 18, 17–20. Wikandari, R., Millati, R., Lennartsson, P.R., Harmayani, E., Taherzadeh, M.J., 2012. Isolation and characterization of zygomycetes fungi from tempe for ethanol production and biomass applications. Appl. Biochem. Biotechnol. 167, 1501–1512. € sten, H.A.B., 2019. Filamentous fungi for the production of enzymes, chemicals and materials. Curr. Wo Opin. Biotechnol. 59, 65–70. Wright, C., Gryganskyi, A.P., Bonito, G., 2016. Fungi in composting. In: Purchase, D. (Ed.), Fungal Applications in Sustainable Environmental Biotechnology. Springer International Publishing, Cham. Xin Li, Q.Y., 2020. Production of fumaric acid from lignocellulose by Rhizopus oryzae. Chem. Ind. For. Prod. 40, 1–7. Xiros, C., Christakopoulos, P., 2009. Enhanced ethanol production from brewer’s spent grain by a Fusarium oxysporum consolidated system. Biotechnol. Biofuels 2, 4. Xiros, C., Topakas, E., Katapodis, P., Christakopoulos, P., 2008. Hydrolysis and fermentation of brewer’s spent grain by Neurospora crassa. Bioresour. Technol. 99, 5427–5435. Xu, Q., Li, S., Fu, Y., Tai, C., Huang, H., 2010. Two-stage utilization of corn straw by Rhizopus oryzae for fumaric acid production. Bioresour. Technol. 101, 6262–6264. Yuwa-Amornpitak, T., Chookietwatana, K., 2018. Bioconversion of waste cooking oil glycerol from cabbage extract to lactic acid by Rhizopus microsporus. Braz. J. Microbiol. 49, 178–184. Zain, N.A.M., Aziman, S.N., Suhaimi, M.S., Idris, A., 2021. Optimization of L(+) lactic acid production from solid pineapple waste (SPW) by Rhizopus oryzae NRRL 395. J. Polym. Environ. 29, 230–249. Zhang, Z.Y., Jin, B., Kelly, J.M., 2007. Production of lactic acid from renewable materials by Rhizopus fungi. Biochem. Eng. J. 35, 251–263. Zhang, L., Li, X., Yong, Q., Yang, S.-T., Ouyang, J., Yu, S., 2015. Simultaneous saccharification and fermentation of xylo-oligosaccharides manufacturing waste residue for l-lactic acid production by Rhizopus oryzae. Biochem. Eng. J. 94, 92–99. Zhao, M., Lu, X., Zong, H., Li, J., Zhuge, B., 2018. Itaconic acid production in microorganisms. Biotechnol. Lett. 40, 455–464. Zhong, J.J., 2011. 2.21—Bioreactor engineering. In: Moo-Young, M. (Ed.), Comprehensive Biotechnology, third ed. Pergamon, Oxford.

3 Fungal biology Soumya Mukherjeea and Shakuntala Ghoraib a

UNI VE RS IT Y OF T OL ED O, T OLE DO , OH , UNI TE D STAT ES b DEPARTMENT OF MIC ROB IOLOGY, RAIDIGHI COLLEGE, RAIDI GHI, INDIA

1. Introduction Kingdom fungi constitute an exceedingly species-rich kingdom, covering almost 100,000 described and about 1.5–5.1 million undescribed species in diverse environments such as forest soil, phyllosphere, aquatic ecosystems, and soils of the pristine polar region (Jumpponen and Jones, 2009; Kagami et al., 2007; Dura´n et al., 2019). Fungi are important components of ecosystems. They play roles of decomposers, mutualists of plants and as parasites to various organisms (Talbot et al., 2008; Allen et al., 2003; Kohler et al., 2015). Humans utilized fungi in terms of applications in agriculture, pharmacology, the food industry, and environmental technologies (Rico-Munoz et al., 2019; Zjawiony, 2004; Cardoso and Kuyper, 2006; Wang and Chen, 2006). Thus, exploration of fungal diversity is worthy of effort and time not only for our ecosystem and ecological community but also to provide invaluable resources for various fields of applied microbiology (Table 1). Classical fungal taxonomy faced a chaotic and turbulent history. Whittaker (1969) proposed a fourth kingdom in the kingdom of life. Fungi that have been previously oscillating between kingdom Protista and Plantae were given a new place as a kingdom. The 2007 classification of kingdom Fungi was the result of collaborative research effort of dozens of mycologists, scientists, and individual projects working globally on fungal taxonomy. Formal recognition of fungal nomenclature including yeasts is governed by the International Code of Botanical Nomenclature (ICBN) as adopted by each International Botanical Congress. Assembling the Fungal Tree of Life (AFTOL) project was funded by the US National Science Foundation. The 2007 phylogenetic classification divided the fungi kingdom into 7 phyla, 10 subphyla, 35 classes, 12 subclasses, and 129 orders. Phylogenetic relationships (relation based on ancestry) are inferred from fossils, comparative morphology, and biochemistry. Constructing phylogenetic trees (evolutionary trees or cladograms) requires molecular data coupled to these traditional forms of data. To be formally recognized by taxonomists, an organism must be described in accordance with internationally accepted rules and given a Latin binomial. The presence of dual reproductive stages of fungal propagation, i.e., sexual (teleomorph stage) and asexual (anamorphs), has been used since century for nomenclature. Morphological details associated with sexual sporulation proved useful in higher fungal classification. The type of fruiting body (basidioma in basidiomycetes, ascoma in Current Developments in Biotechnology and Bioengineering. https://doi.org/10.1016/B978-0-323-91872-5.00017-X Copyright © 2023 Elsevier Inc. All rights reserved.

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Table 1

Some notable production strains.

Fungi

Division

Products

Rhizopus oligosporus

Mucoromycota

Aspergillus oryzae

Ascomycota

Penicillium camemberti Penicillium roqueforti Aspergillus oryzae, Saccharomyces cerevisiae

Ascomycota

Tempeh (Indonesian fermented legume seeds) Miso, koji, sake, (fermented rice, beverages), enzymes Camembert and Roquefort cheese

Saccharomyces cerevisiae

Ascomycota

Ascomycota

Agaricus bisporus, Volvariella volvacea, Pleurotus Basidiomycota ostreatus, Lentinula edodes and many more Blakeslea trispora Zygomycota Aspergillus niger

Ascomycota

Acremonium chrysogenum

Ascomycota

Thermotelomyces thermophila

Ascomycota

Tricoderma reesei

Ascomycota

Penicillium chrysogenum

Ascomycota

Fusarium venenatum

Ascomycota

Candida famata

Ascomycota

Ashbya gossyppi

Ascomycota

Pleurotus ostreatus

Basidiomycota

Ganoderma lucidum

Basidiomycota

Schizophyllum commune

Basidiomycota

Utilago maydis

Basidiomycota

Agaricus bisporus

Basidiomycota

Cantharellus cibarius

Basidiomycota

Imleria badia

Basidiomycota

Lentinula edodes

Basidiomycota

Termitomyces clypeatus

Basidiomycota

References

Ghorai et al. (2009) Ghorai et al. (2009) Ghorai et al. (2009) Soy sauce Ghorai et al. (2009) Rice wine (sake), Chinese liquor, Ghorai et al. animal feed (2009) Edible mushrooms, pharmaceutical, Ghorai et al. and nutraceutical by-products (2009) Vitamins (β-carotene) Cairns et al. (2019) Enzymes, organic acids Cairns et al. (2019) β-Lactam antibiotics Cairns et al. (2019) Enzymes Cairns et al. (2019) Enzymes Cairns et al. (2019) β-Lactam antibiotics, enzymes Cairns et al. (2019) Mycoprotein Cairns et al. (2019) Riboflavin Azizan et al. (2016) Riboflavin Azizan et al. (2016) Composite materials Cairns et al. (2019) Composite material, imitation Cairns et al. leather (2019) Textiles Cairns et al. (2019) Itaconic acid Cairns et al. (2019) Food, lovastatin Kala et al. (2020) Food, lovastatin Kala et al. (2020) Food, lovastatin Kala et al. (2020) Food, lovastatin Kala et al. (2020) Enzymes, food, and feed Ghorai et al. (2009)

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ascomycetes) or the type of ascus (a microscopic, unicellular, frequently globose, saccate, or cylindrical structure) is prominent sources for classification. Variations in ascus structure helps in the classification of these fungi, especially at the level of family and above. Earlier Fungi were usually classified in four divisions: the Chytridiomycota (chytrids), Zygomycota (bread molds), Ascomycota (yeasts and sac fungi), and the Basidiomycota (club fungi).

2. The fungal world “I thought a forest was made up entirely of trees, but now I know that the foundation lies below ground, in the fungi” … Derrick Jensen

Fungi have shorter generation time, larger population size, more active haploid state, no embryonic state, higher chromosome plasticity, higher selective pressure for a reduced genome, and higher evolutionary rate compared to plants and animals (Naranjo-Ortiz and Gabaldon, 2020).

2.1 Growth of fungi Hyphal structures in fungi show polarized growth. Some unicellular fungi like Saccharomyces cerevisiae also demonstrate polarized growth but they do not produce hyphal structures. The components responsible for fungal polarized growth are well conserved. € rper which is composed of Hyphal structures contain one organelle called Spitzenko numerous vesicles originating from Golgi apparatus (Diepeveen et al., 2018). These vesicles are full of enzymes, lipids, and polysaccharides needed for the synthesis of membranes and cell wall. Those vesicles are coordinated via actin and microtubule cytoskeleton. Cell growth is associated with coordinated cycles or oscillations of exocytosis involving polarity markers, exocyst complex, and SNARE proteins (Takeshita, 2016). Dikarya groups are specialized to carry this machinery and studies reveal the conservative nature of this apparatus across all Dikarya. In Zygomycetes fungi, apical vesicle credent € rper (Fisher and Roberson, are less organized aggregates of vesicles compared to Spitzenko 2016). Hyphal structures are septate or nonseptate. Septa formation requires chitin rings and chitin synthase activity. True fungal network formation requires the ability to fuse the hyphal tips or anastomosis. This involves complex cell recognition mechanism while preventing fusion of genetically dissimilar hyphae during vegetative hyphal growth (NaranjoOrtiz and Gabaldon, 2020). Filamentous fungi generally form branches at nearly right angles to the parent hyphae (Carlile et al., 2001). Fungal growth is mostly determined by hyphal growth unit which is the total length of the mycelium divided by the total number of tips. Sometimes, fungal growth pattern is examined based on the mean hyphal segment length of the fungal network. Direction of fungal growth is indicated by the growth angle which can be defined as the difference between the angle of a segment and the angle of its preceding segment

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(Riquelme et al., 1998). Larger values for the mean growth angle are indicative of a complex network full of branches whereas a low value indicates that there is no or minimum change in the growth direction. Five distinguished phases of growth namely the lag, the first transition period, the log, the second transition, and the stationary phase were identified in Rhizopus microspores, Aspergillus fumigatus, and Scedosporium prolificans with varying growth rates (Meletiadis et al., 2001). Transition phases were long and log phases showed least variability with respect to growth rate among the strains. Although entry to the stationary phase or deceleration phase is critical considering its role in the production of industrially important secondary metabolites, this phase is least studied. In some cases, deviation from normal growth curve like hidden diauxic growth may happen due to reuse of released secondary metabolites like polyols, gluconate, or organic acids, etc., by the fungi (Schmitz et al., 2013). Currently, automated methods for fungal growth measurement are becoming popular. Typical sigmoidal growth curve was observed for economically important fungi Coniophora puteana and Rhizoctonia solani depending on mycelial area and number of tips under 16 different environmental conditions (De Ligne et al., 2019). Images of growing fungi at certain time interval were processed and analyzed via algorithms to study spatiotemporal growth dynamics. Environmental effects were measured depending on the Granger causality test, the Mann-Whitney test, and dynamic time warping. Fungal feature tracker, a modern tool, is developed to characterize morphology and growth of filamentous fungi quantitatively (Vidal-Diez de Ulzurrun et al., 2019). Modifications of polar growth and morphology are targeted for the industrial production of secondary metabolites from engineered filamentous fungi (Cairns et al., 2019). Different signaling pathways like the cAMP/PKA signaling pathways, the calcium/calcineurin signaling pathway and RAS signaling, etc., are pivotal in controlling the production rate. Several filamentous fungi are known to produce biofilms when grown on aqueous environment. Aspergillus sp., Alternaria sp., Botrytis sp., Cladosporium sp., and Penicillium sp. are capable of forming biofilms in environment as well as in a laboratory setup (Siqueira and Lima, 2013). Biomass or monolayer formation and exopolysaccharide production was directly co-related. Biofilm production was observed to follow five sequential stages: (i) propagule adsorption, (ii) active attachment to a surface, (iii) microcolony formation I, (iv) microcolony formation II, and (v) dispersal or planktonic phase.

2.2 Nutrition and transport in fungi Although today’s fungi originated from a flagellated unicellular organism with saprophytic or parasitic life style, they represent a wide variety of unicellular to complex multicellular organisms. They behave as osmotrophs with their surrounding environment with the help of numerous secreted proteins (enzymes) and secondary metabolites. Unicellular zoosporic fungi as saprophytic or having predatory-parasitic lifestyle. Those swimming cells normally attached themselves to an available substrate and phagocytic amoeboid extensions are produced which act as feeding structures (Oberwinkler, 2017). Many members of

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Chytridiomycota having polycentric rhizoid structures belong to this category. Nutrient transport in filamentous fungi as mediated via cytoplasmic currents which pass cellular components including nuclei for growing hyphal tips (Naranjo-Ortiz and Gabaldon, 2020). Cytoplasmic waves are used to transport over long distances whereas cytoskeleton-based movement is essential for short-range movements or against the main cytoplasmic flow. They also narrated fungal sensory systems which are similar to that of plants. Key cellular events like reproduction, morphogenesis, virulence, and metabolisms are regulated via light-induced gene expressions. In those cases, fungi have well-regulated wavelength-ratio sensing mechanism and circadian clock in them. Zinc-finger transcription factors named white-collar complex proteins mediate changes in the transcriptome profile. Some yeast and parasitic fungi are devoid of those white-collar proteins (Adam et al., 2018). In some fungi, opsin-like proteins are also involved in regulation of sexual cycle and pathogenesis. Perception of gravity in fungi is controlled by units called statoliths which are composed of oxalate crystals and buoyant lipid structures (Kunzler, 2018; Medina-Castellanos et al., 2018). In major fungal groups like Ascomycota, Basidiomycota, Mucoromycotina, Mortierellomycotina, and Glomeromycota; buoyancy systems are present and they are conserved across long evolutionary distances. Filamentous and zoosporic fungi are found to detect electric fields and respond to it in Ca2+-dependent manner. Multicellular vegetative structures are called rhizomorphs in some fungi. These are vegetative hypha having thread-like aggregates which helps in nutrient distribution over large distances (Krizsan et al., 2019).

2.3 Fungal reproduction Reproduction is the fundamental characteristic of all life forms. It involves formation of daughter or new cells from parent. Fungi adopt different modes for reproduction like vegetative, asexual, parasexual, and sexual. Filamentous fungi can reproduce via sexual or asexual mode. Although sexual reproduction renders many advantages like increased genetic variation, more durable and resistant sexual fruiting bodies, etc., almost one-fifth of all fungi are known to reproduce asexually. Fungal sexual reproduction can be summarized in three steps (Lee et al., 2010). Compatible haploid cells fuse, i.e., plasmogamy, then nuclei of both the haploid cells fuse, i.e., karyogamy, and finally fused diploid cell produces four haploid spores via meiosis. Nuclear fusion initiates just after the cell fusion in the two basal fungal lineages, i.e., Chytridiomycetes and Zygomycetes as well as in some ascomycetes whereas the event of nuclear fusion is delayed after cell fusion in other ascomycetes and in basidiomycetes. The later groups have a stable dikaryotic hyphae stage (especially in basidiomyteces) throughout most of their hyphal growth stage and then nuclear fusion occurs leading to meiosis to finally produce haploid recombinant progeny. Size of the reproductive unit is defined as “subpopulations of nuclei that propagate together as spores, and function as reproductive individuals” and is dynamic and dependent on the environment (Ma et al., 2016).

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2.3.1 Unicellular yeast form Vegetative mode of reproduction involves part of vegetative cells or somatic portion of the fungal hyphae/thallus. Higher fungi can accommodate two forms in their life—unicellular monokaryotic yeast form and filamentous dikaryotic form. Fungi adopting one of these forms are called monomorphic, while those taking up both forms are dimorphic. Yeast form is generated from the budding of a basidiospore and it reproduces asexually by budding, fission, or production of forcefully ejected ballistoconidia (Flegel, 1977). Various modes of vegetative reproduction in yeast are observed like multilateral budding, bipolar budding, unipolar budding, monopolar budding, binary fission, bud fission, budding from stalks, ballistoconidiogenesis, and pseudomycelia (Walker, 1998). Filamentous forms, as the terminology goes, consist of long branching tubular cells known as hyphae which may be septate via compartments or aseptate and grow at the apex (Morrow and Fraser, 2009). Parasexual cycle in wild mitosporic fungi occur through deoxyribonucleic acid (DNA) recombination. It may involve fusion of two haploid mycelia forming heterokaryotic mycelium with more than one genotype in uncontrolled proportions (Wallen and Perlin, 2018). In Candida albicans some DNA repair is performed through recombination in this life cycle. Instead of regular meiosis, tetraploid cells generated through mating of two (diploid) mating types go through concerted chromosome loss (CCL). This is believed to involve chromosome nondisjunction events during mitosis and the aneuploid cells show a wide variety of ploidies including haploid cells. One meiosis-specific recombinase Spo11 is found to be involved in the process. In C. albicans, homothallic mating is also observed (Bennett and Turgeon, 2016). A cell releases pheromone for both mating types which enable the cell to be self-fertile or inducing same sex mating. Unicellular ascomycetes such as yeast grow either as haploid or diploid cells but diploidy is predominant in wild (Lee et al., 2010). Haploid mating types can be either a or α. Mating type of the cell is decided by the genetic material at the mating-type locus. A single MAT locus is the deciding factor of mating-type identity. In case of unicellular ascomycetes like yeast Pichia pastoris; mating type switching occurs in the cell by flipflop inversion mechanism (Wallen and Perlin, 2018). Meiosis in diploid cells is triggered by DNA damage in nutrient limiting condition as through meiosis genetic materials got repaired. In pathogenic ascomycetes, no sexual reproduction is usually observed inside the host and in the wild as well, although they produce genetic components used for sexual reproduction, whereas pathogenic and saprophytic basidiomycetes reproduce sexually. Basidiomycetes yeast can produce conjugation tubes in presence of compatible mating type and eventually fuse to produce a dikaryotic hypha. They also undergo a complex form of mitosis via formation of clamp cells. Meiosis involves nuclear fusion with formation of tetrad of haploid basidiospores in basidium (Casselton and Olesnicky, 1998). Pathogenicity and parasitism are critically linked to the changeable forms of fungi and their modes of reproduction (Madhani and Fink, 1998; Nadal et al., 2008).

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2.3.2 Chytridiomycota They reproduce via asexual mode through the flagellated zoospores from sporangia (James et al., 2006a). Those spores may be mono or polyflagellate and thallus developed from them may form either monocentric or one sporangium from single spore or polycentric or many sporangia from a single zoospore. Sporangia are thin walled but resting spores that germinate later on after a dormant period, are thick-walled structures. Zoosporangia are always produced asexually but resting spores may be formed by sexually or asexually. Meiosis may happen within the resting spores or during germination to form mature sporangium. Majority of the chytrids lack sexual cycle. Release of spores from sporangia is induced by the presence of haem or porphyrins release from ingested plant materials in the rumen. Those flagellated zoospores move toward soluble sugars and/or phenolic acids released from the stomata or lateral spikes of the ingested plant materials by beating of up to 8–17 flagella via chemotaxis. After attachment to the plant material, zoospores shed the flagella and form cyst. Germination from the cyst is mediated by formation of a germ tube from the opposite polar end of flagellar origin. In monocentric fungus, nucleus remains within the cyst which becomes larger to form zoosporangium, so the rhizoids are anucleate. In case of polycentric fungi, nuclei migrates into the rhizoidal portion and multiple sporangia are formed on each thallus. Prominent exceptions to this are several genera like Cyllamyces, etc. (Ozkose et al., 2001). The rhizoid structure penetrates the plant material and takes up nutrients from there for the development and maturation of multinucleate sporangia. These again produce a few (1–2) to many (50–80) zoospores. Induction of zoospore differentiation in the mature sporangium eventually leads to release of the spores after dissolution of the sporangial wall. These fungi may go through aerotolerant structure in their life cycle (Griffith et al., 2009). Sexual reproduction is unusual in case of chytrids. Sometimes rhizoids fuse to transfer nuclei between thalli. Alternately, some swimming mitospores behave as gametes and when two of them fuse, a single cell with two nuclei and two flagella is produced through plasmogamy. When the cell expands a thick-walled meiosporangium is formed which contains meiospores. Meiospores are produced through meiosis after fusion of nuclei.

2.3.3 Zygomycota One mode of asexual reproduction is through mitospores. The method is fast and economical although lack genetic variability in the offspring. Most common form of asexual reproduction involves formation of spores from the tip of the hyphae one by one. The spores are called conidia and corresponding hyphae is called as conidiophores. Aerial reproductive hypha is called sporangiophore. They swell at the tip to form a mitosporangium and the contents divide to form many mitospores inside the shelter. When the sporangium matures, it breaks open, as a result spores are freely released into the air and ready to get deposited in available surfaces. Sexual reproduction in zygomycetes involving formation of zygosporangium generated from the fusion of parental hyphae at the tip and subsequent hardening of the wall

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and production of a zygospore (Lee et al., 2010). Parental mycelia must be compatible in nature, if one is plus mating type, the other one must be minus mating type. Specific pheromone trisporic acid is required for sexual development which is produced from β-carotene in each mating type. Both parental hyphae meet at the tips. Behind the tips, cross walls are formed leading to the formation of structure gametangia which behaves as gametes. The walls dissolve and gametangia fuse via plasmogamy. The fusion cell is called zygosporangium where two nuclei form parental hyphae fuse and generate 2n zygote nuclei. The wall structure of the zygosporangium becomes hard and thick gradually to produce zygospore. 1n recombinant nuclei are generated from 2n nuclei through meiosis and germ sporangium is formed from swelling tip of hyphae grown from zygospore. From the sporangium, 1n meiospores are released into the air and they eventually germinate into hyphal structure when favorable environment is available.

2.3.4 Glomeromycota These are arbuscular mycorrhizae fungi. They produce asexual mitospores. Some species generate mitospores in the mycelial part that reaches to the soil while others produce mitospores inside the root structure between the cells or in the space enclosed by the walls of the host plant cells. Unlike other spores, mitospores are not made inside the sporangia (sac-like structure) but instead are actually the swollen tip of hyphae with cytoplasm and stored food. Their size may be as large as millimeter is diameter and they are distributed nearby by some sort of dispersal mechanism.

2.3.5 Ascomycota Asexual reproduction in the phylum Ascomycota begins with spores (n) (Bennett and Turgeon, 2016). When they get nutrient and favorable conditions, they germinate into mycelia. Hyphal tips form asexual conidia and conidia formation varies in different fungi. Some conidia are like blowing bubbles from a pipe while in other fungi conidiophores are split into short segments. Sexual reproduction cycle in Ascomycota requires two compatible mycelia, plus and minus mating types. Female structure, ascogonium, is larger compare to the male structure, antheridium. During the fusion process or plasmogamy, nuclei move from antheridium to the ascogonium. After fertilization, n + n hyphae generate from fertilized ascogonium and one fruiting structure called ascoma is formed via weaving of the 1n hyphae and n + n hyphae of the ascogonial parent. Mainly three different types of ascoma are found. Ascoma structure varies in different fungi. On one surface of ascoma many n + n hyphae make meosporangia or asci. Ascus generating hypha, ascogenous, bends its tip while growing and makes a hook like structure called crozier which contains nuclei (n + n). Mitotic division of the two nuclei and walls lead to the formation of three cells from the crozier. The penultimate cell containing two nuclei of opposite types is the young ascus. 2n zygote nucleus is formed within the ascus through karyogamy. The cell at the tip of the crozier while bent fuses with the stalk of the hyphae to generate n + n state. In this way, more asci are generated from the same

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hyphae. Then, the zygote nuclei form four recombinant 1n nuclei via meiosis followed by mitotic division ultimately resulting eight meiospores in the cytoplasm. The spores are called ascospores and their release from ascus varies from fungus to fungus. They may be released passively or directly shot from the ascus as one spore at a time or all at once in a sticky mass.

2.3.6 Basidiomycota Basidiomycota fungi reproduce mainly via sexual mode. Asexual spores are also generated but lesser in extent. Culinary delicacy mushrooms are actually sexual fruiting bodies or basidiomata (basidioma in singular). Mating occurs when haploid meiospore in form of mycelium (1n) encounters one compatible 1n mycelium (like one plus and one minus or vice versa) (Coelho et al., 2017). Through plasmogamy, the tips of both the hyphae fuse and the fusion cell bears one nuclei from each parent. As the mycelium of basidiomycetes are septed in nature and in many cases, nuclei can pass through septa to other compartments and divide mitotically, so haploid mycelia are converted to single n + n mycelium. Fruiting bodies or basidiomata are formed in many numbers as fusion cell makes more branches of n + n hyphae. In mushrooms, dikaryotic hyphal development to form basiomata or fruiting bodies through signal exchange is dependent on the hyphal location in the basidiomata. Some dikaryotic hyphae make a stalk, some make protective cap, some produce gills, or spore producing part of the basidioma. Spores are generated from the tips of n + n hyphae present all over the surface of each gill. Swelling of basidium or the tipmost cell of all these hyphae results in 2n zygote nucleus by fusion of the paired nuclei through karyogamy. Four 1n nuclei are formed from the 2n zygote via meiosis. Spores are created through the pressure in the basidium as the wall of the basidium near each 1n nucleus generates a thin stalk or sterigma and the tip of the sterigma grows bigger into a spore. Through the pressure cytoplasm enters into sterigma along with a nucleus. Finally, four basidiospores with different genotypes are produced and spores are released after spore walls are hardened. Dikaryotic stage of life is much longer in basidiomycetes compare to ascomycetes. In mushrooms, dikaryons serve as both feeding mycelium as well as to produce fruiting body but in Ascomycetes dikaryons are short lived and produce fruiting bodies only. So, mushrooms can generate basidiomata many times in its life. Mushrooms maintain the dikaryotic stage by forming: (1) overlapping mitotic spindles, (2) clamp connection, and (3) perforated septum called dolipore septum. Spores are released from sterigma as ballistospores and drift downward to the open air. Two genetic MAT loci determine the fate of mating type in basidiomycota. One encodes for tightly linked pheromone and pheromone receptor P/R locus and the other encodes for HD locus or homeodomain-type transcription factors which decides viability after syngamy. Tetrapolar breeding system is generated when four mating types are produced through meiosis from two unlinked MAT loci. In some, a single MAT locus controls a bipolar system where both the P/R and HD loci are linked or one has lost its function in type determination.

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2.4 Metabolic and genetic complexity in fungi Vast array of enzymes released from fungi enable them to take advantage of using various substrates. Gene duplication, gene exchange (horizontal transfer), and gene loss all contribute to metabolic diversity of fungi (Rokas et al., 2018). Numerous metabolites also help them while interacting with the other members of the ecosystem. They play active roles in cell signaling, pigmentation, osmotic protection, and preventing invaders as toxins, etc. Secondary metabolites are grouped mainly as small nuclear-encoded peptides, nonribosomal peptides, polyketides, terpenoids, and derivatives obtained from the shikimate pathway. Metabolically related as well as nonrelated clustered genes in fungi are diverse and abundant (Marcet-Houben and Gabaldon, 2019). Several regulatory molecules are involved in coordination of the expression of those clustered genes (Akhberdi et al., 2018). Most studied global regulator, the velvet complex proteins, regulate secondary metabolic pathways in Pezizomycotina although they are detected across all fungal groups. Those proteins have significant roles in sexual development of Ascomycota and Basidiomycota. However, S. cerevisiae, C. albicans, and other basidiomycetes leading biotrophic lifestyle are devoid of velvet complex whereas this is present in Yarrowia lipolytica. External factors like nutrient availability, light, pH, or injury, etc., and internal factors like cell type or sexual cycle, etc., regulate the production of metabolites (Keller, 2018). Anaerobic fungi from phylum Neocallimastigomycota living in the midgut or hindgut of gastrointestinal tract of mammalian herbivores, adapt to the anaerobic environment in various ways. They are devoid of mitochondria, cytochromes, and other biochemical features of the oxidative phosphorylation pathway (Youssef et al., 2013). They have special organelles named hydrogenosomes which help in generating energy via metabolism of glucose. These organelles are having similar features to that of mitochondria and believed to be coming from them as well (Muller et al., 2012). Hydrogenosomes contain hydrogenase which produces H2, CO2, formate, and acetate as waste product of metabolism. Those anaerobes produce lactate and ethanol along with the previous products from plant polysaccharides in the gastrointestinal tract of the herbivores through degradation and fermentation. In response to damage, fungi close their septa in order to reduce loss of cytoplasmic content. This also induces promotion of branching and sporulation along with other coordinated events like production of toxic metabolic compounds (Kunzler, 2018; MedinaCastellanos et al., 2018). Regular signaling pathways of eukaryotes like reactive oxygen species (ROS) play several significant roles in fungi. In addition to injury-signaling pathways, chemical mediators against biological intruders, ROS also signals in cell differentiation. ATP in extracellular space signals to leakage of cell. Oxypilin signaling and action potential-like electrical signals travelling across long distance are indicative of damage in fungi. Oxypilins coordinate a number of events in fungi like secondary metabolism, pathogenesis, the sex cycle, morphological switches, and defense against grazing. Complex multicellularity is observed exclusively in the fruiting body bearing fungi like Ascomycetes and Basidiomycetes. Fruiting body development involves overexpression of

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many genes related to cell wall remodeling, DNA synthesis, ribosomes, and lipid metabolism directly or indirectly (Krizsan et al., 2019). Metabolic pathways are nowadays analyzed on the basis of reliable groups of orthologous proteins and mapping those groups on to the metabolic pathways described in KEGG and MetaCyc (Grossetete et al., 2010). Accurate functional annotation of industrially well-exploited fungal genomes like Saccharomyces cerevisiae, Candida albicans, and Yarrowinia lipolytica, etc., available in different databases is essential for selection of reliable set of orthologs. Inparanoid and OrthoMCL are generally used for identifying orthologs. Recently, one user friendly tool FUNGIpath, freely available in http://www.fungipath.u-psud.fr, is found to be more useful in searching orthologs, exploring metabolic pathways or a specific step in a pathway or a complete pathway compared to other databases like Swiss-Prot or KEGG. Fungi living with bacterial endosymbionts like Rhizopus microsporus (Mucoromycotina) and its endobacteria Burkholderia gave more insights to metabolic pathways during their mutually beneficial association (Lastovetsky et al., 2016). In presence of the symbiont, expression of lipid metabolic genes was changed with increase in the levels of triacylglycerol and phosphatidylethanolamine in the host. This upregulation was found to be associated with diacylglycerol kinase activity because its inhibition altered the fungal lipid profile resulting host-microbe interaction to antagonism instead of mutualism. So, the mutual interaction of the fungi with its endosymbionts had significant impact on the metabolic pathways.

2.5 Genome Zoosporic fungi have usually smaller genomes whereas anaerobic Neocallimastigomycotina and some Chytridiomycetes have genome size comparable to or larger than mushrooms (Oberwinkler, 2017). Some small genome chytrids are parasitic in nature whereas its saprophytic ancestor has larger genome which explains that reduction is somehow linked to its adaptation to the new lifestyle. Some Ascomycota and Basidiomycota members are also unicellular. In Basidiomycota, thallus reduction in primarily biotrophic parasites generated those unicellular forms which have high amount of compacted genome with reduced signaling pathways, secondary metabolic pathways and structural components. Polyketide synthetases and nonribosomal peptide synthetases play critical role in conidiation in Aspergillus and other filamentous Ascomycota but these clusters are absent or reduced in yeast and some biotrophic pathogens of plant (Riquelme et al., 2018). Various forms of genome may exist in fungal cell. Many yeasts, e.g., Saccharomyces cerevisiae exist independently as hybrids. Hybrids are defined as “fungal lineages that have emerged from mating between two lineages whose disparity exceeds that of those typically found across the most distance strains of well recognized species” (Peter et al., 2018). These hybrids are very common in industry setup (Mixao and Gabaldon, 2018). They may be generated due to the adaptation to a new environment or sometimes they are related to pathogenicity as evident from several plant pathogens from Ascomycetes

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and Basidiomycetes. Heterokaryosis occurs when two or more genetically distinct nuclear populations coexist within a syncytium. Keeping the nuclear population in control and passage the nuclei to newly formed hyphal branches in the fungal network need critical coordination. In Neurospora tetrasperma heterokaryon state is stably maintained for long period of time in spite of higher growth rate and asynchronous nuclear division. Aneuploidy refers to various ploidy levels within the same genome. This phase serves as transitory, intermediate state when the system adapts to certain conditions (Anderson et al., 2017). Polyploidy or genome duplication in fungi can be either autopolyploidy where all chromosomes have the same genotype during duplication or allopolyploidy where the chromosomes are genetically different (Gerstein et al., 2015). Autopolyploidy generates larger cell which is advantageous in certain situation like reducing the possibility of phagocytic predation. For instance, polyploid vegetative titan cells of Cryptococcus are resistant to vertebrate immune system. In halotolerant, black yeast Hortaea werneckii duplication of whole genome was responsible for the expansion of cationic transporters which were necessary for survival of the fungi in high salinity (Sinha et al., 2017). Closely 4940 core genes (present in all analyzed genomes) were estimated from in 7800 pangenome pool (complete gene pool of a single species) of S. cerevisiae strains from diverse ecosystems (Peter et al., 2018). 2860 flexible genes are located in subtelomeric regions and are associated to cell-cell interactions, secondary metabolism, and stress responses. This variability among strains is clearly indicative of horizontal gene transfer (HGT) between strains in the environment. Such evidence is available from other groups of fungi like Ascomycota. HGT mechanisms in fungi are not clearly understood. Simple transporters or enzymatic pathways and secondary metabolism-related genes are usually transferred through HGT compared to highly interconnected proteins. HGT may drastically change the lifestyle of the fungi as genus Metarrhizium was found to be entomopathogenic from a grass endophyte through HGT (Zhang et al., 2019).

3. Classification of fungi AFTOL project (http://www.aftol.org/) defines the exact phylogenetic relationships of the groups in the fungal kingdom. The modern-day taxonomy, divides true fungi it into nine major lineages: (1) Opisthosporidia, (2) Chytridiomycota, (3) Neocallimastigomycota, (4) Blastocladiomycota, (5) Zoopagomycota, (6) Glomeromycota, (7) Mucoromycota, (8) Ascomycota, and (9) Basidiomycota based on their sexual reproductive structures. Together, these lineages formed a monophyletic clade, the true fungi (Tedersoo and Smith, 2017). Opisthosporidia are called “fungi imperfecti”; are key saprotrophs and parasites of plants, animals and other fungi, playing important roles in ecosystems.

3.1 Opisthosporodia Opisthosporidia are not considered true fungi because of their phylogenetic position that place them as sister to true fungi, and some of their biological peculiarities contradict with

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the classical definition of fungi. One such fact is that the trophonts of Aphelida and Cryptomycota (but not Microsporidia, which are extremely specialized parasites) show amoeba like phagocytosis by engulfing the whole host cytoplasm. Opisthoporadia roofs three main lineages: Aphelidea, Rozellidea, and Microsporidia (or the ARM clade). Species in this clade are mostly intracellular parasites or parasitoids of a wide range of eukaryotes. Karpov et al. (2013) included Aphelidea as the last major lineage to join the family and created the term Opisthosporidia by combining Opisthokont and sporae, in reference to the specialized penetration apparatus of the spore (in Microsporidia) and cyst (in the two other phyla) that characteristic for all three phyla Microsporidia, Cryptomycota, and Aphelida (Karpov et al., 2013).

3.2 Aphelidea Aphelids are a group of obligate endoparasitoids (the infected host cell is consumed and killed) of various algae and diatoms. To date four genera have been described in this group: Aphelidium, Amoebaphelidium, Paraphelidium (freshwater), and Pseudaphelidium (marine environments) (Karpov et al., 2017). Their life cycle consists of a mobile cell that is either flagellated (Aphelidium, Pseudaphelidium), amoeboid (Amoebaphelidium), or both (Paraphelidium). Presence of their posteriorly uniflagellate zoospores raises controversy over the classification of aphelids. The motile zoospore may be amoeboid. The zoospore may be round or oval, with or without pseudopodia (Table 2; Letcher and Powell, 2019). With only a few formally described species, environmental sampling suggests that Aphellidea is indeed a highly diverse and cosmopolitan clade (Karpov et al., 2014).

3.3 Rozellidea Rozella harbors a genus of flagellated parasitoids of zoosporic fungi (Chytridiomycota and Blastocladiomycota), Oomycetes, and some green algae (Gleason et al., 2012). Rozella species are zoosporic biotrophic parasites of oomycetes, chytrids, and Blastocladiomycota. Rozella indulges a zoosporic infectious stage that attaches to the host cell. A. Rozellidea also includes the recently described Paramicrosporidium and Nucleophaga, which are microsporidian-like parasites of amoebozoa (Corsaro et al., 2014). Sequence data obtained from environmental samples, mark their phylogenetical relation to Rozella and have been found present in virtually all aquatic environments, comprising a very high sequence divergence. Taxonomists interpreted such distribution and divergence as the existence of a highly species-rich and ecologically meaningful hidden clade, which could be comparable in diversity to the rest of true fungi. R. allomycis grows inside the host as naked protoplasm, and reproduces through the production of ephemeral zoosporangia or chitinous, thick-walled resting sporangia. Inside the host it produces the cell wall of the zoosporangium, which when matures bursts to form numerous zoospores with a single flagellum. When these zoospores, finds a suitable host, it retracts its flagellum, develops a cell wall, and injects its cytoplasm into the host (phagocytosing). The genome of Rozella allomycis, a parasitoid of the blastoclad Allomyces was published in 2013 (James et al., 2013).

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Table 2 Morphological characters describing spore (size and shape), spore type, flagellum, cyst, and host of Aphelidiaceae. Taxon

Spore size (μm), shape

Flagellum (μm) Cyst

Resting spore size (μm)

Host

Not observed

Chaetophora elegans

7–13  5–6.5, ellipsoidal

Scenedesmus, chlorococcus algae (green algae) Kirchneriella obesa, Ankistrodesmus (green algae) Coleochaete soluta (green alga) Desmodesmus opoliensis (green alga)

Morphological characters and hosts for aphelid taxa Aphelidium: Aph. chaetophorae Aph. chlorococcorum f. chlorococcorum Aph. chlorococcorum f. majus Aph. deformans Aph. desmodesmi

Aph. melosirae

2.7–3, spherical

9

1.5–2, “stiletto” pseudopodia

8

2–3, spherical, conic “stiletto” anterior pseudopodium 2–3, spherical

14

Not known 2, spherical, subspherical,  6 angular numerous thin filopodia 4  6, pleomorphic  10

Aph. tribonematis

2–3, oval, numerous filopodia

Paraphelidium: Pa. letcheri

2–2.5, spherical, with a 8–10 lamellipodium and subfilopodia 2–2.5, oval, a broad anterior  7 lamellipodium; a few lateral and anterior subfilopodia

Pa. tribonematis

Amoeboaphelidium: 2 long Am. achnanthis Am. chlorellavorum 1–2, amoeboid Am. occidentale

6–8

Not known Not known 7–10

1.3–2.7, spherical, subspherical, elongate Am. protococcorum 2–4, spherical to elongate,  7 numerous pseudopodia, thin trichipodia, thick lobopodia Am. radiatum 1–3, spherical, numerous Not filopodia known Pseudaphelidium: Ps. 3  5, elongate drebesii

15

Not observed Sessile or short stalk Stalked

5  8, ellipsoidal

Not 12–30 diam, round observed to oval Stalked Not observed

Sessile

12–14  10, oval

Stalked

Unknown

Sessile

Unknown

Melosira varians (diatom) Sessile or 6–7, spherical, Tribonema gayanum, short residual body Botridiopsis stalk outside intercedens (yellowgreen algae) Sessile or 6–8, spherical, single Tribonema gayanum short wall, residual body stalk outside Stalked 8–10, ellipsoid, Tribonema gayanum two-walled, residual bodies between the two walls Unknown Unknown Achnanthes lanceolata (diatom) Sessile 3–7, spherical Chlorella spp. (green alga) Stalked unknown Scenedesmus dimorphus Sessile 4–6  5–7, oval Scenedesmus, Protococcus, chlorococcus algae

Adapted from Letcher, P.M., Powell, M.J., 2019. A taxonomic summary of Aphelidiaceae. IMA Fungus 10, 4.

Kirchneriella, Ankistrodesmus, chlorococcus algae Thalassiosira punctigera (marine diatom)

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Rozella and Microsporidia both have horizontally acquired Rickettsia-like NTT-ATP/ ADP transporters, but metchnikovellids, Mitosporidium, and Paramicrosporidium do not. The mitochondrial genomes of Mitosporidium and Rozella lack Complex I of the oxidative phosphorylation pathway and are AT-rich. On the contrary, Paramicrosporidium possess all genes of that pathway typically found in fungi. Another instance of potentially horizontally acquired genes is thymidine kinases found in Rozella and Microsporidia, but not in Paramicrosporidium.

3.4 Microsporidia No subdivision of this phylum group is proposed yet because of the lack of well-sampled multi-gene phylogenies within the group. Microsporidia may be a sister group of the rest of the Fungi, is uncertain due to incomplete sampling. Majority of the known genera of Microsporidia infect aquatic animals with host that varied from single-celled protists to vertebrates. Susceptible hosts of microsporidia span across wide taxonomic spectrum, from lower protists to higher mammals. Primarily, Microsporidia are parasites of invertebrates and vertebrates, endosymbionts of ciliates, hyperparasites in protists. Metchnikovellids are specialized parasites of gregarines (Apicomplexa), protistan gut symbionts of many invertebrates. Hyperspora aquatica is a hyperparasite of the paramyxid, Marteilia cochillia, a serious pathogen of European cockles. Microsporidia have very reduced genomes. Some of their characteristics are typical of prokaryotic genomes viz. presence of overlapping genes, mitochondria-derived organelles called mitosomes. Simple cellular morphology, absence of mitochondria and long-branch-attraction phylogenetic artifacts caused by their parasitic nature, led to the belief that Microsporidia was early-branching eukaryotes, whose divergence preceded the acquisition of mitochondria (Corradi and Keeling, 2009). They all form a specialized resistant spore containing a coiled polar filament surrounding the nucleus or diplokaryon and the sporoplasm (its associated cytoplasmic organelles) (Fig. 1). The spore is the only microsporidial form that is extracellular and is the infective stage. The microsporidia spores range from small, oval- or pyriform-shaped, highly resistant varies in length from approximately 1–12 μm. Microsporidia lack canonical Golgi apparatus and their mitochondria have been highly reduced to mitosomes. These mitosomes are unable to generate their own ATP through oxidative phosphorylation, requiring energy to be imported from the host via nucleotide transporters. Microsporidia also lack flagella and an apparent capacity for phagocytosis. Microsporidia undergoes two different phases, one known as proliferative phase and other the sporogonic phase. The only stage of microsporidia outside the host is the infective spores. Infection by microsporidia in economically important invertebrate hosts such as silkworm, honeybee, and shrimp as well as vertebrates such as fish can cause significant economic losses.

3.5 Chytridomycota (Chytrids) Members of the zoosporic true fungi are Blastocladiomycota, Chytridiomycota, and Neocallimastigomycota. Taxonomical identification of Chytrid considerably relies on a

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FIG. 1 Parts of microsporidian spore. (A) Anchoring disk; (B) lamellar-polaroplast; (C) outer exospore; (D) inner endospore; (E) vesicular polaroplast; (F) nucleus; (G) polar tube; and (H) vacuole (posterior). Parts of a specialized resistant spore containing a coiled polar filament surrounding the nucleus or diplokaryon and the sporoplasm (its associated cytoplasmic organelles).

combination of ultrastructure and molecular data because majority of Chytridiomycota species are aquatic habitants and have rarely been cultured for studying and taxonomic purposes. Most were classified as “uncultured” and thus any speculations on a chytrid’s ecological role based on the literature is shifty due to the difficulty of assigning names to environmental sequences that match poorly to the databases. Chytrids are one of the early diverging fungal lineages and is considered to be one of the most ancestral groups of fungi. Their membership in the fungal kingdom is demonstrated by the presence of chitin cell walls, a posterior whiplash flagellum, absorptive nutrition, use of glycogen as an energy storage compound, synthesis of lysine by the α-amino adipic acid (AAA) pathway, Golgi apparatus with stacked cisternae, and nuclear envelope fenestrated at poles during mitosis. General morphological features of chytrids. 1. 2. 3. 4.

Motile asexual zoospores (with a single posterior flagellum). Both a kinetosome and nonfunctional centriole. Nine flagellar props and a microbody-lipid globule complex in zoosporangia. Presence of a thallus that may be holocarpic (where thallus is involved in formation of the sporangium) or eucarpic (only part of the thallus is converted into the fruiting body), monocentric, polycentric, unicellular, or filamentous. 5. Sexual reproduction accompanies zygotic meiosis, that produces motile sexual zoogametes; sexual reproduction not oogamous. 6. Asexual reproduction by zoospores bearing a single posteriorly directed flagellum. 7. Zoospores containing a kinetosome and a nonflagellated centriole.

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8. Thallus monocentric or rhizomycelial polycentric. Chytrids are important pathogens of plants (e.g., Synchitrium), animals (e.g., Batrachochytrium), parasites to several groups of algae (e.g., Chytridium, Dinomyces). Chytrids are efficient decomposers of highly recalcitrant organic matter, such as pollen (e.g., Spizellomyces, Rhyzophidium), cellulose (e.g., Rhizophlyctis), arthropod exoskeletons, and fungal spores. Due to its parasitoidism, existence chytrids are unculturable resulting in very limited sequence information on zoosporic fungi, which poses challenges in obtaining a robust chytrid tree of life (Grossart et al., 2016). A well-resolved phylogenetic backbone of the fungal tree of life is required to describe how the fungal nutritional toolkit has evolved over a billion years. However, with modern day tools and technology this situation is changing. With the use of single-cell-based techniques genomic environmental sampling is steadily increasing. Single-cell genomics method was used for the first time to uncultured mycoparasitic EDF from the Cryptomycota, Chytridiomycota, and Zoopagomycota (Ahrendt et al., 2018). The Chytridiomycota have attracted the attention of mycologists due to their potential for negatively affecting phytoplankton communities, and altering phytoplankton dynamics throughout the season. Kagami et al. showed that Chytridiomycota effectively channeled organic matter and energy to higher trophic levels, a mechanism which has been termed the “mycoloop” (Kagami et al., 2014). Chytridiomycota zoospores are consumed by zooplankton, especially by Daphnia as they serve as excellent food source in lakes, due to their nutritional quality (e.g., high contents of PUFAs and cholesterols) and their high abundance (ranging from 101 to 109 spores) (Kagami et al., 2004). In this way, zoosporic fungi play an important role in shaping aquatic ecosystems by altering food web dynamics, sinking fluxes, or system stability. The parasitic chytrids that infect cyanobacteria potentially improve the nutritional quality of cyanobacteria by adding sterol (Kagami et al., 2007) or by rendering them edible by fragmenting large filaments or colonies. Another example is the parasitic chytrid Dinomyces arenysensis, known to infect dinoflagellates (some of them toxic, such as Alexandrium spp.) in coastal areas and could serve as food for marine zooplankton or the saprotrophic Chytridiomycota that decompose pollen have the potential to facilitate zooplankton growth in lakes where resource subsidies (Masclaux et al., 2013). The roles of Chytridiomycota as parasites, such as parasitism of cyanobacteria and as causative agents of the global amphibian decline, are widely studied. Chytrids present a zoosporic dispersal stage usually growing nonflagellated stage. In spite of the presence of filopodia in several chytrid groups (e.g., Batrachochytrium), true phagocytosis has never been observed. True mycelial growth is restricted to certain genera within the Monoblepharidomycetes (Dee et al., 2015). Chytridiomycota are divided into two main classes: Chytridiomycetes and Monoblepharidomycetes.

3.5.1 Chytridiomycetes ORDER: CHYTRIDIALES; EXAMPLE

GENERA:

CHYTRIDIUM, CHYTRIOMYCES, NOWAKOWSKIELLA.

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FIG. 2 AGF protein domains. Functional annotation of HGT genes/pfams indicated that the majority (63.9%) of events encode metabolic functions, cellular processes, and signaling represent the second most represented HGT events (11.19%), while genes involved in information storage and processing only made up 4.69% of the HGT events identified.

Chytridiomycetes is by far the largest class of zoosporic fungi with 1000 described species. Phylogenetic analyses and ultrastructure study of the zoosporic stage have raised several lineages to the level of orders. Characterized by asexually reproducing by zoospores bearing a single posteriorly directed flagellum; zoospores contain a kinetosome and a nonflagellated centriole; thallus may be monocentric or rhizomycelial polycentric (Fig. 2); sexual reproduction not oogamous. Chytridiomycetes have received considerable attention owing to the deadly parasite Batrachochytrium dendrobatidis that devastated considerable populations of amphibians worldwide (Berger et al., 2005). The genome of Batrachochytrium dendrobatidis, published in 2009, represented the first sequenced chytrid. The chytrid was placed in a new genus, Batrachochytrium under Phylum Chytridiomycota, Class Chytridiomycetes, and Order Chytridiales (Longcore et al., 1999). Researchers proposed two possible hypotheses to explain how a fungus that infects the superficial epidermis has the capacity to kill amphibians (frogs) (Berger et al., 1998). Initially, the chytrid might release proteolytic enzymes or other active compounds that are absorbed through the permeable skin of the frog and secondly, this damage to skin function results in disturbance of electrolyte flux and oxygen, water imbalance which results in death (Voyles et al., 2007). Batrachochytrium dendrobatidis Batrachochytrium dendrobatidis causes a lethal epidermal infection chytridiomycosis, a disease of amphibians, that leads to mass mortality, population declines and almost extinctions. The life cycle of Batrachochytrium dendrobatidis is a simple progression from zoospore to a thallus, which produces a single zoosporangium (a container for zoospores). The contents of the zoosporangium (also known as a sporangium) cleave into new

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zoospores which exit the sporangium through one or more papillae. Sexual reproduction has not been observed. Batrachochytrium dendrobatidis discharges zoospores through an inoperculate opening and exhibits monocentric or colonial growth (Longcore et al., 1999). In amphibians, sporangia infect cells in the stratum granulosum and stratum corneum in the superficial epidermis layer. B. dendrobatidis has two primary life stages: a sessile, reproductive zoosporangium and a motile, uniflagellated zoospore released from the zoosporangium. The zoospores are known to be active only for a short period of time, and can travel short distances of one to two centimeters. The zoospores are capable of chemotaxis, and can move toward a variety of molecules that are present on the amphibian surface, such as sugars, proteins, and amino acids.

3.5.2 Monoblepharidomycetes Monoblepharidomycetes are a group of freshwaters, zoosporic fungi that can present either unicellular or mycelial growth. Monoblepharidomycetes chytrids form true hyphae, and present some typical cytological characteristics, such as the presence of centrioles but € rper, which points to an independent origin of these traits from the absence of Spitzenko other fungi (Dee et al., 2015). An oogonic sexual cycle (i.e., the presence of morphologically different gametes) is common in Monoblepharidomycetes, a unique feature among fungi. The Monoblepharidomycetes is the sister class to the Chytridiomycetes in the phylum Chytridiomycota. The six known genera have thalli that are either monocentric and without rhizoids or produce hyphae with an independent evolutionary origin from the hyphae of higher fungi. Monoblepharidomycetes (Chytridiomycota) displays an exceptional range of body types from crescent-shaped single cells to sprawling hyphae. Hyphae of Monoblepharidomycetes lack a complex aggregation of secretory vesicles at the hyphal apex (i.e., Spit€ rper), have centrosomes as primary microtubule organizing centers and have zenko stacked Golgi cisternae instead of tubular/fenestrated Golgi equivalents. The cytoplasmic distribution of actin in Monoblepharidomycetes is comparable to the arrangement observed previously in other filamentous fungi. Members of this class have a filamentous thallus that is either extensive or simple, unbranched. They often have a holdfast at the base. In contrast to other taxa in their phylum, they reproduce using autospores, although many reproduce through zoospores. Oogamous sexual reproduction may also occur. Asexually, they reproduce either by zoospores or autospores. Zoospores contain a kinetosome that is in parallel to a nonflagellated centriole, a striated disk partially extending around the kinetosome, microtubules radiate anteriorly from the striated disk, a ribosomal aggregation, and rumposome (fenestrated cisterna) adjacent to a microbody (Letcher et al., 2006).

3.6 Neocalimastigomycota CLASS: NEOCALLIMASTIGOMYCETES ORDER: NEOCALLIMASTIGALES; EXAMPLE NEOCALLIMASTIX, CYLLAMYCES SP. AND PECORAMYCES SP.

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Since their discovery by Orpin, 1974, members of the new phylum Neocallimastigomycota intrigued microbiologists as these organisms were reported to be found in digestive tracts of mammalian herbivores, with others potentially inhabiting other anaerobic niches. Taxonomic backbone contains eight genera of strictly anaerobic fungi. Members of this phylum are involved in the rumen function and animal digestion, and possess capacity to convert lignocellulose into bioenergy products (Solomon et al., 2016). Originally, these organisms were grouped under chytridiomycetous fungi but later assigned to higher phylum due to their life cycle (possess a vegetative structure from which zoospores are produced) and a chitin-containing cell walls. Later based on the type species Neocallimastix frontalis, Heath et al. (1983) formally classified them into a new family Neocallimastigaceae in the class Chytridiomycetous and order Spizellomycetales mainly due to the similarities of zoospore ultrastructure to some members of this order. Hibbett et al. (2007) later raised it to phylum containing anaerobic fungi, which are symbionts found in the digestive tracts of larger herbivores also known as the anaerobic gut fungi (AGF). Neocallimastigomycota dwell in the rumen and alimentary tract of herbivorous mammals, and reptiles (e.g., iguana) where they play important roles in the degradation of recalcitrated plant fiber. General characteristic features of Neocallimastogomycota. 1. Presence of monocentric or polycentric thallus. 2. Anaerobic and resides in the digestive system of herbivorous mammals and in other terrestrial and aquatic anaerobic environments. 3. Neocallimastigomycota lack mitochondria but instead contain hydrogenosomes in which the oxidation of NADH to NAD+, leads to formation of H2. 4. Horizontal gene transfer results in development of xylanase (from bacteria) and other glucanase activity. 5. Zoospores posteriorly unflagellate or polyflagellate zoospores. 6. Kinetosome-associated complex composed of a strut, skirt, spur flagellar ring, microtubules form a fan-like shape extending from spur and radiate around nucleus. 7. Flagellar props absent, nuclear envelope remains intact throughout mitosis. Neocallimastigomycota harbors a small group of flagellated, obligate anaerobic, nonparasitic fungi owing to a single family that comprises 18 recognized genera of which some may be paraphyletic (Hibbett et al., 2007). Neocallimastigomycota possess large genome sizes (101 Mb in Orpinomyces), very low GC content (as low as 17% in Orpinomyces), and high content of repetitive elements (Youssef et al., 2013). The low GC content is due to genetic drift triggered by the low effective population sizes, bottlenecks in vertical transmission, and the asexual life style of anaerobic fungi. AGF release asexual motile free zoospores into the herbivorous gut as part of their life cycle. Large AT-biased (78%–84%) genomes along with their fastidious growth condition impose challenges in the genomic and phylogenomic analyses of the AGF. These large genomes harbor-rich repertoire of carbohydrate-degrading enzymes shaped by gene expansions and horizontal gene et al., 2000). It is estimated the most recent common ancestransfer events (Garcia-Vallve tor of the AGF diverged millions years ago, a time frame that coincides with the evolution

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of grasses (Poaceae), as well as the mammalian transition from insectivores to herbivores. This co-occurrence estimation suggests that AGF may have role in shaping the succession of mammalian herbivore transition by improving the efficiency of energy acquisition from recalcitrant plant materials. To endure in this anoxic and prokaryote-dominated environment, AGF members have undergone multiple structures and metabolic adaptations, such as the loss of the mitochondria replaced by a hydrogenosome, loss of respiratory capacities, and substitution of ergosterol with tetrahymanol in the cell membrane (van der Giezen, 2009). Interestingly, all known AGF taxa have a remarkable plant biomass degradation machinery, which aids in competing with other microbes for resources and establishing growth in the herbivorous anaerobic gut. Outside this environment, there is a single report of the presence of these fungi in the gut of a sea urchin based on the morphological identification (Thorsen, 1999).

3.6.1 AGF protein domains and homologous genes A comparative genomic analysis study between AGF and their nonrumen-associated chytrid relatives identified 40 Pfam domains that are unique to the AGF (accounting almost 0.67% of the total number of Pfams (5980) in the AGF pangenome-transcriptome). Functional annotation of HGT genes/pfams indicated that the majority (63.9%) of events encode metabolic functions such as extracellular polysaccharide degradation and central metabolic processes. Genes involved in cellular processes and signaling represent the second most represented HGT events (11.19%), while genes involved in information storage and processing only made up 4.69% of the HGT events identified (Fig. 2). Transcripts acquired by HGT represented >50% of transcripts in anywhere between 13 (Caecomyces) and 20 (Anaeromyces) GH families; 3 (Caecomyces) and 5 (Anaeromyces, Neocallimastix, Orpinomyces, and Feramyces) CE families; and 2 (Caecomyces and Feramyces) and 3 (Anaeromyces, Pecoramyces, Piromyces, Neocallimastix, and Orpinomyces) PL families. The AGF CAZyome encodes enzymes putatively mediating the degradation of 12 different polysaccharides. The predicted function of these domains included anaerobic ribonucleotide reductase (NRDD), metal transport and binding (FeoA and FeoB_C), carbohydrate binding (e.g., CBM_10, CBM-like, and Cthe_2159), glycoside hydrolase (e.g., Glyco_hydro_6 and Glyco_hydro_11), and atypical protein kinase (Cot H). In addition to these unique domains, many additional Pfams enriched the AGF genome. Polysaccharide degradation and monosaccharide fermentations domains like Chitin_binding_1, CBM_1, Cellulase, Glyco_hydro_10, Gly_radical, RicinB_lectin_2, Esterase, and Polysacc_deac_1 were found abundant. Phylogenetic analysis indicated that the AGF polysaccharide lyase domain is distinct and not orthologous to related enzymes in other fungi. In-depth analysis identified 106 Pfam domains that are not present in AGF genomes and transcriptomes but found in sister Chytridiomycota. Domains involved in the biosynthesis of nicotinic acid, uric acid, and photolyase, in purine catabolism, and in pathways of ureidoglycolate and kynurenine are absent in AGF species. Interestingly, most of these missing domains are related to oxidation reactions on cytochromes and mitochondria. Phylogenetic analyses support a horizontal transfer of certain Pfam domain such as Cthe_2159 domain (carbohydrate-binding domain-containing protein) transfer from rumen bacteria into

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AGF, followed by potential gene fusion to deliver eukaryotic specific functions. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut with four bacterial phyla (Firmicutes, Proteobacteria, Bacteroidetes, and Spirochaetes) identified.

3.7 Blastocladiomycota Blastocladiomycota holds a very interesting position. Morphological and ecological similarities initially suggested a common ancestry with the core chytrids. Molecular analysis based on ribosomal DNA sequences and zoospore ultrastructural characters demonstrated it not monophyletic with Chytridiomycota but Blastocladiomycetes split more recently from the fungal backbone than the chytrids. The systematic classification of the Blastocladiomycetes was revised, and was given their own phylum Blastocladiomycota. Major evolutionary changes have accompanied the divergence of the Blastocladiales from the core chytrids. For example, the Blastocladiales have a life cycle with sporic meiosis whereas most core chytrids have zygotic meiosis (Letcher et al., 2006). However, the zoospore is functionally similar to those found among “core chytrids.” General characteristic features of blastoclaiomycota. 1. A single posteriorly directed flagellum, stored lipid, and glycogen reserves, branching thallus with pseudosepta. 2. A characteristic assemblage of lipids, microbodies, membrane cisterna called the sidebody complex. 3. A membrane-bounded ribosomal cap covering the anterior surface of a cone-shaped nucleus. 4. Blastocladiomycota present alternation of gametophytic and sporophytic generations. 5. Three types of life cycle (a) The Euallomyces life cycle; has alternating haploid gametophytic and diploid sporophytic generations. (b) The Cystogenes life cycle has a large, dominant, asexual sporophyte that produces thin-walled zoosporangia and resistant sporangia whereas the sexual gametophyte is a small, spherical, thin-walled cyst that produces variable numbers of isogametes that fuse in pairs forming biflagellate zoospores and the biflagellate zoospores develop into asexual thalli. (c) The Brachyallomyces life cycle, also called short-cycled, has no gametophytic or sexual thalli and reproduced only asexually. Two popular model organisms of Blastocladiomycota are Allomyces macrogynus and Blastocladiella emersonii, which are saprotophs with well-defined and well-studied alternation of generations. Other representatives of these genera are Physoderma (parasitic on higher plants), Blastocladiella, and Coelomomyces (obligate endoparasite of insects with alternating sporangia and gametangia stages in mosquito larvae and copepod hosts). CLASS: BLASTOCLADIOMYCETES of Blastocladiomycota contains a single-order, Blastocladiales, and four morphologically defined families bearing minor changes validated by molecular studies (Porter et al., 2011).

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89

FAMILY: CATENARIACEAE contains both saprobes and pathogens (includes the genera Catenaria, Catenophlyctis, and Catenomyces). FAMILY: COELOMOMYCETACEAE contains pathogens of invertebrates. FAMILY: FAMILY BLASTOCLADIACEAE (genus Allomyces). FAMILY: SOROCHYTRIACEAE contains a pathogen of tardigrades.

Later in Tedersoo et al. (2018), introduced another class; Class Physodermatomycetes, including Order Physodermatales. Family Physodermataceae contains obligate parasites of plants; (genera, Physoderma and Urophlyctis) an endobiotic polycentric thallus that produces thick-walled resting spores within the host plant. The thick-walled resting spore is meant for unfavorable conditions. Typically, blastocladian zoospores have a distinctive ribosomal nuclear cap, and in some species, a large side body containing lipid globules. Environmental sampling has detected ample Blastocladiomycota clades in aquatic environments. Its ability to grow in pure culture and its position as a relative of plant parasites make it a potentially interesting organism to study genes associated with parasitism.

3.8 Zygomycetous fungi Zygomycete fungi were classified under a single phylum, Zygomycota that reproduces sexually by zygospores and asexually by sporangia, except some show absence of multicellular sporocarps, and production of coenocytic hyphae. Phylogenetic classification includes 2 phyla, 6 subphyla, 4 classes, and 16 orders. Zygomycetous fungi formed two main lineages, one that is mostly parasites of opisthokonts (Zoopagomycota) and a second that is composed mostly of plant symbionts and saprotrophs (Glomeromycota + Mucoromycota; Table 3). Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina, and Zoopagomycotina. Phylum Mucoromycota comprises Glomeromycotina, Mortierellomycotina, and Mucoromycotina and is sister to phyla Dikarya.

3.9 Zoopagomycota This phylum is the earliest diverging group of nonflagellated fungi that includes three main lineages, i.e., ENTOMOPHTHOROMYCOTINA, ZOOPAGOMYCOTINA, and KICKXELLOMYCOTINA (Spatafora et al., 2016). Ø Ø Ø

ENTOMOPHTHOROMYCOTINA: Monophylatic lineage representing insect pathogens mostly along with nematodes and mites. ZOOPAGOMYCOTINA: Obligate parasites of zygomycete fungi and microscopic soil animals like nematodes, rotifers, etc. KICKXELLOMYCOTINA: Includes four zygomycetes orders Asellariales, Dimargaritales, Harpeellales, and Kickxellales.

Members of theses lineages have the ability to form true mycelia. Most members are either saprotrophs or parasites of metazoans, amoebae or other fungi, including highly specialized forms.

Table 3

Phylogenic classification of zygomycete fungi.

Zoopagomycota

Mucoromycota

Zygomycete fungi Subphyla Incertae sedis Life form/Host types

Entomophthoro Mycotinaa Pathogens, saprobes, animal, arthropod

Mucoro mycotina Saprotrophic mycorrhizalor parasitic plant

Zygospore

Zygospore

Zygospore

Trichospores, sporangia, merosporangia Bifurcate septa with lenticular plug

Conidia

Sporangia, sporangioles

Sporangia

Resembles chlamydo-spore

Complete septa, bifurcate septa/ coenocytic; hyphal bodies €rper Spitzenko

Coenocytic

Coenocytic

Coenocytic

Apical vesicle crescent Spindle pole body Industrial enzyme (Tako et al., 2015)

Apical vesicle crescent –

Apical vesicle crescent –

Polyunsaturated fatty acid (Wagner et al., 2013) Present (few) Mortierellales

Biofertilizer (Aguilar-Paredes et al., 2020)

Zoopago mycotina

Kickxello mycotina

Obligate parasites animal, fungi, nematode, rotifers, amoebae

Animal, fungi

Sexual reproduction Asexual reproduction

Zygospore Sporangia conidia, arthrospores cllamydospores

Hyphae type

Coenocytic

Hyphal tip morphology Mictotubules/ centrioles Biotechnology application

Unsampled

Fruiting body Order

a

Unsampled.

Apical vesicle crescent Centriole-like

Centriole-like

Ecological study (amoebophagous fungi in permafrost soils) (NaranjoOrtiz and Gabaldon, 2019)

Metal homeostasis (Shine et al., 2015)

Biological control (Carla Baron et al., 2019)

Absent Zoopagales

Absent Asellariales, Kickxellales, Dimargatitales, Harpellales

Absent b Basidiobolomycetes Entomophthoromycetes Neozygito-mycetes

Present (few) Endognales, Mucorales, and Mortierellales

Mortierello mycotina Saprotrophs, nonpathogenic except Mortierella wolfii, plant Zygospore

Glomero mycotina Arbuscularmycorhizza, plant

Unknown

Present (few) Paraglomerales Diversisporales Glomerales Archaeosporales

Raised to the rank of phylum as “Entomophthoromycota” in a scientific paper by Humber (2012). Raised to class Basidiobolomycetes. Adapted and modified from Spatafora, J., Chang, Y., Benny, G., Lazarus, K., Smith, M., Berbee, M., Bonito, G., Corradi, N., Grigoriev, I., Gryganskyi, A., James, T., O’Donnell, K., Roberson, R., Taylor, T., Uehling, J., Vilgalys, R., White, M., Stajich, J., 2016. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108, 1028–1046.

b

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3.9.1 Entomophthoromycotina Entomophthoromycotina includes three classes (BASIDIOBOLOMYCETES, NEOZYGITOMYCETES ENTOMOPHTHOROMYCETES) (Humber, 2012). Ø Ø Ø

BASIDIOBOLOMYCETES: representive genera Drechslerosporium, Schizangiella, Basidiobolu. NEOZYGITOMYCETES: representative genus Neozygites. ENTOMOPHTHOROMYCETES: representative genus Conidiobolus.

All are saprobic and insect pathogenic fungi. The thallus may have either coenocytic or septate hyphae, which may fragment to form hyphal bodies or it may comprise only hyphal bodies. Asexual reproduction is through conidiogenesis from branched or unbranched conidiophores. Primary conidia are forcibly discharged and secondary conidia are either forcibly or passively released. Sexual reproduction is either by forming zygospores by gametangial copulation, involving hyphal compartments or hyphal bodies (Humber, 2012). Sterol data revealed sterols of different zoosporic and zygosporic forms exhibit structural diversity. Cholesterol and 24-ethyl-Δ5 sterols found in zoosporic taxa, and 24-methyl sterols in zygosporic fungi. Each of the three monophyletic lineages of zygosporic fungi has distinctive major sterols, ergosterol in Mucorales, 22-dihydroergosterol in Dimargaritales, Harpellales, and Kickxellales (DHK clade), and 24-methyl cholesterol in Entomophthorales. Entomophthoromycotina present 24-methyl cholesterol as their main membrane sterol (Weete et al., 2010). So far, Basidiobolus of class Basidiobolomycetes is the only genus in the Entomophthoromycotina to bear septate hyphae. Basidiobolus and Conidiobolus of class Entomophthoromycetes are unique among the zygomycetous fungi for possessing a true € rper. Ultrastructural image revealed a dense cluster of vesicles at the hyphal Spitzenko apex. The hyphal apex exhibited phase-dark inclusion exhibited independent motility within the hyphal apex and its presence and position were correlated to the rate and direction of hyphal growth. The hyphal apex of Basidiobolus sp. did not contain γ-tubulin (Manning et al., 2007).

3.9.2 Zoopagomycotina Zoopagomycotina include mycoparasites, predators, or parasites of small invertebrates and amoebae. Special haustoria structures are produced in association with hosts. The hyphal diameter is characteristically narrow in thalli that are branched or unbranched. Only limited species could be successfully maintained in axenic culture. Sexual reproduction, is by gametangial conjugation, forming globose zygospores on apposed differentiated or undifferentiated suspensor cells. Asexual reproduction is by arthrospores, chlamydospores, conidia, or multispored merosporangia that may be simple or branched (Walther et al., 2019). Zoopagomycotina comprises a single order, Zoopagales, that includes 5 families and around 20 genera.

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3.9.3 Kickxellomycotina Subphylum Kickxellomycotina was created by combining poorly documented fungal groups united by the presence of septated mycelia that present unique septal pores with a lenticular plug. These pore plugs as well as the characteristics of the sporangia account for diagnostic traits for this group within the subphylum (Tretter et al., 2014). The group comprises four recognized orders: Ø Ø Ø Ø

ORDER: KICKXELLALES; for example genera: Kickxella, Coemansia, Linderina, Spirodactylon. ORDER: DIMARGARITALES; for example genera: Dimargaris, Dispira, Tieghemiomyces. ORDER: HARPELLALES; for example genera: Harpella, Furculomyces, Legeriomyces, Smittium. ORDER: ASELLARIALES; for example genera: Asellaria, Orchesellaria.

Mycelium is symmetrically divided into compartments by bifurcate septa that have lenticular occlusions. Sexual reproduction involves the formation of diversly shaped zygospores by gametangial conjugation of relatively undifferentiated sexual hyphal compartments. Sporophores may be produced from septate, simple, or branched somatic hyphae. Asexual reproduction involves the production of uni- or multispored merosporangia from sporocladium, sporiferous branchlets, or an undifferentiated sporophore apex. Species may be saprobes, mycoparasites, and symbionts of insects. The genus Coemansia of the Order Kickxellales (Kickxellaceae, Kickxellales); is a dung-associated saprotroph with intrincate asexual structures. It was the first sequenced Kickxellomycotina (Chuang et al., 2017). Septal ontogeny in Linderina pennispora is initiated by the ingrowth of material from the inner of the two layers of the cell wall. The growing point of the septum bifurcates and continues growth forming a lenticular cavity into which the septal plug is deposited. This type of septal development occurs in all septa except those produced between the pseudophialides and the merosporangia and spores. The latter septal type initially is formed as previously described, but then additional wall material is produced both above and below the septum. In the merosporangiospore, three layers of wall material are produced. The inner two layers give rise to the spore spines and at maturity all wall layers coalesce and form a single, thick spore wall. Extra wall material in the apex of the pseudophialide gives rise to a multilobed and mottled vacuole that shrivels just before spore liberation. Mature merosporangiospores are the only structures with spore spines. Aerial spines are produced on all structures except the merosporangiospores, although a relatively larger number of the aerial spines are produced on the aerial hyphae than on the pseudophialides and the sporocladia (Benny and Aldrich, 2011).

3.10 Glomeromycota Members of the Glomeromycota species are well known for forming arbuscular mycorrhizas (AMs) in the roots of vascular land plants. Morphological features are the soil-borne sporocarps (spore clusters) that are found in or near colonized plant roots. Earlier studies

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placed Glomeromycota as the sister clade to Dikarya (Ascomycota + Basidiomycota + € βler et al., 2001). Later Glomeromycota was separated from Entorrhizomycota) (Schu the rest of Zygomycota based on ribosomal protein phylogenies. Species of Glomeromycotina produce coenocytic hyphae that harbor bacterial endosymbionts belonging to members of the family Gigasporaceae and Mollicutes (Mollicutesrelated endobacteria MRE) in their cytoplasm. During coevolution, MRE formed distinct, monophyletic evolutionary lineages within their fungal hosts with a 16S rRNA gene (16S) s et al., 2015). Asexually formed sequence divergence of up to 20% (Torres-Corte chlamydospore-like spores are borne on specialized hyphae. These spores are large, multinucleated, and filled with lipid and protein globules. Spore morphology defines the different groups. Most species produce spores directly in soil or in the roots, but several species in different lineages make macroscopic sporocarps. This phylum species live as obligate symbionts of land plants, forming a particular type of symbiosis termed arbuscular mycorrhizae. Arbuscules are distinguishing structures of AMF and serve as the site of nutrient exchange and transfer in arbuscular mycorrhizae. They are modified, highly branched haustorium-like cells that are produced in cortical plant root cells. The fungal mycelia grow inside the root of the plant penetrating the host cells. The host plant exerts influence over the proliferation of intercellular hyphal and arbuscule formation. The fungus helps the plant in acquiring of phosphorus, nitrogen, and water in exchange for photosynthesis-derived metabolites. The mycelium is always nonseptate and presents anastomoses (Redecker et al., 2013). Members of this group have 24-ethyl-cholesterol as the main membrane sterol, apparently lacking ergosterol. Ø Ø Ø Ø

ORDER: ORDER: ORDER: ORDER:

ARCHAEOSPORALES; for example genera: Archaeospora, Geosiphon. DIVERSISPORALES; for example genera: Acaulosporaceae, Diversispora, Pacispora. GLOMERALES; for example genus: Glomus. PARAGLOMERALES; for example genus: Paraglomus.

Recent molecular studies have suggested a separate phylum is appropriate for the AM fungi, the Glomeromycota, and this is the position taken by the AFTOL study. The ICBN requires the name of a family or order to be formed from the genitive singular of a legitimate name of an included genus. The genitive of the type genus Glomus is Glomeris, and so the name of the family should be Glomeraceae and order Glomerales (rather than “Glomales”).

3.11 Mucoromycota Phylum Mucoromycota, currently listed along with clade zygomycetes under incertae sedis comprises three orders under subdivision Mucoromycotina. Sexual reproduction is through zygospore production by gametangial conjugation. Zygospores tend to be globose, smooth or ornamented, and produced on opposed or apposed suspensor cells with or without appendages. Asexual reproduction involves chlamydospores and spores produced in sporangia and sporangioles. Hyphae has large diameter and coenocytic.

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Ø

ORDER: MUCORALES; for example genera: Mucor, Parasitella, Phycomyces, Pilobolus, Rhizopus. ORDER: ENDOGONALES; for example genera: Endogone, Peridiospora, Sclerogone, Youngiomyces. ORDER: MORTIERELLALES; for example genera: Mortierella, Dissophora, Modicella.

Ø Ø

Mucoromycota is characterized by plant-associated nutritional modes (plant symbionts, decomposers of plant debris, plant pathogens, etc.) but have rare ecological interactions with animals (as opportunistic infections).

3.11.1 Mortierellomycotina Mortierellomycotina are diferentiated from Mucoromycotina by the morphology of the zygospore and the absence of a columella which is centrally vacuolated part of hyphae bearing spores, typically a basally inflated sporangiophore (Smith et al., 2013). Species of Mortierella live as saprotrophs in soil, on decaying leaves and other organic materials. Most species of Mortierellomycotina form microscopic colonies but few in the genus Modicella make multicellular sporocarps. Compared with Mucor-like fungi, the mitosporangia are typically smaller and contain fewer spores and lack a columella. Mortierellomycotina reproduce asexually by sporangia and form zygospores (naked or surrounded by nest like hyphae) that are the developed through plasmogamy between gametangia belonging to complementary mating types. Mortierella species are producers of fatty acids especially polyunsaturated fatty-acid like, arachidonic acid, and they frequently harbor bacterial endosymbionts (Higashiyama et al., 2002; Sato et al., 2010).

3.11.2 Mucoromycotina Mucoromycotina subphyla taxonomic placement is still considered as incertae sedis by some mycologists and these groups were originally clustered as Zygomycota. Mucoromycotina fungi represent the majority of zygomycetous fungi in pure culture. Species can be isolated from soil, dung, plant debris, and sugar-rich plant parts (e.g., fruits). Sexual reproduction within Mucoromycotina is by prototypical zygospore formation. It involves the production of zygospores by apposed gametangia within a simple sequestrate or enclosed sporocarp. Asexual reproduction involves the copious production of sporangia and/or sporangioles. Primary cell walls component of Mucoromycotina is chitosan, a deacetylated form of chitin lida et al., 2015). Presence of an inflated swelling of a sporangiophore termed a columella (Me is synapomorphic for the subphylum. Porous, plasmodesmata-containing septa sometimes appear in reproductive structures and senescent hyphae. Mucorales members often referred to as pin molds, produce sporangia held up on hyphae, called sporangiophores. Sporangiophores are upright (simple or ramified) hyphae that support sac-like sporangia filled with asexual sporangiospores. The sporangiospores germinate to form the haploid hyphae of a new mycelium.

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Endogonales covers both ectomycorrhizal and saprobic species. Current findings suggest that ectomycorrhizae have probably evolved twice within Endogonales (Tedersoo and Smith, 2013), once as an independent origin of mycorrhizae relative to the arbuscular mycorrhizae of Glomeromycotina and second as ectomycorrhizae of Dikarya. Like many of Mucoromycota, they harbor endohyphal bacteria.

3.12 Dikarya The name was derived from the Greek word di- (two) and karyon (nut or kernel, interpreted by biologists to refer to nuclei). Instead of usual pattern of phylum name ending in mycota such as Dikaryomycota or Neomycota, the clade was named Dikaryon following the phylogeny-based classification of Hibbett et al. (2007) which has been adopted both in Ainsworth & Bisby’s Dictionary of the Fungi and the GenBank taxonomy (http://www.ncbi.nlm.nih.gov/guide/taxonomy). Monophyly of Dikarya is strongly documented by independent and combined analyses of nuclear ribosomal RNA genes, RNA polymerase II subunits, and whole genomes sequencing (James et al., 2006b). Dikarya are characterized to have a sexual cycle that includes hyphal fusion uncoupled with meiosis, which produces hyphae that contain two independent nuclear populations (dikaryotic hyphae). Beside these features like the presence of septate hyphae, ergosterol as the building block of the membrane sterol, and several lineages that are able to form multicellular reproductive or vegetative structures such as cytoplasmic fusion of two haploid monokaryotic hyphae giving rise to dikaryotic condition defines the putative synapomorphy of this group nomenclature. Clamp connections of Basidiomycota and croziers of Ascomycota, are structures that function in the distribution and allocation of nuclei to daughter cells following mitosis in dikaryotic hyphae, are homologous and represents an additional synapomorphy. Evenly septate hyphae are typical synapomorph to this group, because Mucoromycota, its sister taxon, have predominantly coenocytic hyphae. From the above description, Nagy et al. (2014) proposed that if clamps/croziers and septate hyphae of Basidiomycota and Ascomycota are homologous, then the ancestor of Dikarya must have been filamentous (Nagy et al., 2014).

3.12.1 Ascomycota Derived from the Greek askos (sac) + mykes (fungus) the name Ascomycota rather than the synonyms Ascomycetes (class) and Ascomycotina (subphylum), was termed following the phylogeny-based classification of Hibbett et al. (2007), similar to Basidiomycota. Ascomycota comprises three mutually exclusive subclades (Schoch et al., 2009). Taphrinomycotina, Saccharomycotina, and Pezizomycotina pezizomycotina include all ascomaproducing taxa. The fossil record of Ascomycota dates back to Devonian period, with Paleopyrenomycites and Prototaxites taitii dating from the Middle Ordovician until the Late Devonian molecular phylogenies of the fossil record have estimated the origin of Ascomycota around 0.40–1.3 billion years before present (Taylor and Berbee, 2006).

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General characteristic features of Ascomycota. Ascomycota includes diverse organisms from unicellular yeasts to complex cup fungi. Half of all members of the phylum Ascomycota form symbiotic associations with algae to form lichens (Kumar et al., 2011). 1. Sexual reproduction leads to formation of meiospores (ascospores) within sac-shaped meiosporangia (asci) by the process of free cell formation. 2. Free cell formation involves the production of an enveloping membrane system, which is derived from either the ascus plasmalemma or the nuclear envelope and delimits ascospore initials. 3. Ascomycota are devoid of flagella and exhibit intranuclear mitosis with spindle pole bodies instead of centrioles. 4. Most Ascomycota have filamentous septate hyphae fenced by septal walls that have septal pores. 5. The cell walls of the ascomycetes contain chitin and β-glucans. A unique character of the Ascomycota (but not present in all ascomycetes) is the presence of membrane bound structure with a crystaline protein matrix called Woronin bodies on each side of the septa. Asexual reproduction produces mitospores or vegetative reproductive spores called the conidiospores.

3.12.2 Basidiomycota Why did the mushroom come to the party? because he’s a fungi! Derived from the Latin word -basis (means base, support) plus -idium, refers to the basidium, a “little pedestal,” on which the basidiospores develop. The most pronounced difference between the ascomycota and basidiomycota is the extended dikaryotic phase of some of the basiomycota. Similar to ascomycota the name basidiomycota was adapted by Hibbet et al., as well as in Ainsworth & Bisby’s Dictionary of the Fungi, and the GenBank taxonomy (http://www. ncbi.nlm.nih.gov/guide/taxonomy) (Hibbett et al., 2007; Kirk et al., 2008). Three major subdivision, Pucciniomycotina (rusts—Pucciniales and relatives), Ustilaginomycotina (smuts—Ustilaginales and relatives), and Agaricomycotina which includes mushrooms Agaricomycetes, jelly fungi (Auriculariales, Dacrymycetales, Tremellales) and others have been allotted under this and is strongly supported by phylogenetic analyses of multilocus molecular data (James et al., 2006b). Genome-based datasets strongly support the monophyletic descend of Basidomycota which was also corroborated in an analysis of nonmolecular characters by Zhao et al. (2017) and Nagy et al. (2016). In gist Basidiomycota is form of extended, free-living dikaryotic mycelium where the production of meiospores on basidia is putative synapomorphies. General characteristic features of Basidomycota. 1. Basidiomycota reproduces sexually via the formation of specialized club-shaped end cells called basidia that normally bear external meiospores (usually four). These

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3. 4.

5. 6.

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specialized spores are called basidiospores borne on distinctive basidiocarps or basidioma. The basidiospores are the dispersive spores and they are forced out by hydrostatic pressure between the sterigma and the basidiospore on the basidium. In these cases, they are called ballistospores. The hymenium is the tissue layer of the fungi fruiting body from which the basidia arise. Mycelium that grows from a basidiospore is haploid. Haploid mycelia fuse via plasmogamy until the hyphae contains a pair of compatible nuclei (dikaryon), hence called dikaryotic. This dikaryotic stage can last for years and maintenance of the dikaryotic status in dikaryons in Basidiomycota is facilitated by the formation of clamp connections. Dikaryotic mycelium grows as an expanding circle and feeds on its substrate for organic matter and nutrients during its expansion. With time, the older dikaryotic mycelia expand in circles as a ring (called fairy ring), which also becomes the source of the basidiocarps.

The Basidiomycotina is the most diverse subphylum in the Basidiomycota. Tree ear is an example of this taxa. Basidiomycotina can be differentiated on the basis of their basidiocarps, which show great disparity in form. The Basidiomycota fungi range from common edible mushroom forms to some of deadly plant pathogens. The symbiotic basidiomycota such as rusts (Subphylum Urediniomycotina) and smuts (Subphylum Ustilagomycotina), attack wheat and other crops and are main groups of plant pathogens. The rusts (e.g., wheat rust and white pine blister rust) alternate between two hosts (heteroecious) and have five different kinds of spores (macrocyclic) in their life cycles. In Puccinia graminis, karyogamy occurs in the teliospore (fourth spore) after which it undergoes meiosis with each four cells bearing one basidiospore each. The basidiospores then after disperse and restart the infection process (Begerow et al., 2006). Not all symbiotic Basidiomycota are harmful to their partners. For instance, some Basidiomycota form ectomycorrhizae, which are symbiotic associations with the roots of vascular plants. Ectomycorrhizal Basidiomycota help to transfer mineral nutrients from the soil to the plant, and in exchange they receive carbon source like sugars produced in photosynthesis. The basidiomycete toxin phalloidin (from the mushroom Amanita phalloides) binds actin, which is a component of microfilaments. This prevents depolymerization of actin fibers. Gradually phalloidin destroy the liver cells and causes nephrosis.

4. Conclusions and perspectives Ever since the discovery of George Beadle and Edward Tatum “one gene, one enzyme” hypothesis based on experiments on bread mold Neurospora crassa, fungi continued to be the preferred model organism for genetic experiments largely because they are less expensive than any other eukaryotic organism and also because of ease of culture, definite

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life cycles, short generation time gap, etc. Fungi comprise a highly heterogenous community from unicellular microscopic entity yeast to complex multicellular macroscopic filamentous structures. They represent parasitic anaerobes in the animal gut as well as saprophytic aerobes in wild. Their taxonomic origin has been revised numerous times in recent past. Some chytrid members are given new phylum status whereas old phylums are dissolved. Phylum AGF/Neocallimastigomycota, distinct from the chytrid fungi, possess several unique traits that make their study fascinating yet challenging to mycologists. Much of the interest in these fungi relates to the genes/enzymes important for biorefining and biofuel production, notably xylose isomerases and glycosyl hydrolases (xylanases, cellulases). In Prague, Kate and her colleagues have explored the use of anaerobic fungi to improve the hydrolytic phase of biogas production. They have also investigated which fungi are present in the cow manure used to prime the biogas fermentations. Most exploited industrial strains are mainly from Ascomycota and Basidiomycota. Moreover, some members of Ascomycota like unicellular S. cerevisiae and heterothallic filamentous Neurospora crassa are overanalyzed as model organisms. Fungi showcase a good deal of complexity in cellular, metabolic, and genomic organization along with dearth of functional knowledge in every aspect of all the representative members from different phylum. Considering the number of unidentified micro and macrofungi, we are far away from harnessing full potential of this monophyletic community.

Acknowledgments Dr. Shakuntala Ghorai is thankful to Dr. Sasabindu Jana, Principal, Raidighi College, for his constant encouragement and support in all academic endeavors.

References Adam, A., Deimel, S., Pardo-Medina, J., Garcia-Martinez, J., Konte, T., Limon, M.C., Avalos, J., Terpitz, U., 2018. Protein activity of the Fusarium fujikuroi rhodopsins CarO and OpsA and their relation to fungus-plant interaction. Int. J. Mol. Sci. 19 (1), 215. Aguilar-Paredes, A., Valdes, G., Nuti, M., 2020. Ecosystem functions of microbial consortia in sustainable agriculture. Agronomy 10, 1902. Ahrendt, S., Quandt, A., Ciobanu, D., Clum, A., Salamov, A., Andreopoulos, B., Cheng, J.-F., Woyke, T., Pelin, A., Henrissat, B., Reynolds, N., Benny, G., Smith, M., James, T., Grigoriev, I., 2018. Leveragibg single-cell genomics to expand the fungal tree of life. Nat. Microbiol. 3 (12), 1417–1428. Akhberdi, O., Zhang, Q., Wang, D., Wang, H., Hao, X., Liu, Y., Wei, D., Zhu, X., 2018. Distinct roles of velvet complex in the development, stress tolerance, and secondary metabolism in Pestalotiopsis microspora, a taxol producer. Genes (Basel) 9 (3), 164. Allen, M., Swenson, W., Querejeta, J., Egerton-Warburton, L.M., Treseder, K., 2003. Ecology of miccorrhizae: a conceptual framework for complex interactions among plants and fungi. Annu. Rev. Phytopathol. 41, 271–303. Anderson, M., Saha, A., Haseeb, A., Bennett, R., 2017. A chromosome 4 trisomy contributes to increased fluconazole resistance in clinical isolate of Candida albicans. Microbiology 163 (6), 856–865.

Chapter 3 • Fungal biology

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Azizan, M.S., Zamani, A., Stahmann, K.-P., Ng, C., 2016. Fungal metabolites and their industrial importance: a brief review. Malays. J. Biochem. Mol. Biol. 2, 15–23. Begerow, D., Stoll, M., Bauer, R., 2006. A phylogenetic hypothesis of Ustilaginomycotina based on multiple gene analyses and morphological data. Mycologia 98 (6), 906–916. Bennett, R., Turgeon, B.G., 2016. Fungal sex: the ascomycota; microbiology. Spectrum 4 (5). FUNK-00052016. Benny, G., Aldrich, H., 2011. Ultrastructural observations on septal and merosporangial ontogeny in Linderina pennispora (Kickxellales; Zygomycetes). Can. J. Bot. 53 (20), 2325–2335. Berger, L., Speare, R., Daszak, P., Green, E., Cunningham, A., Goggin, L., Slocombe, R., Ragan, M., Hyatt, A., McDonald, K., Hines, H., Lips, K., Marantelli, G., Parkes, H., 1998. Chytridiomycosis causes amphibian mortality associated with population declines in the rain forests of Australia and Central America. Proc. Natl. Acad. Sci. U. S. A. 95 (15), 9031–9036. Berger, L., Hyatt, A., Speare, R., Longcore, J., 2005. Life cycle stages of the amphibian chytrid Batrachochytrium dendrobatidis. Dis. Aquat. Org. 68 (1), 51–63. Cairns, T., Zheng, X., Zheng, P., Sun, J., Meyer, V., 2019. Moulding the mould: understanding and reprogramming filamentous fungal growth and morphogenesis for next generation cell factories. Biotechnol. Biofuels 12 (77). Cardoso, I., Kuyper, T., 2006. Mycorrhizas and tropical soil fertility. Agric. Ecosyst. Environ. 116 (1–2), 72–84. Carla Baron, N., Cid Rogobelo, E., Cunha Zied, D., 2019. Filamentous fungi in biological control: current status and future perspective. Chil. J. Agric. Res. 79 (2), 307–315. Carlile, M., Watkinson, S., Gooday, G., 2001. The Fungi, seond ed. Academic Press, United Kingdom. Casselton, L., Olesnicky, N., 1998. Molecular genetics of mating recognition in Basidiomycete fungi. Microbiol. Mol. Biol. Rev. 62 (1), 55–70. Chuang, S.-C., Ho, H.-M., Reynolds, N., Smith, M., Benny, G., Chien, C.-Y., Tsai, J.-L., 2017. Preliminary phylogeny of Coemansia (Kickxellales), with descriptions of four new species from Taiwan. Mycologia 109, 815–831. Coelho, M., Bakkeren, G., Sun, S., Hood, M., Giraud, T., 2017. Fungal sex: the basidiomycota. Microbiol. Spectr. 5 (3). Corradi, N., Keeling, P., 2009. Microsporidia: a journey through radical taxonomical revisions. Fungal Biol. Rev. 23, 1–8. € ller, K.-D., Michel, R., 2014. Microsporidia-like Corsaro, D., Walochnik, J., Venditti, D., Steinmann, J., Mu parasites of amoebae belong to the early fungal lineage rozellomycota. Parasitol. Res. 113 (5), 1909–1918. De Ligne, L., de Ulzurrun, V.-D., Guillermo, Baetens, J., den Bulcke, V., Jan, Acker, J., De Baets, B., 2019. Analysis of spatio-temporal fungal growth dynamics under different environmental conditions. IMA Fungus 10 (7). Dee, J., Mollicone, M., Longcore, J., Roberson, R., Berbee, M., 2015. Cytology and molecular phylogenetics of Monoblepharidomycetes provide evidence for multiple independent origins of the hyphal habit in the fungi. Mycologia 107, 710–728. Diepeveen, E., Gehrmann, T., Pourquie, V., Abeel, T., Laan, L., 2018. Patterns of conservation and diversification in the fungal polarization network. Genome Biol. Evol. 10 (7), 1765–1782. Dura´n, P., Barra, P., Jorquera, M., Viscardi, S., Fernandez, C., Paz, C., de la Luz Mora, M., Bol, R., 2019. Occurrence of soil fungi in Antarctic pristine environments. Front. Bioeng. Biotechnol. 7, 28. Fisher, K., Roberson, R., 2016. Hyphal tip cytoplasmic organization in four zygomycetes fungi. Mycologia 108 (3), 533–542.

100

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Flegel, T.W., 1977. Let’s call a yeast a yeast. Can. J. Microbiol. 23 (8), 945–946. , S., Romeu, A., Palau, J., 2000. Horizontal gene transfer of glycosyl hydrolases of the rumen Garcia-Vallve fungi. Mol. Biol. Evol. 17 (3), 352–361. Gerstein, A., Fu, M., Mukaremera, L., Li, Z., Ormerod, K., Fraser, J., Berman, J., Nielsen, K., 2015. Polyploid titan cells produce haploid and aneuploid progeny to promote stress adaptation. mBio 6 (5), e0134015. Ghorai, S., Banik, S.P., Verma, D., Chowdhury, S., Mukherjee, S., Khowala, S., 2009. Fungal biotechnology in food and feed processing. Food Res. Int. 42, 577–587. Gleason, F., Carney, L., Lilje, O., Glockling, S., 2012. Ecological potentials of species of Rozella (Cryptomycota). Fungal Ecol. 5 (6), 651–656. Griffith, G.W., Ozkose, E., Theodorou, M., Davies, D., 2009. Diversity of anaerobic fungal populations in cattle revealed by selective enrichment culture using different carbon sources. Fungal Ecol. 2 (2), 87–97. Grossart, H.-P., Wurzbacher, C., James, T., Kagami, M., 2016. Discovery of dark matter fungi in aquatic ecosystems demands a reappraisal of the phylogeny and ecology of zoosporic fungi. Fungal Ecol. 19, 28–38. Grossetete, S., Labedan, B., Lespinet, O., 2010. FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology. BMC Genomics 11 (81). Heath, B., Bauchop, T., Skipp, R., 1983. Assignment of the rumen anaerobe Neocallimastix frontalis to the Spizellomycetales (Chytridiomycetes) on the basis of its polyflagellate zoospore ultrastructure. Can. J. Bot. 61 (1), 295–307. Hibbett, D., Binder, M., Bischoff, J., Blackwell, M., Cannon, P., Eriksson, O., et al., 2007. A higher-level phylogenetic classification of the fungi. Mycol. Res. 111 (5), 509–547. Higashiyama, K., Fujikawa, S., Park, E., Shimizu, S., 2002. Production of arachidonic acid by Mortierella fungi. Biotechnol. Bioprocess Eng. 7, 252–262. Humber, R., 2012. Entomophthoromycota: a new phylum and reclassification for entomophthoroid fungi. Mycotaxon 120, 477–492. James, T., Kauff, F., Schoch, C., Matheny, B., Hofstetter, V., Cox, C., et al., 2006a. Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 443, 818–822. James, T., Letcher, P., Longcore, J., Mozley-Standridge, S., Porter, D., Powell, M., Griffith, G., Vilgalys, R., 2006b. A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). Mycologia 98 (6), 860–871. James, T., Pelin, A., Bonen, L., Ahrendt, S., Sain, D., Corradi, N., Stajich, J., 2013. Shared signatures of parasitism and phylogenomics unite cryptomycota and microsporidia. Curr. Biol. 23 (16), 1548–1553. Jumpponen, A., Jones, K., 2009. Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytol. 184 (2), 438–448. Kagami, M., van Donk, E., de Bruin, A., Rijkeboer, M., Ibelings, B., 2004. Daphnia can protect diatoms from fungal parasitism. Limnol. Oceanogr. 49, 680–685. Kagami, M., de Bruin, A., Ibelings, B., Van Donk, E., 2007. Parasitic chytrids: their effects on phytoplankton communities and food-web dynamics. Hydrobiologia 578, 113–129. Kagami, M., Miki, T., Takimoto, G., 2014. Mycoloop: chytrids in aquatic food webs. Front. Microbiol. 5, 166. Kala, K., Kryczyk-Poprawa, A., Rzewinska, A., Muszynska, B., 2020. Fruiting bodies of selected edible mushrooms as a potential source of lovastatin. Eur. Food Res. Technol. 246, 713–722. Karpov, S., Mikhailov, K., Mirzaeva, G., Mirabdullaev, I., 2013. Obligately phagotrophic aphelids turned out to branch with the earliest-diverging fungi. Protist 164 (2), 195–205.

Chapter 3 • Fungal biology

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Karpov, S., Mamkaeva, M., Aleoshin, V., Nassonova, E., Lilje, O., Gleason, F., 2014. Morphology, phylogeny, and ecology of the aphelids (Aphelidea, Opisthokonta) and proposal for the new superphylum Opisthosporidia. Front. Microbiol. 5, 112. Karpov, S., Mamanazarova, K., Popova, O., Aleoshin, V., Timothy, J., Mamkaeva, M., Tcvetkova, V., Vishnyakov, A., Longcore, J., 2017. Monoblepharidomycetes diversity includes new parasitic and saprotrophic species with highly intronized rDNA. Fungal Biol. 121, 729–741. Keller, N., 2018. Fungal secondary metabolism: regulation, function and drug discovery. Nat. Rev. Microbiol. 17, 167–180. Kirk, P., Cannon, P., Minter, D., Stalpers, J., 2008. Ainsworth & Bisby’s Dictionary of the Fungi, tenth ed. CAB International, Wallingford. Kohler, J., Casadevall, A., Perfect, J., 2015. The spectrum of fungi that infects humans. Cold Spring Harb. Perspect. Med. 5 (1), a019273. Krizsan, K., Almasi, E., Merenyi, Z., Sahu, N., Viragh, M., Koszo, T., Mondo, S., Kiss, B., Balint, B., Kues, U., Barry, K., Cseklye, J., Hegedus, B., Henrissat, B., Johnson, J., et al., 2019. Transcriptomic atlas of mushroom development highlights an independent origin of complex multicellularity. Proc. Natl. Acad. Sci. U. S. A. 116 (15), 7409–7418. Kumar, T.K., Crow, J., Wennblom, T., Abril, M., Letcher, P., Blackwell, M., Roberson, R., McLaughlin, D., 2011. An ontology of fungal subcellular traits. Am. J. Bot. 98, 1504–1510. Kunzler, M., 2018. How fungi defend themselves against microbial competitors and animal predators. PLoS Pathog. 14 (9), e1007184. Lastovetsky, O., Gaspar, M., Mondo, S., LaButtic, K., Sandor, L., Grigoriev, I., Henry, S., Pawlowsk, T., 2016. Lipid metabolic changes in an early divergent fungus govern the establishment of a mutualistic symbiosis with endobacteria. Proc. Natl. Acad. Sci. U. S. A. 113 (52), 15102–15107. Lee, S., Ni, M., Li, W., Shertz, C., Heitman, J., 2010. The evolution of sex: a perspective from the fungal kingdom. Microbiol. Mol. Biol. Rev. 74 (2), 298–340. Letcher, P.M., Martha, P.J., Churchill, P., Chambers, J., 2006. Ultrastructural and molecular phylogenetic delineation of a new order, the Rhizophydiales (Chytridiomycota). Mycol. Res. 110 (8), 898–915. Letcher, P.M., Powell, M.J., 2019. A taxonomic summary of Aphelidiaceae. IMA Fungus 10 (4). https://doi. org/10.1186/s43008-019-0005-7. Longcore, J., Pessier, A., Nichols, D., 1999. Batrachochytrium dendrobatidis gen. et sp. nov., a Chytrid pathogenic to amphibians. Mycologia 91, 219–227. Ma, L., Song, B., Curran, T., Phong, N., Dressaire, E., Roper, M., 2016. Defining individual size in the model filamentous fungus Neurospora crassa. Proc. R. Soc. B 283, 20152470. Madhani, H.D., Fink, G.R., 1998. The control of filamentous differentiation and virulence in fungi. Trends Cell Biol. 8 (9), 348–353. Manning, R., Waters, S., Callaghan, A., 2007. Saprotrophy of Conidiobolus and Basidiobolus in leaf litter. Mycol. Res. 111, 1437–1449. Marcet-Houben, M., Gabaldon, T., 2019. Evolutionary and functional patterns of shared gene neighbourhood in fungi. Nat. Microbiol. 4 (12), 2383–2392. Masclaux, H., Perga, M.-E., Kagami, M., Desvilettes, C., Bourdier, G., Bec, A., 2013. How pollen organic matter enters freshwater food webs. Limnol. Oceanogr. 58, 1185–1195. Medina-Castellanos, E., Villalobos-Escobedo, J., Riquelme, M., Read, N., Abreu-Goodger, C., HerreraEstrella, A., 2018. Danger signals activate a putative innate immune system during regeneration in a filamentous fungus. PLoS Genet. 14 (11), e1007390. Meletiadis, J., Meis, J., Mouton, J., Verweij, P., 2001. Analysis of growth characteristics of filamentous fungi in different nutrient media. J. Clin. Microbiol. 39 (2), 478–484.

102

Current Developments in Biotechnology and Bioengineering

Melida, H., Sain, D., Stajich, J., Bulone, V., 2015. Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches. Environ. Microbiol. 17, 1649–1662. Mixao, V., Gabaldon, T., 2018. Hybridization and emergence in opportunistic human yeast pathogens. Yeast 35 (1), 5–20. Morrow, C., Fraser, J., 2009. Sexual reproduction and dimorphism in the pathogenic basidiomycetes. FEMS Yeast Res. 9 (2), 161–177. Muller, M., Mentel, M., van Hellemond, J.J., Henze, K., Woehle, C., Gould, S.B., Yu, R.-Y., van der Giezen, M., Tielens, A., Martin, W., 2012. Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol. Mol. Biol. Rev. 76 (2), 444–495. Nadal, M., Garcia-Pedrajas, M., Gold, S., 2008. Dimorphism in fungal plant pathogens. FEMS Microbiol. Lett. 284 (2), 127–134. Nagy, L., Ohm, R., Kov’acs, G., Floudas, D., Riley, R., Gacser, A., et al., 2014. Phylogenomics reveals latent homology behind the convergent evolution of yeast forms. Nat. Commun. 5, 4471. Nagy, L., Riley, R., Tritt, A., Adam, C., Daum, C., Floudas, D., Sun, H., et al., 2016. Comparative genomics of early-diverging mushroom-forming fungi provides insights into the origins of lignocellulose decay capabilities. Mol. Biol. Evol. 33 (4), 959–970. Naranjo-Ortiz, M., Gabaldon, T., 2019. Fungal evolution: diversity, taxonomy and phylogeny of the fungi. Biol. Rev. 94, 2101–2137. Naranjo-Ortiz, M., Gabaldon, T., 2020. Fungal evolution: cellular, genomic and metabolic complexity. Biol. Rev. Camb. Philos. Soc. 95 (5), 1198–1232. Oberwinkler, F., 2017. Yeasts in Pucciniomycotina. Mycol. Prog. 16, 831–856. Orpin, C.G., 1974. The rumen flagellate Callimastix frontalis: does sequestration occur? J. Gen. Microbiol. 84, 395–398. Ozkose, E., Thomas, B., Davies, D., Griffith, G., Theodorou, M., 2001. Cyllamyces aberensis gen.nov.sp.nov., a new anaerobic gut fungus with branched sporangiophores isolated from cattle. Can. J. Bot. 79 (6), 666–673. Peter, J., De Chiara, M., Friedrich, A., Yue, J.-X., Pflieger, D., Bergstrom, A., Sigwalt, A., Barre, B., Freel, K., Llored, A., Cruaud, C., Labadie, K., Aury, J.-M., Istace, B., Lebrigand, K., et al., 2018. Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Nature 556, 339–344. Porter, T., Martin, W., James, T., Longcore, J., Gleason, F., Adler, P., Letcher, P., Vilgalys, R., 2011. Molecular phylogeny of the Blastocladiomycota (fungi) based on nuclear ribosomal DNA. Fungal Biol. 115, 381–392. € ssler, A., Stockinger, H., Stu € rmer, S., Morton, J., Walker, C., 2013. An evidence-based conRedecker, D., Schu sensus for the classification of arbuscular mycorrhizal fungi (Glomeromycota). Mycorrhiza 23 (7), 515–531. Rico-Munoz, E., Samson, R., Houbraken, J., 2019. Mould spoilage of foods and beverages: using the right methodology. Food Microbiol. 81, 51–62. Riquelme, M., Reynaga-Pena, C., Gierz, G., Bartnicki-Garcia, S., 1998. What determines growth direction in fungal hyphae? Fungal Genet. Biol. 24 (1–2), 101–109. Riquelme, M., Aquirre, J., Bartnicki-Garcia, S., Braus, G., Feldbrugge, M., Fleig, U., Hansberg, W., HerreraEstrella, A., Kamper, J., Kuck, U., Mourino-Perez, R., Takeshita, N., Fischer, R., 2018. Fungal morphogenesis, from the polarized growth of hyphae to complex reproduction and infection structures. Microbiol. Mol. Biol. Rev. 82 (2), e00068-17. Rokas, A., Wisecaver, J., Lind, A., 2018. The birth, evolution and death of metabolic gene clusters in fungi. Nat. Rev. Microbiol. 16, 731–744. Sato, Y., Narisawa, K., Tsuruta, K., Umezu, M., Nishizawa, T., Tanaka, K., Yamaguchi, K., Komatsuzaki, M., Ohta, H., 2010. Detection of betaproteobacteria inside the mycelium of the fungus Mortierella elongate. Microbes Environ. 25 (4), 321–324.

Chapter 3 • Fungal biology

103

Schmitz, K., Peter, V., Meinert, S., Kornfeld, G., Hardiman, T., Wiechert, W., Noack, S., 2013. Simultaneous utilization of glucose and gluconate in Penicillium chrysogenum during overflow metabolism. Biotechnol. Bioeng. 110 (12), 3235–3243. Schoch, C., Sung, G.-H., Lopez-Giraldez, F., Townsend, J., Miadlikowska, J., et al., 2009. The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Syst. Biol. 58, 224–239. € βler, A., Schwarzott, D., Walker, C., 2001. A new fungal phylum, the Glomeromycota: phylogeny and Schu evolution. Mycol. Res. 105, 1413–1421. Shine, A., Shakya, V., Idnurm, A., 2015. Phytochelatin synthase is required for tolerating metal toxicity in a basidiomycete yeast and is conserved factor involved in metal homeostasis in fungi. Fungal Biol. Biotechnol. 2, 3. Sinha, S., Flibotte, S., Neira, M., Formby, S., Plemenitas, A., Cimerman, N., Lenassi, M., Gostincar, C., Stajich, J., Nislow, C., 2017. Insight into the recent genome duplication of the halophilic yeast Hortaea werneckii: combining an improved genome with gene expression and chromatin structure. GE3 7 (7), 2015–2022. Siqueira, V., Lima, N., 2013. Biofilm formation by filamentous fungi recovered from a water system. J. Mycol. 2013, 152941. Smith, M., Gryganskyi, A., Bonito, G., Nouhra, E., Moreno-Arroyod, B., Bennya, G., 2013. Phylogenetic analysis of the genus Modicella reveals an independent evolutionary origin of sporocarp-forming fungi in the Mortierellales. Fungal Genet. Biol. 61, 61–68. Solomon, K., Haitjema, C., Henske, J., Gilmore, S., Borges-Rivera, D., Lipzen, A., Brewer, H., Purvine, S., Wright, A., Theodorou, M., Grigoriev, I., Regev, A., Thompson, D., O’Malley, M., 2016. Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes. Science 351 (6278), 1192–1195. Spatafora, J., Chang, Y., Benny, G., Lazarus, K., Smith, M., Berbee, M., Bonito, G., Corradi, N., Grigoriev, I., Gryganskyi, A., James, T., O’Donnell, K., Roberson, R., Taylor, T., Uehling, J., Vilgalys, R., White, M., Stajich, J., 2016. A phylum-level phylogenetic classification of zygomycete fungi based on genomescale data. Mycologia 108, 1028–1046. Takeshita, N., 2016. Coordinated process of polarized growth in filamentous fungi. Biosci. Biotechnol. Biochem. 80 (9), 1693–1699. Tako, M., Kotogan, A., Krisch, J., Vagvolgyi, C., Mondal, K., Papp, T., 2015. Enhanced production of industrial enzymes in Mucoromycotina fungi during solid-state fermentation of agricultural wastes/byproducts. Acta Biol. Hung. 66 (3), 348–360. Talbot, J., Allison, S., Treseder, K., 2008. Decomposers in disguise: mycorrhizal fungi as regulators of soil C dynamics in ecosystems under global change. Funct. Ecol. 22, 955–963. Taylor, J., Berbee, M., 2006. Dating divergences in the fungal tree of life: review and new analyses. Mycologia 98, 838–849. Tedersoo, L., Smith, M., 2013. Lineages of ectomycorrhizal fungi revisited: foraging strategies and novel lineages revealed by sequences from belowground. Fungal Biol. Rev. 27, 83–99. Tedersoo, L., Smith, M., 2017. Ectomycorrhizal fungal lineages: detection of four new groups and notes on consistent recognition of ectomycorrhizal taxa in high-throughput sequencing studies. Ecol. Stud. 230, 125–142. €ring, M., Schigel, D., May, T., Ryberg, M., Tedersoo, L., Sa´nchez-Ramı´rez, S., Ko˜ljalg, U., Bahram, M., Do Abarenkov, K., 2018. High-level classification of the fungi and a tool for evolutionary ecological analyses. Fungal Divers. 90, 135–159. Thorsen, M., 1999. Abundance and biomass of the gut-living microorganisms (bacteria, protozoa and fungi) in the irregular sea urchin Echinocardium cordatum (Spatangoida: Echinodermata). Mar. Biol. 133, 353–360.

104

Current Developments in Biotechnology and Bioengineering

s, G., Ghignone, S., Bonfante, P., Schu € ßler, A., 2015. Mosaic genome of endobacteria in arbusTorres-Corte cular mycorrhizal fungi: transkingdom gene transfer in an ancient mycoplasma-fungus association. Proc. Natl. Acad. Sci. U. S. A. 112 (25), 7785–7790. Tretter, E., Johnson, E., Benny, G., Lichtwardt, R., Wang, Y., Kandel, P., Novak, S., Smith, J., White, M., 2014. An eight-gene molecular phylogeny of the Kickxellomycotina, including the first phylogenetic placement of Asellariales. Mycologia 106, 912–935. van der Giezen, M., 2009. Hydrogenosomes and mitosomes: conservation and evolution of functions. J. Eukaryot. Microbiol. 56 (3), 221–231. Vidal-Diez de Ulzurrun, G., Huang, T.-Y., Chang, C.-W., Lin, H.-C., Hsueh, Y.-P., 2019. Fungal feature tracker (FFT): a tool for quantitatively characterizing the morphology and growth of filamentous fungi. PLoS Comput. Biol. 15 (10), e1007428. Voyles, J., Berger, L., Young, S., Speare, R., Webb, R., Warner, J., Rudd, D., Campbell, R., Skerratt, L., 2007. Electrolyte depletion and osmotic imbalance in amphibians with chytridiomycosis. Dis. Aquat. Org. 77 (2), 113–118. Wagner, L., Stielow, L., Hoffman, K., Petkovits, T., Papp, T., Vagvolgyi, C., de Hoog, G.S., Verkley, G., Voigt, K., 2013. A comprehensive molecular phylogeny of the Mortierellales (Mortierellomycotina) based on nuclear ribosomal DNA. Persoonia 30, 77–93. Walker, G., 1998. Yeast Physiology and Biotechnology. John Wiley & Sons, Chichester. Wallen, R.M., Perlin, M., 2018. An overview of the function and maintenance of sexual reproduction in dikaryotic fungi. Front. Microbiol. 9, 503. Walther, G., Wagner, L., Kurzai, O., 2019. Updates on the taxonomy of mucorales with an emphasis on clinically important taxa. J. Fungi 5 (4), 106. Wang, J., Chen, C., 2006. Biosorption of heavy metals by Saccharomyces cerevisiae: a review. Biotechnol. Adv. 24 (5), 427–451. Weete, J., Abril, M., Blackwell, M., 2010. Phylogenetic distribution of fungal sterols. PLoS One 5 (5), e10899. Whittaker, R., 1969. New concepts of kingdoms or organisms. Evolutionary relations are better represented by new classifications than by the traditional two kingdoms. Science 163 (3863), 150–160. Youssef, N., Couger, M.B., Struchtemeyer, C., Liggenstoffer, A., Prade, R., Najar, F., Atiyeh, H., Wilkins, M., Elshahed, M., 2013. The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader. Appl. Environ. Microbiol. 79 (15), 4620–4634. Zhang, Q., Chen, X., Xu, C., Zhao, H., Zhang, X., Zeng, G., Qian, Y., Liu, R., Guo, N., Mi, W., Meng, Y., St. Leger, R., Fang, W., 2019. Horizontal gene transfer allowed the emergence of broad host range entomopathogens. Proc. Natl. Acad. Sci. U. S. A. 116 (16), 7982–7989. Zhao, R.-L., Li, G.-J., S’anchez-Ram’irez, S., Stata, M., Yang, Z.-L., et al., 2017. A six-gene phylogenetic overview of Basidiomycota and allied phyla with estimated divergence times of higher taxa and a phyloproteomics perspective. Fungal Divers. 84, 43–74. Zjawiony, J., 2004. Biologically active compounds from Aphyllophorales (polypor) fungi. J. Nat. Prod. 67 (2), 300–310.

4 Mycotoxins Manikhardaa, Hanifah Nuryani Lioeb, Rachma Wikandaria, and Endang Sutriswati Rahayua DEPARTMENT OF FOOD AND AGRICULTURAL PRODUCT T ECHNOLOGY, UNI VERSITAS GADJ AH M A D A , Y OG Y A K A R T A, I ND O N E S I A b DEPARTME NT OF FOOD SCIENCE AND TECHNOLOGY, IPB UNIVERSITY, BOGOR, INDONESIA

a

1. Introduction Mycotoxins, first coined in 1962 after an incident involving aflatoxin (AF) and costing the death of approximately 100,000 turkey poults in London, are defined as toxin synthesized by filamentous fungi species as secondary metabolites that might pose a health hazard to human or vertebrates of other animal groups in low concentration and usually consists of low molecular compounds (Ashiq, 2015; Bennett et al., 2003). However, it is important to note that not all fungal toxic secondary metabolite is defined as mycotoxin. For example, an antibiotic is a fungal product that is mainly poisonous to bacteria. The same goes for other fungal toxins harmful to plants, but they are not classified as mycotoxins. The presence of filamentous fungi also does not always imply mycotoxin occurrence because the fungi might also grow without secreting toxins. Compared to other fungal by-products, mycotoxins have a wide selection of hosts and targets that cross-plant species. Currently, about 500 mycotoxins are recognized. Mycotoxins classification is usually based on the fungal producers, chemical configurations, and (or) action mechanism. However, one type of mycotoxins can be produced by several different species. Similarly, a single species of fungi might generate one or several types of mycotoxins. Furthermore, a systematic definition of modified mycotoxins and “masked mycotoxins” had been proposed into four hierarchical levels to distinguish the unbound and unmodified mycotoxins from biologically or chemically modified mycotoxins and matrix-bound mycotoxins (Rychlik et al., 2014). Molds are a major spoilage agent of foods and feedstuffs. They cause the reduction of crop yield and quality with significant economic losses and contamination of grains with mycotoxins that are harmful to people and livestock. Mycotoxins contamination in food and feed still becomes a headline due to the negative impact on the health and economy of the country. Moldy food is easily recognized by the naked eye from the color of conidia, spore, mycelia of the fungi. However, some could not be easily detected and need further analysis in the laboratory, such as direct or dilution plating methods. Among the different molds or fungi, there are toxigenic and nontoxigenic molds/fungi. Toxigenic ones produce mycotoxins. Current Developments in Biotechnology and Bioengineering. https://doi.org/10.1016/B978-0-323-91872-5.00008-9 Copyright © 2023 Elsevier Inc. All rights reserved.

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The presence of mycotoxin produced by filamentous fungi in food or feed could exert adverse health effects. Though the appearance of moldy food could be observed visually, mycotoxin contamination is barely detected by the naked eyes. The ingestion of mycotoxins can be direct via consuming contaminated products or indirect via consuming the mycotoxin residue in animal products. The lethal effect of mycotoxins can occur shortly after exposure at certain levels. While at lower levels, several disorders or immunity impairment can occur depending on the type and concentration of the mycotoxin exposure, the health status of the individual ingesting the mycotoxin, alcohol consumption, duration of exposure, and coexposure to other toxins (Ashiq, 2015; Bennett et al., 2003). Thus, the severity of mycotoxin poisoning can be compounded by vitamin deficiency, caloric deprivation, alcohol abuse, and infectious disease status. This phenomenon denotes that mycotoxins affect people’s health (Weidenborner, 2008). The list of some mycotoxins and their health effects are summarized in Table 1. Some studies also had reviewed the mycotoxin effect on reproductive health in Africa (Eze et al., 2018), and epidemiological studies of mycotoxin exposure and cancer risk (Claeys et al., 2020). Table 1

Health risk/clinical manifestation of mycotoxins.

Mycotoxins

Health effect

Aflatoxins (B1, Liver lesions, cirrhosis, primary B2, B3, G1, hepatocellular carcinoma, G2, M1, P1) Kwashiorkor, Reye’s syndrome, immunosuppression The adverse effect of AF is usually due to chronic exposure to one’s diet Fumonisins Esophageal carcinoma, neural tube defect

Ochratoxin A

Endemic nephropathy, urothelial tumors

Concentration

Incidence

References

1–5 μg/kg (9 samples), 5–20 μg/ kg (3 samples), 31 μg/ kg (1 sample)

Incidence: 13/37 Country: Czechoslovakia 1/10–6/10 death rates of hepatitis in China and Africa Incidence: 14/32 country: Spain, USA, South Africa, China Incidence: 4/24 Country: Bulgaria

Fukal et al. (1990) and Reddy et al. (2010)

4.8–85.5 μg/L

25–27 μg/kg

Deoxynivalenol Nausea, vomiting, abdominal pain, 5–100 μg/kg diarrhea, dizziness, headache, (5 samples) immunosuppression Zearalenone Premature puberty in girls, cervical 2–8 μg/kg cancer, breast cancer

Patulin

Damage of gastrointestinal, respiratory systems, DNA, many enzymes

2.6 μg/kg

Reddy et al. (2010), Shepard (2006), and Torres et al. (1998)

Petkova-Bocharova and Castegnaro (1985) and Reddy et al. (2010) Incidence: 5/7 Eskola et al. (2000), country: Finland, Reddy et al. (2010), India and Shepard (2006) Incidence: 1/7 Claeys et al. (2020), Country: Finland, Eskola et al. (2000), US and Reddy et al. (2010) Incidence: 1/16 Bergner-Lang et al. (1983), Piva et al. Country: (2006), and Reddy Germany, Italy et al. (2010)

Chapter 4 • Mycotoxins 107

In the case of AF exposure in Indonesia, a preliminary study of AF risk assessment had been conducted in the Temanggung region, a corn-based food consumption. Almost every day, people in this area consume corn in the form of sekelan (corn-based food) as carbohydrates sources. AFB1 in ready-to-eat sekelan was about 0.96–0.98 ppb (lower than the LOD 1.75 ppb, using enzyme-linked immunosorbent assay (ELISA) methods). With the daily consumption rate of sekelan about 117.1–358.7 g/person per day, it was estimated that the AFB1 exposure value was 79 ng/kg bodyweight per day. According to JECFA (1998), estimation for cancer liver was 0.01–0.30 cases/year per 100.000 people. Therefore estimation for liver cancer, with a population of 8.000 people in the region, is about 0.06–1.80 cases/year per population (Mahdy et al., 2013). The exposure of mycotoxins in developing countries is possibly higher than that of developed countries since developed countries implement strict regulations for mycotoxins. Therefore, this situation forces developing countries to keep their most contaminated food domestically for their consumption while exporting their best crops (Wu, 2006). For instance, AF exposure for Indonesian people is about 9–122 ng/kg body weight per day , and for South Asian people, in general, is about 30–100 ng/kg body weight per day . For comparison, AF exposure for European (in general) is 0–4 ng/kg body weight per day . Liver cancer, is the third leading cause of cancer death worldwide (WHO, 2004). Mycotoxin contamination implies considerable economic loss due to losses in human health, animals and livestock well-being, as well as agricultural commodities (Hussein and Brasel, 2001). Because the lesser stock of commodities complies with the tolerable levels of mycotoxins, it leads to accumulation of rejected products, while conceivably it would necessitate higher cost to provide mycotoxin-safe foods (Ashiq, 2015). Therefore, mycotoxins are responsible for millions of dollars in annual economic losses (Table 2). The impacts of fungi and mycotoxins, apparently AFs in maize and peanut that is still relevant to other fungal and mycotoxins contaminated food had been specified in a report (Lubulwa and Davis, 1994), i.e., (a) the decline in agricultural products quality; (b) decomposition of the agricultural products; (c) negative health impacts on humans who consume mycotoxin-contaminated food; (d) livestock well-being and its impact on the productivity; and (e) loss of trade markets due to regulations restricting the trade of mycotoxin-contaminated products. Feed contaminated by mycotoxins is worsening the health of the animal or even lethal, thus causing significant losses in animal production and animal welfare and might result in the toxins carrying over to the animal-derived products such as meat, milk, or eggs. However, the level might be lower than that found in plant-derived products (Fink-Gremmels, 2006). Strict regulation is needed to maintain human health. On the other hand, too rigid regulation might be resulted in higher economic losses due to rejection. Implementation of more strict regulations from food importers does not have a significant effect on their health. For instance, reducing the limit of AF from 20 to 10 μg/kg only decreases the risk of mortality due to hepatitis B and C by two in a billion annually (Henry et al., 1999). Nevertheless, it significantly impacts the exporting countries as more products are rejected, and they need to keep their contaminated product for themselves. Hence, it is important

108

Current Developments in Biotechnology and Bioengineering

Table 2 Mycotoxins Aflatoxins

Economic impact related to mycotoxin incidence. Cases/ commodities Maize, wheat, rice, sorghum, groundnuts, tree nuts, figs

Economic impact ($)

References

In 2009, maize prices in Kenya plummeted by half. EU mycotoxins regulation was predicted to reduce 64% of African export for agricultural products, approximately 670 million US$ in value yearly. Gambia’s cumulative financial loss on domestic and international trade from 2000 to 2014 was about 23 million US$, on average, about 1.52 million US$ yearly. Presumably, 1.2 billion US$ loss is caused by aflatoxin contamination globally per year, with 38% of this loss (450 million US$) came from African nations N.A.

Bankole and Adebanjo (2003), ECOACAP (2014), IITA (2012), Marechera and Ndwiga (2015), and Reddy et al. (2010)

Deoxynivalenol Maize, wheat, cereals, cereal products Fumonisins Maize, maize The international implementation of products, sorghum 2 mg/kg fumonisin regulation in food would cause export losses to corn exporting nations (USA, China, Argentine) around $20 million to $40 million annually. If the standard of 0.5 mg/kg fumonisin in corn is applied, the global annual market loss will increase to $200 million through product rejection Ochratoxin A Cereals, dried vine N.A. fruit, wine, coffee Patulin Apples, apple juice N.A. Zearalenone Maize, wheat N.A. cereals, cereal products

Reddy et al. (2010)

Reddy et al. (2010) and Wu (2006)

Reddy et al. (2010) Reddy et al. (2010) Reddy et al. (2010) and Shepard (2006)

to do a risk assessment in order to determine the regulation limit of mycotoxin, so it will be beneficial for both food importers and exporters.

2. Major groups of mycotoxins: chemistry and processing stability Among 500 mycotoxins are recognized to date, the common mycotoxins in foods are described in Table 3. The major mycotoxins producing fungal genera were Aspergillus,

Table 3

Type, producing fungi, and stability of different mycotoxins.

Mycotoxin

Chemical structure

Producing fungi Aspergillus flavus, A. parasiticus, A. bombycis, A. ochraceus, A. pseudotamari

Aflatoxin B1, aflatoxin B2, aflatoxin B3 (parasiticol), aflatoxin D1, aflatoxin G1, and their derivates (aflatoxin M1, aflatoxin P1, aflatoxin Q1, and aflatoxicol)

Aflatoxin B1 (AFB1)

Aflatoxin M1 (AFM1)

Aflatoxin G1 (AFG1)

Aflatoxin P1 (AFP1)

Aflatoxicol

Chemistry and processing stability References The AFs are heterocyclic compounds with dihydrodifurano or tetrahydrodifurano moieties attached to a substituted coumarin moiety. These toxins are highly oxygenated. They are also highly fluorescent under UV light and could be recognized by their fluorescing characteristics. Both AFB1 and AFB2 showed blue fluorescence, and AFG1 and AFG2 showed yellowgreen fluorescence More than 20 kinds of AFs and their derivatives had been recognized. AFB1 has the highest prevalence among the AFs group. AFB2a is the metabolites resulted from AFB1 detoxification with the least acute toxicity among the major aflatoxins. AFG2a is derived as the metabolite product of AFG1 The metabolite derivatives of AFB1 are aflatoxicol A, AFM1, AFP1, and AFQ1, among others. Aflatoxicol A might also be synthesized biologically in Tetrahymena pyriformis, Dactylium dendroides, and Rhizopus spp. AFM1 is secreted in urine and milk. AFM1 has

Bennett et al. (2003), Castells et al. (2005), Cole and Cox (1981), Park et al. (2005), Raters and Matissek (2008), and Reddy et al. (2010)

Continued

Table 3

Type, producing fungi, and stability of different mycotoxins—cont’d

Mycotoxin

Chemical structure

Producing fungi

Alternaria spp., A. tenuis, A. dauco, A. cucumerina

Alternaria toxins (alternariol, altenuisol, alternariol methyl ether, altenuene, altenusin, dehydroaltenusin, altertoxin I, altertoxin II)

Alternariol (AOH)

Altenuene (ALT)

Chemistry and processing stability References less effect than AFB1. AFP1 is the main urinary metabolite of AFB1 with less toxicity. AFQ1 is the major metabolites from AFB1 and less toxic AFs are almost completely degraded at heating temperatures of 160°C and above. An average AFB1 reduction of 34% was exhibited in normal cooking of contaminated rice. The extrusion process reported reducing total AFs around 50%–95% or more Dry baking reduces Alternaria toxins better than wet baking. Alternariol monomethyl ether (AME) is the most stable compared to alternariol (AOH) and altenuene (ALT), with ALT being the least stable. In sunflower flour, rising temperature to 100°C barely degraded AOH and AME; keeping the temperature at 121°C for 60 min could decrease the toxins. However, the heat-treated material exhibited adverse effects in rats. Alternaria toxins are very stable and hard to break down in fruits and their processed products

Cole and Cox (1981), Ferna´ndez-Cruz et al. (2010), Lee et al. (2015), Logrieco et al. (2009), Ostry (2008), and Siegel et al. (2010)

Cytochalasins (cytochalasins group consists of cytochalasins E, cytochalasins G, cytochalasins A, cytochalasins B, cytochalasins F, cytochalasins H, cytochalasins C, and cytochalasins D); Cytochalasin A chaetoglobosin group consists of chaetoglobosin A, chaetoglobosin B, chaetoglobosin C, chaetoglobosin D, chaetoglobosin E, chaetoglobosin F, chaetoglobosin G, chaetoglobosin J, and chaetoglobosin K; deoxaphomin, proxiphomin, Cytochalasin C protophomin, zygosporin D, zygosporin E, zygosporin F, zygosporin G

Rosellinia necutrix, Aspergillus clavatus, Nigrosabulum spp., Helminthosporium dermatiodeum, Phoma spp., Hormiscium spp., Phomopsis spp., Metarrhizium anisopliae, Zygosporium masonii, Chaetomium globosum, Diplodia macrospora

Citrinin

Penicillium citrinum Thorn, P. implicatum Biourge, P. lividum Westling, P. fellutanum Biourge, P. jenseni Zaleski, P. citrioviride Biourge, P. expansum, P. notatum, P. viridicatum Westling, P. steckii, Aspergillus terreus Thorn, A. niveus Blockwitz, A. candidus

Citrinin

Cytochalasins are characterized by the phenylalanine or tryptophan moiety attached to a perhydrosoindole moiety that is connected to a polyketide ring system comprising a lactone (cytochalasin A), a carbocyclic (cytochalasin C), and a cyclic carbonate (cytochalasin E) moiety. This group can be divided into several subgroups based on their chemical structures. Cytochalasins inhibit cytoplasmic cleavage that leads to massive polynucleate cells Citrinin is a quinone methide with two intramolecular hydrogen bonds. Citrinin can be broken down in acidic or alkaline solution and by heating. The degradations of citrinin in wet and dry conditions occur at >100 and >175°C, respectively. The concentration of citrinin in Monascus is reduced by half after 20 min of boiling, which indicates that citrinin is heat sensitive and unstable in an aqueous solution. This might be correlated with the low level of citrinin in processed foods

Cole and Cox (1981), Ferna´ndez-Cruz et al. (2010), Lee et al. (2015), Logrieco et al. (2009), Ostry (2008), and Siegel et al. (2010)

Ali et al. (2015b), Berde and €rmer (1978), Cole and Stu Cox (1981), Fajardo et al. (1995), Hamuel (2015), Krska et al. (2008), Merkel et al. (2012), Pierri et al. (1982), Silva et al. (2021), Wang et al. (2017), and Xu et al. (2006)

Continued

Table 3

Type, producing fungi, and stability of different mycotoxins—cont’d

Mycotoxin

Chemical structure

Ergot alkaloids (Ergocornine, Ergocristine, α-Ergokryptine, Ergometrine, Ergosine, Ergotamine)

Ergotamine

Producing fungi

Chemistry and processing stability References

Acremonium sp., Claviceps This group of mycotoxins Hussein and Brasel (2001) purpurea has a comparable structure to lysergic acid diethylamide, a hallucinogenic medicine. There are three types of ergot alkaloids (EA), including clavine, watersoluble, and water-insoluble lysergic acid. EAs contain a C9]C10 double bond readily exhibits epimerization. The left-hand rotation is called ergopeptines (e.g., ergotamine), whereas the right-hand rotation is called ergopeptinine (e.g., ergotaminine). Epimerization of EA could occur at cold storage for 14 days in barley and rye extracts. EA could be decomposed by 2%–30%, and the epimeric ratio change during the baking of cookies. In general, EAs are quite stable as it still presents after cooking. For instance, processing flour into pan bread only gives a slight effect on EA. However, cooking in an alkali solution could enhance the removal of EA

Fumonisins (fumonisin B1 (FB1), hydrolyzed (HBF1), fumonisin B2, fumonisin B3, 3-epi-fumonisin B3)

F. verticillioides, F. proliferatum

Fumonisin B1

Fumonisin B2

Fumonisin B3

Fumonisin possesses a longchain hydrocarbon comparable to that of sphingosine and sphinganine, thus determines their toxicity mode of action. The most toxic of the group is fumonisin B1 (FB1). Fumonisin removal depends on the time and temperature of processing. Though appearing to have heatstable properties, and even its bioavailability might increase during heat treatment, the fumonisin level seems to decline as the processing temperatures raised. In the cooking processes at 125°C or lower (i.e., baking and canning), the decrease of fumonisin is low (25%–30%), while the processes at 175°C and higher (i.e., frying and hot extrusion), losses are greater (90% or more). Besides heating, fumonisin levels could be reduced by baking, frying, roasting, nixtamalization, and extrusion cooking of foods

Castells et al. (2005), Cole and Cox (1981), De Girolamo et al. (2016), Hussein and Brasel (2001), and Reddy et al. (2010)

Continued

Table 3

Type, producing fungi, and stability of different mycotoxins—cont’d

Mycotoxin

Chemical structure

Producing fungi F. acuminatum, F. concentricum, F. proliferatum, F. verticillioides, F. oxysporum, F. tricinctum

Fusarium cyclodepsipeptide beauvericins (BEAs), enniatins (ENNs) consist of enniatin A1 and enniatin B1, beauvenniatins (BEAs), and allobeauvericins (ALLOBEAs)

Beauvericins (BEA)

Enniatin A1 (ENN A1)

Fusaproliferin (FUSA)

Fusaproliferin (FUSA)

Chemistry and processing stability References

BEAs, ENNs, BEAEs, and allobeauvericins (ALLOBEAs) consist of three N-methyl amino acids and three hydroxy acid groups. The biosynthesis of cyclodepsipeptides involves a multidomain nonribosomal peptide synthase (NRPS) which is consisted of enzymatic modules used to prolong the proteinogenic and nonproteinogenic amino acids, as well as carboxyl and hydroxy acids. ENNs could be reduced by thermal treatment and common industrial processes, including bread-making, beer-making, brewing or malting processes, and cooking. However, this mycotoxin cannot be completely removed during processing Fusarium proliferatum, FUSA is a bicyclic F. subglutinans, sesterterpene. It is F. antophilum, F. begoniae, synthesized from acetyl-CoA F. bulbicola, F. circinatum, subunits through the F. concentricum, isoprenoid pathway via F. succisae, F. udum common terpene intermediates. It can be degraded at 80, 120, and 180°C under wet conditions. However, the complete degradation occurred at 240°C only under dry conditions. Besides heating, FUSA can

Bushley and Turgeon (2010), Gallo et al. (2013), Herrmann et al. (1996), Huang et al. (2020), Meca et al. (2012), Schoevers et al. (2016), Tolosa et al. (2017), Urbaniak et al. (2020), and Zˇuzˇek et al. (2016)

Logrieco et al. (1996), Manetti et al. (1995), Moretti et al. (2007), Ritieni et al. (1997, 1999), and Santini et al. (1996)

Fusarin C

Fusarin C

Moniliformin (MON)

Moniliformin

Ochratoxins (ochratoxin A, ochratoxin B, mellein, 4-hydroxymellein, 4-hydroxyochratoxin A, ochratoxin C)

Ochratoxin A (OTA)

Mellein

be reduced by treating the samples with a saturated solution of dichloroisocyanuric acid F. verticillioides, Fusarins possess a polyketide F. oxysporum backbone and are distinguished by their different substitution at the 2-pyrrolidone part. Fusarin C was observed to be acutely toxic. The degradation of Fusarin C occurs rapidly as the pH increased and losses stability on light exposure Fusarium moniliforme Moniliformin consists of a Sheldon, F. moniliforme sodium or potassium salt of var. subglutimans, 1-hydroxycyclobut-1-ene-3, F. graminearum, 4-dione. This toxin can F. fusarioides, contaminate the next F. proliferatum, Gibberella batches of the plants and fujikuroi could remain in the soil for years A 27% reduction of MON in the extrusion process of corn grits was observed. Heat treatment for 60 min at 175° C combined with pH 10 also showed to reduce MON Aspergillus ochraceus Wilh. This group is characterized (NRRL 3174) by the presence of 3,4A. carbonarius, dihydro-3-methyl A. sulphureus (NRRL 4077), isocoumarin moiety A. melleus (NRRL 3519; attached to L-β3520), A. oniki, Penicillium phenylalanine by an amide verrucosum, P. viridicatum bond. Ochratoxin A (OTA) (ATCC 18411) and its methyl and ethyl esters are the major toxic compounds from this group, while the rest of the members showed little or no toxicity

Bryden et al. (2001), Desjardins (2006), Han et al. (2014), Leslie and Summerell (2006), and Zhu and Jeffrey (1992)

Castells et al. (2005), Cole and Cox (1981), and Pineda-Valdes and Bullerman (2000)

Castells et al. (2005), Cole and Cox (1981), and Skudamore and Banks (2004)

Continued

Table 3 Mycotoxin

Type, producing fungi, and stability of different mycotoxins—cont’d Chemical structure

Producing fungi

Ochratoxin C

Patulin

Patulin

Penicillium expansum (P. leucopus), P. patulum Bainier (P. urticae; P. griseofulvum), P. claviforme P. equinum (P. terrestre) P. novae-zeelandiae, P. lapidosum, P. granulatum, (P. divergens), P. lanosum, P. melinii, P. cyclopium, P. cyaneo-fulvum, P. roqueforti, Aspergillus clavatus, A. giganteus, A. terreus, Byssochlamys nivea (Gymnoascus spp.)

Chemistry and processing stability References OTA seems to be heat stable up to 180°C, thus reduction of OTA in baked wheat products found to be 66%. While soaking and boiling beans reduced the amount of OTA up to 64% and 45%, respectively. The extrusion process on the wheat whole meal decreased 8%–39% of OTA. The removal of bran and offal part of the contaminated wheat could also reduce OTA in bread making, while the heat treatment during baking showed less effect on the toxin reduction Patulin is dissolved in water, alcohols, acetone, ethyl acetate, chloroform; while showing little solubility in ethyl ether, benzene; and hardly dissolved in petroleum ether. Though it is less stable in polar solvents, its biological potency is lost at alkaline pH. Yeast fermentation showed successful degradation of patulin. Physical selection by excluding rotten and lower quality apples can lessen the concentration of patulin. The presence of vitamin C can also gradually reduce patulin in apple juice

Cole and Cox (1981), Peraica et al. (2002), Reddy et al. (2010), Scott (1998), and Skudamore and Banks (2004)

Penicillic acid (PA)

Penicillic acid

PR-Imine

PR-Imine

Penicillium lividum, P. puberulum, P. griseum, P. simplicissimum, P. cyclopium, P. thomii P. roqueforti (P. suavolens), P. martensii, P. fenelliae, P. aurantio-virens, P. janthinellum, P. viridicatum, P. palitans, P. baarnense, P. madriti, P. lilacinum, P. canescens, P. chrysogenum, P. olivinoviride, Aspergillus ochraceus, A. sulphureus, A. melleus, A. scelrotiorum, A. alliaceus, A. ostianus, Paecilomyces ehrlichii Penicillium roqueforti

Penicillic acid (PA) present in corns with high moisture preserved at cold temperatures. PA showed low oral toxicity and easily decomposed at 100°C

Bianchini and Bullerman (2014), Cole and Cox (1981), Ismaiel and Papenbrock (2015), and Li et al. (2015)

PR toxin consists of a bicyclic sesquiterpene with functional groups attached, namely, (CH3COO
), aldehyde (–CHO), and ketone complemented with two epoxide rings. Though having a toxic effect, PR toxin is unstable and could be transformed into less toxic derivatives like PR imine, PR amide, and/or PR acid, depending on the circumstances in the blue cheese making at the low O2 level

Chang et al. (1993), Hymery et al. (2014), Siemens and Zawistowski (1993), and Wei et al. (1975)

Continued

Table 3 Mycotoxin

Type, producing fungi, and stability of different mycotoxins—cont’d Chemical structure

Roquefortines (chlororugulovasine A, chlororugulovasine Β, rugulovasine A, rugulovasine Β, fumigaclavine A (SM-2), roquefortine A (isofumigaclavine A), fumigaclavine Β, roquefortine Β (isofumigaclavine B), fumigaclavine C (SM-1), Roquefortine A roquefortine C) Rubratoxin (rubratoxin A, rubratoxin B)

Rubratoxin A

Sterigmatocystins (Sterigmatocystin, dihydrosterigmatocystin, O-methylsterigmatocystin, dihydro-Omethylsterigmatocystin, aspertoxin, 5-methoxysterigmatocystin, Sterimagtocystin dihydrodemethylsterigmatocystin)

Producing fungi

Chemistry and processing stability References

Aspergillus fumigatus, Penicillium islandicum, P. concavorugulosum, P. roquefortii, Rhizopus arrhizus

Roquefortines are alkaloids Cole and Cox (1981) usually found in the production of Roquefort cheese (or another variant of blue cheese)

Penicillium rubrum

Rubratoxins consist of complex nonadrides with lactone rings and anhydrides. Rubratoxin A is relatively stable for 2 years. Treatment with low pH at 60°C for 30 min showed no substantial degradation. However, degradation of rubratoxin B through yeast fermentation has been found to be effective Aspergillus versicolor (Vuill.) Sterigmatocystins (STs) are Tiraboschi, A. nidulans distinguished by a xanthone (Eidam) Wint., Bipolaris moiety attached to a sorokiniana, A. aurantiodihydrofurano or hrunneus, tetrahydrodurano moiety. A. quadrilineatus, A. ustus The variations in Bainier, A. variecolor, Also unsaturation of positions 2 an intermediate in the and 3 of the difurano ring biosynthesis of aflatoxins by system and substitution A. parasiticus and A. flavus group on positions 6, 7, and

Bokhari and Aly (2009), Cole and Cox (1981), Septien et al. (1993), Takahashi et al. (1984), and Versˇilovskis and Bartkevics (2012)

Bokhari and Aly (2009), Cole and Cox (1981), Septien et al. (1993), Takahashi et al. (1984), and Versˇilovskis and Bartkevics (2012)

Dihydrosterimagtocystin

Tremorgen (fumitremorgins consist of fumitremorgin A, fumitremorgin Β, fumitremorgin C (SM-Q), verruculogen, 15-acetoxy verruculogen, TR-2; Penitrems consist of penitrem A, and penitrem Β, lolitrem B, paspalitrems consist of paxilline, paspaline, paspalicine, paspalinine, paspalitrem A, paspalitrem Β and aflatrem; tryptoquivalines (tryptoquivaline, nortryptoquivalone (tryptoquivalone), nortryptoquivaline deoxytryptoquivaline deoxynortryptoquivalone and deoxynortryptoquivaline; tryptoquivaline E, tryptoquivaline F, tryptoquivaline G, tryptoquivaline H, tryptoquivaline I, tryptoquivaline J, tryptoquivaline

Fumitremorgins A

Penitrem A

10 of the xanthone system and/or a substitution on position 3 of the difurano system define the differences among STs. ST is the most acutely toxic and carcinogenic among the member. This toxin dissolves in chloroform and pyridine. Some processing steps like milling, baking, and roasting might lower the toxin concentration. However, in bread manufacturing ST was found to be stable Penicillium spp., Tremorgens with indole P. verruculosum, moiety from tryptophan can P. crustosum, P. palitans, be divided into four P. puberulum, subgroups according to their P. spinolosum, Claviceps chemical structures, i.e., spp., C. paspali, Aspergillus penitrems, fumitremorgins, spp., A. fumigatus, paspalitrems, and A. caespitosus, A. tenuis, tryptoquivalines group. A. lolii Some metabolites that are chemically correlated but do not exhibit tremorgenicity also comprised tremorgens, namely tetramic acid groups and other related nontremorgenic metabolites

Cole and Cox (1981), ElBanna et al. (1983), Hussein and Brasel (2001), Reddy et al. (2010), Scott et al. (1984), and Visconti et al. (2004)

Paspalitrem A Continued

Table 3 Mycotoxin

Type, producing fungi, and stability of different mycotoxins—cont’d Chemical structure

L, tryptoquivaline M, and tryptoquivaline N; related nontremorgenic metabolites (deoxybrevianamide Ε, preechinulin, neoechinulin, neoechinulin Ε, neoechinulin D, cryptoechinulin G, neoechinulin Tryptoquivaline A, neoechinulin Β, neoechinulin C, isoechinulin A, isoechinulin Β, isoechinulin C, cryptoechinulin A, echinulin, and austamide; Tetramic acid group Tenuazonic acid Cyclopiazonic acid Cyclopiazonic acid Cyclopiazonic acid imine Bissecodehydrocyclopiazonic acid Trichothecenes (12,13epoxytrichothec-9-enes (trichodermol or roridin C, verrucarol, scirpentriol, T-2 tetraol, trichodermin, T2-toxin monoacetoxyscirpenol, diacetoxyscirpenol (DAS), neosolaniol, neosolaniol monoacetate, HT-2 toxin, diacetyl HT-2 toxin or T-2 triol, T-2 toxin, 4,15-diacetylverrucarol, 7αT-2 triol hydroxydiacetoxyscirpenol, 7α,8αdihydroxydiacetoxyscirpenol,

Producing fungi

Chemistry and processing stability References

Myrothecium roridum, M. verrucaria, Fusarium roseum, F. equiseti, F. poae, F. sporotrichioides, F. sulphureum, F. tricinctum, F. sambucinum, F. lateritium, F. graminearum, F. semitectum, F. diversisporum, F. scirpi, F. solani, F. avenaceum, F. culmorum, F. langsethiae, Giberella

This group is distinguished by sesquiterpenes with the presence of a 12,13epoxytrichothec-9-ene ring system with distinctive constituents on positions 3, 4, 7, 8, and 15. The members of this group are divided into four subgroups based on their chemical structure depend on the presence of carbonyl function at C-8 and macrocyclic ester bridge

Bretz et al. (2005), Castells et al. (2005), Cole and Cox (1981), Krska et al. (2014), Kuchenbuch et al. (2018), and Ueno et al. (1983)

calonectrin, 15-deacetylcalonectrin, acetyl T-2 toxin, crotocin, crotocol, trichothecene, 4β,8α-15triacetoxy-12,13epoxytrichothec-9-ene-3α-72diol, and triacetoxyscirpenol), T-2 tetraol 8-ketotrichothecenes (deoxynivalenol (DON), nivalenol (NIV), deoxynivalenol monoacetate, fusarenon-X, trichotecin, nivalenol diacetate, trichothecolone, and trichodermone), macrocyclic diester of verrucarol (satratoxin G, Deoxynivalenol (DON) satratoxin H, roridin A, roridin D, roridin E, roridin H, vertisporin, isororidin, 7β,8β-epoxyisororidin E, 7β,8β-epoxyroridin H, 7β,8β,20 ,30 -diepoxyroridin H, and baccharin) and macrocyclic triesters of verrucarol (verrucarin Nivalenol (NIV) A, verrucarin B, 20 dehydroverrucarin A, verrucarin J, and verrucarin K)

Satratoxin H

intricans, Trichoderma lignorum, T. viride, Calonectria nivalis, Trichothecium roseum, Cephalosporium crotocinigenum, Verticimonosporium diffractum, Cylindrocarpon spp., Phomopsis spp.

T-2 toxin and DAS were considered the most toxic of the group. In contrast to DON and nivalenol that soluble in polar solvents, T-2 and DAS are soluble in nonpolar ones Trichothecene group also exhibits biological activities, namely antibacterial, antiviral, antifungal, cytostatic, insecticidal, phytotoxic, and animal and human toxicity to some extent. This group also shows cytotoxicity to mammalian cell culture Trichothecenes display inhibitory activity to protein and DNA synthesis. DON is observed to be highly stable during baking. DON degradation in pasta increases with an increasing percentage of water used. The extrusion process reported reducing 42%– 99.5% DON. Nivalenol (NIV) could be degraded with long time heating at high temperatures Curtobacterium sp. strain 114-2 could transform T-2 toxin and HT-2 toxin into their less toxic derivative, T-2 triol. T-2 Degradation up to 45% in T-2 toxin and 20% in HT-2 toxin were observed in the thermal process of biscuit manufacturing Continued

Table 3

Type, producing fungi, and stability of different mycotoxins—cont’d

Mycotoxin Versicolorins (versicolorin A, versicolorin B, versicolorin C, averufin, norsolorinic acid, versiconal hemiacetal acetate, versiconol acetate, versiconol, nidurufin, dimethylnidurufin, aversin, O-methylaversin)

Chemical structure

Producing fungi Aspergillus versicolor, A. parasiticus, A. ustus, A. nidulans

Versicolorin A

Versicolorin C

Versiconol acetate

Aspergillus sulphureus, A. melleus, A. ochraceus, Penicillium viridicatum, P. cyclopium

Viomellein

Chemistry and processing stability References Versicolorin exhibits little or Cole and Cox (1981) no acute toxicity to vertebrae. The presence of dhydrofurano and tetrahydrofuran moieties is similar to that of aflatoxins and sterigmatocystins. The number and position of substituents on the anthraquinone ring distinguished the members in this group. Some members of versicolorins are also mentioned as precursors of aflatoxins (e.g., versicolorin C, norsolorinic acid, averufin, versiconal hemiacetal acetate, versiconol acetate, versiconol, nidurufin, dimethylnidurufin, aversin, O-methylaversin) Cole and Cox (1981)

Viomellein Xanthomegnin

Xanthomegnin

Aspergillus ochraceus, A. melleus, A. sulphureus, Penicillium viridicatum, P. cyclopium, Trichophyton rubrum, T. megnini, T. violaceum, Microsporum cookei

Xanthomegnin could cause Cole and Cox (1981) and nephropathy and mortality Gupta et al. (2000) in animals. This toxin gives of red color underneath T. rubrum culture. The presence of this toxin can be found in infected skin and nails

Zearalenone (ZEA)

Zearalenone (ZEA)

Fusarium roseum (F. graminearum, Gibberella zeae) F. tricinctum F. lateritium F. oxysporum F. culmorum F. moniliforme F. equiseti F. gibbosum F. avenaceum F. nivale F. sambucinum var. Coeruleum

Zearalenone (ZEA) could affect the female reproduction system, namely hyperestrogenism, as well as males. ZEA is thermally stable, but extrusion cooking of cereals found to partially degrade ZEA. Moreover, the extrusion process of corn grits could decrease 66%– 83% of ZEA

Castells et al. (2005), Cole and Cox (1981), Gupta et al. (2018), and Numanoglu et al. (2012)

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Penicillium, Fusarium, and some Alternaria (Reddy et al., 2010). The major mycotoxins in foods were AFs, fumonisins (FMNs), zearalenone (ZEA), ochratoxin A (OTA), citrinin (CIT), and trichothecenes (TCT). Some members of TCTs are deoxynivalenol (DON) and nivalenol (NIV) (Shepard, 2006; Pickova et al., 2020). Mycotoxins can also become airborne spread, namely AFs (A. flavus, A. parasiticus), DON, and other TCTs (Fusarium spp.), ochratoxins (A. ochraceus), sterigmatocystin (A. versicolor), and satratoxins (S. chartarum) (Hintikka et al., 2006). Many mycotoxins tend to accumulate in the lipid fraction of animals or plants due to their lipophilic nature (Hussein and Brasel, 2001). AF is the most extensively studied mycotoxins, which could be found in many commodities. This toxin poses a threat as carcinogenic, teratogenic, genotoxic, immunosuppressive, acute diseases, and even mortality at certain doses and conditions; therefore, a strict rule was applied regarding AFs in international trade. The four major occurring AFs are AF B1, B2, G1, and G2. AFB1, known as the major AF, synthesized by the toxigenic strains and also the most potent carcinogenic. Some other AFs like AFB2a, AFG2a, AFQ1, and AFP1 are biotransformation derivatives from the major AFs (Table 3). A. flavus group, which potentials in producing AF, carries nor-1, aflR, and omtB genes, is responsible for AF metabolism (Rahayu et al., 2016).

3. Occurrence of mycotoxins in food Since decades ago, surveys related to mycotoxins contamination in some commodities have been conducted. Table 4 presents the occurrence of mycotoxin in various commodities, including cereals, legumes, fruits, spices, etc. As presented in Table 4, various commodities are infected by various toxins such as AF, ochratoxin, FMN, ZEA, DON, patulin, TCTs, and sterigmatocystin. AF, ochratoxin, and FMN are the most commonly found mycotoxins in those commodities. AF contaminations are found in the range of 0.26–1632 μg/kg. Meanwhile, the OTA and FMN are in the range of 0.03–907.5 μg/kg and 0.374–4537 μg/kg, respectively. According to RASSF, mycotoxin became the most reported hazard, with 534 notifications in 2019. Cereals are important carbohydrate and protein sources. Because they are highly nutritious, they are susceptible to mold growth and mycotoxin contamination. The mycotoxins in the cereals are dominated by DON, ZEA, and fumonisin, AF, and ochratoxin. These toxins are produced by Fusarium spp, Aspergillus spp, and Penicillium spp, which are commonly found in a warm-climate region. The mycotoxin could be produced at different stages, including vegetation of the plant by field fungi, harvesting, and storage of the plant by storage fungi. The mycotoxin contamination in the raw material can be transferred to the final product. The incidences global occurrence of DON, ZEA, and FMN in cereals ranging from 50% to 76%, 15% to 50%, 39% to 95%, respectively, were reported (Lee and Ryu, 2017). In addition, van der Fels-Klerx reported that the occurrence of DON in North West European cereal grains commodities in 11% samples were over the legal limit set by European Commission (van der Fels-Klerx et al., 2012). The co-occurrence of mycotoxin, in which one sample contains more than one type of toxin, is found in several

Chapter 4 • Mycotoxins 125

Table 4

Occurrence of mycotoxin in various commodities.

Commodities

Type of mycotoxin Level (μg/kg) References

Cereals Maize Rice grain Corn Cereals (raw materials and derived products) Wheat-based products Half maize, half rye bread Maize bread Wheat bread Maize flour Rye flour Wheat flour Corn Corn Maize grain Maize grits Maize flour Cornflakes Sweet maize Wheat grain Wheat flour Wheat Maize milling products Grains for human consumption Wheat milling products Bread and rolls Pasta Breakfast cereals Fine bakery wares Sweet corn Brewing barley Wheat Wheat and wheat flour Barley Oat Rye and rye flour Maize Biscuits Bread Pasta Breakfast cereals Brewing barley

Aflatoxin B1 Aflatoxin B1 Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Fumonisins Fumonisin B1 Fumonisin B1 Fumonisin B1 Fumonisin B1 Fumonisin B1 Fumonisin B1 Fumonisin B1 Fumonisin B1 Zearalenone Zearalenone Zearalenone Zearalenone Zearalenone Zearalenone Zearalenone Zearalenone Zearalenone Zearalenone Deoxynivalenol Deoxynivalenol Deoxynivalenol Deoxynivalenol Deoxynivalenol Deoxynivalenol Deoxynivalenol Deoxynivalenol Deoxynivalenol Deoxynivalenol Deoxynivalenol

0.26 26–33 0.093 0.29 1.36–21.17 0.89 0.42 0.12 0.67–2.75 0.77 0.26–0.85 71,121 0.374 346.4 347.6 408.5 31.5 12.4 71.2 64.4 3049 14 5.7 13 5.2 5.8 5.7 7.7 4.8 100–2300 41,157 205 37 95 42 594 50.6 88.9 141.2 198.8 310–15,500

EFSA (2007) Serrano et al. (2012) Simatupang et al. (2014) SCOOP (2002a) Kumar et al. (2012) Paı´ga et al. (2012) Paı´ga et al. (2012) Paı´ga et al. (2012) Spahiu et al. (2018) Spahiu et al. (2018) Spahiu et al. (2018) Lee and Ryu (2017) Rahayu et al. (2015) SCOOP (2003) SCOOP (2003) SCOOP (2003) SCOOP (2003) SCOOP (2003) SCOOP (2003) SCOOP (2003) Lee and Ryu (2017) EFSA (2011) EFSA (2011) EFSA (2011) EFSA (2011) EFSA (2011) EFSA (2011) EFSA (2011) EFSA (2011) Piacentini et al. (2018) Ji et al. (2014) SCOOP (2003) SCOOP (2003) SCOOP (2003) SCOOP (2003) SCOOP (2003) SCOOP (2003) SCOOP (2003) SCOOP (2003) SCOOP (2003) Piacentini et al. (2018)

Aflatoxin B1 Aflatoxin B1 Aflatoxin B1

1.46 22.2 0.95

EFSA (2007) EFSA (2007) EFSA (2007)

Legumes Almonds Brazil nuts Hazelnuts

Continued

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Table 4

Occurrence of mycotoxin in various commodities—cont’d

Commodities

Type of mycotoxin Level (μg/kg) References

Cashews Peanuts Pistachios Soybean Soybean

Aflatoxin B1 Aflatoxin B1 Aflatoxin B1 Ochratoxin A Fumonisin B1

0.42 1.93 16.8 0.045 0.067

EFSA (2007) EFSA (2007) EFSA (2007) Simatupang et al. (2014) Rahayu et al. (2015)

Ochratoxin A Patulin Patulin Zearalenone

2.30 15.6 4.9 72

SCOOP (2002a) SCOOP (2002b) SCOOP (2002b) EFSA (2011)

Aflatoxin B1 Aflatoxin B1 Aflatoxin B1 Aflatoxin B1 Aflatoxin B1 Aflatoxin B1 Aflatoxin B1 Aflatoxin B1 Aflatoxin B1 Aflatoxin B1 Aflatoxin B1 Aflatoxin B1 Aflatoxin B1 Aflatoxin B1 Aflatoxin B2 Aflatoxin B2 Aflatoxin B2 Aflatoxin B2 Aflatoxin B2 Aflatoxin B2 Aflatoxin G1 Aflatoxin G1 Aflatoxin G1 Aflatoxin G1 Aflatoxin G1 Aflatoxin G1 Aflatoxin G1 Aflatoxin G1 Aflatoxin G2 Aflatoxin G2 Aflatoxin G2 Aflatoxin G2 Aflatoxin G2 Ochratoxin A Ochratoxin A Ochratoxin A

1.46 1632.2 39.3–139.5 155.7 75.8 57.0 56.8 39.8 27.4 26.5 21.7 18.2 16.8 11.0 2.6–33.3 μ 9.9 2.5 2.3 1.7 1.6 318.1 157.5 41.2 31.5 12.9 10.5 8.1 7.0 45.4 16.0 7.6 1.5 0.4 1.15 907.5 177.4

EFSA (2007) Dharmaputra et al. (2015) Wikandari et al. (2020) Gambacorta et al. (2018) Zahra et al. (2018) Migahed et al. (2017) Migahed et al. (2017) Khazaeli et al. (2017) Migahed et al. (2017) Azzoune et al. (2015) Ali et al. (2015a) Migahed et al. (2017) Migahed et al. (2017) Ali et al. (2015a) Wikandari et al. (2020) Gambacorta et al. (2018) Migahed et al. (2017) Ali et al. (2015a) Ali et al. (2015a) Ali et al. (2015a) Gambacorta et al. (2018) Migahed et al. (2017) Migahed et al. (2017) Migahed et al. (2017) Migahed et al. (2017) Migahed et al. (2017) Migahed et al. (2017) Alsharif et al. (2019) Gambacorta et al. (2018) Migahed et al. (2017) Migahed et al. (2017) ray (2015) Karaaslan and Arslang ray (2015) Karaaslan and Arslang SCOOP (2002a) Manda et al. (2016) Gambacorta et al. (2018)

Fruits Dried fruits Apple juice Apple puree Vegetable oils Spices Spices Nutmeg Chili Paprika Black pepper Licorice Black cumin Ginger Parsley Saffron Fennel Mustard Thyme Coriander Chili Paprika Parsley Fennel Turmeric Coriander Paprika Anise Thyme Black pepper Rosemary Mustard Parsley Chili Paprika Black pepper Mustard Chili Cinnamon Spices Chili Paprika

Chapter 4 • Mycotoxins 127

Table 4

Occurrence of mycotoxin in various commodities—cont’d

Commodities

Type of mycotoxin Level (μg/kg) References

Black pepper Cardamom Nutmeg Licorice Cumin Cinnamon Ginger Curry Turmeric Garlic white pepper Onion Garlic Mint Paprika Dawadawa Black pepper Thyme Licorice Nutmeg Onion Chili Paprika Dawadawa Paprika Licorice Paprika Dawadawa Paprika Paprika Dawadawa Thyme Licorice Oregano Paprika Thyme Black pepper Chili

Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Fumonisin B1 Fumonisin B1 Fumonisin B1 Fumonisin B1 Fumonisin B1 Fumonisin B1 Fumonisin B1 Fumonisin B1 Fumonisin B1 Fumonisin B2 Fumonisin B2 Fumonisin B2 Fumonisin B2 Trichothecenes Trichothecenes Trichothecenes Trichothecenes Trichothecenes Zearalenone Zearalenone Zearalenone Zearalenone Sterigmatocystin Sterigmatocystin Sterigmatocystin Sterigmatocystin Sterigmatocystin

79.0 78.0 60.7 36.7 20.4 16.1 12.7 9.6 8.5 5.1 4.9 591.0 540.0 256.0 243.9 165.0 135.0 125.0 39.3 25.0 4537.0 425.0 176.9 170.0 59.8 11.0 243.9 32.0 27.1 53.6 86.0 209.0 8.8 28.0 18.0 14 49.0 32

Jacxsens and De Meulenaer (2016) Gherbawy and Shebany (2018) Ostry et al. (2015) Ostry et al. (2015) Ali et al. (2015a) Jalili (2016) Ostry et al. (2015) Ali et al. (2015a) Jalili (2016) El Darra et al. (2019) Nguegwouo et al. (2018) Motloung et al. (2018) Tonti et al. (2017) €rer Soyogul et al. (2016) Gu Gambacorta et al. (2018) Chilaka et al. (2018) Jacxsens and De Meulenaer (2016) €rer Soyogul et al. (2016) Gu Huang et al. (2018) Reinholds et al. (2017) Motloung et al. (2018) Motloung et al. (2018) Gambacorta et al. (2018) Chilaka et al. (2018) Gambacorta et al. (2018) Huang et al. (2018) Gambacorta et al. (2018) Chilaka et al. (2018) Gambacorta et al. (2018) Gambacorta et al. (2018) Chilaka et al. (2018) Reinholds et al. (2017) Huang et al. (2018) Reinholds et al. (2017) Motloung et al. (2018) Reinholds et al. (2017) Jacxsens and De Meulenaer (2016) Jacxsens and De Meulenaer (2016)

Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Ochratoxin A Zearalenone Zearalenone

0.20 1.62 0.72 0.03 0.36 0.24 9.0 1.0

SCOOP (2002a) SCOOP (2002a) SCOOP (2002a) SCOOP (2002a) SCOOP (2002a) SCOOP (2002a) EFSA (2011) EFSA (2011)

Others Meat products Green coffee Roasted coffee Beer Wine Cocoa and derived products Biscuits Beer

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FIG. 1 Mycotoxigenic fungi and their mycotoxin in different samples.

samples. The mixture of toxins is reported to have additive or synergetic effects. Thus, they have a more adverse effect on human health (Alborch et al., 2012). Spices are important agricultural commodities, particularly in developing countries. Asia is the top spices producer, which contributes up to 95.1% of global spices (Thanushree et al., 2019). As presented in Table 4, spices contain a diverse type of mycotoxin at contamination levels ranging from 1.46 to 4537 μg/kg. The dominant mycotoxins in spices are AFs and ochratoxins. The incidence of mycotoxins in spices ranging from 47% to 100% (Zinedine et al., 2006). According to RASFF, from 2015 to 2019, mycotoxin notification of spices was in the third rank with 219 notifications. Among the notification, approximately 80.2% and 19.8% belong to AF and ochratoxin, respectively. The mycotoxin-contaminated spices were dominated by chili (51.3%) and nutmeg (20.5%). Table 4 indicates that the occurrence of mycotoxin contamination is relatively high in many types of spices as the maximum limits of total AF and ochratoxin A in spices are 10 and 15–80 μg/kg, respectively, according to EU legislation. The occurrence of mycotoxin is related to the presence of mycotoxigenic mold. Several fungi have been isolated and identified based on morphological and molecular characteristics. Key genes responsible for mycotoxin metabolisms are usually used in this study to confirm the potency of strains in mycotoxin metabolisms. Fig. 1 shows a picture of mold growth in media using the direct plating method, identified mold species, and mycotoxins.

3.1 International regulation Due to the harmful effect of mycotoxin both on human and animal health, many countries have established regulations related to mycotoxin in food and feed. In 1995, CODEX set a

Chapter 4 • Mycotoxins 129

standard related to mycotoxin, including regulation of AFs, DON, ochratoxins, FMN, and patulin. The number of countries with known specific regulations on mycotoxin has significantly increased from 33 countries in 1981 to 100 countries (corresponding to 85% of world inhabitants) in 2003 (Van Egmond et al., 2007). In addition, the percentage of the inhabitants of each region with known regulation varies from 59% in Africa (15 countries), 88% in Asia (26 countries), 99% in Europe (39 countries), 91% in Latin America (19 countries) to 100% in North America (2 countries) (Food and Agriculture Organization, 2004). The regulation of mycotoxin varies between countries, commodities, and types of mycotoxin. The type of mycotoxins which are regulated includes AFs (B1, B2, G1, and G2), AF M1, TCTs (DON, diacetoxyscirpenol, T-2 toxin, and HT-2 toxin), FMNs (B1, B2, and B3), agaric acid, ergot alkaloids, OTA, patulin, phomopsins, sterigmatocystin, and ZEA (Van Egmond et al., 2007). The maximum limit of each type of mycotoxin is summarized in Table 5. Several factors considered in setting limits for mycotoxins include scientific factors and socioeconomic issues. The scientific factors are the availability of toxicological data and occurrence data and detailed knowledge about possibilities for sampling and analysis. Comparing the regulation in 1995, the regulations in 2003 cover more types of mycotoxins, commodities, and products, whereas the tolerance limits generally tend to decrease. Not only the maximum limit, but the regulation also covers more detailed information regarding official procedures for sampling and analytical methodology. The mycotoxin test procedures consist of several steps, including taking a given size of the sample from the lot, comminution, removal of subsample, mycotoxin extraction, and quantification. The size of the incremental sample depending on the weight of the lot. For instance, for a lot of cereals and cereals products less than 50 kg, the number of incremental samples is 3–100 with the weight of the aggregate sample of 1–10 kg. Meanwhile, for lot weight of 50 tons and 300 tons, the number of incremental samples is 100 with the weight of the aggregate sample of 10 kg (European Comission, 2014). There are several analytical techniques to determine the mycotoxin include fluorometry, ELISAspectrophotometry, GC-MS, GC, liquid chromatography (LC), thin-layer chromatography

Table 5 Worldwide regulation limit of different types of mycotoxin (Food and Agriculture Organization, 2004). Type of mycotoxins

Worldwide regulation limit (μg/kg)

Limit by most countries (μg/kg)

Aflatoxin B1 Aflatoxin total Aflatoxin M1 in milk Patulin in fruits Ochratoxin A in cereals Deoxynivalenol in wheat and cereals Zearalenone Fumonisin

1–20 0–35 0.05–15 5–100 3–50 300–2000 50–1000 1000–3000

2 (applied by 29 out of 61 countries) 4 (applied by 29 out of 76 countries) 0.05 (applied by 34 out of 60 countries) 50 (applied by 44 out of 48 countries) 5 (applied by 29 out of 37 countries) 750 (applied by 19 out of 37 countries) 1000 (applied by 8 out of 17 countries) 1000 (applied by 4 out of 6 countries)

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(TLC), and minicolumn chromatography. Among them, LC and TLC are the most frequently used for mycotoxin regulatory analysis (Food and Agriculture Organization, 2004).

4. Toxigenic fungi and factors affecting mycotoxins production Mold contamination and toxins production in agricultural commodities occur during preharvest, postharvest, storage, and supply chain. Fungal species that produces toxins are called toxigenic fungi. The phenotypic and metabolic plasticity of toxigenic fungi enables them to grow a various important crops and to thrive on different environmental conditions (Moretti et al., 2017). Most mold contaminants are present in agricultural products, i.e., in cereals (e.g., maize and rice), legumes (e.g., peanut and soybean), coffee, cocoa, and spices (e.g., nutmeg and chili). Moreover, molds can also be found to contaminate marine products such as dried salted fish. Some molds contaminated certain agricultural commodities over others due to the differences in the substrate types. For example, peanuts were highly contaminated by AF producer Aspergillus flavus, while maize beside A. flavus was also contaminated by Fusarium. Ochratoxin producing A. niger was dominant in cocoa and coffee beans. Various classifications are used in categorizing factors that affect the incidence of mycotoxigenic mold and mycotoxins production in the food chain. These factors are divided into three main groups, i.e., intrinsic factor and extrinsic factor. However, the human factor is also very important, particularly the awareness related to mycotoxins and their hazards.

4.1 Intrinsic factors Intrinsic factors are those inherent to the type and properties of foods or the substrate for fungal growth that can be divided into three categories: chemical, biological, and physical factors. Chemical factors involve moisture content, substrate type, plant type, and nutrient composition. Biological factor comprises the structure and defense mechanism of the plant. Meanwhile, physical factors include water activity, pH, and activity of electrons (Eh). Biosynthesis of mycotoxins can be derived through polyketide route (e.g., AFs and patulin), terpene route (e.g., TCTs) or amino acids (e.g., ergot toxins and gliotoxins) among others. Mycotoxins are secondary metabolites that are by-products of secondary metabolism or biosynthesis. Generally, fungi are likely to perform secondary metabolism when they are in suboptimal conditions, because in optimal condition the fungi would perform their primary metabolism (Steyn, 1980). Casquete et al. (2017) observed that the AFs production started around 2 days after the end of lag phase. In our study, after 10 days of inoculation on soybean, A. flavus could produce AFs B1 between 12 and 381 ng/g at 20°C, 1 to 935 ng/g at 30°C, and from not detected to 60 ng/g at 40°C with humidity range of 70%–90%. At 10 day of 20, 30, and 40°C of 80%– 90%, sporulation has been occurred (observed in our research, data not reported in the journal). The 10 days growth was at the maximum growth stage before entering the lag

Chapter 4 • Mycotoxins 131

phase (Pratiwi et al., 2015). Other study also showed that the 10-day growth was at the maximum stage of the fungal growth (Ahmed et al., 2016), this condition give a fact that AF B1 production can be easily observed at the fungal maximum growth. It is important to note that the mycotoxins production depends on several factors, such as pH, temperature and water activity. For instance, at room temperature (25°C) with water activity of 0.95 and pH 5, the AFs started to be produced around 2 days after lag phase. However, under similar condition, no mycotoxins are detected at temperature of 15°C (Casquete et al., 2017). Other factors should be considered in mycotoxin production, namely microbial interaction, growth factors, growth kinetics, and toxins concentrations.

4.2 Extrinsic factors The extrinsic factors affecting mycotoxin production include duration of fungal growth, aeration, humidity, temperature, storage conditions (Ashiq, 2015) soil condition (type of soil and fungal diversity), climates (dry or rainy season), and agricultural treatment (fertilization, irrigation, plant density, and time of harvest). In addition, stress factors such as lack of water, insect infestation, and other pests’ attack could trigger the formation of toxins (Sanchis and Magan, 2004). Each fungal species requires different optimum conditions for growth and mycotoxin production (Council for Agricultural Sciences and Technology (CAST), 2003). However, in general, hot and humid are the significant factors contributing to mycotoxin production (Ashiq, 2015).

5. Prevention and reduction of mycotoxins Codex Alimentarius prepares general guidelines or standard operating procedures for good farming and livestock practices, good harvest and post-harvest practices, good storage practices, as well as good manufacturing practices (GMPs). These good practices were socialized to farmers, retailers, and food processors through training on management control of AF. This management control was based on real problems identified starting from the farm, preharvest, harvest, postharvest, storage, processing up to market or consumers (food safety from farm to table). The most effective effort to control mycotoxins contamination in the food process is the use of good raw material, as possible, free mycotoxins, which can be obtained with appropriate pre- and postharvest handling. Implementation of good practices should be done at every stage of the supply chain. Haque et al. also had proposed a control strategy for mycotoxin contamination (Haque et al., 2020). Each mycotoxin type might require different risk management strategies, particularly on preharvest and dietary levels. Hazard analysis and critical control point (HACCP) requirements must be complied with to ensure the safety of the final product. The implementation of good practices should be accompanied by monitoring and evaluation. Several performance indicators are targeted, such as increasing the productivity, quality, and safety (low AF level) of the commodities, increasing market share, increasing awareness of the AF problem, and income of farmers.

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5.1 Prevention of mycotoxins 5.1.1 Good agricultural practices Good agricultural practice (GAP) is a primary line against mycotoxin contamination in the field, followed by GMPs for handling and storage after harvesting. Codex Alimentarius has released a code of practice for the prevention and reduction of mycotoxin contamination in cereals in 2014 (Of et al., 2014). The guidance includes planting, preharvest, postharvest, storage, and transport from storage. For planting, it is recommended to rotate the crops, using fungal-resistant seeds or resistant varieties, analyzing the need to use fertilizer, removing old seeds, determining a suitable time for planting, preventing water stress in plants, and avoiding overcrowding of the plants. In addition, it is also suggested to begin with good soil preparation, application of competitive nontoxigenic fungal strains to the soil, adequate fertilizer and irrigation, and good pest and disease controls are required for healthy plants (Adeyeye, 2016; Dorner and Cole, 2002; Sarrocco et al., 2019). Insect infestation causes damage to the grain, thus accelerating mold infection and mycotoxin production. The application of insecticides and fungicides can prevent mold growth and mycotoxin production. In addition, weeds can also be vectors for mold, especially soil-borne pathogens such as F. graminearum and F. moniliforme. Weeds can be mechanically removed using herbicides or other safer ways. During preharvest, it is recommended to apply GAP to ensure that cultivars are adapted to local environments, to breed for insect resistance, to forecast mycotoxin formation, timely harvesting, to control weeds using mechanical, registered herbicides, or other safe methods, to minimize mechanical damage, to ensure the adequate supply of water, to ensure the equipment used for harvesting are functional, and to harvest at low moisture and full maturity. At this stage, irrigation and soil conditions should be controlled since drought stress and soil fertility greatly affect the intensity of mold attack and the production of mycotoxins. Managing the temperature and soil moisture plays an important role in the control of mycotoxin contamination. High water content and soil moisture are excellent for spore germination and mold proliferation. In peanut plants, drought stress in the reproductive stage is very sensitive to A. flavus and AF contamination. While in corn plants, drought stress and high humidity level are ideal for the occurrence of proliferation F. moniliforme and FMN production. Harvest is preferably conducted in the dry season and after the seed is fully matured. Young seeds or grains contain lots of water support for mold growth. Water content at harvest time should be adjusted to a certain range, for corn 23%–25%, sorghum 12%–17%, soybean 11%–15%, and groundnut 35%–50% (Maryam, 2006). Too early or too late harvest increased contamination of mold in agricultural produce. Equipment used during harvest or for transportation to the drying and storage area must be cleaned to minimize the population of insects and molds. In addition, it is suggested to implement GMP and HACCP, avoid mechanical damage, and cleaning the seed.

Chapter 4 • Mycotoxins 133

Agricultural produce should be dried as soon as possible within a period of not more than 24–28 h after harvesting until it reaches adequate moisture content for storage to prevent the growth of mold and the production of mycotoxins. Drying can be done traditionally by employing sunlight, hanging the produce in the open air or indoors with little heating/curing, especially for products that are easily infected with molds, and by using a drying machine. Sortation is done through visual observation, by separating good produce from damaged ones. Produce could be mechanically damaged or deteriorated by insects, mold infections, or rotten. Agricultural produce should be dried to certain moisture content for storage. In temperate countries, the ideal moisture content is 3.5 (4–60°C). Solutions at pH 7.0 are even stable after 30 min of boiling. Toxicological data are widely available about this red pigment. This includes patents containing information about acute oral toxicity in mice 90-day sub-chronical toxicological study, acute dermal irritation, acute eye irritation, anti-tumor activity, micronucleus test in mice, AMES test (Salmonella typhimurium reverse mutation assay), estimation of antibiotic activity, and test results of estimation of five mycotoxins [WO 9,950,434; CZ 285,721; EP 1,070,136; US 6,340,586 cited in Sardaryan et al. (2004)]. After evaluating all the documents provided by the company, the Codex Alimentarius Commission made the following statement on the occasion of its Rotterdam meeting on March 11–15, 2002: “… there will not be any objections to use the red coloring matter Arpink Red” in – – – – –

meat products and meat product analogs in the amount up to 100 mg/kg non-alcoholic drinks in the amount up to 100 mg/kg alcoholic drinks in the amount up to 200 mg/kg milk products and ice creams in the amount up to 150 mg/kg confectionery in the amount up to 300 mg/kg

Subsequently, this biotechnologically produced anthraquinone was sold and used in Czech Republic for several years. The joint FAO/WHO Expert Committee on Food Additives (JECFA) evaluation process made some progress, and the legal situation concerning Arpink Red™ was discussed during the 63rd Annual JECFA meeting in Geneva, June 8–17, 2004. Additional data were requested, however, the company Ascolor appeared to stop its activities, and a new company, named Natural Red™, was established in 2012.

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Pros and cons are quite difficult to judge in this case, as private companies using a fungal strain that is not publicly available, have conducted the whole development. No academic paper has been published, and much information, in particular, confirmation of genus/species of the fungal strain, chemical structure of the anthraquinone pigment(s), and absence of mycotoxins (e.g., secalonic acid D) is lacking.

5.2 Other fungal anthraquinones Anthraquinones are widely spread throughout the kingdom of fungi (For example, in Aspergillus sp., Eurotium sp., Fusarium sp., Dreschlera sp., Penicillium sp., Emericella purpurea, Curvularia lunata, Mycosphaerella rubella, Microsporum sp., etc.), and thus might serve as alternative sources independent of agro-climatic conditions (Caro et al., 2012; Gessler et al., 2013). This is in contrast to plant- and animal-derived sources. Anthraquinones exhibit a broad range of biological activities, including bacteriostatic, fungicidal, antiviral, herbicidal, and insecticidal effects (Gessler et al., 2013). Presumably, in fungi, these compounds are involved in interspecific interactions. For example, anthraquinones synthesized by endophytic fungi protect the host plant from insects or other microorganisms (Gessler et al., 2013). The present picture of fungal anthraquinones is quite complex, with a great variety of chemical structures (Fig. 4), a huge number of factors or parameters which may have impact on the composition of quinoidal pigments biosynthesized by a particular species. Among them, e.g., habitat, light, pH, temperature, O2 transfer, liquid/solid media, culture medium, C and N sources, C:N ratio, presence of organic acids, mineral salts, and inoculum have been considered (Caro et al., 2012). Today, research priority is focused on a small number of fungal anthraquinoneproducing species meeting the following profile of requirements established by Mapari et al. (2009a) during the identification of potentially safe fungal cell factories for the production of polyketide natural food colorants using chemotaxonomic rationale: – – –

fungus shall be non-pathogenic to humans fungus shall be non-toxigenic under a broad range of production conditions fungus shall be able to produce in liquid media

6. Fungi from marine ecological niches as novel sources of chemically diverse pigments Recent literature abundantly reports the interest for marine organisms with respect to the production of new molecules and, among them, new pigments. Indeed, many marine ecological niches are still unexplored and it seems plausible that unique features of marine environments such as high salinity, low temperature, lack of light, and high pressure can be the inducers of unique substances synthesized by marine microorganisms. The potential of marine microorganisms to produce unique and original molecules could therefore

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Altersolanol A, Alternaria sp.

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no common name, Fusarium oxysporum

NaO3 S

Cynodontin, Dreshslera avenae

3-O-Methyl alaternin sulfate, Ampelomyces sp.

FIG. 4 Some anthraquinones from fungal origin (color of the box reflects color of the main pigment produced by the fungus).

come from specific metabolic or genetic adaptation processes to meet very specific combinations of physico-chemical parameters. For now, the highest diversity of marine fungi seems to be found in tropical regions, mainly in tropical mangroves which are extensively studied because of their high richness in organic matter favorable to the development of these heterotrophic microorganisms. Anyway, it seems obvious that in extreme

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environments the fungal species with pigmented cell walls in the spores and mycelium, can tolerate dehydration-hydration cycles and high solar radiation better than the moniliaceous fungi, whose cells are devoid of pigments. For example, melanin, a black phenolic pigment which has a significant antioxidant activity and sporopollenin (brown product of oxidative polymerization of β-carotene) are very common in many fungi (dematiaceous hyphomycetes) and may protect the biological structures, giving them an excellent durability and a high potential for survival in hostile environments. Another example is the deep green pigment cycloleucomelone (terphenylquinone) from an A. niger strain isolated from the mediterranean sponge Axinella damicornis, as well as from its terrestrial counterparts (Hiort et al., 2004). Marine fungi are also able to produce bright colors, from yellow to red, mainly belonging to polyketides. Indeed, several review papers illustrate that polyketides seem to dominate marine natural products of fungal origin (Ebel, 2010). As examples, yellow pigments physcion and macrosporin, have been reported to be extracted from the endophytic Alternaria sp., isolated from the fruit of the marine mangrove tree Aegiceras corniculatum in Zhanjiang, Guangdong (South China Sea) (Huang et al., 2011). The orange questin, the yellow asperflavin, and the brown 2-O-methyleurotinone have been reported to be produced by Eurotium rubrum from the inner tissue of the stem of the marine mangrove plant Hibiscus tiliaceus near Hainan Island (China) (Li et al., 2009). Also, the yellow oils citromycetin and 2,3-dihydrocitromycetin have been isolated from a marine derived Penicillium bilaii (Capon et al., 2007). The examples of other molecules that can also color fungal structures or be excreted as secondary metabolites include tetrahydroauroglaucin (yellow) and isodihydroauroglaucin (orange) which have been extracted from Eurotium sp., an isolate from leaves of the mangrove plant Porteresia coarctata (Dnyaneshwar et al., 2002). The yellow compounds flavoglaucin including the mycotoxin citrinin have been shown to be produced by the marine-derived fungus Microsporum sp. in Korea (Li et al., 2006). A fungus of the genus Periconia isolated from hypersaline environment (solar saline in Puerto Rico) subjected to high solar radiations has been shown to produce a still unidentified, and unusual blue pigment (Cantrell et al., 2006). To date, most of the studies on the marine fungi have highlighted that these fungal genera and species are facultative and not obligate microorganisms. With regards to the industrial production of dyes, this may be considered as an advantage because strictly marine fungal species (able to grow only in the marine environment) are often difficult to culture at a large scale (Ebel, 2010). The feature to culture at a large scale is highly required for the industrial production of biochemicals including the pigments. Ubiquitous strains including the members of the genera Aspergillus and Penicillium are frequently encountered in marine habitats and usually produce enough biomass for chemical studies or industrial exploitations. These two genera have been intensively investigated for decades in the quest for interesting secondary metabolites both from the terrestrial and the marine origin. Among these secondary metabolites, some are considered as new, although in many cases, they are biogenetically closely related to natural products described previously from their terrestrial counterparts. For example, the so

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called novel yellow 2,3-dihydrocitromycetin from the marine-derived isolate of Penicillium bilaii, collected from the Australian Huon estuary (Port Huon, Tasmania) has also been identified from a soil isolate of Penicillium striatisporum (Capon et al., 2007). Up-to-now a few unique colored compounds have not yet been found their counterparts produced from the terrestrial isolates. The examples are the brown bisdihydroanthracenone derivative, eurorubrin or the new orange anthraquinone glycoside [3-O-(α-D-ribofuranosyl)-questin] from Eurotium rubrum, isolated from the inner tissue of the stem of the mangrove plant H. tiliaceus around Hainan Island (China). Seemingly, no terrestrial counterpart has been discovered yet for the new yellow compound dimethoxy-1methyl-2-(3-oxobutyl) anthrakunthone produced by the mangrove’s endophytic Fusarium sp. ZZF60 isolated from the South China Sea (Huang et al., 2010), or for the red alterporriols: K, L & M from the endophytic Alternaria sp. found in the fruit of the mangrove’s shrub Aegiceras corniculatum (Zhanjiang Guangdong, South China Sea) (Huang et al., 2011). Penicillium commune G2M isolated from the mangrove plant H. tiliaceus (Hainan Island, China) has also been reported to synthesize a pale-yellow oil characterized as 1-O-(2,4-dihydroxy-6 methylbenzoyl)-glycerol (Yan et al., 2010), and Penicillium sp. JP-1 from the inner bark of an Aegiceras corniculatum tree collected in Fujian (China) has been claimed to produce a red pigment named penicillenone (Lin et al., 2008). Finally, the yellow anthracene-glycoside asperflavin-ribofuranoside from the marine-derived fungus Microsporum sp. (Korea) (Li et al., 2006) appears only to be produced by marine fungi. Many marine fungi have been reported to be endophytes and to make associations with higher life forms (plants, algae, corals). Examples have shown that under these conditions the fungi may proceed to biochemically mimic the host organism (Strobel et al., 1996). This is not surprising since the fungi have to deal with the marine environment and the biological context of the host. Algae can then be considered as valuable sources for the isolation of pigment producing marine fungi to the extent that many algae are pigmented. Therefore, the algicolous fungi may produce unusual and novel dyeing molecules. In addition, co-cultivation of marine fungi with other microorganisms from the same ecosystem has been proved to be successful in activating silent gene clusters to produce bioactive secondary metabolites (Brakhage and Schroeckh, 2011). Even if the microorganism can be easily genetically manipulated and simply scaled-up for metabolite production, the modification of cultivation parameters such as media composition can also possibly induce and regulate secondary metabolite biosynthesis (Calvo et al., 2002). Inactivation or enhancement of selected steps of a biosynthetic pathway by a chemical approach can then be an alternative tool to metabolic engineering, using mutations or genetic transformation techniques. One of the main advantages of using inhibitor and precursor feeding is that the genetic and epigenetic background of the cell remains unchanged. However, the overexpression of a transcriptional factor controlling a metabolic pathway can affect the expression of certain genes or modify some cellular processes. The use of such techniques requires a thorough knowledge of the biosynthetic pathways and the enzymes involved.

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FIG. 5 Products from filamentous fungi and their various applications.

Thus, filamentous fungi seem very versatile and could be used for various applications (Fig. 5).

7. Conclusions and perspectives The current use and the potential of using filamentous fungi as pigment and natural colorant sources for food applications is promising considering the ever-rising demand by the consumers to replace their synthetic counterparts. Filamentous fungi are readily available raw materials that can be tailored to make microbial cell factories for the production of food grade pigments because of their chemical and color versatility in their pigment profile, easier large-scale-controlled cultivation, growth on agro-industrial residues and

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a long-term history of well-known production strains for the production of a variety of other biochemicals including colorants. Emphasis has been put on the screening for specific pigments such as natural blue, or red colorant for cochineal extract/carminic acid/ carmine partial replacement by the food colorant industries. In this regard the hydroxyanthraquinoid pigments and/or novel chemical classes from marine pigment producing fungi could be an interesting avenue to be explored further. As in the case of other food additives and/or ingredients, all sources of natural pigments and colorants (plants, minerals, insects, microalgae, microorganisms) will coexist in the market, with market shares depending on consumer’s expectations, industrial prices, and availability.

Acknowledgments  would like to thank the Conseil Re gional de La Re union, Re union island, France, and the Laurent Dufosse gional de Bretagne, Brittany, France, for financial support of research activities dedicated to Conseil Re microbial pigments.

References Arai, T., Koganei, K., Umemura, S., Kojima, R., Kato, J., Kasumi, T., Ogihara, J., 2013. Importance of the ammonia assimilation by Penicillium purpurogenum in amino derivative Monascus pigment, PP-V, production. AMB Express 3, 19. Bechtold, T., 2009. Natural colorants – quinoid, naphthoquinoid and anthraquinoid dyes. In: Bechtold, T., Mussak, R. (Eds.), Handbook of Natural Colorants. John Wiley and Sons, pp. 151–182 (Chapter 10). Brakhage, A.A., Schroeckh, V., 2011. Fungal secondary metabolites – strategies to activate silent gene clusters. Fungal Genet. Biol. 48, 15–22. Calvo, A.M., Wilson, R.A., Bok, J.W., Keller, N.P., 2002. Relationship between secondary metabolism and fungal development. Microbiol. Mol. Biol. Rev. 66, 447–459. Cantrell, S.A., Casillas-Martinez, L., Molina, M., 2006. Characterization of fungi from hypersaline environments of solar salterns using morphological and molecular techniques. Mycol. Res. 110, 962–970. Capon, R.J., Stewart, M., Ratnayake, R., Lacey, E., Gill, J.H., 2007. Citromycetins and bilains A-C: new aromatic polyketides and diketopiperazines from Australian marine-derived and terrestrial Penicillium spp. J. Nat. Prod. 70, 1746–1752. , L., 2012. Natural hydroxyanthraquinoid Caro, Y., Anamale, L., Fouillaud, M., Laurent, P., Petit, T., Dufosse pigments as potent food grade colorants: an overview. Nat. Prod. Bioprospect. 2, 174–193. Dnyaneshwar, G., Devi, P., Supriya, T., Naik, C.G., Parameswaran, P.S., 2002. Fungal metabolites: tetrahydroauroglaucin and isodihydroauroglaucin from the marine fungus, Eurotium sp. In: Sree, A., Rao, Y.R., Nanda, B., Misra, V.N. (Eds.), Proceedings of National Conference on Utilization of Bioresources NATCUB-2002 October 24–25, 2002. Regional Research Laboratory, Bhubaneswar, pp. 453–457. Ebel, R., 2010. Natural product diversity from marine fungi. In: Mander, L., Lui, H.-W. (Eds.), Comprehensive Natural Products II. Elsevier, pp. 223–262 (Chapter 2.08). Feng, Y., Shao, Y., Chen, F., 2012. Monascus pigments. Appl. Microbiol. Biotechnol. 96, 1421–1440. Frisvad, J.C., Smedsgaard, J., Larsen, T.O., Samson, R.A., 2004. Mycotoxins, drugs and other extrolites produced by species in Penicillium subgenus Penicillium. Stud. Mycol. 49, 201–241.

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Frisvad, J.C., Yilmaz, N., Thrane, U., Rasmussen, K.B., Houbraken, J., Samson, R.A., 2013. Talaromyces atroroseus, a new species efficiently producing industrially relevant red pigments. PLoS One 8 (12), e84102. Fu, G., Xu, Y., Li, Y., Tan, W., 2007. Construction of a replacement vector to disrupt pksCT gene for the mycotoxin citrinin biosynthesis in Monascus aurantiacus and maintain food red pigment production. Asia Pac. J. Clin. Nutr. 16 (Suppl. 1), 137–142. Gao, J.M., Yang, S.X., Qin, J.C., 2013. Azaphilones: chemistry and biology. Chem. Rev. 113, 4755–4811. Gessler, N.N., Egorova, A.S., Belozerskaya, T.A., 2013. Fungal anthraquinones. Appl. Biochem. Microbiol. 49, 109–123. Gmoser, R., Ferreira, J.A., Lundin, M., Taherzadeh, M.J., Lennartsson, P.R., 2018. Pigment production by the edible filamentous fungus Neurospora intermedia. Fermentation 4 (113), 11. https://doi.org/10.3390/ fermentation4010011. Hiort, J., Maksimenka, K., Reichert, M., Perovic-Ottstadt, S., Lin, W.H., Wray, V., Steube, K., Schaumann, K., Weber, H., Proksch, P., 2004. New natural products from the sponge-derived fungus Aspergillus niger. J. Nat. Prod. 67, 1532–1543. Huang, Z., Yang, R., Guo, Z., She, Z., Lin, Y., 2010. New anthraquinone derivative produced by cultivation of mangrove endophytic fungus Fusarium sp. ZZF60 from the South China Sea. Chin. J. Appl. Chem. 27, 394–397. Huang, C.H., Pan, J.H., Chen, B., Yu, M., Huang, H.B., Zhu, X., Lu, Y.J., She, Z.G., Lin, Y.C., 2011. Three bianthraquinone derivatives from the mangrove endophytic fungus Alternaria sp ZJ9-6B from the South China Sea. Mar. Drugs 9, 832–843. Isbrandt, T., Tolborg, G., Ødum, A., Workman, M., Larsen, T.O., 2020. Atrorosins: a new subgroup of Monascus pigments from Talaromyces atroroseus. Appl. Microbiol. Biotechnol. 104 (2), 615–622. Jia, X.Q., Xu, Z.N., Zhou, L.P., Sung, C.K., 2010. Elimination of the mycotoxin citrinin production in the industrial important strain Monascus purpureus SM001. Metab. Eng. 12, 1–7. Kalra, R., Conlan, X.A., Goel, M., 2020. Fungi as a potential source of pigments: harnessing filamentous fungi. Front. Chem. 8, 369. Kumar, M., Dwivedi, P., Sharma, A.K., Sankar, M., Patil, R.D., Singh, N.D., 2014. Apoptosis and lipid peroxidation in ochratoxin A- and citrinin-induced nephrotoxicity in rabbits. Toxicol. Ind. Health 30, 90–98. Li, Y., Li, X., Lee, U., Kang, J.S., Choi, H.D., Son, B.W., 2006. A new radical scavenging anthracene glycoside, asperflavin ribofuranoside, and polyketides from a marine isolate of the fungus Microsporum. Chem. Pharm. Bull. 54, 882–883. Li, D.L., Li, X.M., Wang, B.G., 2009. Natural anthraquinone derivatives from a marine mangrove plantderived endophytic fungus Eurotium rubrum: structural elucidation and DPPH radical scavenging activity. J. Microbiol. Biotechnol. 19, 675–680. Lin, Z., Zhu, T., Fang, Y., Gu, Q., Zhu, W., 2008. Polyketides from Penicillium sp. JP-1, an endophytic fungus associated with the mangrove plant Aegiceras corniculatum. Phytochemistry 69, 1273–1278. Mapari, S.A.S., Nielsen, K.F., Larsen, T.O., Frisvad, J.C., Meyer, A.S., Thrane, U., 2005. Exploring fungal biodiversity for the production of water-soluble pigments as potential natural food colorants. Curr. Opin. Biotechnol. 16, 231–238. Mapari, S.A.S., Hansen, M.E., Meyer, A.S., Thrane, U., 2008a. Computerized screening for novel producers of Monascus-like food pigments in Penicillium species. J. Agric. Food Chem. 56, 9981–9989. Mapari, S.A.S., Meyer, A.S., Thrane, U., 2008b. Evaluation of Epicoccum nigrum for growth morphology and production of natural colorants in liquid media and on a solid rice medium. Biotechnol. Lett. 30, 2183–2190.

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Mapari, S.A.S., Meyer, A.S., Thrane, U., Frisvad, J.C., 2009a. Identification of potentially safe promising fungal cell factories for the production of polyketide natural food colorants using chemotaxonomic rationale. Microb. Cell Factories 8, 24. Mapari, S.A.S., Meyer, A.S., Thrane, U., 2009b. Photostability of natural orange-red and yellow fungal pigments in liquid food model systems. J. Agric. Food Chem. 57, 6253–6261. Mapari, S.A.S., Meyer, A.S., Thrane, U., Frisvad, J.C., 2012. Production of Monascus-Like Pigments. European Patent EP 2010/2262862 A2. Mendez, A., Perez, C., Montanez, J.C., Martinez, G., Aguilar, C.N., 2011. Red pigment production by Penicillium purpurogenum GH2 is influenced by pH and temperature. J Zhejiang Univ Sci B 12, 961–968. Park, Y.H., Lee, I.Y., Kim, S.W., Lee, J.H., Jeong, J.C., 2000. Production Method of β-Carotene From Blakeslea trispora. Korean Patent KR20000031738. Pereira, D.G., Tonso, A., Kilikian, B.V., 2008. Effect of dissolved oxygen concentration on red pigment and citrinin production by Monascus purpureus ATCC 36928. Braz. J. Chem. Eng. 25, 247–253. Santos-Ebinuma, V.C., Roberto, I.C., Fransisca, M., Teixeira, S., Pessoa Jr., A., 2013. Improving of red colorants production by a new Penicillium purpurogenum strain in submerged culture and the effect of different parameters in their stability. Biotechnol. Prog. https://doi.org/10.1021/btpr.1720. Sardaryan, E., Zihlova, H., Strnad, R., Cermakova, Z., 2004. Arpink red – meet a new natural red food col, L. (Ed.), Pigments in Food, More Than Colours…. Universite  de orant of microbial origin. In: Dufosse Bretagne Occidentale Publ., Quimper, France, pp. 207–208. Strobel, G.A., Hess, W.M., Ford, E., Sidhu, R.S., Yang, X., 1996. Taxol from fungal endophytes and the issue of biodiversity. J. Ind. Microbiol. Biotechnol. 17, 417–423. Wang, J., Huang, Y., Shao, Y., 2021. From traditional application to genetic mechanism: opinions on Monascus research in the new milestone. Front. Microbiol. 12, 659907. Whittaker, J.A., Johnson, R.I., Finnigan, T.J.A., Avery, S.V., Dyer, P.S., 2020. The biotechnology of quorn mycoprotein: past, present and future challenges. In: Nevalainen, H. (Ed.), Grand Challenges in Biology and Biotechnology. Springer Publisher, pp. 59–79, https://doi.org/10.1007/978-3-030-29541-7_3. Woo, P.C., Lam, C.W., Tam, E.W., Lee, K.C., Yung, K.K., Leung, C.K., Sze, K.H., Lau, S.K., Yuen, K.Y., 2014. The biosynthetic pathway for a thousand-year-old natural food colorant and citrinin in Penicillium marneffei. Sci. Rep. 4, 6728. https://doi.org/10.1038/srep06728. Yan, H.J., Gao, S.S., Li, C.S., Li, X.M., Wang, B.G., 2010. Chemical constituents of a marine-derived endophytic fungus Penicillium commune G2M. Molecules 15, 3270–3275. Yang, Y., Liu, B., Du, X., Li, P., Liang, B., Cheng, X., Du, L., Huang, D., Wang, L., Wang, S., 2015. Complete genome sequence and transcriptomics analyses reveal pigment biosynthesis and regulatory mechanisms in an industrial strain, Monascus purpureus YY-1. Sci. Rep. 5, 8331. https://doi.org/10.1038/ srep08331. Yilmaz, N., Houbraken, J., Hoekstra, E.S., Frisvad, J.C., Visagie, C.M., Samson, R.A., 2012. Delimitation and characterization of Talaromyces purpurogenus and related species. Persoonia 29, 39–54.

12 Filamentous fungi for food Rachma Wikandaria, Manikhardaa, Ratih Dewanti-Hariyadib, and Mohammad J. Taherzadehc a

DEPARTMENT OF FOOD AND AGRICULTURAL PRODUCT T ECHNOLOGY, UNI VERSITAS GADJ AH M A D A , Y OG Y A K A R T A, I ND O N E S I A b DEPARTME NT OF FOOD SCIENCE AND TECHNOLOGY, IPB U N I VE R S I T Y , B OGOR, INDONESIA c SW EDISH C ENTR E FOR R ESOUR CE RECOVE RY, UNIVER SIT Y ˚ S , SW EDEN OF BORA˚ S, BOR A

1. Introduction The United Nations (UN) figures the global population to reach 9.7 billions by 2050, which consequently increases the food demand, particularly protein-rich diets (United Nations, 2019). Animal protein is an important protein source, hence the world demand for animal protein is predicted to be doubled in 2050 (FAO, 2019), which results in raising concerns for sustainability and food security. It is generally accepted that animal-based foods give higher negative impact on the environment since they are more greenhouse gases (GHGs) intense than plant-based foods (Tilman and Clark, 2014). The rise of animal-based food demand puts more pressure on land and water usage as well as losses of biodiversity and other essential ecosystem services (Van Zanten et al., 2016). In terms of health, overconsumption of processed meat is linked to a high intake of saturated fatty acids, which harms our health. Besides environmental and health concerns, ethical issues related to animal production drives a dietary shift toward reduction of meat consumption. Therefore, an alternative source of protein that provides high protein quality with a low environmental impact is desired. Filamentous fungi have been consumed for centuries in several countries in the form of fermented foods. For instance, tempe, a fermented soybean by filamentous fungi is the staple source of protein in Indonesia. Pure biomass of filamentous fungi was introduced to the market 3.5 decades ago and obtained a positive response as a promising meat replacer, and now there are several companies with their products on the market. Filamentous fungi have similar quality of protein to several animal-based foods with a significantly lower requirement of land and water usage; thus, it can be considered as a more environmentally friendly protein. In addition, filamentous fungi can grow in a wide range of substrates, thus enabling them to convert organic wastes into a rich and diverse set of valuable products. This is in accordance with the concept of a sustainable bio-circular economy which has gained interest in very recent years. This chapter presents the application of filamentous fungi as food, the protein quality, the environmental impact, the safety issue, the production of filamentous fungi-based food both in traditional and in modern Current Developments in Biotechnology and Bioengineering. https://doi.org/10.1016/B978-0-323-91872-5.00007-7 Copyright © 2023 Elsevier Inc. All rights reserved.

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FIG. 1 Various filamentous fungi-based food products (the fungal-based sausage was provided by Swedish Company Millow).

industry, as well as the prospects and the challenges in developing filamentous fungibased food. The applications of filamentous fungi for food are summarized in Fig. 1. Filamentous fungi can be consumed as sole biomass in the form of mycoprotein, in which Quorn is one successful example. They can be consumed with their growing substrates in the form of fermented food such as tempe, soy sauce, miso, oncom, etc. Furthermore, filamentous fungi are also used for making food ingredients including coloring agents, flavor enhancers, and enzymes.

2. Filamentous fungi as protein source 2.1 Protein quality of various protein sources Proteins are among the essential nutrients in the human diet. Proteins are available in a variety of foods, which are mainly classified into animal- and plant-based proteins. Several important animal protein sources include cattle, poultry, goat, pig, seafood, egg, and milk. Meanwhile, plant-based protein sources are dominated by soybean, bean,

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nuts, and pulses (Hertzler et al., 2020; Vogelsang-O’Dwyer et al., 2021). Despite the aforementioned protein sources, there are several emerging protein source alternatives such as insects, cultured meat, and fungal protein (Hadi and Brightwell, 2021). There are several factors to be considered when selecting protein sources, including nutritional quality, price, safety, as well as health and environmental impacts. The nutritional quality of protein is evaluated according to protein content and quality. The protein quality is related to protein digestibility and bioavailability (Schoenlechner et al., 2008). The digestibility of protein is a crucial factor as it describes how the protein is best utilized in the human body, which can be presented in the value of net protein utilization (NPU) and protein digestibility-corrected amino acid score (PDCAAS). NPU measures protein quality by calculating the nitrogen used for tissue formation divided by the nitrogen ingested from food (Hoffman and Falvo, 2004); thus, it provides information on how efficiently the body utilizes protein consumed in the diet. Besides the protein content, the essential amino acid (EAA) content in a protein source is also necessary to be considered. EAAs are amino acids that cannot be produced by the human body and must be ingested from our diet. The PDCAAS compares the EAA content of a test protein with that of a reference EAA pattern and a correction for differences in protein digestibility (Schaafsma, 2005). The bioavailability of the protein is affected by unfavorable compounds which inhibit nutrient absorption, which is called antinutritional factors (Ram et al., 2020). The safety of protein is related to the presence of toxic and allergenic compounds. An example of an antinutritional factor is phytic acid, whereas the toxic compound com^mara and Madruga, 2001). The nutritional quality monly found in plants is cyanic acid (Ca and the safety of various protein sources are presented in Table 1. Protein digestibility shown by NPU and PDCAAS is relatively higher in animal protein than in plant-based protein (Table 1). However, animal proteins are usually high in saturated fat and cholesterol, which have a negative impact on human health. Animal proteins may pose food safety risks, including heavy metals in wild fish (Hayes et al., 2016; MoraEscobedo et al., 2018) and environmental contaminants frequently found in meat as the contaminants are highly soluble in fat (Gonza´lez et al., 2020). Besides, it has been reported that high animal protein intake could increase the risk of cardiovascular disease, cancer (De Souza et al., 2015; Song et al., 2016), kidney stones (Tracy et al., 2014), and mortality (Virtanen et al., 2019). In addition, consuming 106 CFU/g increase while inoculation after fermentation and steaming led to an increase in the bacterial counts up to 108 CFU/g and detection of S. aureus enterotoxins in some samples. Additionally, Salmonella typhimurium also grew well during the fermentation (>106 CFU/g increase in 1 d), although it grew relatively slowly at 25 and 15°C in tempe inoculated after fermentation and steaming. The study recommends that high level of hygiene during tempe fermentation and refrigeration (5°C) of the product following fermentation are to be applied to prevent potential outbreaks (Tanaka et al., 1985). In the USA, an outbreak (n ¼ 8) due to Salmonella paratyphi linked to tempe consumption was reported in 2012 (Griese et al., 2013). The S. paratyphi was also found in the starter culture and this poses a risk of contamination. Concerns pertaining food safety hazard of tempe have been reported in the USA. It is suggested that the starter culture was contaminated with S. paratyphi (Marasas, 2001), and prompted the authority to recall the contaminated batch of tempe.

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Tempe with the most food safety concerns is tempe bongkrek, i.e., tempe made from coconut press cake (instead of soybean) which is fermented using Rhizopus oligosporus. Tempe bongkrek poisoning is caused by bongkrekic acid produced by contaminating bacterium Burkholderia gladioli (previously known as Burkholderia cocovenenans). An outbreak due to consumption of tempe bongkrek has caused death of nearly 2000 people since 1951. In addition, the endosymbiont bacterium of Rhizopus microsporus used for making tempe such as Burkholderia produces a toxin, namely rhizonin which is a hepatotoxic cycloprotein (Partida-Martinez et al., 2007).

6. Industrial production of filamentous fungi-based food Filamentous fungi have been applied as food source worldwide. In the Western world, the fungal biomass is mainly used to produce meat-free protein such as Quorn. Meanwhile in Asia, several filamentous fungi play an important role in production of fermented food. In this section, industrial production is divided into two groups, namely traditional and modern processes.

6.1 Traditional processes of food from filamentous fungi 6.1.1 Tempe Tempe is one example of filamentous fungi-based product which is mainly produced by traditional methods. In Indonesia, there are over 100,000 tempe producers representing mostly small and medium enterprises with a capacity of 10–2000 kg soybean per day. Tempe has a significant contribution to economic growth of Indonesia as it creates millions of direct and indirect jobs with business turnover of billions USD. Several businesses are related to tempe including supplier, distributor, transporter, and retailer. Approximately half of soybean usage in Indonesia is for tempe productions (PUSIDO Badan Standardisasi Nasional, 2012). Kopti is an association of tempe enterprises in Indonesia that established in 1975 to assure the quality of tempe material and provide training for its members on how to produce tempe. Tempe is one of the staple proteins for Indonesia mainly due to its affordable price. The raising of global attention on tempe is mainly driven by its nutritional values as plantbased protein. Tempe is introduced in other countries mainly by Indonesian immigrants although in some cases by their citizens who visited or lived in Indonesia. Tempe was firstly available in the European Market in 1946, since then the number of tempe factories increased and in 1984, 18 tempe factories were reported. Similarly, in America, the number of tempe companies raised by more than four times, from 13 to 53 during 5 years (1979–84) (Shurtleff and Aoyagi, 1984). This fact makes tempe to be the fastest-growing soyfood market in the USA. Tempe and its derived products that dominate the US sales include regular soy tempe (33%), tempe burgers and other second-generation tempe products (48%), and soy and grain tempe (19%) (Shurtleff and Aoyagi, 1984). In 1984, the eight largest companies outside its origin country were located in Japan, The Netherlands, and the USS with average weekly production between 2100 and 6885 kg/week (Shurtleff and Aoyagi, 1984).

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In general, the process of making tempe consists of soaking, boiling, dehulling, cooling, inoculation, packaging, and incubation. In traditional methods, dehulling is commonly done using wet method, i.e., by soaking the beans to loosen the hull and let the hull floating or with dry method by mechanical abrasion. Meanwhile at the industrial scale, dehulling is done using motor-driven disc impactor and fermentation is done in a tray (Nout, 2005). In traditional production, two different starter cultures are generally used: laru, i.e., fungi grown in cooked rice then dried and usar, i.e., fungi grown on certain leaves and let dry (Fig. 3). The diversity of tempe microflora leads to inconsistency of tempe quality which becomes a problem in large-scale production.

6.1.2 Soy sauce The top producer of soy sauce is China which contributes to more than 60% of the global € kenberg, 2017). Soy sauce is made by traditional small-scale industry and in production (Ho a large-scale modern factory. Aroma is a crucial property in soy sauce affecting consumer selection and distinguishes soy sauce from different origins. Aroma is generated during fermentation and it is influenced by raw materials, processing methods, and microorganism. In traditional soy sauce production, the koji and moromi fermentation occur spontaneously using an indigenous microflora as the processes are performed in nonsterile conditions. The microbial community in traditional soy sauce may be more complex than in the controlled industrialized process, thus they produce distinctive flavors which makes traditional soy sauce to be sold at a higher price (Yang et al., 2017). However, as the microflora is poorly controlled, the quality of the product is inconsistent and consequently, the market share of traditional products has been constantly diminishing. Soy sauce is mainly made from yellow or black soybean. The process and equipment used for traditional soy sauce are presented below: a) Sortation and boiling The sortation is conducted manually mainly to remove gravel and other contaminants. The soybean is then soaked overnight. The soaked soybean is then boiled for 1–5 h. The aim of this step is to soften the beans; hence, the mycelium of the fungi can be easily penetrated into the bean and hydrolyze the protein into amino acids and flavoring compounds that contribute to the taste of the soy sauce. This step is also essential to reduce the pathogens in the soybean and to increase the digestibility of the protein. After boiling, the softened bean is rapidly spread in a bamboo tray to remove the excess water and heat to prevent spoilage (Sardjono, 2016). b) Koji fermentation After the temperature of the bean reaches room temperature, sometimes it is mixed with wheat or rice flour. The bamboo tray is then covered by other bamboo trays, gunny sacks, or rice straw for approximately a week. This step is known as koji fermentation which is aimed to form the flavor compound. In traditional soy sauce production, the koji fermentation occurs spontaneously by microbes living in the air, from previously used trays and

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FIG. 3 Production of traditional tempe culture “Usar”: (A) Hibiscus tiliaceus leaves; (B) spreading the boiled soybean on the leaves; (C) covering the soybean with the leaves; (D) incubation at room temperature; (E) sporulation; and (F) ready to use Usar (personal documentation taken by Anang Juni Yastanto).

covered materials. The water activity (aw) is set at 0.95–0.97 to obtain optimum condition of koji fermentation. If the aw is lower, the fungi start to form spores which cease the enzyme production. During koji fermentation, the temperature increased, thus it needs agitation. During fermentation, the oxygen diffuses slowly to grow and prevent sporulation. After sufficient growth of the molds, the koji product is crumbled to remove the

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mycelium followed by sun drying. The dried beans are then put in plastic, ceramic, and wooden vessels (Sardjono, 2016). c) Moromi fermentation In this stage, a brine solution is added to the dried koji product in the vessel with a ratio of 1 part of koji product to 4–6 parts of brine solution. The brine solution is made by dissolving crude sea salt in water. The vessel is put outside under the sun and stirred regularly. It is covered during rainfall and at night to maintain the temperature. This process aims to enhance the flavor formation, prolong the shelf-life, and select appropriate microorganisms. The brine solution varies from 18% to 24%. The fermentation duration varies from months to years. It has been suggested that a period of 150 days is optimum for flavor formation in traditional Chinese-type of soy sauce (Gao et al., 2010). d) Filtration and cooking The brine is then filtered using a cloth and subjected to cooking. Cooking is aimed to kill pathogens and improve the shelf life. In traditional soy sauce fermentation, cooking is commonly conducted at 60–80°C for 30 min. However, it is recommended to cook at 80°C for 30 min to obtain the optimum flavors (Gao et al., 2010). In Indonesian soy sauce, caramelized palm or cane sugar is added during cooking to make a sweet soy sauce which is a more common type of soy sauce. Besides sugars, sometimes spices, monosodium glutamate, and thickening agent are also added at this stage. After cooking, the solution is filtered again and subjected to bottling. 1 kg of soybean could produce approximately 10 L of soy sauce.

6.2 Modern processes 6.2.1 Modern process of tempe production The number of modern tempe factories has been raising consistently. As the largest tempe producer in the world, approximately 2.4 million tons of tempe were produced per day in Indonesia in 2012 (PUSIDO Badan Standardisasi Nasional, 2012). There are several methods for tempe productions in modern tempe factories, which are mainly classified into dry and wet method depending on the method of dehulling. In the wet method, the soybean is firstly soaked followed by dehulling manually or using mechanical rubber, hull removal, and soaking, while in the dry process the soybean is dehulled by mechanical abrasion, followed by hull removal and soaking. The remaining process for wet and dry processes are similar. They include cooking, inoculation, packaging, and incubation. Wet process offers an advantage as it is conducted manually by workers so it does not require a major equipment and the mechanical damage of the soybean can be minimized. However, this process is considered less hygienic and significantly higher water usage compared to the dry method. Generally, the step of making tempe in modern process is similar to that of traditional one. However, in modern processes, some factories use dry method, inoculum powder,

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and higher sanitary level of the production process. Modern tempe factories use a standardized inoculum in the form of powder which contains a single culture of a certain strain of Rhizopus, thus the quality is more homogenous. In addition, the higher sanitary level in modern tempe production is applied by using stainless-steel food-grade equipment and practicing personal hygiene for the workers. The different hygienic and sanitary level of tempe production is related to the presence of biologically active compound in tempe. Tamam et al. (2019) reported that tempe produced in a good sanitation level has more bioactive peptides (with antihypertensive, antidiabetic, antioxidative, and antitumor properties) than that of tempe produced using moderate or poor sanitation level. This might be due to that the metabolite profiles are mostly influenced by the starter culture (Kadar et al., 2020), hence the direct physical contact of the worker’s hand with the soybean which introduces the contamination should be avoided. In brief, several steps of tempe production in modern factories include soaking, boiling, dehulling, cooling, inoculating, packaging, and incubation (Fig. 4). The soybean is soaked overnight in a steel vessel and it is followed by boiling for 30 min using large pressure cooker and continuous soybean cooking machine, dehulling using a grinder followed by soaking for 24 h. Subsequently, the bean is boiled for 1 h and drained in a perforated steel table. After cooling, 1 kg of inoculum is added to 1500 kg soybeans. The inoculated soybeans are then transported on a conveyor to a package machine that divided the soybeans by weight into perforated plastic bags. Incubation takes place for 24 h.

Soaking 1

Boiling 1

Incubation

Packaging

Dehulling

Inoculation

Soaking 2

Boiling 2

FIG. 4 Modern tempe processing (pictures taken from tempe factory UD Super Dangsul, Yogyakarta, Indonesia).

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6.2.2 Production of Quorn Large-scale production of Quorn is started by growing F. venenatum on media containing glucose, vitamins, trace minerals, and ammonia. The fermentation takes place in an 14,000 L airlift fermenter operated in a continuous mode. The freeze-dried culture of Fusarium venenatum is grown in a lab-scale fermenter prior to transfer to the main airlift fermentor. Several fermentation parameters are strictly controlled including pH, temperature, dissolved oxygen, nutrient concentration, and growth rate (Trinci, 1991). The fermentation temperature is kept at 28–30°C and the pH is maintained at 6.0. These conditions resulted in a specific growth rate of 0.17–0.20 h1 and yielded 300–350 kg biomass h1 (Wiebe, 2002). The fermentation usually occurs for 6 weeks. The fermentation broth is heated at optimum temperature of 72–74°C for 30–45 min to reduce the RNA content from 10% to 1%, which is below the limit required by the World Health Organization (2%). Subsequently, the mycelial biomass is heated at 90°C for preservation. It is followed by centrifugation to collect the biomass and further concentrated by vacuum chilling to obtain 24% of total solid (Finnigan, 2011). At this point, the mycoprotein is ready to be further processed into Quorn food. To create Quorn piece and mince, the processing steps are similar, however, the ingredient is slightly different. The processing steps include mixing, forming, cooking, and freezing. The mycoprotein is firstly mixed with egg albumin, malt extract, and water for making Quorn mince, however, the malt extract is replaced by natural flavor in Quorn piece. The egg albumin is needed to form fibrous bundles. Subsequently, the temperature is increased to 90°C in order to denature the egg, which is then fixed the texture after forming. It is followed by freezing at 10°C for 30 min to settle the fibrous bundle. The ice crystal growth during the freezing force the mycelium together and create the fibrous bundle. This fibrous bundle creates an eating quality of meat which differentiate Quorn from other meat-free protein. After freezing, the product is packed and kept in cold storage. The production scheme is illustrated in Fig. 5.

FIG. 5 Production of mycoprotein. Adapted from Finnigan, T.J.A., 2011. Mycoprotein: origins, production and properties. In: Handbook of Food Proteins. Woodhead Publishing Limited. https://doi.org/10.1533/9780857093639.335.

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7. Conclusions and perspectives Filamentous fungi holds a wide applications in food due to its high nutritional quality with low environmental impact. Although their excellent properties, development of filamentous fungi-based food faces some challenges including the mycotoxin issue, allergen, neophobia, and high production cost. Several attempts hence are needed to address those challenges such as avoiding mycotoxin-producing fungi, conducting comprehensive allergenic studies, formulating filamentous fungi into tasty familiar products, involving an influencer, role model, or officials in the health and food sector for promotion by explaining the nutritional value, safety, and sustainability. The introduction of filamentous fungi in the market as a nutritious family member of mushroom and truffle could eliminate the new phobia. Advanced technologies which could decrease the production cost are needed to increase the acceptance of this product in the market. In addition, filamentous fungi have been shown to give a positive impact on human health thus it becomes a good candidate as a functional food. Furthermore, filamentous fungi could grow in agricultural waste and food by-products which convert low-cost material into nutritious, healthy, and tasty products. The excellent nutritional value together with its environmentally friendly protein would drive the demand for this protein, particularly if it is supported by policies and regulations.

Acknowledgment This work was supported by the Ministry of Research and Technology of Indonesia through the grant of PDUPT with the contract number of 2847/UN1.DITLIT/DIT-LIT/PT/2020.

References Adebiyi, J.A., 2019. Food fermentation and mycotoxin detoxification: an African perspective. Food Control 106, 106731. Adejoh, J., Idoko, F., Ujah, E., Okoh, M., 2020. Cyanide content analysis in selected food crops (soya beans, maize, white beans), nuts (ground nut, tiger nut) cultivated and consumed in Nigeria and, espouse of environmental toxicants as epigene (s) modifier. Chem. Sci. Eng. Res. 2 (4), 26–33. https://doi.org/ 10.36686/Ariviyal.CSER.2020.02.04.017. Afifah, D.N., Sulchan, M., Syah, D., Suhartono, M.T., 2015. The use of red oncom powder as potential production media for fibrinogenolytic protease derived from Bacillus licheniformis RO3. Procedia Food Sci. 3, 453–464. https://doi.org/10.1016/j.profoo.2015.01.050. Ahnan-Winarno, A.D., Winarno, F.G., Gibbons, J., 2021. Tempeh: a semicentennial review on its health benefits, fermentation, safety, processing, sustainability, and affordability. Compr. Rev. Food Sci. Food Saf. 20 (2), 1717–1767. https://doi.org/10.1111/1541-4337.12710. Akihisa, T., Tokuda, H., Yasukawa, K., Ukiya, M., Kiyota, A., Sakamoto, N., Suzuki, T., Tanabe, N., Nishino, H., 2005. Azaphilones, furanoisophthalides, and amino acids from the extracts of Monascus pilosus-fermented rice (red mold rice) and their chemopreventive effects. J. Agric. Food Chem. 53, 562. Allen, A.M., Hof, A.R., 2019. Paying the price for the meat we eat. Environ. Sci. Policy 97 (February), 90–94. https://doi.org/10.1016/j.envsci.2019.04.010. Archer, D.B., 2000. Filamentous fungi as microbial cell factories for food use. Curr. Opin. Biotechnol. 11 (5), 478–483. https://doi.org/10.1016/S0958-1669(00)00129-4.

386

Current Developments in Biotechnology and Bioengineering

Archer, D.B., Connerton, I.F., MacKenzie, D.A., 2008. Filamentous fungi for production of food additives and processing aids. Adv. Biochem. Eng. Biotechnol. 111 (February), 99–147. https://doi.org/ 10.1007/978-3-540-70536-9. Ardo, Y., 2007. Blue cheese. In: McSweeney, P. (Ed.), Cheese Problem Solved. CRC Press, pp. 284–288. Aruna, K., Shah, J., Birmole, R., 2014. Production and partial characterization of alkaline protease from Bacillus tequilensis strains CSGAB0139 isolated from spoilt cottage cheese. Int. J. Appl. Biol. Pharm. 5, 201–221. Ashu, E., Forsythe, A., Vogan, A., Xu, J., 2015. Filamentous fungi in fermented foods. In: Didier, M., Ramesh, R. (Eds.), Fermented Foods, Part I: Biochemistry and Biotechnology. CRC Press. Assohoun, M., Djeni, T., Koussemon-Camara, M., Brou, K., 2013. Effect of fermentation process on nutritional composition and aflatoxins concentration of Doklu, a fermented maize based food. Food Nutr. Sci. 4 (11), 1120–1127. Astuti, M., Meliala, A., Dalais, F.S., Wahlqvist, M.L., 2000. Tempe, a nutritious and healthy food from Indonesia. Asia Pac. J. Clin. Nutr. 9 (4), 322–325. https://doi.org/10.1046/j.1440-6047.2000.00176.x. Azeem, A., Neelagund, Y., Rathod, V., 1999. Biotechnological production of oil: fatty acid composition of microbial oil. Plant Foods Hum. Nutr. 53 (4), 381–386. Badan Pusat Statistik, 2021. Rata-Rata Konsumsi per Kapita Seminggu Beberapa Macam Bahan Makanan Penting, 2007–2021. https://www.bps.go.id/statictable/2014/09/08/950/rata-rata-konsumsi-perkapita-seminggu-beberapa-macam-bahan-makanan-penting-2007-2019.html. (Accessed 29 March 2021). Barus, T., Suwanto, A., Wahyudi, A.T., Wijaya, H., 2008. Role of bacteria in tempe bitter taste formation; microbiological and molecular biological analysis based on 16S rRNA gene. Microbiol. Indones. 2, 17–21. https://doi.org/10.5454/mi.2.1.4. 1. Bender, A.E., Matthews, R., 1981. Adverse reactions to foods. Br. J. Nutr. 46, 403–407. Berlian, Z., Aini, F., 2016. Uji kadar alkohol pada tapai ketan putih dan singkong melalui fermentasi dengan dosis ragi yang berbeda. J. Biota 2 (1), 106–111. Beuchat, L.R., 2018. Oncom (fermented peanut press cake). In: Reddy, N.R., Pierson, M., Salunkhe, D. (Eds.), Legume-Based Fermented Foods. CRC Press, pp. 136–144. Bintanah, S., Muis, S.F., Purwanto, A.P., Kusuma, H.S., 2019. Combination of tempe and bran flours towards nutritional content as an antihyperlipidemic and antistress oxidative. IOP Conf. Ser.: Earth Environ. Sci. 292 (1), 12050. Blanco, C.A., Caballero, I., Barrios, R., Rojas, A., 2014. Innovations in the brewing industry: light beer. Int. J. Food Sci. Nutr. 65 (6), 655–660. Boa, E., 2007. Wild Edible Fungi a Global Overview of Their Use and Importance to People. Bokulich, N.A., Ohta, M., Lee, M., Mills, D.A., 2014. Indigenous bacteria and fungi drive traditional kimoto sake fermentations. Appl. Environ. Microbiol. 80 (17), 5522–5529. Boonsong, S., Klaypradit, W., Wilaipun, P., 2016. Antioxidant activities of extracts from five edible mushrooms using different extractants. Agric. Nat. Resour. 50 (2), 89–97. https://doi.org/10.1016/j. anres.2015.07.002. Borzekowski, A., Anggriawan, R., Auliyati, M., Kunte, H.J., Koch, M., Rohn, S., Karlovsky, P., Maul, R., 2019. Formation of zearalenone metabolites in tempeh fermentation. Molecules 24, 2697. Boye, J., Wijesinha-Bettoni, R., Burlingame, B., 2012. Protein quality evaluation twenty years after the introduction of the protein digestibility corrected amino acid score method. Br. J. Nutr. 108 (S2), S183–S211. Bui-Klimke, T.R., Wu, F., 2015. Ochratoxin A and human health risk: a review of the evidence. Crit. Rev. Food Sci. Nutr. 55 (13), 1860–1869.

Chapter 12 • Filamentous fungi for food

387

Bujang, A., Taib, N.A., 2014. Changes on amino acids content in soybean, garbanzo bean and groundnut during pre-treatments and tempe making. Sains Malays. 43 (4), 551–557. Burd, N.A., Beals, J.W., Martinez, I.G., Salvador, A.F., Skinner, S.K., 2019. Food-first approach to enhance the regulation of post-exercise skeletal muscle protein synthesis and remodeling. Sports Med. 49 (1), 59–68. Camacho, N.A., Aguilar, G., 2003. Production, purification, and characterization of a low-molecular-mass xylanase from Aspergillus sp. and its application in baking. Appl. Biochem. Biotechnol. 104 (3), 159–171. ^mara, F.S., Madruga, M.S., 2001. Cyanic acid, phytic acid, total tannin and aflatoxin contents of a BraCa zilian (Natal) multimistura preparation. Rev. Nutr. 14 (1), 33–36. € , Y.M., 2017. Blue cheese. In: McSweeney, P.L.H., Cantor, M.D., van den Tempel, T., Hansen, T.K., Ardo Fox, P.F., Cotter, P.D., Everett, D.W. (Eds.), Cheese: Chemistry, Physics and Microbiology, fourth ed. Academic Press, pp. 929–954, https://doi.org/10.1016/B978-0-12-417012-4.00037-5. Caro, Y., Venkatachalam, M., Lebeau, J., Fouillaud, M., Dufoss e, L., 2015. Pigments and colorants from filrillon, J.-M., Ramawat, K.G. (Eds.), Fungal Metabolites. Springer International amentous fungi. In: Me Publishing, pp. 499–568.  Castanheira, E.G., Freire, F., 2013. Greenhouse gas assessment of soybean production: implications of land use change and different cultivation systems. J. Clean. Prod. 54, 49–60. Castrillo´n, A.M., Pilar Navarro, M., Trinidad Garcı´a-Arias, M., 1996. Tuna protein nutritional quality changes after canning. J. Food Sci. 61 (6), 1250–1253. https://doi.org/10.1111/j.1365-2621.1996. tb10972.x. Cesari, V., Zucali, M., Sandrucci, A., Tamburini, A., Bava, L., Toschi, I., 2017. Environmental impact assessment of an Italian vertically integrated broiler system through a life cycle approach. J. Clean. Prod. 143, 904–911. Cesari, V., Zucali, M., Bava, L., Gislon, G., Tamburini, A., Toschi, I., 2018. Environmental impact of rabbit meat: the effect of production efficiency. Meat Sci. 145, 447–454. Cheng, Y.-Q., Hu, Q., Li, L.-T., Saito, M., Yin, L.-J., 2009. Production of sufu, a traditional Chinese fermented soybean food, by fermentation with Mucor flavus at low temperature. Food Sci. Technol. Res. 15 (4), 347–352. Cian, R.E., Fajardo, M.A., Alaiz, M., Vioque, J., Gonza´lez, R.J., Drago, S.R., 2014. Chemical composition, nutritional and antioxidant properties of the red edible seaweed Porphyra columbina. Int. J. Food Sci. Nutr. 65 (3), 299–305. Codex Alimentarius Commission, 2019. General Standard for Contaminants and Toxins in Food and Feed (Cxs 193-1995). Food and Agriculture Organization, pp. 1–66. Copetti, M.V., 2019. Fungi as industrial producers of food ingredients. Curr. Opin. Food Sci. 25, 52–56. https://doi.org/10.1016/j.cofs.2019.02.006. Dabbour, I.R., Takruri, H.R., 2002. Protein digestibility using corrected amino acid score method (PDCAAS) of four types of mushrooms grown in Jordan. Plant Foods Hum. Nutr. 57 (1), 13–24. Dayal, J.S., Ponniah, A.G., Khan, H.I., Babu, E.P.M., Ambasankar, K., Vasagam, K.P.K., 2013. Shrimps—a nutritional perspective. Curr. Sci., 1487–1491. de Gavelle, E., Huneau, J.F., Bianchi, C.M., Verger, E.O., Mariotti, F., 2017. Protein adequacy is primarily a matter of protein quantity, not quality: modeling an increase in plant: animal protein ratio in French adults. Nutrients 9 (12). https://doi.org/10.3390/nu9121333. de Gier, S., Verhoeckx, K., 2018. Insect (food) allergy and allergens. Mol. Immunol. 100 (May), 82–106. https://doi.org/10.1016/j.molimm.2018.03.015. € neDe Souza, R.J., Mente, A., Maroleanu, A., Cozma, A.I., Ha, V., Kishibe, T., Uleryk, E., Budylowski, P., Schu mann, H., Beyene, J., Anand, S.S., 2015. Intake of saturated and trans unsaturated fatty acids and risk of

388

Current Developments in Biotechnology and Bioengineering

all cause mortality, cardiovascular disease, and type 2 diabetes: systematic review and meta-analysis of observational studies. BMJ 351, 1–16. https://doi.org/10.1136/bmj.h3978. Departemen Kesehatan Republik Indonesia, 1995. Daftar Komposisi Zat Gizi Pangan Indonesia. Dervilly, G., Leclercq, C., Zimmermann, D., Roue, C., Thibault, J.-F., Saulnier, L., 2002. Isolation and characterization of high molar mass water-soluble arabinoxylans from barley and barley malt. Carbohydr. Polym. 47 (2), 143–149. Diez-Simon, C., Eichelsheim, C., Mumm, R., Hall, R.D., 2020. Chemical and sensory characteristics of soy sauce: a review. J. Agric. Food Chem. 68 (42), 11612–11630. https://doi.org/10.1021/acs.jafc.0c04274. Dinesh Babu, P., Bhakyaraj, R., Vidhyalakshmi, R., 2009. A low cost nutritious food “tempeh”—a review. World J. Dairy Food Sci. 4 (1), 22–27. Du, H., Guo, Y., Bennett, D.A., Bragg, F., Bian, Z., Chadni, M., Yu, C., Chen, Y., Tan, Y., Millwood, I.Y., Gan, W., Yang, L., Yao, P., Luo, G., Li, J., Qin, Y., Lv, J., Lin, X., Key, T., et al., 2020. Red meat, poultry and fish consumption and risk of diabetes: a 9 year prospective cohort study of the China Kadoorie biobank. Diabetologia 63 (4), 767–779. https://doi.org/10.1007/s00125-020-05091-x. , L., 2018. Red colourants from filamentous fungi: are they ready for the food industry? J. Food Dufosse Compos. Anal. 69 (April 2017), 156–161. https://doi.org/10.1016/j.jfca.2017.11.002. , L., Fouillaud, M., Caro, Y., Mapari, S.A.S., Sutthiwong, N., 2014. Filamentous fungi are large-scale Dufosse producers of pigments and colorants for the food industry. Curr. Opin. Biotechnol. 26, 56–61. https:// doi.org/10.1016/j.copbio.2013.09.007. Dunuwila, P., Rodrigo, V.H.L., Goto, N., Ifdholy, M., Romli, M., Wiloso, E., 2019. Global warming impact and energy analysis of tempeh made from local and imported soybean. Indonesian J. Life Cycle Assess. Sustain. 2 (2), 1–11. Ebine, H., 1986. Miso. In: Reddy, N., Pierson, M., Salunkhe, D. (Eds.), Legume-Based Fermented Food. CRC Press, pp. 47–68. Edward, D., Cumming, J.H., 2010. The protein quality of mycoprotein. Proc. Nutr. Soc. 69, E331. El Sheikha, A., Montet, D., 2016. Fermented foods-artisan household technology to biotechnology era. In: Montet, D., Ray, R.C. (Eds.), Fermented Foods: Part I Biochemistry and Biotechnology. CRC Press, pp. 1–15. FAO, 2017. Greenhouse Gas Emissions From Aquaculture. Food and Agriculture Organization of The United Nations. FAO, 2019. Meat & Meat Products. FAO. FAOSTAT, 2020. Mushrooms and Truffles. 3A449#FAO. (Accessed 27 March 2021).

http://data.un.org/Data.aspx?d¼FAO&f¼itemCode%

FAOSTAT, 2021. Production quantity of crops and livestock products. https://www.fao.org/faostat/en/ #data. (Accessed 25 January 2021). Feng, Y., Chen, X.M., Zhao, M., He, Z., Sun, L., Wang, C.Y., Ding, W.F., 2018. Edible insects in China: utilization and prospects. Insect Sci. 25 (2), 184–198. https://doi.org/10.1111/1744-7917.12449. Finnigan, T.J.A., 2011. Mycoprotein: origins, production and properties. In: Handbook of Food Proteins. Woodhead Publishing Limited, https://doi.org/10.1533/9780857093639.335. Finnigan, T., Needham, L., Abbott, C., 2017. Mycoprotein: a healthy new protein with a low environmental impact. In: Sustainable Protein Sources. Elsevier, pp. 305–325. Forum Tempe Indonesia, 2017. Activity Report the Indonesian Tempe Forum FY 2017. http://www. forumtempe.org/images/Materials/Activity-Report-FTI-2017.pdf. Frandsen, R.J., Nielsen, N.J., Maolanon, N., Sorensen, J.C., Olsson, S., Nielsen, J., Giese, H., 2006. The biosynthetic pathway for aurofusarin in Fusarium graminearum reveals a close link between the naphthoquinones and naphthopyrones. Mol. Microbiol. 61, 1069–1080.

Chapter 12 • Filamentous fungi for food

389

Galli, B.D., Martin, J.G.P., da Silva, P.P.M., Porto, E., Spoto, M.H.F., 2016. Sensory quality of Camembert-type cheese: relationship between starter cultures and ripening molds. Int. J. Food Microbiol. 234, 71–75. https://doi.org/10.1016/j.ijfoodmicro.2016.06.025. Gandjar, I., 1999. Fermentation of the far east. In: Robinson, R.K. (Ed.), Encyclopedia of Food Microbiology. Elsevier, pp. 767–773. Gao, X.L., Cui, C., Zhao, H.F., Zhao, M.M., Yang, L., Ren, J.Y., 2010. Changes in volatile aroma compounds of traditional Chinese-type soy sauce during moromi fermentation and heat treatment. Food Sci. Biotechnol. 19 (4), 889–898. https://doi.org/10.1007/s10068-010-0126-7. Garcı´a-Garibay, M., Go´mez-Ruiz, L., Cruz-Guerrero, A.E., Ba´rzana, E., 2014. Single cell protein: the algae. In: Encyclopedia of Food Microbiology, second ed. Vol. 3, pp. 425–430, https://doi.org/10.1016/B9780-12-384730-0.00309-8. Gilani, G.S., 2012. Background on international activities on protein quality assessment of foods. Br. J. Nutr. 108 (S2), S168–S182. Gmoser, R., Ferreira, J.A., Lundin, M., Taherzadeh, M., Lennartsson, P., 2018. Pigment production by the edible filamentous fungus neurospora intermedia. Fermentation 4 (11), 1–15. https://doi.org/10.3390/ fermentation4010011. Gonza´lez, N., Marque`s, M., Nadal, M., Domingo, J.L., 2020. Meat consumption: which are the current global risks? A review of recent (2010–2020) evidences. Food Res. Int. 137 (April), 109341. https:// doi.org/10.1016/j.foodres.2020.109341. Grassin, C., Fauquembergue, P., 1996. Fruit juices. In: Godfrey, T., West, S. (Eds.), Industrial Enzymology. MacMillan Press, pp. 226–264. Greiner, R., Konietzny, U., 2006. Phytase for food application. Food Technol. Biotechnol. 44 (2), 125–140. Griese, S., Fleischauer, A.T., MacFarquhar, J.K., Moore, Z., Harrelson, C., Valiani, A., Morrison, S.E., Sweat, D., Maillard, J.M., Griffin, D., Springer, D., Mikoleit, M., Newton, A.E., Jackson, B., Nguyen, T.A., Bosch, S., Davies, M., 2013. Gastroenteritis outbreak associated with unpasteurized tempeh. Emerg. Infect. Dis. 19 (9). Gunasekaran, S., Poorniammal, R., 2008. Optimization of fermentation conditions for red pigment production from Penicillium sp. under submerged cultivation. Afr. J. Biotechnol. 7 (12), 1894–1898. Hadi, J., Brightwell, G., 2021. Safety of alternative proteins: technological, environmental and regulatory aspects of cultured meat, plant-based meat, insect protein and single-cell protein. Foods 10 (6), 1226. Hakim, M.L., Sumantri, A., 2018. Statistics of Food Consumption 2018. Center for Agricultural Data and Information System, Secretariate General – Ministry of Agriculture. Halling, R.E., 2006. Wild edible fungi: a global overview of their use and importance to people. Non-wood Forest products 17. Econ. Bot. 60 (1). https://doi.org/10.1663/0013-0001(2006)60[99:wefago]2.0.co;2. Halloran, A., Hanboonsong, Y., Roos, N., Bruun, S., 2017. Life cycle assessment of cricket farming in NorthEastern Thailand. J. Clean. Prod. 156, 83–94. Hanft, F., Koehler, P., 2006. Studies on the effect of glucose oxidase in bread making. J. Sci. Food Agric. 86 (11), 1699–1704. Hashempour-Baltork, F., Khosravi-Darani, K., Hosseini, H., Farshi, P., Reihani, S.F.S., 2020. Mycoproteins as safe meat substitutes. J. Clean. Prod. 253, 119958. https://doi.org/10.1016/j.jclepro.2020.119958. Hayes, M., Mora, L., Hussey, K., Aluko, R.E., 2016. Boarfish protein recovery using the pH shift process and generation of protein hydrolysates with ACE-I and antihypertensive bioactivities in spontaneously hypertensive rats (SHRs). Innov. Food Sci. Emerg. Technol. 37, 253–260. Helm, R.M., Cockrell, G., Connaughton, C., Sampson, H.A., Bannon, G.A., Beilinson, V., Nielsen, N.C., Burks, A.W., 2000. A soybean G2 glycinin allergen. Int. Arch. Allergy Immunol. 123 (3), 213–219. https://doi.org/10.1159/000024446.

390

Current Developments in Biotechnology and Bioengineering

Henchion, M., Hayes, M., Mullen, A., Fenelon, M., Tiwari, B., 2017. Future protein supply and demand: strategies and factors influencing a sustainable equilibrium. Foods 6 (7), 53. https://doi.org/ 10.3390/foods6070053. Hermana, Mahmud, M., Karyadi, D., 1999. Compotiton value of food. In: The Complete Handbook of Tempe. The American Soybean Association. Hertzler, S.R., Lieblein-Boff, J.C., Weiler, M., Allgeier, C., 2020. Plant proteins: assessing their nutritional quality and effects on health and physical function. Nutrients 12 (12), 3704. Hesseltine, C.W., Wang, H.L., 1980. The importance of traditional fermented foods. Bioscience 30 (6), 402–404. Hjort, C.M, 2006. Production of food additives using filamentous fungi. In: Heller, K.J. (Ed.), Genetically Engineered Food. Method and Detection. Wiley VCH, pp. 95–108. Hocquette, A., Lambert, C., Singuin, C., Peterolff, L., Wagner, Z., Bonny, S.P.F., Lebert, A., Hocquette, J.F., 2015. Educated consumers don’t believe artificial meat is the solution to the problems with the meat industry. J. Integr. Agric. 14 (11), 273–284. Hoffman, J.R., Falvo, M.J., 2004. Protein—which is best? J. Sports Sci. Med. 3 (3), 118. € kenberg, J., 2017. Soy Sauce—China’s Brown Gold. https://www.alfalaval.com/media/stories/foodHo processing/soy-sauce-chinas-brown-gold/. Homolkova´, D., Plachy´, V., Dvora´ cek, V., Hu cko, B., Mudr´ık, Z., 2019. Nutrient digestibility of wheat in rats and chickens depending on the Rye 1B/1R translocation of wheat varieties. Sci. Agric. Bohem. 50 (3), 176–180. https://doi.org/10.2478/sab-2019-0024. Hsu, Y.-W., Hsu, L.-C., Liang, Y.-H., Kuo, Y.-H., Pan, T.-M., 2010. Monaphilones A-C, three new antiproliferative azaphilone derivatives from Monascus purpureus NTU 568. J. Agric. Food Chem. 58, 8211–8216. IARC, 1993. IARC Monographs on the Evaluation of Carcinogenic Risks to Humans: Some Naturally. IARC. €rtz, A.M.L., Overvad, K., Dahm, C.C., 2019. Substitution of red meat with Ibsen, D.B., Warberg, C.K., Wu poultry or fish and risk of type 2 diabetes: a Danish cohort study. Eur. J. Nutr. 58 (7), 2705–2712. Ingale, S., Shrivastava, S.K., 2011. Nutritional study of new variety of groundnut (Arachis hypogaea L.) JL-24 seeds. Afr. J. Food Sci. 5 (8), 490–498. INSC, 2009. National Standard of Maximum Mycotoxin Content in Food (SNI 7385:2009) (In Bahasa Indonesia). Indonesian National Council for Standarization, Jakarta. 24 pp. Iwe, M.O., Michael, N., Madu, N.E., Obasi, N.E., Onwuka, G.I., Nwabueze, T.U., Onuh, J.O., 2017. Physicochemical and pasting properties high quality cassava flour (HQCF) and wheat flour blends. Agrotechnology 6 (2), 167. Jacobson, M.F., DePorter, J., 2018. Self-reported adverse reactions associated with mycoprotein (Quornbrand) containing foods. Ann. Allergy Asthma Immunol. 120 (6), 626–630. https://doi.org/10.1016/j. anai.2018.03.020. James, J., Simpson, B.K., Marshall, M.R., 1996. Application of enzymes in food processing. Crit. Rev. Food Sci. Nutr. 36 (5), 437–463. https://doi.org/10.1080/10408399609527735. Jongema, Y., 2015. List of Edible Insect Species of the World. https://www.wur.nl/en/Research-Results/Chairgroups/Plant-Sciences/Laboratory-of-Entomology/Edible-insects/Worldwide-species-list.htm. Joshi, V.K., Attri, D., Bala, A., Bhushan, S., 2003. Microbial pigments. Indian J. Biotechnol. 2, 362–369. Kadar, A.D., Astawan, M., Putri, S.P., Fukusaki, E., 2020. Metabolomics based study of the effect of raw materials to the end product of tempe—an indonesian fermented soybean. Meta 10 (9), 1–11. https://doi.org/10.3390/metabo10090367. Kamal, S., Pandey, J., Ghignone, S., Varma, A., 2009. Mushroom biology and biotechnology an overview. In: Chauhan, A.K., Varma, A. (Eds.), A Textbook of Molecular Biotechnology, third ed. I. K. International Publishing House Pvt, pp. 573–628.

Chapter 12 • Filamentous fungi for food

391

Kanti, A., Sudiana, I.M., 2016. Comparison of Neurospora crassa and Neurospora sitophila for phytase production at various fermentation temperatures. Biodiversitas 17 (2), 769–775. https://doi.org/10.13057/ biodiv/d170253. Karkle, E.N.L., Beleia, A., 2010. Effect of soaking and cooking on phytate concentration, minerals, and texture of food-type soybeans. Food Sci. Technol. 30 (4), 1056–1060. Kataoka, S., 2005. Functional effects of Japanese style fermented soy sauce (shoyu) and its components. J. Biosci. Bioeng. 100 (3), 227–234. https://doi.org/10.1263/jbb.100.227. Kazer, J., Orfanos, G., Gallop, C., 2021. Quorn Footprint Comparison Report. Carbon Trust, p. 24. KEMENKES, 2017. Tabel komposisi pangan Indonesia 2017. Keuth, S., Bisping, B., 1993. Formation of vitamins by pure cultures of tempe moulds and bacteria during the Tempe solid substrate fermentation. J. Appl. Bacteriol. 75 (5), 427–434. https://doi.org/10.1111/ j.1365-2672.1993.tb02798.x. Kew, M.C., 2013. Synergistic interaction between aflatoxin and hepatitis B virus in hepatocarcinogenesis. In: Aflatoxins. IntechOpen. Knecht, A., Humpf, H.-U., 2006. Cytotoxic and antimitotic effects of N-containing Monascus metabolites studied using immortalized human kidney epithelial cells. Mol. Nutr. Food Res. 50, 406–412. Kong, Y., Zhang, L.L., Zhang, Y.Y., Sun, B.G., Sun, Y., Zhao, J., Chen, H.T., 2018. Evaluation of non-volatile taste components in commercial soy sauces. Int. J. Food Prop. 21 (1), 1854–1866. https://doi.org/ 10.1080/10942912.2018.1497061. Kumar, V.V., 2018. Aflatoxins: properties, toxicity and detoxification. Nutr. Food Sci. Int. J. 6 (5), 1–4. Lagrange, V., 2004. Reference Manual for U. S. Whey and Lactose Products. U.S. Dairy Export Council. http://usdec.files.cms-plus.com/PDFs/2008ReferenceManuals/Whey_Lactose_Reference_Manual_ Complete2_Optimized.pdf. , L., Caro, Y., 2017. Production and Lebeau, J., Venkatachalam, M., Fouillaud, M., Petit, T., Vinale, F., Dufosse new extraction method of polyketide red pigments produced by ascomycetous fungi from terrestrial and marine habitats. J. Fungi 3 (3). https://doi.org/10.3390/jof3030034. Lee, B.Q., Khor, S.M., 2015. 3-Chloropropane-1, 2-diol (3-MCPD) in soy sauce: a review on the formation, reduction, and detection of this potential carcinogen. Compr. Rev. Food Sci. Food Saf. 14. https://doi. org/10.1111/1541-4337.12120. Leisegang, R., Nevoigt, E., Spielvogel, A., Kristan, G., Niederhaus, A., Stahl, U., 2006. Fermentation of food by means of genetically modified yeast and filamentous fungi. In: Heller, K.J. (Ed.), Genetically Engineered Food. Method and Detection. Wiley VCH, pp. 62–94. Lin, C.P., Huang, P.C., 1986. Comparison of control diets containing various protein levels for determining net protein utilization by rats. J. Nutr. 116 (2), 216–222. https://doi.org/10.1093/jn/116.2.216. Lioe, H.N., Selamat, J., Yasuda, M., 2010. Soy sauce and its umami taste: a link from the past to current situation. J. Food Sci. 75 (3). https://doi.org/10.1111/j.1750-3841.2010.01529.x. Lombrana, M., Moralejo, F., Pinto, R., Martin, J.F., 2004. Modulation of Aspergillus awamori thaumatin secretion by modification of bipA gene expression. Appl. Environ. Microbiol. 70 (9), 5145–5152. Luning, P.A., Devlieghere, F., Verhe, R., 2007. Safety in the Agri-Food Chain. Wageningen Academic Publisher. Loret, M.-O., Morel, S., 2010. Isolation and structural characterization of two new metabolites from Monascus. J. Agric. Food Chem. 58, 1800–1803. Maing, I.-Y., Ayres, J.C., Koehler, P.E., 1973. Persistence of aflatoxin during the fermentation of soy sauce. Appl. Microbiol. 25 (6), 1015–1017. https://doi.org/10.1128/am.25.6.1015-1017.1973. Majesty, D., Ijeoma, E., Winner, K., Prince, O., 2019. Nutritional, anti-nutritional and biochemical studies on the oyster mushroom, Pleurotus ostreatus. EC Nutr. 14 (1), 36–59. Mapari, S.A.S., Meyer, A.S., Frisvad, J.C., & Thrane, U. (n.d.). Production of Monascus-like azaphilone pigments (Patent No. European Patent EP2262862 B1).

392

Current Developments in Biotechnology and Bioengineering

Mapari, S.A.S., Thrane, U., Meyer, A.S., 2010. Fungal polyketide azaphilone pigments as future natural food colorants? Trends Biotechnol. 28 (6), 300–307. https://doi.org/10.1016/j.tibtech.2010.03.004. Marasabessy, I., Sudirjo, F., 2017. Seaweed fortification on crispy enbal as local food of Kei Islands. IOP Conf. Ser.: Earth Environ. Sci. 89 (1), 1–5. Marasas, W., 2001. Recent research on fumonisins: a historical perspective. Environ. Health Perspect. 114, 237–241. Martinez-Medina, G.A., Cha´vez-Gonza´lez, M.L., Verma, D.K., Prado-Barraga´n, L.A., Martı´nez-Herna´ndez, J.L., Flores-Gallegos, A.C., Thakur, M., Srivastav, P.P., Aguilar, C.N., 2021. Bio-funcional components in mushrooms, a health opportunity: ergothionine and huitlacohe as recent trends. J. Funct. Foods 77. https://doi.org/10.1016/j.jff.2020.104326. Matsuo, M., 2000. Plasma cholesterol reduction by defatted soy ontjom (fermented with Neurospora intermedia) in rats fed a cholesterol-free diet. J. Nutr. Sci. Vitaminol. 46 (1), 30–33. https://doi.org/10.3177/ jnsv.46.30. McCormick, S.P., Stanley, A.M., Stover, N.A., 2011. Trichothecenes: from simple to complex mycotoxins. Toxins 3, 802–814. ˆ .S.M., Martins-Meyer, T.S., Figueiredo, E., Lobo, B.W.P., Dellamora-Ortiz, G.M., 2013. Enzymes in Miguel, A bakery: current and future trends. Food Ind., 278–321. Missmer, S.A., Suarez, L., Felkner, M., Wang, E., Merrill, A.H., Rothman, K.J., Hendricks, K.A., 2006. Exposure to fumonisins and the occurrence of neural tube defects along the Texas–Mexico border. Environ. Health Perspect. 114, 237–241. Mitchell, G.V., Jenkins, M.Y., Grundel, E., 1989. Protein efficiency ratios and net protein ratios of selected protein foods. Plant Foods Hum. Nutr. 39 (1), 53–58. Mo, H., Kariluoto, S., Piironen, V., Zhu, Y., Sanders, M.G., Vincken, J.P., Wolkers-Rooijackers, J., Nout, M.J.R., 2013. Effect of soybean processing on content and bioaccessibility of folate, vitamin B12 and isoflavones in tofu and tempe. Food Chem. 141 (3), 2418–2425. https://doi.org/10.1016/j. foodchem.2013.05.017. € zer, N., Hermansen, J.E., Knudsen, M.T., 2020. Mogensen, L., Heusale, H., Sinkko, T., Poutanen, K., So Potential to reduce GHG emissions and land use by substituting animal-based proteins by foods containing oat protein concentrate. J. Clean. Prod. 274. https://doi.org/10.1016/j.jclepro.2020.122914. rrez, A.D., Castro-Rosas, J., Mun ˜ oz-Llandes, Mora-Escobedo, R., Robles-Ramı´rez, M.D.C., Roma´n-Gutie C.B., Guzma´n-Ortiz, F.A., 2018. Peptides and microorganisms isolated from soybean sources with antimicrobial activity. In: Soybean-Biomass, Yield and Productivity. IntechOpen. ndez-Zavala, A., Morales-Oyervides, L., Ruiz-Sa´nchez, J.P., Oliveira, J.C., Sousa-Gallagher, M.J., Me , L., Montan ˜ ez, J., 2020. Biotechnological approaches for the production of natGiuffrida, D., Dufosse ural colorants by talaromyces/penicillium: a review. Biotechnol. Adv. 43 (July). https://doi.org/ 10.1016/j.biotechadv.2020.107601. Moresi, M., Parente, E., 2014. Fermentation (industrial): production of some organic acids (citric, gluconic, lactic, and propionic). In: Encyclopedia of Food Microbiology: Second Edition. vol. 1. Elsevier, https:// doi.org/10.1016/B978-0-12-384730-0.00111-7. Nadathur, S.R., Wanasundara, J.P.D., Scanlin, L., 2016. Sustainable Protein Sources. Elsevier. Negra˜o, C.C., Mizubuti, I.Y., Morita, M.C., Colli, C., Ida, E.I., Shimokomaki, M., 2005. Biological evaluation of mechanically deboned chicken meat protein quality. Food Chem. 90 (4), 579–583. Nout, M.J.R., 2005. Tempe fermentation, innovation and functionality: update into the third millenium. J. Appl. Microbiol. 98 (4), 789–805. Nout, M.J.R., Aidoo, K.E., 2002. Asian fungal fermented food. In: Industrial Applications. Springer, pp. 23–47. Nurdini, A.L., Nuraida, L., Suwanto, A., Suliantari., 2015. Microbial growth dynamics during tempe fermentation in two different home industries. Int. Food Res. J. 22 (4), 1668–1674.

Chapter 12 • Filamentous fungi for food

393

Nurjannah, N., Nurhikmah, N., 2020. Pengaruh konsentrasi ragi dan lama fermentasi terhadap mutu tape singkong (Manihot esculenta crantz). J. Borneo Saintek 3 (2), 73–78. O’Donnell, K., Cigelnik, E., Casper, H.H., 1998. Molecular phylogenetic, morphological, and mycotoxin dam veneta support reidentification of the quorn mycoprotein fungus as Fusariunatum. Fungal Genet. Biol. 23 (1), 57–67. Oatway, L., Vasanthan, T., Helm, J.H., 2001. Phytic acid. Food Rev. Int. 17 (4), 419–431. Ogasawara, M., Yamada, Y., Egi, M., 2006. Taste enhancer from the long-term ripening of miso (soybean paste). Food Chem. 99 (4), 736–741. https://doi.org/10.1016/j.foodchem.2005.08.051. Ogbodo, U.O., Ugwuanyi, J.O., 2017. Production, use, and prospects of microbial food colorants. In: Microbial Production of Food Ingredients and Additives. Elsevier Inc., https://doi.org/10.1016/b978-0-12811520-6.00007-6. Oibiokpa, F.I., Akanya, H.O., Jigam, A.A., Saidu, A.N., Egwim, E.C., 2018. Protein quality of four indigenous edible insect species in Nigeria. Food Sci. Human Wellness 7 (2), 175–183. https://doi.org/10.1016/j. fshw.2018.05.003. Okouchi, R., Sakanoi, Y., Tsuduki, T., 2019. Miso (fermented soybean paste) suppresses visceral fat accumulation in mice, especially in combination with exercise. Nutrients 11 (3). https://doi.org/10.3390/ nu11030560. Oonincx, D.G.A.B., van Itterbeeck, J., Heetkamp, M.J.W., van den Brand, H., van Loon, J.J.A., van Huis, A., 2010. An exploration on greenhouse gas and ammonia production by insect species suitable for animal or human consumption. PLoS One 5 (12), 1–7. https://doi.org/10.1371/journal.pone.0014445. Ough, C.S., 1975. Further investigations with glucose oxidase-catalase enzyme systems for use with wine. Am. J. Enol. Vitic. 26 (1), 30–36. Palmer, S., 1989. Recommended dietary allowances, tenth edition. Eur. J. Clin. Nutr. 44 (Suppl. 2), 13–21. Papoutsis, K., Grasso, S., Menon, A., Brunton, N.P., Lyng, J.G., Jacquier, J.C., Bhuyan, D.J., 2020. Recovery of ergosterol and vitamin D2 from mushroom waste—potential valorization by food and pharmaceutical industries. Trends Food Sci. Technol. 99 (March), 351–366. https://doi.org/10.1016/j. tifs.2020.03.005. Partida-Martinez, L.P., De Looß, C.F., Ishida, K., Ishida, M., Roth, M., Buder, K., Hertweck, C., 2007. Rhizonin, the first mycotoxin isolated from the zygomycota, is not a fungal metabolite but is produced by bacterial endosymbionts. Appl. Environ. Microbiol. 73 (3), 793–797. https://doi.org/10.1128/ AEM.01784-06. Patakova, P., 2013. Monascus secondary metabolites: production and biological activity. J. Ind. Microbiol. Biotechnol. 40 (2), 169–181. https://doi.org/10.1007/s10295-012-1216-8. Payne, G.A., Brown, M.P., 1998. Genetics and physiology of aflatoxin biosynthesis. Rev. Phytopathol. 36 (1), 329–362. Polak-Sliwiniska, M., Paszczyk, B., 2021. Trichothecenes in food and feed, relevance to human and animal health and methods of detection: a systematic review. Molecules 26, 454. Polizeli, M., Rizatti, A.C., Monti, R., Terenzi, H.F., Jorge, J.A., 2005. Xylanases from fungi: properties and industrial applications. Appl. Microbiol. Biotechnol. 67 (5), 577–591. Post, M.J., Hocquette, J.F., 2017. New sources of animal proteins: in vitro meat. In: New Aspects of Meat Quality. Elsevier Ltd, https://doi.org/10.1016/B978-0-08-100593-4/00017-5. Quorn. (n.d.). Nutritional Profile of Quorn™ Mycoprotein. PUSIDO Badan Standardisasi Nasional, 2012. Tempe: Persembahan Indonesia untuk Dunia. Badan Standardisasi Nasional. Qureshi, T.M., Vermeer, C., Vegarud, G.E., Abrahamsen, R.K., Skeie, S., 2013. Formation of biogenic amines and vitamin K contents in the Norwegian autochthonous cheese Gamalost during ripening. Dairy Sci. Technol. 93 (3), 303–314.

394

Current Developments in Biotechnology and Bioengineering

Ram, S., Narwal, S., Gupta, O.P., Pandey, V., Singh, G.P., 2020. Anti-nutritional factors and bioavailability: approaches, challenges, and opportunities. In: Gupta, O.P., Pandey, V., Narwal, S., Sharma, P., Ram, S., Singh, G.P. (Eds.), Wheat and Barley Grain Biofortification, Woodhead Publishing Series in Food Science, Technology and Nutrition. Woodhead Publishing, pp. 101–128, https://doi.org/10.1016/B978-012-818444-8.00004-3 (Chapter 4). Ratledge, C., 2004. Fatty acid biosynthesis in microorganisms being used for single cell oil production. Biochimie 85 (11), 807–815. Reddy, K.R.N., Salleh, B., Saad, B., Abbas, H.K., Abel, C.A., Shier, W.T., 2010. An overview of mycotoxin contamination in foods and its implications for human health. Toxin Rev. 29 (1), 3–26. € ling, W.F.M., Timotius, K.H., Budhi Prasetyo, A., Stouthamer, A.H., Van Verseveld, H.W., 1994. Changes in Ro microflora and biochemical composition during the Baceman stage of traditional indonesian Kecap (soy sauce) production. J. Ferment. Bioeng. 77 (1), 62–70. https://doi.org/10.1016/0922-338X(94) 90210-0. Jongrungruangchok, S., Kittakoop, P., Yongsmith, B., Bavovada, R., Tanasupawat, S., Lartpornmatulee, N., Thebtaranonth, Y., 2004. Azaphilone pigments from a yellow mutant of the fungus Monascus kaoliang. Phytochemistry 65, 2569–2575. , J., Sranacharoenpong, K., Harwatt, H., Wien, M., Soret, S., 2015. The environmental cost of protein Sabate food choices. Public Health Nutr. 18 (11), 2067–2073. https://doi.org/10.1017/S1368980014002377. Sadler, M.J., 1994. Fungal protein. In: New and Developing Sources of Food Proteins. Springer, pp. 343–362, https://doi.org/10.1007/978-1-4615-2652-0_11. Sadler, M.J., 2003. Mycoprotein. In: Caballero, B. (Ed.), Encyclopedia of Food Sciences and Nutrition, second ed. Academic Press, pp. 4072–4079. Sa´nchez-Moya, T., Martı´nez-Herna´ndez, V.M., Lo´pez-Nicola´s, R., Gonza´lez-Bermu´dez, C.A., Ros-Berruezo, G., Frontela-Saseta, C., 2019. Effect of soaking and inositol phosphate content on in vitro mineral availability in edible seaweeds. J. Appl. Phycol. 31 (3), 1981–1989. Sancholle, M., Losel, D., 1996. Lipids in fungal biotechnology. In: Kuck, U. (Ed.), The Mycota II. Genetics and Biotechnology. Springer, pp. 339–367. Sardjono, 2016. Teknologi Proses Fermentasi Kecap (Tinjauan Singkat Aspek Teknologi dan Mikrobiologi). Kanisius. Sastraatmaja, D.D., Tomita, F., Kasai, T., 2002. Production of high-quality Oncom, a traditional Indonesian fermented food, by the inoculation with selected mold strains in the form of pure culture and solid inoculum. J. Grad. School Agron. Hokkaido Univ. 70, 111–127. Savage, G.P., Deo, S., 1989. The nutritional value of peas (Pisum sativum). A literature review. Nutr. Abstr. Rev. 59 (2), 66–83. Schaafsma, G., 2005. The protein digestibility-corrected amino acid score (PDCAAS)—a concept for describing protein quality in foods and food ingredients: a critical review. J. AOAC Int. 88 (3), 988–994. Schoenlechner, R., Siebenhandl, S., Berghofer, E., 2008. Pseudocereals. In: Arendt, E.K., Dal Bello, F. (Eds.), Gluten-Free Cereal Products and Beverages, Food Science and Technology 2008. Academic Press, pp. 149–190, https://doi.org/10.1016/B978-012373739-7.50009-5. VI (Chapter 7). € sler, H., de Boer, J., Boersema, J.J., 2012. Can we cut out the meat of the dish? Constructing consumerScho oriented pathways towards meat substitution. Appetite 58 (1), 39–47. https://doi.org/10.1016/j. appet.2011.09.009. Schweiggert-Weisz, U., Eisner, P., Bader-Mittermaier, S., Osen, R., 2020. Food proteins from plants and fungi. Curr. Opin. Food Sci. 32, 156–162. https://doi.org/10.1016/j.cofs.2020.08.003. Scott, P., 2012. Recent research on fumonisins: a review. Food Addit. Contam. 2 (2), 242–248.

Chapter 12 • Filamentous fungi for food

395

Sharp, T., 1993. Quorn myco-protein: the development of a new food and its contribution to the diet. In: van der Heij, D.G., Lowik, M.R.H., Ockhuizen, T. (Eds.), Food and Nutrition Policy in Europe. Pudoc Scientific Publisher, pp. 149–151. Shukla, S., Kim, M., 2016. Determination of biogenic amines and total aflatoxins: quality index of starter culture soy sauce samples. Food Sci. Biotechnol. 25 (4), 1221–1224. https://doi.org/10.1007/s10068016-0194-4. Shurtleff, W., Aoyagi, A., 1984. History of Tempeh., p. 101. http://search.ebscohost.com/login.aspx? direct¼true&db¼ffh&AN¼1985-04-J-0098&site¼ehost-live. Sirbu, T., 2011. The searching of active catalase producers among the microscopic fungi. Analele Univ. din Oradea Fasc. Biol. 18 (2), 164–167. Six, L., De Wilde, B., Vermeiren, F., Van Hemelryck, S., Vercaeren, M., Zamagni, A., Masoni, P., Dewulf, J., De Meester, S., 2017. Using the product environmental footprint for supply chain management: lessons learned from a case study on pork. Int. J. Life Cycle Assess. 22 (9), 1354–1372. Sokolowski, C.M., Higgins, S., Vishwanathan, M., Evans, E.M., 2020. The relationship between animal and plant protein intake and overall diet quality in young adults. Clin. Nutr. 39 (8), 2609–2616. https://doi. org/10.1016/j.clnu.2019.11.035. Solomons, G.L., 1986. Microbial proteins and regulatory clearance for RHM myco-protein. In: Moo-Young, M., Gregory, K.F. (Eds.), Microbial Biomass Proteins. Elsevier, pp. 19–26. Song, M., Fung, T.T., Hu, F.B., Willett, W.C., Longo, V.D., Chan, A.T., Giovannucci, E.L., 2016. Association of animal and plant protein intake with all-cause and cause-specific mortality. JAMA Intern. Med. 176 (10), 1453–1463. https://doi.org/10.1001/jamainternmed.2016.4182. Song, Y.R., Jeong, D.Y., Baik, S.H., 2015. Monitoring of yeast communities and volatile flavor changes during traditional Korean soy sauce fermentation. J. Food Sci. 80 (9), 2005–2014. https://doi.org/ 10.1111/1750-3841.12995. Spinnler, H., Leclercq-Perlat, M., 2007. White-mould cheese. In: McSweeney, P. (Ed.), Cheese Problem Solved. CRC Press, pp. 268–269. Stone, A.K., Tanaka, T., Nickerson, M.T., 2019. Protein quality and physicochemical properties of commercial cricket and mealworm powders. J. Food Sci. Technol. 56 (7), 3355–3363. Sukumaran, R.K., Singhania, R.R., Pandey, A., 2005. Microbial Cellulases-Production, Applications and Challenges. Tallapragada, P., Dikshit, R., 2017. Microbial production of secondary metabolites as food ingredients. In: Microbial Production of Food Ingredients and Additives. Elsevier Inc., https://doi.org/10.1016/b9780-12-811520-6.00011-8. Tamam, B., Syah, D., Suhartono, M.T., Kusuma, W.A., Tachibana, S., Lioe, H.N., 2019. Proteomic study of bioactive peptides from tempe. J. Biosci. Bioeng. 128 (2), 241–248. https://doi.org/10.1016/j. jbiosc.2019.01.019. Tanaka, N., Kovats, S.K., Guggisberg, J.A., Meske, L.M., Doyle, M., 1985. Evaluation of the microbiological safety of tempeh made from unacidified soybeans. J. Food Prot. 48 (5), 438–441. Taylor, R.C., Omed, H., Edwards-Jones, G., 2014. The greenhouse emissions footprint of free-range eggs. Poult. Sci. 93 (1), 231–237. Thoma, G., Popp, J., Nutter, D., Shonnard, D., Ulrich, R., Matlock, M., Kim, D.S., Neiderman, Z., Kemper, N., East, C., 2013. Greenhouse gas emissions from milk production and consumption in the United States: a cradle-to-grave life cycle assessment circa 2008. Int. Dairy J. 31, S3–S14. Tilman, D., Clark, M., 2014. Global diets link environmental sustainability and human health. Nature 515 (7528), 518–522.

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Tinarwo, J., Mvumi, B.M., Saidi, P.T., Benhura, C., Manditsera, F.A., 2021. Effect of heat treatment on selected macronutrients in the wild harvested edible ground cricket, Henicus whellani Chopard. Int. J. Trop. Insect Sci. https://doi.org/10.1007/s42690-020-00375-6. Tobler, C., Visschers, V.H.M., Siegrist, M., 2011. Eating green. Consumers’ willingness to adopt ecological food consumption behaviors. Appetite 57 (3), 674–682. https://doi.org/10.1016/j.appet.2011.08.010. Toelstede, S., Hofmann, T., 2009. Kokumi-active glutamyl peptides in cheeses and their biogeneration by penicillium roquefortii. J. Agric. Food Chem. 57 (9), 3738–3748. https://doi.org/10.1021/jf900280j. Tracy, C.R., Best, S., Bagrodia, A., Poindexter, J.R., Adams-Huet, B., Sakhaee, K., Maalouf, N., Pak, C.Y.C., Pearle, M.S., 2014. Animal protein and the risk of kidney stones: a comparative metabolic study of animal protein sources. J. Urol. 192 (1), 137–141. https://doi.org/10.1016/j.juro.2014.01.093. Tran, H., Juergens, A., 2020. Mushroom Toxicity. StatPearls Publishing. Trinci, A.P., 1991. Quorn mycoprotein. Mycologist 5, 106–109. Udomsil, N., Imsoonthornruksa, S., Gosalawit, C., Ketudat-Cairns, M., 2019. Nutritional values and functional properties of house cricket (Acheta domesticus) and field cricket (Gryllus bimaculatus). Food Sci. Technol. Res. 25 (4), 597–605. https://doi.org/10.3136/fstr.25.597. United Nations, 2019. World Population Prospects 2019. US Dairy Export Council, 1999. Reference Manual for U.S. Whey Products, second ed. United State Dairy Export Council. USDA, 2021. FoodData Central. Utami, R., Wijaya, C.H., Lioe, H.N., 2016. Taste of water-soluble extracts obtained from over-fermented tempe. Int. J. Food Prop. 19 (9), 2063–2073. https://doi.org/10.1080/10942912.2015.1104509. Valencia del Toro, G., Vega, R.C., Garin-Aguilar, M.E., Lara, H.L., 2004. Biological quality of proteins from three strains of Pleurotus spp. Food Chem. 94 (4), 494–497. https://doi.org/10.1016/j. foodchem.2004.11.053. rez, T., Paredes-Lo´pez, O., 2015. Edible mushrooms: improving human Valverde, M.E., Herna´ndez-Pe health and promoting quality life. Int. J. Microbiol. 2015, 376387. van Vliet, S., Burd, N.A., van Loon, L.J.C., 2015. The skeletal muscle anabolic response to plant-versus animal-based protein consumption. J. Nutr. 145 (9), 1981–1991. Van Zanten, H.H.E., Mollenhorst, H., Klootwijk, C.W., van Middelaar, C.E., de Boer, I.J.M., 2016. Global food supply: land use efficiency of livestock systems. Int. J. Life Cycle Assess. 21, 747–758. Velmurugan, P., Lee, Y.H., Venil, C.K., Lakshmanaperumalsamy, P., Chae, J.C., Oh, B.T., 2010. Effect of light on growth, intracellular and extracellular pigment production by five pigment-producing filamentous fungi in synthetic medium. J. Biosci. Bioeng. 109 (4), 346–350. https://doi.org/10.1016/j. jbiosc.2009.10.003. Virtanen, H.E.K., Voutilainen, S., Koskinen, T.T., Mursu, J., Kokko, P., Ylilauri, M.P.T., Tuomainen, T.P., Salonen, J.T., Virtanen, J.K., 2019. Dietary proteins and protein sources and risk of death: the Kuopio ischaemic heart disease risk factor study. Am. J. Clin. Nutr. 109 (5), 1462–1471. https://doi.org/10.1093/ ajcn/nqz025. Vogelsang-O’Dwyer, M., Zannini, E., Arendt, E.K., 2021. Production of pulse protein ingredients and their application in plant-based milk alternatives. Trends Food Sci. Technol. 110, 364–374. https://doi.org/ 10.1016/j.tifs.2021.01.090. Warkentin, T.D., Delgerjav, O., Arganosa, G., Rehman, A.U., Bett, K.E., Anbessa, Y., Rossnagel, B., Raboy, V., 2012. Development and characterization of low-phytate pea. Crop Sci. 52 (1), 74–78. Warrilow, A., Mellor, D., McKune, A., Pumpa, K., 2019. Dietary fat, fibre, satiation, and satiety—a systematic review of acute studies. Eur. J. Clin. Nutr. 73 (3), 333–344. https://doi.org/10.1038/s41430-018-0295-7. Wiebe, M., 2002. Myco-protein from fusarium venenatum: a well-established product for human consumption. Appl. Microbiol. Biotechnol. 58 (4), 421–427. https://doi.org/10.1007/s00253-002-0931-x.

Chapter 12 • Filamentous fungi for food

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Wiebe, M.G., 2004. Quorn™ myco-protein—overview of a successful fungal product. Mycologist 18 (1), 17–20. https://doi.org/10.1017/S0269915X04001089. Wiedemann, S., McGahan, E., Murphy, C., Yan, M.-J., Henry, B., Thoma, G., Ledgard, S., 2015. Environmental impacts and resource use of Australian beef and lamb exported to the USA determined using life cycle assessment. J. Clean. Prod. 94, 67–75. Wikanta, W., 2019. Membuat Oncom Praktis dan Aman Aflatoksin. Rajawali Pers. Xu, D., Wang, H., Zhang, Y., Niu, W., Yang, Z., Sun, X., 2012. Quantitative risk assessment of aflatoxin B1in fermented soy sauce in China using Monte Carlo technique. Fresenius Environ. Bull. 21, 895–900. Yagoub, A.A., Abdalla, A.A., 2007. Effect of domestic processing methods on chemical composition, in vitro digestibility of protein and starch and functional properties of bambara groundnut (Voandzeia subterranea) seed. Res. J. Agric. Biol. Sci. 3 (1), 24–34. Yang, Y., Deng, Y., Jin, Y., Liu, Y., Xia, B., Sun, Q., 2017. Dynamics of microbial community during the extremely long-term fermentation process of a traditional soy sauce. J. Sci. Food Agric. 97 (10), 3220–3227. https://doi.org/10.1002/jsfa.8169. Yasuda, M., 2011. Fermented tofu, tofuyo. In: Ng, T.-B. (Ed.), Soybean—Biochemistry, Chemistry and Physiology. IntechOpen, pp. 299–322. Yoneya, T., 2003. Fermented soy products: tempe, nattos, miso and soy sauce. In: Hui, Y., Ghazala, S., Murell, K., Nip, W. (Eds.), Handbook of Vegetable Preservation and Processing. CRC Press. Zarkadas, C.G., Voldeng, H.D., Yu, Z.R., Shang, K., Pattison, P.L., 1997. Comparison of the protein quality of five new northern adapted natto soybean cultivars by amino acid analysis. J. Agric. Food Chem. 45 (6), 2013–2019. https://doi.org/10.1021/jf9604697. Zhang, J., Tatsumi, E., Fan, J., Li, L., 2007. Chemical components of Aspergillus-type Douchi, a Chinese traditional fermented soybean product, change during the fermentation process. Int. J. Food Sci. Technol. 42 (3), 263–268. Zhang, Y., He, S., Simpson, B.K., 2018. Enzymes in food bioprocessing—novel food enzymes, applications, and related techniques. Curr. Opin. Food Sci. 19, 30–35. Zhu, Z., Momeu, C., Zakhartsev, M., Schwaneberg, U., 2006. Making glucose oxidase fit for biofuel cell applications by directed protein evolution. Biosens. Bioelectron. 21 (11), 2046–2051.

13 Filamentous fungi as animal and fish feed ingredients Sajjad Karimi, Jorge A. Ferreira, and Mohammad J. Taherzadeh ˚ S , SW EDEN SWE DISH C ENTRE FOR RE SOUR CE R ECOVE RY, UNIVERS ITY O F BORA˚ S, BOR A

1. Introduction There is no doubt that providing food for the population is one of the biggest challenges concerning the governments for the future. This issue will be more critical when reports show that population will grow beyond 9 billion people by 2050 (FAO, 2018). Supplying huge amount of food and energy resources for this growing population from one side and generation of giant amount of waste from other side, make the situation even more complicated. Farm products, including animal-based protein producing sector is cooperated as a significant part of protein supplying for human. However, putting pressure on domestic animal farms in order to increase production, concomitantly rises the need for high quality feed ingredient. Among feed ingredients, protein source ingredients are the most valuable component. Utilization of food-grade protein source ingredient such as fishmeal and other agricultural products, e.g., soybean meal, sunflower meal, etc., for animal feed is not sustainable. Fishmeal, the most common protein source ingredient, is commonly produce from pelagic fish species such as anchovy, sardine, jack mackerel, or capelin, which their stock resources declined since last decades (FAO, 2018). Limitations of supply, rapid expansion in different farming sectors and increase in the demand has resulted in incredible increase in fishmeal price. Even though, different alternative protein sources such as soybean meal have introduced as new feed ingredient, these feedstuff do not meet the nutritional requirements of farmed animals. On the other hand, competition with their application as food, limited land, and water resources for agricultural purposes are still obstacles in the way of these alternatives as suitable resources for animal feed (Karimi et al., 2018). Therefore, a great effort has been given to find an appropriate alternative protein source ingredient for animal feed. Various commercial feed recipes assigned to different animals, contain protein, fat, minerals, vitamins, etc. Feed composition and formulation is greatly affected by several biotic factors, e.g., animal species, life stage, health status, etc. (NRC, 2011). Feed ingredient, however, generally vary from simple elements to complex compounds and chemicals. However, as the basic classification, they grouped in three macronutrient groups, protein, fat, and carbohydrates. It must be taken into account that a variety of additives Current Developments in Biotechnology and Bioengineering. https://doi.org/10.1016/B978-0-323-91872-5.00002-8 Copyright © 2023 Elsevier Inc. All rights reserved.

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such as vitamins, minerals, antioxidant agents, etc., need to be added to the recipes to meet all nutritional requirement. From both animal health and growth standing points, protein source ingredient is the most important part in the feed. In addition, since protein source ingredient is the most expensive component composing animal feed, it can be as key factor determining final feed production cost (Sanchez-Muros et al., 2014). Inclusion of ingredients entitle additives can enhance feed quality and lower feed production cost. Recently, filamentous fungal biomass has proposed as one of promising renewable protein sources with the application in animal feed (Karimi et al., 2018). In this chapter different aspects of its feed application will be discussed.

2. Animal compound feed The term “compound feed” refers to the feed type that formulated based on the nutritional requirements of each individual animal (Hardy, 2010). Nutritional quality of feed attributed to the specific animal can be evaluated previously in the experiments and accordingly a range of different raw material of varied sources are mixed and processed by processing equipment. Development in the knowledge of animal specific requirements in the terms of amino acids, fatty acids, minerals, and vitamins, resulted in formulating more accurate diet for each animal species. There is no doubt that protein supply is the most important part in animal feed production. Currently, fishmeal is the preferred protein supplement to the animal diet and therefore, its nutritional properties is described in next section.

2.1 Fishmeal Fishmeal is a nutrient-rich feed ingredient with high digestibility that is the preferred animal protein supplement in the diets of domestic animals, especially fish and shrimp (Bimbo and Crowther, 1992). It contains high quantities of energy per kilogram and is a unique source of protein, lipids (oils), minerals, and vitamins. Fishmeal can be manufactured from wide range of aquatic animals but is generally made from wild catches, small marine fish that contain a high percentage of bones and oil, and therefore, they not consider for direct human consumption. These fishes can be termed as “industrial fish” since most of them are caught with the only purpose of fishmeal and fish oil production. Highquality fishmeal normally contains between 60% and 72% crude protein by weight. Typical diets for fish may contain from 32% to 45% total protein by weight, and diets for shrimp may contain 25%–42% total protein. The percentages of inclusion rate of fishmeal in diets for carp and tilapia may be from 5% to 7%, and up to 40% to 55% in trout, salmon, and some marine fishes. A typical inclusion rate of fishmeal in terrestrial livestock diets is usually 5% or less on a dry matter basis (FAO, 2018). Any complete diet must contain some protein, but the nutritional value of the protein relates directly to its amino acid composition and digestibility. The amino acid profile of fishmeal is what makes this feed ingredient attractive as a protein supplement. Although

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most of the oil usually gets extracted during processing of the fishmeal, the remaining lipid typically represents between 6% and 10% by weight but can range from 4% to 20% (Olsen and Hasan, 2012). Fishmeal is an excellent source of the essential polyunsaturated fatty acids (PUFAs) in both the omega-3 and omega-6 families of fatty acids. Fishmeal and oil contain more omega-3, than omega-6 fatty acids. In contrast, most plant lipids contain higher concentrations of omega-6 fatty acids. Fishmeal also contains valuable phospholipids, fat-soluble vitamins, and steroid hormones (Kris-Etherton et al., 2002).

2.2 Economic and environmental aspects of fishmeal as feed ingredient The fishmeal and fish oil industries are among few major animal industries existing nowadays that still relies greatly on a wild catches. The supply is currently stable at 6.0–6.5 million tons yearly. Roughly, 4–5 tons of whole fish are required to produce 1 ton of dry fishmeal (Olsen and Hasan, 2012). The majority of fishmeal produced is incorporated into commercial diets fed to fish, shrimp, swine, poultry, dairy cattle, and other animals such as mink (Fig. 1). It is unlikely that supplies of commercially available fishmeal and oil will be able to keep pace with the projected increase in worldwide production of aquaculture and terrestrial animal feeds. In most recent years, aquaculture has used approximately 46% of the total annual fishmeal production, a figure that is expected to rise as demand for aquaculture products increases in the next decade (FAO, 2018). The best approach in feed formulation is to use high-quality feedstuffs to manufacture a diet that meets the nutritional and energy requirements of the aquaculture species in question. If a portion or all of the fishmeal in a diet can be replaced successfully with other high-quality protein sources, doing so will contribute greatly toward protecting the surrounding environment and promoting a sustainable aquaculture industry. New information on nutrient requirements of aquatic organisms coupled with advances in feed technology indicates that species-specific fish diets can be made by partial or total replacement of fishmeal with other plant and animal proteins.

FIG. 1 Comparison of the status of fishmeal consumption in different sectors of animal farming (between 2002 and 2010). Data collected from Olsen, R., Hasan, M., 2012. A limited supply of fishmeal: impact on future increases in global aquaculture production. Trends Food Sci. Technol. 27, 120–128.

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Balancing nutrients in diets by using the minimum amount of fishmeal to meet specific amino acid requirements for fast growth and reproduction and reducing feed costs constitute one of the principal objectives in formulation of fish feeds. The animal feed production industry, such as aquaculture industry, must continue to seek out alternative sources of high-quality plant and animal-based protein ingredients for their feedstuffs. Presently, this is an active area of research in aquaculture nutrition. If supplies of fishmeal do not increase, the “fishmeal trap” will start to constrain producers of shrimp and carnivorous fish as the world market price of fishmeal increases in response to increasing demand. As presented in Table 1, average inclusion of fishmeal in commercial compounded feed from 1995 to 2010 in major groups of farmed species had an impressive reduction. The increased knowledge has also resulted in improved feed conversion ratios (FCR). For example, the reported FCR of fed carps dependent upon industrial compounded aquafeed was 2.0 in 1995 and is predicted to be reduced to 1.7 in 2015, for marine shrimps from 2.0 to 1.5 and salmon from 1.5 to 1.3 (Olsen and Hasan, 2012). FAO (2018) reported that the inclusion of fishmeal would continue to decrease in compounded feed for farmed fish and shrimps in the future. From 2010 to 2020, the average levels of fishmeal in the feed are projected to be reduced further from 16% to 8% for shrimps, from 26% to 12% for marine fish, from 22% to 12% for salmon and from 2% to 3% to 1% in carps and tilapias.

2.3 Alternatives to the fishmeal Plant proteins have been and will probably continue to be the main choice as replacement of fishmeal in aquaculture diets. However, plant protein meals have several nutritional drawbacks compared to fishmeal particularly in diets prepared for the carnivorous species which are not adapted to plant feed. In addition to a relatively low content of proteins, the presence of antinutritional components will reduce the digestion or absorption of nutrients, counteract the function of vitamins and may even induce toxicity (Francis et al., 2001; Krogdahl et al., 2010; Tacon and Hasan, 2007). Soybean meal is a by-product of the soybean oil industry. Soybean meal is used as a source of protein by the animal feed industry, either for direct use at farm level, or blended in the mixed feeds. Soybean meal protein levels generally reach around 44%–48% of the total dry matter as compared to 62%–70% in the case of fishmeal (the richest source of protein available for feeding animals). Soybean and other legume meals, which are widely used in the diets of most farm animals such as pigs and chickens, are a good source of lysine and tryptophan but are limiting in the sulfur-containing amino acids methionine and cysteine (Bakke-McKellep et al., 2007). Plant-based proteins, even when properly processed, are usually not as digestible as fishmeal; and their inclusion rate into the diet is often limited as it results in depressed growth rates and feed intake (Karimi et al., 2019). Proteins in cereal grains and other plant concentrates do not contain complete amino acid profiles and usually are deficient in the essential amino acids (EAAs) lysine and methionine. Overall protein digestibility values for fishmeal are consistently above

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Table 1 Production of main farmed fish in the world, commercial feed consumption, FCRa during the years 1995–2020. Species group

Total production

% on commercial feed

Average FCRa

% of fishmeal in feed

Total feed usedb

Total fishmeal usedb

1995 2005 2010 2015 2020

925 2664 4113 6043 8087

75 89 95 97 100

2.0 1.8 1.6 1.5 1.4

28 24 16 12 8

1387 4268 6251 8793 11,322

388 1024 1000 1055 906

1995 2005 2010 2015 2020

533 1402 2137 3140 4613

50 70 73 75 80

2.0 1.9 1.9 1.8 1.8

50 38 26 18 12

533 2050 2964 4239 6643

267 779 771 763 797

1995 2005 2010 2015 2020

537 1382 1734 2213 2825

100 100 100 100 100

1.5 1.3 1.3 1.3 1.3

45 35 22 16 12

806 1796 2255 2877 3672

363 629 496 460 441

1995 2005 2010 2015 2020

5154 9100 11,670 14,190 16,459

20 45 50 55 60

2.0 1.8 1.8 1.7 1.6

10 8 2 1 1

2062 7371 10,503 13,275 15,801

206 590 210 133 158

1995 2005 2010 2015 2020

704 1980 3386 5453 8012

70 80 85 90 95

2.0 1.8 1.7 1.6 1.6

10 8 3 2 1

985 2852 4893 7852 12,178

99 228 147 157 122

5773 18,337 26,866 37,036 49,613

1323 3250 2624 2568 2424

Year

Marine shrimp

Marine fish

Salmon

Fed carpc

Tilapia

Sum of all five groups 1995 2005 2010 2015 2020 a

7853 16,528 23,040 31,047 39,996

FCR: feed conversion ratio (total feed intake/total increase in biomass). In 1000 tons. c Excluding silver carp, bighead carp, and Indian major carp. Data adapted from Tacon, A., Hasan, M., 2007. Global synthesis of feeds and nutrients for sustainable aquaculture development. Study and Analysis of Feeds and Fertilizers for Sustainable Aquaculture Development, vol. 497. FAO, pp. 3–17. b

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95%. In comparison protein digestibility for many plant-based proteins varies greatly, for example, from 77% to 96%, depending on the species of plant (Tacon, 2004). The structural nature of plants is totally different from that of animals. Proteins isolated from plants are associated with indigestible nonstructural carbohydrates (oligosaccharides) and structural fiber components (cellulose), which are not associated with animal proteins. Presence of these components is thought to be contributing obstacles to efficient utilization of proteins in many economically plant-based feedstuffs. The lack of nutritional inhibitors or antinutritional factors in fishmeal also makes this meal more attractive than plant proteins for use in aquaculture diets. Antinutritional factors are compounds that interfere with nutrient digestion, uptake, or metabolism and can also be toxic. For example, a naturally occurring antinutritional factor in uncooked soybeans is the Kunitz trypsin-inhibitor that prevents the enzyme trypsin from breaking down dietary proteins in the intestine of animals. Lathyrogens in chickpeas also disrupt collagen formation. Collagen is the most abundant protein present in animals, making up most of connective tissue and providing structural support. Another very important problem with plant-based protein alternatives for fishmeal is low acceptability (palatability) by animal resulted in nutrient leaching and low feed intake (Francis et al., 2001; Krogdahl et al., 2010). Apart from plant proteins, there are other protein sources which may substitute for fishmeal in aquaculture feed. Terrestrial animal by-product meals such as meat and bone meal, blood meal, and poultry by-product meals are considered feed ingredients of good nutritional quality. It has been estimated that potential quantities of these by-products are two to three times higher than that of fishmeal (Tacon and Metian, 2015). For safety reasons, it is important animal feeds of the same animal species. The ban on using by-products from warm-blooded animals in fish feed in many countries stems from the fear of transmissible spongiform encephalopathies (TSEs) disease transmission (Tacon and Hasan, 2007). Varieties of animal by-products have been used as protein sources for livestock. As high-quality protein sources, blood meal, and plasma protein (spray dried plasma) have been used successfully in nursery diets, and have also been used to stimulate feed consumption in early weaned pigs (Hansen et al., 1993; Kats et al., 1994). However, blood products, and also milk products, are expensive and more likely existence of pathogens limited their application as animal feed ingredient. Recently, single-cell proteins (SCPs), a novel protein source, has introduced as promising alternative ingredient for fishmeal. Different nutritional characteristics of this valuable protein source is discussed in next sections.

3. Single-cell proteins (SCPs) The term SCP is referred to the bulk of dead, dried biomass of single-cell organisms (Nalage et al., 2016). SCP can be prepared from different organisms, e.g., microalgae, bacteria, and fungi. SCPs enclose many positive nutritional characteristics such as high-quality proteins, vitamins, pigments, structural polysaccharides which make it potential to be used in the animal feed as sustainable and renewable feed component

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( Jones et al., 2020). Inclusion of SCP can address the nutritional shortcoming of inclusion of plant-based meals and reduce the need for fishmeal in the feed. In addition to the nutritional properties, SCP is considered as promising pre/probiotics (Glencross et al., 2020). General properties for the organisms to be considered as suitable SCP is listed below (Anupama and Ravindra, 2000): – – – – –

No infectious to the plants and animals Capable to include in feed/food Containing of high nutritional value components No toxic compounds Low production cost

Recently developed SCP-grade food product, Mycoprotein, is an alternative product for meat which is produced from filamentous fungi, Fusarium venenatum. A well-known market brand Quorn is commercially approved to supply as food since 1983 and nowadays is accepted by costumers as high quality food. Introduction of SCP-based animal feed ingredient in the same concept can aid animal farming industry and indirectly improve human food security by producing higher quality meat. Filamentous fungi are a protein-rich and fast growing microorganism. Its application as SCP has investigated by a few studies. For example, nutritional value of Rhizopus oryzae has explored and as a conclusion, researchers reported that dietary filamentous fungi can have positive effects on fish health (Abro et al., 2014; Bankefors et al., 2011).

4. Fungi kingdom The Kingdom fungi comprised by eukaryotic and heterotroph organisms accounting to around 1.5 million species. Based on the last taxonomical classification, in the Kingdom of fungi is divided into eight main phyla, Chytridiomycota, Zygomycota, Glomeomycota, Ascomycota, Basidiomycota, Blastocladiomycota, Microsporidia, and Neocallimastigomycota (Kendrick, 2017). According to the lifecycle, fungi can be categorized in three distinct groups, namely, unicellular, macrofilamentous and multicellular filamentous fungi. From the ecological standpoint, they play a very significant role in the nature, where they contribute to the recycling of nutrients (Wakai et al., 2017). Macrofilamentous fungi refer mainly to mushrooms and truffles. Many of them are commonly included in human diet due to beneficial nutritional composition and favorable taste (Boland et al., 2012). Multicellular filamentous fungi (often referred as molds) include some species industrially used for production of a wide range of products such as organic acids, enzymes, and antibiotics. Furthermore, some species have been used for production of food products. For instance, Aspergillus spp., Neurospora spp., Rhizopus spp., Fusarium spp., and Monascus spp. are categorized as generally recognized as safe (GRAS) and have food applications. For instance Sake, Shoyu, and Miso are the fermented products using Aspergillus spp. and Neurospora spp. have been used traditionally in some indigenous East Asian food, Oncom. Fusarium venenatum is the well-famous strain of edible filamentous fungi

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involved in mycoprotein production known as Quorn. During growth, microscopic spores elongate and branch out creating a 3D macroscopic structure easily recovered from the medium. The use of filamentous fungal biomass for food applications is related to the extended group of nutrients present. Those include high protein content, good PUFAs, vitamins, minerals, and antioxidant and immune stimulant components. Filamentous fungi are enabled to degrade complex substrates due to the production of various enzymes such as amylases, lipases, proteases, pectinases, phytases, etc. Considering their nutritional composition and range of substrates that can be used for growth, filamentous fungi have extensively been investigated for valorization of low-value substrates through their conversion into valuable products. One of the products produced, the filamentous fungal biomass, has increasingly been considered a potential alternative protein source. Filamentous fungi can be cultivated either in submerged cultivation of solid-state fermentation. Food products such as Quorn are produced through submerged fermentation, while tempeh, tofu, and oncom are produced via solid-state fermentation. The product obtained via solid-state fermentation is normally a mixture of fungal filaments and remaining substrate, whereas in submerged fermentation a purer filamentous fungal biomass can be obtained via submerged fermentation via close control of cultivations conditions and content of suspended solids. High content of the latter normally leads to entanglement with fungal filaments; hence influencing the final composition of the fungal biomass. This can have both positive and negative impacts depending on the final applications and composition of the suspended solids.

5. Fungal biomass composition as animal feed nutrient 5.1 Protein and amino acid profile Filamentous fungal biomass carry valuable amount of protein. As a general fact, protein level in highly related to the species as well as cultivation factors, e.g., substrate composition, oxygen availability, pH, etc., but 30%–50% (w/w) dry biomass of most of filamentous fungi is crude protein (Table 2) (Karimi et al., 2019). Therefore, fungal biomass is evaluated as suitable protein source ingredient for animal feed. From nutritional stand point, they are considered as most important constituent in all feed types both since proteins are included in many important biological and economic processes. Proteins connect to the wide range of functions within organisms, such as catalyzing metabolic reactions, deoxyribonucleic acid (DNA) replication, stimuli response, cell shape and structure and transporting molecules from one location to another. Hence, proteins are among essential macronutrient for every living organisms to maintain growth and health ( Joint FAO WHO UNU Expert Consultation on Protein and Amino Acid Requirements in Human Nutrition. Food and Agriculture Organization of the United Nations, World Health Oorganization, and United Nations University, 2007). Apart from protein concentration, protein quality is mainly related to the amino acid composition. In fact, true protein concentration is directly attributed to the amino acid profile in the biomass. In the other word, proteins are carriers for amino acids. The main

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Table 2 Protein content present in the biomass originated from cultivation of filamentous fungi in various substrates. Protein content (% of dry weight)

References

39 46

Barker et al. (1981) Jin et al. (1999)

50–60 30.4 28 47–63

Ferreira et al. (2012) Mitra et al. (2012) Liang et al. (2012) Wikandari et al. (2012)

Spent sulfite liquor

30–50

Lennartsson (2012)

Vinasse

49.7

Wheat ethanol stillage

Corn ethanol stillage Wheat ethanol stillage

56 48 55 43 43

Nitayavardhana et al. (2013) Ferreira et al. (2014)

Wheat bran Dairy waste

40 40

Yunus et al. (2015) Mahboubi et al. (2017)

Wheat lignocellulosic residues

50

Nair (2017)

Fungi

Substrate

Aspergillus oryzae Rhizopus oligosporus

Palm oil waste Starch processing wastewater Spent sulfite liquor Corn ethanol stillage Corn ethanol stillage Tempeh

Rhizopus sp. Mucor circinelloides Pythium irregulare Rhizopus, Mucor, Rhizomucor Mucor indicus Rhizopus sp. Rhizopus oryzae Neurospora intermedia Aspergillus oryzae Rhizopus sp. Rhizopus oligosporus Aspergillus oryzae Neurospora intermedia Rhizopus oligosporus Neurospora intermedia Aspergillus oryzae Neurospora intermedia

Rasmussen et al. (2014) Ba´tori et al. (2015)

functions of amino acids in the organism are (a) protein synthesis, (b) being substrate for necessary metabolite synthesis, e.g., peptides (glutathione, carnosine, etc.), neurotransmitters, NO, CO, H2S, and (c) energy supplier throughout amino acid oxidation (Deutz et al., 2014). However, they also incorporate in rebuilding of various type of proteins (Wu, 2016). Even though amino acids, indirectly have impact on animal health by providing metabolic compounds, it is confirmed that large number of amino acids can manipulate animal immunity system through different mechanisms. EAAs and conditionally EAAs must be provided by the diet because the organisms have not capacity to produce them in the body. In opposite, a number of amino acids can be synthesized in the body de novo (non-EAAs; NEAAs). These amino acids is more or less similar in animals including humans, while there is small differences between then regarding being essential or not (Table 3). Several parameters can affect amino acid synthesize in animal bodies, e.g., availability of substrate, animal species, life stage, physiological condition, gut microbiome, environmental factors, and health status of animal (NRC, 2011). The term “functional amino acids” (FAAs) refer to the given amino acids (arginine, glutamine, glycine, BCAA, proline, etc.) which are included in the regulation of significant physiological reactions can affect and enhance growth and health, effective reproduction success and tissue development. In this concept, even NEAA may consider as required compound to supply in the feed (Wu, 2010).

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Table 3 Profile of different groups of amino acids in different animals, namely in mammals, poultry, and fish (Wu, 2010; Halver, 2013). Mammals

Poultry

Fish

EAA

NEAA

CEAA

EAA

NEAA

CEAA

EAA

NEAA

CEAA

Arg Cys His Ile Leu Lys Met Phe Thr Trp Tyr Val

Ala Asn Asp Ser

Gln Glu Gly Pro Tau

Arg Cys Gly His Ile Leu Lys Met Phe Pro Thr Trp Tyr Val

Ala Asn Asp Ser

Gln Glu Tau

Arg Cys His Ile Leu Lys Met Phe Pro Thr Trp Tyr Val

Ala Asn Asp Ser

Gln Glu Gly Tau

Beyond amino acid composition, balance in amino acid composition is another issue in protein suitability evaluation. Imbalanced feed in regard to amino acid profile may result in amino acid antagonism and toxicity, which in long-time period consumption can reduce feed intake, induce aggressive behavior and lower growth (Dwyer, 2003). Karimi et al. (2019) have studied amino acid composition of three filamentous fungi. As it is presented in Fig. 2 fungal biomass is rich in arginine, methionine, phenylalanine, threonine, glutamine, branched-chain amino acids (BCAAs: leucine, isoleucine, and valine), alanine, asparagine, cysteine, and tyrosine. In addition, the concentrations for proline and glycine, which are categorized as functional amino acids, are in higher level comparing with plant-based protein sources including soybean meal. Fishmeal and soybean meal, the two most usual protein supplementation sources in aqua-feed, contain 62%–70% and 46%–50% crude protein, respectively. Considering this, new protein sources, such as fungal biomass, with comparatively high-protein content (see Fig. 2 for a comparison), have the potential to be used as an alternative protein source for fishmeal and soya.

5.2 Fat and fatty acid content Filamentous fungal biomass, in similar to other fungi, contain fat which is accumulated intracellularly (Passoth, 2017). Different filamentous fungi species are capable to store various range of fats. For example, oleaginous fungi are capable to produce and store high concentrations of lipids, up to 80% of cell dry biomass. This characteristic, existence of lipids in this high level, makes them attractive source for broad spectrum of applications such as biofuel, chemical, and food/feed additives production. For instance, fatty acids

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100% 90% 80% 70% 60%

a

50% 40% 30% 20% 10% 0% AO

NI

RO

FM

Arginine

Histidine

Isoleucine

Leucine

Methionine

Phenylalanine

Threonine

Valine

SBM

Lysine

100% 90% 80% 70% 60% 50%

b

40% 30% 20% 10% 0% AO

NI

RO

FM

SBM

Alanine

Aspargine

Cysteine

Glutamine

Glycin

Proline

Serine

Tyrosine

FIG. 2 Comparison of profiles of EAAs (A) and NEAAs (B) found in filamentous fungi (Aspergillus oryzae (AO), Neurospora intermedia (NI), Rhizopus oryzae (RO)), fishmeal (FM), and soybean meal (SBM) (Karimi et al., 2019).

including omega-3 and -6, fatty alcohols, alkanes, and carotenes can be isolated from fungal biomass (Passoth, 2017). Lipids are among macronutrients together with carbohydrates and proteins. In general, they are energy sources for living cells, but since they are compartment of cell membrane, they play several vital roles in cell integrity and transportations (FAO, 2010). Furthermore, fatty acids are essential substances for many important processes in living organisms, which directly affect growth, heath, and performance. Lipids exist in the complex with other biocompounds and form different biomolecules such as lipoproteins and glycolipids which are critical in the cell functionality (Burlingame et al., 2009).

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Different types of fat, triglycerides, phospholipids, and cholesteryl esters, contain fatty acids. Fatty acids are important to keep cell functionality; hence, they are dietary necessary substances. Basically, fatty acids are formed in either saturated (saturated fatty acids; SFAs) or unsaturated fatty acids. Those of unsaturated fatty acids with more than one double bond PUFAs are valuable molecules in every organisms (Kim et al., 2016). Among PUFAs, the 18–20 or more carbon fatty acids are of particular importance (since plants and some organisms are not capable to synthesize them) and called long-chain polyunsaturated fatty acids (LC-PUFAs) which are nutritionally significant and this group have key roles in animal health maintenance (Blondeau et al., 2014). Filamentous fungi contain high value PUFAs; and therefore, regarded as suitable alternative source providing PUFAs in feed (Asadollahzadeh et al., 2018). Basically, animals including human are able to synthesize LC-PUFAs such as arachidonic acid (20:4n-6; AA), eicosapentaenoic acid (20:5n-3; EPA), and docosahexaenoic acid (22:6n-3; DHA) from C18 fatty acids. However, production rate is not sufficient, particularly in the case of incidence of disease (Bhardwaj et al., 2011). Therefore, either consumption of PUFAs as dietary supplement in the form of pure PUFA or PUFAs-rich products can boost health status. Filamentous fungal biomass, e.g., oleaginous fungi are reported to synthesize omega-3 FAs including EPA and DHA. For example, the genus Mortierella has found to synthesize wide range of PUFAs and gamma-linolenic acid (18:3n-6) was commercially produced using them. Arachidonic acid is commercially produced by M. alpine (Passoth, 2017). Karimi et al. (2019) studied ascomycetes and zygomycetes fatty acid content. Collected data from lipid analysis is presented in Fig. 3. Oleic acid, linoleic acid, and palmitic acid were exist in considerable concentrations and arachidonic acid, alpha linolenic acid (ALA) also were detected in lower amount. Optimization of cultivation conditions such as pH, temperature, aeration rate, etc., and utilization of suitable substrate for cultivation as well as selection of high potential fungi species in lipid synthesize and storage, can improve lipid and fatty acid production by filamentous fungi. Linoleic acid can bioconvert to the arachidonic acid and ALA is the precursor substrate for biosynthesis of EPA and DHA, most important derivatives of fatty acids in disease responses. Aforementioned LC-PUFAs, have several roles, which are mainly important that is described in the next section.

5.2.1 Arachidonic acid (AA) As a fundamental component of cell membrane, it is necessary element in all stages of cell development and growth specifically in bad cell conditions (Das, 2018). AA effect is mainly on membrane fluidity and permeability and therefore can control cell signaling which is done by control of in/out flux of protein to the cell. In addition, it can enhance ion entrance and exit to the cell throughout regulation of sodium-potassium channels (Seah et al., 2017). AA positively affect immune system by activation of immune cells such as eosinophils, neutrophils, macrophages, and consequently respiratory burst mechanism is approved as an impact of exogenous and endogenous supplementation of AA.

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100% 90% 80% 70% 60%

a

50% 40% 30% 20% 10% 0% AO

NI

RO

FM

SBM

C14:0 (Myristic acid)

C16:0 (Palmitic acid)

C16:1 (Palmitoleic acid)

C18:0 (Stearic acid)

C18:1 (Oleic acid)

C18:2 (Linolelaidic acid)

C18:3 (Linolenic acid)

C20:0 (Arachidic acid)

100% 90% 80% 70%

b

60% 50% 40% 30% 20% 10% 0% AO % SFA

NI % MUFA

RO % PUFA

FIG. 3 (A) Comparison of the profile of fatty acids found in filamentous fungi (Aspergillus oryzae (AO), Neurospora intermedia (NI), Rhizopus oryzae (RO)), fishmeal (FM), and soybean meal (SBM). (B) The fraction of saturated fatty acids (SFAs), monounsaturated fatty acids (MUFAs), and polyunsaturated fatty acids (PUFAs) is presented in the lower figure (Karimi et al., 2019).

AA together with other three types of oxygenases: cyclooxygenases (COX), lipoxygenases (LOX), and cytochrome p450 can react with molecular oxygen, which led to eicosanoids and other inflammatory compounds synthesize. AA and its derivatives such as prostaglandins (PGs) also are included in muscle cells generation (Gomez Candela et al., 2011). Bae et al. (2010) evaluated the impact of adding different levels of ARA in the diet of juvenile eel, Anguilla japonica, to investigate growth rates and carcass quality. After 12 weeks feeding trial, growth promoting (both specific growth rate (SGR) and weight gain (WG)) have been reported as result. In addition to growth promoting effect, it has been found that dietary ARA, improve reproduction success in fish. Viability of larvae, higher

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hatching success and increase in egg size are the main improved features in yellow tail, Seriola dorsalis fed with ARA in the diet (Stuart et al., 2017). Turbot juvenile fish fed with the diet containing ARA as a single HUFA (0.78% of diet dry weight) showed better growth rate and survival when these parameters compared with the fish fed with reference diet (Castell et al., 1994). In the other study, gilthead sea bream, it has been confirmed that, feed containing higher levels of ARA can enhance fish growth and survival (Fountoulaki et al., 2003) and immunity system (Koven et al., 2001). Fountoulaki et al. (2003) stated that 1% inclusion of ARA can improve fish growth significantly, while fish fed with 1.8% extra ARA had higher survival rates. Koven et al. (2001) found that when fish (gilthead sea bream) larvae fed with the ARA-enriched rotifers, they were more resistant against acute stresses such as handling, etc.

5.2.2 Linoleic acid (LA) In parallel to the elucidation of relationship between diet and health, a new idea has emerged as functional lipids. LA is 18-carbon chain FA that contains two-double bounds and it is classified as n-6 FAs. The first and main health beneficial of LA in the literature is obesity prevention. Reduced energy intake, enhancement in fat metabolism, changes in skeletal metabolism have reported as the major effect, which lead to antiobesity effects of LA (Bhardwaj et al., 2011). Although there is still doubt on the positive impact of LA on prevention of cardiovascular disease (CVD) but its consumption has confirmed in a number of studies to reduce CVD risk (Kim et al., 2016; Kus-Yamashita et al., 2016; Morenga and Montez, 2017). Anticancer effects of LA consumption also have been investigated. While McGowan et al. (2013) have reported positive effect of LA consumption 10 days prior to the surgery in breast cancer, however, there is other studies, which are in contrast with this findings. LA has showed to reduce undesired effects of immune activation and inflammatory responses. Replacement of soybean oil with commercially enriched LA oil in growing finishing pigs resulted in higher quality in pig bacon fattening and meat quality (Marijana et al., 2012). Ebeid et al. (2011) found that chickens fed with the diet consist of various levels of LA, had increased amount of omega-3 and -6 PUFAs in egg yolk. Paulino et al. (2018) fed the juvenile tambaquic (Colossoma macropomam) with the higher rate of LA/ALA, ranging from 3.1 to 26.9. The researchers reported that higher rates of LA/ALA significantly improve fillet quality indices such as EPA, DHA, and ARA content which is suitable for human as costumers.

5.2.3 Alpha linolenic acid (ALA) As another member of functional FAs, ALA, which is belonging to the n-3 FAs, is the precursor for other most important LC-PUFAs, EPA, and DHA. It is highly documented that
rrez et al., 2019). ALA has neuroprotective and antiinflammatory properties (Gutie Omega-3 FAs are essential to promote brain development and maintain normal health
rrez et al., 2019). Like other of mammalian, human are not capable to synthelevel (Gutie size ALA de novo and therefore it should obtain from the diet. Consumption of ALA-rich

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diet has been shown to have reduction impact on low-density lipoprotein (LDL) which is the main cause of atherosclerosis and coronary heart disease (CHD). In addition, it is demonstrated that it has antiarrhythmic properties and ALA consumption can protect against CVD (Blondeau et al., 2014). Increasing levels of ALA in the diet resulted in higher concentrations of ALA in the liver and fillet of baramondi, Lates calcarifer (Tu et al., 2012). Higher growth rate and lower mortality is reported in postpartum piglets by consumption of ALA (Roszkos et al., 2020). In another study, it is found that dietary ALA can improve reproduction success. In this work, feeding pigs with the diet containing ALA resulted in enhancement in oocyte maturation and embryo development. Total cell count of blastocyst improved by consumption of ALA (Sampels et al., 2010).

5.2.4 Oleic acid Oleic acid (18:1n-9) has a double bound on carbon 9 position. A number of studies showed that oleic acid is efficient bioactive compound in prevention of ischemic heart disease. In addition, it is stated that consumption of oleic acid in the diet has inhibitory effect on platelet aggregation. The people consumed oleic acid had lower total plasma cholesterol as well as immunomodulatory effect via affecting neutrophil function and production of reactive oxygen species and T-cell proliferation promoting effect (Lopez-Huertas, 2010). It is mentioned in the literature that balanced ratio of PUFA to SFA in food/feed must be supplied. In this regard, the ratio of 0.45 of PUFA/SFA has reported to be safe and below that is considered as nonhealthy (Gomez Candela et al., 2011). Considering high concentrations of PUFA in filamentous fungi, for example in Karimi et al. is more than 1, filamentous fungal biomass could be an interesting source to meet the requirements.

5.3 Cell wall components Filamentous fungi similar to plants, some of algae and bacteria consist a functional rigid cell wall. Although the general functions that described for filamentous fungi cell wall is highly similar to that of described for other organisms, its composition may be different with other organisms. Furthermore, cell wall composition become different among various species in the kingdom fungi during the evolution process (Quintin, 2018). In addition, there is evidence regarding cell wall structure and composition alteration in respect to fungi ontogeny stages such as sporulation or development (aging of fungal culture) and environmental condition, e.g., nutritious circumstances (Snarr et al., 2017). To emphasize on the importance of cell wall of filamentous fungi, it is interesting to mention that cell wall comprise around 30% of cell dry weight and roughly, 20% of total genetic material is to regulate cell wall composition and structure. In general, the cell wall is largely composed of polysaccharides. However, small proportions of proteins and lipids also are present. In this section, functional compound present in filamentous cell wall will discuss (Bowman and Free, 2006).

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5.3.1 Glucans Glucan is a polymer made of glucose building blocks. Glucans are acting like a flexible cement to maintain cell wall flexibility. Glucans are the most containing polysaccharides in the fungal cell walls. There are various types of glucans, e.g., β-1,3, β-1,6, and α-1,3 glucans. In α-glucans, sugars building blocks are linked together via α-1,3-bond while β-1,3 and β-1,6 bond are used to make β-glucans. Although in some cases small amount of β-1,4glucan bonds also have been detected in a number of fungi species. The most common glucans among the fungi cell wall are β-glucans where β-1,3-glucans are present in zygomycetes, basidiomycetes, and ascomycetes, whereas, β-1,6-glucans are founded in ascomycetes and basidiomycetes (Bowman and Free, 2006). Glucans are arranged generally in large linear molecules in the form of microfibrils contributing to the cell wall strength (Cabib et al., 1988). Biological response modulators including immunostimulants have been intensively explored in animal production industries, recently. Glucans are among the most studied immunostimulants in aquaculture. In Channel catfish, Ictalurus punctatus, applying 0.05% of beta-glucan showed effective immunostimulant properties. In this study, phagocytic activity, reactive cells to nitroblue tetrazolium (NbT) were significantly stimulated. The author concluded that adding 0.05% beta-glucan to the commercial feed can enhance innate immune system in the channel catfish (Sa´nchez-Martı´nez et al., 2017). In several other studies in fish, beta-glucan has to confirmed to stimulate nonspecific immune system by improving immune factors such as phagocytic activity, respiratory burst activity, nitric oxide, complement, and lysozyme activity and white blood cell count (Bridle et al., 2005; Zaragoza et al., 2011; Jaafar et al., 2011). Application of beta-glucan in chicks also showed that dietary beta-glucan can actively aid immune system against A. salmonella thyphimurium by increase in villus height and gablet cell numbers ( Jacob and Pescatore, 2017). Paul et al. (2012) reported that glucans extracted from the fungi pleuratusflorida can stimulate immune system and protect broiler chickens against Newcastle disease.

5.3.2 Chitin Chitin is homopolymer of β-1,4-N-acetylglucosamine which is the second most abundant biopolymer after cellulose in the nature. It is connected to the rigidity and cell shape. Chitin basically composes lower amount of cell wall composition comparing with glucans. However, almost in many of fungi species, chitin is present. Considering the chain arrangement of chitin into the microfibrils, three types of chitin exist in the nature, β, α, and γ which only α-chitin is occurred in fungal cell wall. Chitin is present in variable concentrations in fungi cell wall ranging from 2% in Saccharomyces cerevisiae to 60% in Allomyces macrogynus. However, average amount of 20% is considered in fungal cell wall (Lopez-Romero and Ruiz-Herrera, 1986). Application of chitin as immunostimulant has investigated in a number of studies. Various parameters of nonspecific immune system such as super oxidase anion production, myeloperoxidase activity, nitric oxide production were elevated in different fish species such as catla, Catla catla (Sangma and Kamilya,

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2015), gilthead sea bream, Sparus auratus (Esteban et al., 2000), and rainbow trout, Oncorhynchus mykiss (Vahedi and Ghodratizadeh, 2011).

5.3.3 Chitosan Chitosan is a polymer of glucosamine and diacetyl chitobiose which are bound via β-1,4bonds. Mainly, chitosan is founded in zygomycetes, ascomycetes, and basidiomycetes species. Chitosan can be synthesized throughout the deacetylation of acyl glucosamine of chitin (Cabib et al., 1988). Chitosan functions is assumed to be enhancing the accumulation processes of negatively charged molecules in the cell wall and protecting chitin against enzymatic hydrolyses of chitinases due to elastic features of chitosan (Beauvais
, 2018). and Latge Chitosan has been confirmed to improve immune function in animal feeding studies. It has been reported that, relative weight of thymus, serum level of IGF-1, INS, GH, T3, T4, IgM, IgA, complement system were significantly improved by supplementation of chitosan in the Huoyan geese diet (Miao et al., 2019). Chitosan also in approved to actively stimulate immune system in fish and shell fish. Injection of 2 and 4 μg/g of chitosan significantly increased hemocyte cells and respiratory burst activity after 2 days and phagocytic activity after 1 day (Wang and Chen, 2005). In another study, 1% supplementation of chitosan in the feed, improved superoxidase anion production, and elevate lysozyme activity in common carp (Gopalakannan and Arul, 2006).

5.3.4 Mannose Mannose is another component of filamentous fungi cell wall. Mannan polysaccharides are frequently found in almost all of fungi species. They are commonly associated with wall proteins. One of greatly confirmed application of filamentous fungal cell wall polysaccharides is use as immunostimulants. Interestingly, cell wall biopolymers such as chitin, chitosan, glucans, etc., can improve immunity status of animals (Hernandez Chavez et al., 2017; Karimi et al., 2018; Sakai, 1999). Immunostimulants are the substances that improve resistance of organism against infectious substances and organisms. They boost innate immunity responses to protect the organism against stressful condition and disease incidence. Generally, immune mechanisms are common in higher vertebrates including mammals, aquatic animals, etc. (Wei et al., 2016) and consist of a group of cellular and humoral-based factors that can act to protect the organism against invading pathogens such as microorganisms; toxins, etc. Almost in large number of organisms, immune system comprises innate and adaptive responses, which both of these systems can react via cellular and humoral mechanisms. Innate immune system is the most general reactions and consist of physical barriers such as skin and mucus, other chemical factors like complement systems, antimicrobial enzymes, e.g., lysozyme, interleukins as well as cellular mechanisms such as granulocytes, monocytes, macrophages, and natural killer cells ( Jin et al., 2018). Often the bioactive compounds found in fungal cell wall, which discussed earlier, can trigger immune system particularly as antigen-like substances to immune responses

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induction by production of some specific antibody. The other mechanism that the immunostimulants are involved in is without any antigenic property and instead they enhance immune response of other antigens nonspecifically.

5.4 Minerals It is greatly approved that filamentous fungi similar to other organisms such as algae and bacteria are able to achieve different concentrations of various elements from the surrounding substrate (Beever and Burns, 1981). Different species of filamentous fungi contain valuable minerals. Although the concentrations are variable due to several parameters such as species, type of living (wild or cultured), cultivation conditions, life stage, living environment, and substrate, however, considerable amount of macro and microminerals composition have reported in the literature in filamentous fungal biomass (Siddiquee et al., 2015). Karimi et al. (2019) reported that filamentous fungi species, Aspergillus oryzae, Neurospora intermedia, and Rhizopus oryzae, contain Ca, K, P, and S were in considerable level while Mg and Na content also were detected in lower amount. In addition to the mentioned elements, iron, zinc, magnesium, and selenium, which are categorized as microminerals, reported to be included in fungal biomass. Their availability in the fungal biomass is directly related to the growth stages and its uptake level decrease over the cultivation time (Boriova´ et al., 2014). Generally, minerals such as P, K, Ca, and S are involved in very wide range of functions in organisms. Instance, P is a part of nucleotide, skeleton, cell membrane phospholipids, coenzymes, DNA, ribonucleic acid (RNA) and has buffering effect (Takeda et al., 2012). In addition, P is a component of nucleotides, skeletal tissues, phospholipids, coenzymes, DNA, RNA, and special enzymes involved in energy production (Bloomfield, 1997). Moreover, P has a buffering effect and helps an organism maintain a normal pH (Fairweather-Tait and Cashman, 2015). Ca is involved in blood clotting (vertebrates), muscle functions (such as contractions), nerve impulse transmission, osmoregulation, membrane permeability, hormone, and enzyme secretions, and acts as a structural component of teeth and bones. K is an essential macromineral used particularly to balance the acid-base equilibrium, as well as for osmoregulation and maintaining muscle and nerve activity (He and MacGregor, 2008). If these minerals are not supplied at sufficient levels in the diet, the organism will become susceptible to different pathological problems. For example, a deficiency in P will lead to a reduction in growth capacity and feed conversion, skeletal malformation, intermediary metabolism impairment, a reduction in tissue hardness, a reduction in antibody production, and reduced weight gain (Fairweather-Tait and Cashman, 2015; Yamauchi et al., 1996). Other minerals and particularly microminerals such as selenium, zinc, iron, and magnesium are considered as essential microminerals and must be included in animal diet. For example, selenium has significant roles in seleno-proteins, which are effective in cell signaling regulation, intracellular hemostasis, and several other important physiological processes (Fairweather-Tait and Cashman, 2015). As mentioned before, filamentous fungi are capable to absorb chemicals from surrounding substrate. These elements could be heavy metals also, however, there is evidence

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that describe such chemical elements such as arsenic, tellurium, etc., could not store in high concentrations in filamentous fungal cells, because living filamentous fungal cells transform them to alkylated or methylated compound effectively. Throughout such biotransformation, generated methylated compounds are in the gas form and highly volatile. Therefore, they release from the cell to the substrate under the definition of bio volatilization (Boriova´ et al., 2014).

5.5 Pigments Natural pigment are known as the colorant substances, which are produced by living organisms while it can be stored in the cell and/or excreted to the substrate. Plants, a number of animals, bacteria, and filamentous fungi are capable to store pigment. Higher water solubility, possibility of production over the whole year regardless of seasonal variation and higher efficiency in production during the time are the advantages of microbial including filamentous fungi pigment production over other methods. Moreover, independency of environmental condition and capability of production under controlled cultivation circumstances are added to the advantages of natural pigment production by microbial sources like filamentous fungi (Siqueira, 2015). Filamentous fungi are known as pigment producers. Considering GRAS nature of edible filamentous fungi, they are accounted to be a promising feed grade pigment producers. Filamentous fungal pigments are grouped in two major classes, carotenoids and polyketides, including carotenoids, melanines, azaphilones, anthraquinones, flavin, phenazine, quinones, etc. Polyketide pathway is employed by Monascus spp. whereas other type of filamentous fungi such as N. intermedia produces carotenoids instead. Pigments can be synthesized nonbiologically, however, due to the problems arising from their toxicity and not environment friendly being, natural pigments are growing in acceptance to introduce in the market (Gmoser et al., 2017). Pigments produced via fermentation process by various fungi such as Monascus, Penicillium oxalicum, Ashbya gossypii, Blakeselea trispora are already available in the market (Esteves Torres et al., 2016). Monascus is well famous genus of filamentous fungi for its natural pigment production. Major pigments which are produced by Monascus, including M. purpureus and M. ruber, they mostly belong to azaphione pigments which give the color ranging from yellow, orange to red. Pigments aid filamentous fungi to overcome the problems arising from exposure to the high intensity light and
, 2017). ultraviolet radiations, invading organisms such as bacteria and insects (Dufosse Animals have lack of the genetic information that code pigment synthesize; and therefore, it is necessary to add the pigments in their diet. Therefore, pigments and in particular natural types of pigments are becoming one of most desired additives to include in animal feed. Pigments serve as several important functions in organisms. In plant, they attract the light to make the photosynthesis possible. In addition, they are precursors for retinoid and retinoic acid which they are required for vision and cell signaling in the animals body. Adding color to egg yolk and fish flesh has led to increase in customer preferences (Karimi et al., 2018). In addition to these applications, antioxidant activity of pigment and mainly carotenoids is greatly accepted, and it is suggested that its consumption in diet can reduce

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the risk of CVD, cancer, eye disease, and health disorders (Fiedor and Burda, 2014). Several potential applications have been described for filamentous fungal pigments including addition in animal feed, e.g., fish and poultry feed purpose to improve sensory attributes in flesh and egg yolk and skin. Filamentous fungi pigments as other pigments, which are already used in the industry, can use as colorant in leather, textile, drug, cosmetic, food, and feed packaging industries (Gmoser et al., 2017).

5.6 Antioxidant agents Filamentous fungi possess different molecules such as phenolic acids, phenyl propanoids, and flavonoids as well as other polymeric compounds such as lignin, melanin, and tannins, which are demonstrated as antioxidant compounds. Polyphenolic substances have been demonstrated to aid cell to protect against oxidative stresses by different mechanisms including inhibiting and/or scavengering free radicals and reactive oxygen species. Reactive oxygen species are generated normally because of living cellular metabolism. Although they can improve immune defense, cellular functionality, and metabolic pathways in lower concentrations, its high concentration can be deteriolous to the cell and living organism. Every living organism can protect against the damages caused by reactive oxygen species in normal condition using endogenous antioxidants system but higher concentrations of accumulated reactive oxygen species in different physiological body condition can oats be covered by endogenous protection system. Filamentous fungi have been demonstrated to be valuable sources of natural antioxidant. Generally, it has been shown that fermentation can increase antioxidant activity of feed. For example, fermented rice bran with Rhizopus oryzae increase free phenolic compound by 100%; and therefore, antioxidant activity improved. Arora and Chandra (2010) have been reported that Aspergillus sp. and Monascus purpureus can be considered as valuable sources for phenolic compounds. Antioxidant capacity of phenolic compounds is mostly dependent on redox ability of the phenolic compounds feed phenolic hydroxyl group and the capacity to the localized electron from chemical structure. Oxidative stresses are related to wide range of disease particularly neurodegenerative disease. Oxidative stress induced by excess reactive oxidative species in vivo has reported to damage carbohydrates, lipids, proteins, and nucleic acid (NA) and cause different disease such as cancer, arteriosclerosis, and complicating disorders of diabetic peoples. Taste, color, and flavor of feed also changes by oxidative damage, in particular in lipid peroxidation during preservation time. Thus, affectively decrease feed quality, nutrient value, and biofunctionality. Basically, synthetic antioxidant compounds such as α-tocopherol, ascorbic acid, and BHA are added to the feed products to stop or at least reduce oxidative reactions. Antioxidants have been confirmed to negatively affect oxidative stress and therefore prevent or decrease the incidence of aforementioned disease. Filamentous fungi contain antioxidant substances that can suppress reactive oxygen species generation and prevent relevant disease incidence and improve health status in animals.

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5.7 Vitamins Vitamins are essential elements which animals cannot synthesize them de novo; therefore, it is needed to be supplemented by the feed (NRC, 2011). Filamentous fungi require vitamins for metabolism and they are able to synthesize a number of vitamins. Fungi including mushrooms are a good source of vitamins. They are rich in a number of vitamins such as B-complex and vitamin D reported that fungal biomass contain considerable contents of vitamin C, folic acid, B1 (thiamine), B2 (Riboflavin), and niacin larırmak, 2007). (C ¸ ag Filamentous fungi Ashbya gossypii have utilized for commercial production of B2 (Riboflavin) (Aguiar et al., 2015). Riboflavin is a precursor for flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential cofactors for numerous enzymes such as dehydrogenases, oxidases, oxidoreductases that participate in a range of redox reactions critical for major biological process. This vitamin is commercially used as a yellow colorant and to make favorable aroma and taste used as animal feed additive. Riboflavin was produced synthetically for many years but its production shifted toward the microbial synthesis nowadays. According to the studies, A. gossypii can produce 5 g/L while 14–20 g/L production also reported for B2 production by A. gossypii in the literature (Aguiar et al., 2015). Vitamin B6 is the term that refers to all biological forms of pyridoxine including pyridoxine, pyridoxal, pyridoxal 5-phosphate, and pyridoxamine. It is required co-factor in very important enzymatic functions mainly in amino acid metabolism. It is reported that B6 may have antioxidant properties as well. Variety of animals including most of fish species are not capable to synthesize vitamin C because of not having the enzyme: L-gulonolactone oxidase required in the vitamin C synthesize pathway (Lee, 2015; Lee et al., 2015). Major symptoms of ascorbate deficiency in fish include reduced growth, scoliosis, lordosis, internal and fin hemorrhage, distorted gill filaments, fin erosion, anorexia, and increased mortality (Lee et al., 2015). Vitamin C is necessary in broad spectrum of physiological functions including growth, development, reproduction, wound healing, response to stressors, and nutrient metabolism such as lipid through its function in carnitine biosynthesis. Because of antioxidant activity, vitamin C plays important role in the immune system and in combating with to infectious diseases of fish (Halver and Hardy, 2002). Vitamin C also is involved in the production of catecholamine in fish which control stress responses trough endocrine. Therefore, in situation of exposure to stressful condition, ascorbic acid requirement is needed in higher concentrations and if required concentrations be provided stress-induced downregulation of the immune system will compensate (NRC, 2011).

5.8 Nucleotides Nucleotides exert numerous important physiological and biochemical functions including incorporation into genetic material, mediating energy metabolism, and cell signaling. In addition, they are necessary components of coenzymes, allosteric receptors, and

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agonists in the cell level (Carver and Allan Walker, 1995). Therefore, while they can be synthesized in the body, their inclusion in the daily diet has health beneficial to the animal and numerous studies have shown evidences that dietary nucleotide deficiency may hurt liver, heart, intestine, and impair immune responses. Accordingly it seems that dietary supplemented nucleotides improve lymphocyte maturation, activation and proliferation, macrophage phagocytosis, immunoglobulin responses, and expression of kind of cytokines either in human and variety of animal (Grimble and Westwood, 2001). Importance of supplementation of dietary nucleotides in fish diet has highlighted since Burrells et al. (2001) reported described how its dietary inclusion can have positive impacts on various salmonid species. In a number of studies with fish it has confirmed that dietary nucleotides can enhance innate immunity system via improve on the immune responses at humoral and cellular levels. Sakai et al. (2008) noticed that feeding the fish, Cyprinus carpio, with the diet containing commercial nucleotides in the increases in serum complement (alternative pathway), lysozyme activity, phagocytosis, and superoxide anion production of head kidney phagocytes. In addition, Li et al. (2004) and Cheng et al. (2010) have shown that blood neutrophil oxidative radical production and head kidney macrophage superoxide anion production were in higher level comparing with the fish fed with common feed. Supplementation of nucleotides increases head kidney leucocyte super oxidase anion production and plasma lysozyme activity. The authors concluded that inclusion of 120–140 mg nucleotide/kg in the diet improve immune system in tilapia (Shiau et al., 2015). In addition to boosting immunity system, several health beneficial reported by adding nucleotides to the fish diet. Enhanced resistance against pathogens, better growth rates and integrity in gut-intestinal tract, boosted and quicker response to the vaccination, increasing capacity of osmoregulation and overall, enhancement in fish performance are among reported consequences of supplementation of nucleotides in the fish diet (Li and Gatlin, 2006).

5.9 Prebiotics Prebiotics are known as nondigestible substances that can positively influence the host by improve growth and/or promoting the metabolism of one or a group bacteria present in the intestine microbiome that promote organisms immunity, and therefore, keep balance in the host’s intestine (Gibson and Roberfroid, 1995). The definition of prebiotics term was modified by Gibson et al. (2004) to “selectively fermented ingredients that allow specific changes, both in the composition and/or activity in the gastrointestinal microbiota that confers benefits upon host well-being and health.” Thus mentioned dietary additive compounds indirectly and gradually change the microbiota in the host gastrointestinal (GI) tract. As discussed earlier in the section for immunostimulants, fungal cell wall composed of oligosaccharide biopolymers such mannan-oligosaccharides and fructooligosaccharides which their prebiotic effects are confirmed (Davani-Davari et al., 2019). Application of prebiotics in aquaculture gained great attention recently to improve

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production capacity, increased nutrient utilization efficiency, and increase infectious disease resistance. Prebiotics seems to represent a high potent alternative to the traditional approaches used to treat the disease.

6. Animal feed Filamentous fungal biomass as feedstuff to be used in chicken diet has investigated in a few researches. Rezaei et al. (2019) fed 70 broiler chickens with Neurospora intermedia to evaluate its digestibility, they used fungal biomass as 30% of total diet which was composed of wheat-soybean meal-based control diet. According to their reported results, there were no significant differences in feed intake and body weight gain at the end of experiment. Based on their result digestibility values for crude and amino acids, cysteine, methionine, and threonine were as the same level as other protein sources commonly used in animal feed. In another research, broiler chicken has fed with tea fungus (consortium of two yeasts, Pichia sp., Zygosaccharomyces sp., and bacterium Acetobacter sp.). Different levels of inclusion (0, 50, 100, 150, 200 and 250 g/kg) were applied to evaluate chicken performance when tea fungus utilized as feed ingredient. Authors reported that, 150 g/kg inclusion in poultry feed enhanced feed intake, weight gain, and performance efficiency factor and carcass quality. As the control test, they reported that there was no abnormalities in histopathological examinations of liver and moreover, 100% of chickens survived during the trial (Murugesan et al., 2005). There are only a few studies described fungal fermented feed application in ruminants. Fungal treated rice straw with Comprinus fimetarius resulted in improved digestibility of cell wall and liquor feed intake in goats (Cone et al., 1996). In addition, Shrivastava et al. (2011) fed goats with fungal treated substrate and as a result, higher digestibility values in dry matter, organic matter. Crude protein, hemicellulose and cellulose were reported. In another study, sheep has fed with C. subvermispora treated bamboo in the compound feed containing Alfa alfa hay, wheat bran, and soy bean meal. In this study, higher digestibility of fungal treated bamboo in the organic matter, NDF and ADF digestion measured when it is compared with untreated bamboo. Fermented soybean and soybean meal have been studies in poultry nutrition. Hirabayashi et al. (1998) reported that fermented soybean meal with Aspergillus improves weight gain and phosphorous retention in chicks. Likewise, it was reported that feeding fermented soybean meal with Aspergillus to broilers enhances the daily feed intake, daily body weight gain, the activity of the enzymes trypsin, lipase, and protease, and increases the villus height (Feng et al., 2007a, b). In addition, Aspergillus oryzae can be used to lessen the antinutritional effects of potential feedstuffs. Fermentation using Aspergillus oryzae and Neurospora sitophila of both Jatropha seed meal and jatropha seed cake could be one way to enhance their nutritional properties and to reduce the amount of toxins and antinutritive compounds (Wina et al., 2010). Yang et al. (2007) fed piglets with different types of soybean products. According to their results, piglets fed with fungal (A. oryzae) fermented soy protein grow as well as other

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treatments including soy protein concentrate which is more expensive than soybean. Moreover, authors noticed that fermented product of soy protein-enhanced piglet performance comparing with those fed unfermented soy proteins. Similar result found when weanling pigs fed with fermented soybean. They reported that digestibility was higher in fermented soy bean than common soybean. Standard ideal digestibility for most of indispensable amino acids was greater in fermented soybean meal than fishmeal-based diet and only Lys, Thr, and Trp were not significantly greater. Overall, they conclude that inclusion of 10% fermented soybean meal can replace fishmeal, chicken meal, or poultry by-product meal without any adverse effect in digestibility and final weight. More digestibility of phosphorous has been reported by the authors comparing with soybean meal that diminish need of adding inorganic phosphorous in the diet. A. awamori, isolated from Japanese fermented food, Koji, has been evaluated in broilers chicken (Saleh et al., 2011). In this study, 15-day (365  3 g) broiler chicken was fed with the diet supplemented with A. awamori at various levels of 0.01%, 0.05%, and 0.1% of feed. Feeding with mentioned diets containing fungi, resulted in higher weight gain, decrease in saturated fatty acids, and increase in unsaturated fatty acids in the muscle. Overall, enhanced growth performance observed when fungal biomass added to the diet. Authors noticed that A. awamori can be utilized as a useful probiotic agent in the broiler chicken farms. Application of A. oryzae has been investigated in order to use as probiotic compound against salmonella contamination in poultry (KyungWoo et al., 2006). They found that, when diet supplemented with A. oryzae, it had inhibitory effect on colonization of salmonella and E. coli in the chickens gut. The author stated that, since, A. oryzae is a favorable substrate for different positive-effect bacterial strains, such as lactobacillus, they can support higher concentrations of such bacterial community in the gut microbiome. Effect of feeding of fungal biomass to the fish has received great attention recently. Wagner et al. (2019) replaced 40% of fishmeal with Zygomycetes (R. oryzae) to investigate its influence on fat and fatty acids content and composition of arctic charr (Salvelinus alpinus). They found that when fungal biomass supplemented in the feed, positively lowered liver lipid content and higher concentrations of DHA in the liver observed comparing with the reference diet. Nile tilapia have fed with two diets containing different concentrations (106 and 8 10 CFUg 1) of A. oryzae to assess probiotic effects of filamentous fungi (Dawood et al., 2019). After 60 days feeding trial, significant improvement in weight gain and feed efficiency reported. When fish fed A. oryzae, challenged with hypoxia stress, higher activity of antioxidant enzymes (SOD and GPX) and higher blood antimicrobial capacity (bactericidal and phagocytosis activity) against A. hydrophila observed. Also elevated serum protein, nitro bluetetrazolium, immunoglobulin, and lysozyme activity were observed as beneficial health effect of A. oryzae in the feed. The authors concluded that A. oryzae supplementation in fish feed can significantly boost immunity status of Nile tilapia against hypoxia stress. Apparent digestibility of R. oryzae investigated in Perca fluvitialis (Eurasian perch) and S. alpinus (Arctic charr) (Langeland et al., 2014). Digestibility coefficient for crude protein,

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amino acid, gross energy was not significantly different with the reference diet in Arctic charr. Same result found regarding the Eurasian perch. Penaeus vannamei fed with defatted groundnut oil cake fermented by filamentous fungi, A. niger as a replacement of fishmeal ( Jannathulla et al., 2018). After the 45-day growth trial, data showed that when cake added to the feed was not fermented by A. niger, in the level of 50 g/kg had no significant adverse effect on growth, while fermented cake by filamentous fungi allowed the researchers to add 100 g/kg in the diet. FCR, protein efficiency ratio, and apparent protein utilization were improved by inclusion of fermented cake. Growth performance, feed intake, carcass composition of rainbow trout have monitored when fish fed fermented wheat grains (Pascual et al., 2018). Pleurotus ostreatus (PWD) and Lentinus edodes (LWD) were filamentous fungi species used in order to perform fermentation. Fish growth, feed intake and efficiency, nutrient retention efficiency for crude protein, crude fat and phosphorus, body lipid content were increased using feed contain fermented materials.

7. Applications of fungal biomass as feed In addition to the specific cell structure differences of various fungal species, other factors, such as culture conditions, cultivation media, etc., contribute to the final composition of fungal biomass (Gopalakrishnan et al., 2012). These differences in the protein, lipid, vitamin, pigment, etc., of fungal biomass challenge the introduction of a standardized method for their application in fish feed. As a number of filamentous fungi strains in genera such as Aspergillus, Fusarium, Monascus, Neurospora, and Rhizopus are categorized as GRAS by the United States Food and Drug Administration (USFDA), their application as animal feed and even human food is allowed (Ferreira et al., 2013). However, different measures should be taken into consideration when applying them as a fish feed supplement. One of the factors that may limit the application of fungal biomass as mammalian food is its high content of NAs, which may cause an increase in plasma uric acid in the long-term, leading to gout and kidney stone formation (Rumsey et al., 1992). However, fish species such as salmonids have the ability to produce high levels of active liver uricase that enables them to metabolize NA without health risks (Kinsella et al., 1985). Filamentous fungi may produce mycotoxins such as aflatoxin, ochratoxin, citrinin, and fusarin (Bennett and Klich, 2003). Therefore, special attention must be paid to prevent the inclusion of mycotoxins as an ingredient in fish feed. In addition, a number of fungal species, including Fusarium, Aspergillus, Exophiala, Scytalidium, and Mucor have been isolated as opportunistic filamentous fungal pathogens from various fish and shellfish species such as Atlantic salmon (Salmo salar) and rainbow trout (Onchorhynchus mykiss) (Ramaiah, 2006). Considering the problems pointed out related to fungal mycotoxins and pathogenicity, it is critical that the fungal biomass that is to be used in fish feed is properly dried and treated prior to application as a fish feed supplement. Another issue with the application of fungal biomass cultivated on waste streams is that filamentous fungi are highly tolerant to xenobiotic compounds present in waste streams. The high efficiency

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of filamentous fungi in absorption and adsorption of various environmental pollutants has introduced them as a low cost bioremediation solution (Tisˇma et al., 2010). Different species of white rot fungi have been used for removal of various types of pollutants such as phenols ( Justino et al., 2009), polycyclic aromatic hydrocarbons (Quintero et al., 2007), dyes (Faraco et al., 2009), and heavy metals such as lead and cadmium (Sankaran et al., 2010). Kapoor et al. (1999) successfully removed different heavy metal ions including lead, cadmium, copper, and nickel from the culture media using A. niger. In another study, Delgado et al. (1998) used Fusarium sp. for the removal of nickel, cadmium, and copper from wastewater. However, there is evidence that describe such chemical elements such as arsenic, tellurium, etc., could not store in high concentrations in filamentous fungal cells, because living filamentous fungal cells transform them to alkylated or methylated compound effectively. Throughout such biotransformation, generated methylated compounds are in the gas form and highly volatile. Therefore, they release from the cell to the substrate under the definition of biovolatilization (Boriova´ et al., 2014). In order to prevent xenobiotic compounds such as heavy metals from reaching our dining tables through fish fed with filamentous fungi, it is imperative to assure that fungi has been cultivated on by-product and waste streams with no health threatening compounds.

8. Economic and environmental aspects Animal proteins such as cattle, pork, and fish meat are incomparable constituents of almost human daily diet. Therefore, demands for such protein products are growing in parallel with the ever growing population of the world and force meat production industries to provide more products in the market. Scaling-up in production and supply of meat and seafood needs to be accomplished with expansion in providing high-quality feed ingredient. Currently, fishmeal and soybean meal are the common sources for protein utilized in animal feed industries. Natural resources to provide fishmeal are limited and according to the current situation, other agricultural products, such as soybean meal, etc., must compensate the shortage of fishmeal. However, high amount of water and land consumption to farm, competition with human feed and biologic problems with the use of such product as feed ingredient, e.g., low digestibility, health problems, and antinutrient content have limited their application as animal feed ingredient. Filamentous fungi have been proposed as alternative proteins sources. Fungal biomass contains a range of other compounds with nutritional relevance including EAAs, fat, PUFAs, vitamins, minerals, β-glucans, and chitosan. Presence of various kinds of bioactive compounds in fungal biomass, not only can supply essential proteins for farming animals, it can promote animal health by providing essential component involving in animal health and immunity. Increase in production, product quality and food security and enhancement in economic aspects is considered as a step forward toward animal protein production in sustainable way which is consequence expected from the application of high quality feed ingredient. On the other hand,

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potential to grow filamentous fungi on industrial and municipal side streams, residuals, and wastes tackle down the production cost issue arising from high cost of synthetic substrate and also can contribute positively to waste management and to the environmental footprint of the food production chain.

9. Conclusions and perspectives Inclusion of filamentous fungal biomass in the animal feed can aid to improve nutritional properties of animal compound feed. Production of such valuable nutrient source by utilization of low-value streams generated by industrial sector as substrate can address their environmental footprint and give the opportunity of supplying a renewable high quality protein source ingredient in feed production sector. The application of filamentous fungal biomass as a potential alternative to fishmeal can remediate some of the challenges obstacle aquaculture industry expansion. From the other stand point, production of valueadded bioproducts via fungal bioconversion of organic-rich waste streams opens new windows for circular economy. Presence of considerable concentrations of protein, fatty acids, pigments, and immunostimulants in the fungal biomass can contribute to the nutrient quality of fish feed. However, it is noteworthy that as the biomass obtained from the different fungal strains differs in amount and type of constituents, standardization of the application of fungal biomass in fish feed still requires extensive research work. Even though, the research field can benefit from a broader investigation of animal species in order to evaluate the potential of application of filamentous fungal biomass as additive in common feed diets. This would strengthen fungal biomass potential as animal feed ingredient and screen its application versatility. In addition to this, in the future, technoeconomic and life-cycle assessment investigations is highly required in regard to evaluating the application of filamentous fungal biomass as animal feed source. This will emphasize on the potential impact of filamentous fungi on the valorization of low-value residues and on the compound feed industry sector.

Acknowledgments €xtverket through a European Regional Development Fund. This work was supported by the Tillva

References Abro, R., Moazzami, A.A., Lindberg, J.E., Lundh, T., 2014. Metabolic insights in Arctic charr (Salvelinus alpinus) fed with zygomycetes and fish meal diets as assessed in liver using nuclear magnetic resonance (NMR) spectroscopy. Int. Aquat. Res. 6, 63. Aguiar, T., Silva, R., Domingues, L., 2015. Ashbya gossypii beyond industrial riboflavin production: a historical perspective and emerging biotechnological applications. Biotechnol. Adv. 33, 1774–1786. Anupama, Ravindra, P., 2000. Value-added food: single cell protein. Biotechnol. Adv. 18, 459–479. Arora, D.S., Chandra, P., 2010. Assay of antioxidant potential of two aspergillus isolates by different methods under various physio-chemical conditions. Braz. J. Microbiol. 41, 765–777.

426

Current Developments in Biotechnology and Bioengineering

Asadollahzadeh, M., Ghasemian, A., Saraeian, A., Resalati, H., Taherzadeh, M.J., 2018. Production of fungal biomass protein by filamentous fungi cultivation on liquid waste streams from pulping process. Bioresources 13, 5013–5031. Bae, J.-Y., Kim, D.-J., Yoo, K.-Y., Kim, S.-G., Lee, J.-Y., Bai, S., 2010. Effects of dietary arachidonic acid (20:4n6) levels on growth performance and fatty acid composition of juvenile eel, Anguilla japonica. Asian Australas. J. Anim. Sci. 23, 508–514. Bakke-McKellep, A.M., Penn, M.H., Salas, P.M., Refstie, S., Sperstad, S., Landsverk, T., Ringo, E., Krogdahl, A., 2007. Effects of dietary soyabean meal, inulin and oxytetracycline on intestinal microbiota and epithelial cell stress, apoptosis and proliferation in the teleost Atlantic salmon (Salmo salar L.). Br. J. Nutr. 97, 699–713. € m, C., 2011. Bankefors, J., Kaszowska, M., Schlechtriem, C., Pickova, J., Edebo, L., Kiessling, A., Sandstro A comparison of the metabolic profile on intact tissue and extracts of muscle and liver of juvenile Atlantic salmon (Salmo salar L.)—application to a short feeding study. Food Chem. 129, 1397–1405. Barker, T.W., Drouliscos, N.J., Worgan, J.T., 1981. Composition and nutritional evaluation of Aspergillus oryzae biomass grown on palm oil processing effluents. J. Sci. Food Agric. 32, 1014–1020. Ba´tori, V., Ferreira, J.A., Taherzadeh, M.J., Lennartsson, P.R., 2015. Ethanol and protein from ethanol plant by-products using edible fungi Neurospora intermedia and Aspergillus oryzae. Biomed. Res. Int. 2015, 176371.
, J.-P., 2018. Special issue: fungal cell wall. J. Fungi 4, 91. Beauvais, A., Latge Beever, R.E., Burns, D.J.W., 1981. Phosphorus uptake, storage and utilization by fungi. In: Woolhouse, H.W. (Ed.), Advances in Botanical Research. Academic Press. Bennett, J.W., Klich, M., 2003. Mycotoxins. Clin. Microbiol. Rev. 16, 497. Bhardwaj, S., Passi, S., Misra, A., 2011. Overview of trans fatty acids: biochemistry and health effects. Diabetes Metab. Syndr. 5, 161–164. Bimbo, A., Crowther, J., 1992. Fish meal and oil: current uses. J. Am. Oil Chem. Soc. 69, 221–227. Blondeau, N., Lipsky, R., Bourourou, M., Duncan, M., Gorelick, P., Marini, A., 2014. Alpha-linolenic acid: an omega-3 fatty acid with neuroprotective properties: ready for use in the stroke clinic? Biomed. Res. Int. 2015, 519830. Bloomfield, S., 1997. Calcium and phosphorus in health and disease. Med. Sci. Sports Exerc. 29, 160. Boland, M., Rae, A., Vereijken, J., Meuwissen, M., Fischer, A., Boekel, M., Rutherfurd, S., Gruppen, H., Moughan, P., Hendriks, W., 2012. The future supply of animal-derived protein for human consumption. Trends Food Sci. Technol. 29, 62–73.  ˇ ansky´, S., Matu ´ sˇ, P., Bujdosˇ, M., Simonovicova, A., 2014. Bioaccumulation and biovolatiBoriova´, K., Cern lization of various elements using filamentous fungus Scopulariopsis brevicaulis. Lett. Appl. Microbiol. 59, 217–223. Bowman, S.M., Free, S.J., 2006. The structure and synthesis of the fungal cell wall. BioEssays 28, 799–808. Bridle, A.R., Carter, C., Morrison, R., Nowak, B.F., 2005. The effect of β-glucan administration on macrophage respiratory burst activity and Atlantic salmon, Salmo salar L., challenged with amoebic gill disease—evidence of inherent resistance. J. Fish Dis. 28, 347–356. Burlingame, B., Nishida, C., Uauy, R., Weisell, R., 2009. Fats and fatty acids in human nutrition: introduction. Ann. Nutr. Metab. 55, 5–7. Burrells, C., Williams, P.D., Southgate, P.J., Wadsworth, S., 2001. Dietary nucleotides: a novel supplement in fish feeds: 2. Effects on vaccination, salt water transfer, growth rates and physiology of Atlantic salmon (Salmo salar L.). Aquaculture 199, 171–184. Cabib, E., Bowers, B., Sburlati, A., Silverman, S.J., 1988. Fungal cell-wall synthesis—the construction of a biological structure. Microbiol. Sci. 5, 370–375.

Chapter 13 • Filamentous fungi as animal and fish feed ingredients

427

larırmak, N., 2007. The nutrients of exotic mushrooms (Lentinula edodes and Pleurotus species) and C ¸ ag an estimated approach to the volatile compounds. Food Chem. 105, 1188–1194. Carver, J.D., Allan Walker, W., 1995. The role of nucleotides in human nutrition. J. Nutr. Biochem. 6, 58–72. Castell, J.D., Bell, J.G., Tocher, D.R., Sargent, J.R., 1994. Effects of purified diets containing different combinations of arachidonic and docosahexaenoic acid on survival, growth and fatty acid composition of juvenile turbot (Scophthalmus maximus). Aquaculture 128, 315–333. Cheng, Z., Buentello, A., Gatlin, D., 2010. Dietary nucleotides influence immune responses and intestinal morphology of red drum Sciaenops ocellatus. Fish Shellfish Immunol. 30, 143–147. Cone, J.W., Van Gelder, A.H., Visscher, G.J.W., Oudshoorn, L., 1996. Influence of rumen fluid and substrate concentration on fermentation kinetics measured with a fully automated time related gas production apparatus. Anim. Feed Sci. Technol. 61, 113–128. Das, U., 2018. Arachidonic acid in health and disease with focus on hypertension and diabetes mellitus. J. Adv. Res. 11, 43–55. Davani-Davari, D., Negahdaripour, M., Karimzadeh, I., Seifan, M., Mohkam, M., Masoumi, S.J., Berenjian, A., Younes, G., 2019. Prebiotics: definition, types, sources, mechanisms, and clinical applications. Foods 8, 92. Dawood, M., Eweedah, N., Moustafa, E., Farahat, E., 2019. Probiotic effects of aspergillus oryzae on the oxidative status, heat shock protein, and immune related gene expression of Nile tilapia (Oreochromis niloticus) under hypoxia challenge. Aquaculture 520, 734669. Delgado, A., Anselmo, A.M., Novais, J.M., 1998. Heavy metal biosorption by dried powdered mycelium of Fusarium flocciferum. Water Environ. Res. 70, 370–375. Deutz, N., Bauer, J., Barazzoni, R., Biolo, G., Boirie, Y., Bosy-Westphal, A., Cederholm, T., Cruz-Jentoft, A., Krznari
c, Z., Nair, K., Singer, P., Teta, D., Tipton, K., Calder, P., 2014. Protein intake and exercise for optimal muscle function with aging: recommendations from the ESPEN expert group. Clin. Nutr. 33, 929–936. Dufoss
e, L., 2017. Red colorants from filamentous fungi: are they ready for the food industry? J. Food Compos. Anal. 69, 151–161. Dwyer, J., 2003. Dietary requirements of adults. In: Caballero, B. (Ed.), Encyclopedia of Food Sciences and Nutrition, second ed. Academic Press, Oxford. Ebeid, T., Fayoud, A., Abou El-Soud, S., Eid, Y., El-Habbak, M., 2011. The effect of omega-3 enriched meat production on lipid peroxidation, antioxidative status, immune response and tibia bone characteristics in Japanese quail. Czech J. Anim. Sci. 56, 314–324. Esteban, M.A., Mulero, V., Cuesta, A., Ortun˜o, J., Meseguer, J., 2000. Effects of injecting chitin particles on the innate immune response of gilthead seabream (Sparus aurata L.). Fish Shellfish Immunol. 10, 543–554. Esteves Torres, F., Zaccarim, B., De Lencastre Novaes, L., Jozala, A., Santos, C., Francisca Simas Teixeira, M., Ebinuma, V., 2016. Natural colorants from filamentous fungi. Appl. Microbiol. Biotechnol. 100, 2511–2521. Fairweather-Tait, S.J., Cashman, K., 2015. Minerals and trace elements. In: Nutrition for the Primary Care Provider. 111. Karger, pp. 45–52. FAO, 2010. Fats and Fatty Acids in Human Nutrition: Report of an Expert Consultation. FAO, 2018. The State of World Fisheries and Aquaculture 2018. FAO, Rome. Faraco, V., Pezzella, C., Miele, A., Giardina, P., Sannia, G., 2009. Bio-remediation of colored industrial wastewaters by the white-rot fungi Phanerochaete chrysosporium and Pleurotus ostreatus and their enzymes. Biodegradation 20, 209–220. Feng, J., Liu, X., Xu, Z., Liu, Y., Lu, Y., 2007a. Effects of Aspergillus oryzae 3.042 fermented soybean meal on growth performance and plasma biochemical parameters in broilers. Anim. Feed Sci. Technol. 134, 235–242.

428

Current Developments in Biotechnology and Bioengineering

Feng, J., Liu, X., Xu, Z., Wang, Y.Z., Liu, J.-X., 2007b. Effects of fermented soybean meal on digestive enzyme activities and intestinal morphology in broilers. Poult. Sci. 86, 1149–1154. Ferreira, J.A., Lennartsson, P.R., Niklasson, C., Lundin, M., Edebo, L., Taherzadeh, M.J., 2012. Spent sulphite liquor for cultivation of an edible Rhizopus sp. Bioresources 7, 173–188. Ferreira, J.A., Lennartsson, P.R., Edebo, L., Taherzadeh, M.J., 2013. Zygomycetes-based biorefinery: present status and future prospects. Bioresour. Technol. 135, 523–532. Ferreira, J.A., Lennartsson, P.R., Taherzadeh, M.J., 2014. Production of ethanol and biomass from thin stillage using food-grade Zygomycetes and Ascomycetes filamentous fungi. Energies 7, 3872–3885. Fiedor, J., Burda, K., 2014. Potential role of carotenoids as antioxidants in human health and disease. Nutrients 6, 466–488. Fountoulaki, E., Alexis, M.N., Nengas, I., Venou, B., 2003. Effects of dietary arachidonic acid (20:4n-6), on growth, body composition, and tissue fatty acid profile of gilthead bream fingerlings (Sparus aurata L.). Aquaculture 225, 309–323. Francis, G., Makkar, H., Becker, K., 2001. Antinutritional factors present in plant-derived alternate fish feed ingredients and their effects in fish. Aquaculture 199, 197–227. Gibson, G.R., Roberfroid, M.B., 1995. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J. Nutr. 125, 1401–1412. Gibson, G.R., Probert, H.M., Loo, J.V., Rastall, R.A., Roberfroid, M.B., 2004. Dietary modulation of the human colonic microbiota: updating the concept of prebiotics. Nutr. Res. Rev. 17, 259–275. Glencross, B., Huyben, D., Schrama, J., 2020. The application of single-cell ingredients in aquaculture feeds—a review. Aust. Fish. 5, 22. Gmoser, R., Ferreira, J.A., Lennartsson, P.R., Taherzadeh, M.J., 2017. Filamentous ascomycetes fungi as a source of natural pigments. Fungal Biol. Biotechnol. 4, 4. Gomez Candela, C., Bermejo Lopez, L.M., Loria Kohen, V., 2011. Importance of a balanced omega 6/omega 3 ratio for the maintenance of health: nutritional recommendations. Nutr. Hosp. 26, 323–329. Gopalakannan, A., Arul, V., 2006. Immunomodulatory effects of dietary intake of chitin, chitosan and levamisole on the immune system of Cyprinus carpio and control of Aeromonas hydrophila infection in ponds. Aquaculture 255, 179–187. Gopalakrishnan, K., Van Leeuwen, H., Brown, R., 2012. Sustainable Bioenergy and Bioproducts: Value Added Engineering Applications. Springer. 001. Grimble, G., Westwood, O., 2001. Nucleotides as immunomodulators in clinical nutrition. Curr. Opin. Clin. Nutr. Metab. Care 4, 57–64. Guti
errez, S., Svahn, S.L., Johansson, M.E., 2019. Effects of omega-3 fatty acids on immune cells. Int. J. Mol. Sci. 20, 5028. Halver, J., 2013. Fish Nutrition. Elsevier. Halver, J.E., Hardy, R.W., 2002. Fish Nutrition. Elsevier. Hansen, J.A., Nelssen, J.L., Goodband, R.D., Weeden, T.L., 1993. Evaluation of animal protein supplements in diets of early-weaned pigs. J. Anim. Sci. 71, 1853–1862. Hardy, R.W., 2010. Utilization of plant proteins in fish diets: effects of global demand and supplies of fishmeal. Aquac. Res. 41, 770–776. He, F.J., MacGregor, G.A., 2008. Beneficial effects of potassium on human health. Physiol. Plant. 133, 725–735. Hernandez Chavez, M., P
erez Garcı´a, L., Nino-Vega, G., Mora, H., 2017. Fungal strategies to evade the host immune recognition. J. Fungi 3, 51. Hirabayashi, M., Matsui, T., Yano, H., Nakajima, T., 1998. Fermentation of soybean meal with Aspergillus usamii reduces phosphorus excretion in chicks. Poult. Sci. 77, 552–556.

Chapter 13 • Filamentous fungi as animal and fish feed ingredients

429

Jaafar, R., Skov, J., Kania, P., Buchmann, K., 2011. Dose dependent effects of dietary immunostimulants on rainbow trout immune parameters and susceptibility to the parasite Ichthyophthirius multifiliis. J. Aquac. Res. Dev. S3, 1–8. Jacob, J., Pescatore, A., 2017. Glucans and the poultry immune system. Am. J. Immunol. 13, 45–49. Jannathulla, R., Dayal, J., Kondusamy, A., Eugine, A., Muralidhar, M., 2018. Fungus, Aspergillus niger, fermented groundnut oil cake as a fishmeal alternative in the diet of Penaeus vannamei. Aquac. Res. 49, 2891–2902. Jin, B., Van Leeuwen, H.J., Patel, B., Doelle, H.W., Yu, Q., 1999. Production of fungal protein and glucoamylase by Rhizopus oligosporus from starch processing wastewater. Process Biochem. 34, 59–65. Jin, Y., Li, P., Wang, F., 2018. β-Glucans as potential immunoadjuvants: a review on the adjuvanticity, structure-activity relationship and receptor recognition properties. Vaccine 36, 5235–5244. Joint FAO WHO UNU Expert Consultation on Protein and Amino Acid Requirements in Human Nutrition. Food and Agriculture Organization of the United Nations, World Health Oorganization & United Nations University, 2007. Protein and Amino Acid Requirements in Human Nutrition: Report of a Joint FAO/WHO/UNU Expert Consultation. World Health Organization, Geneva. Jones, S.W., Karpol, A., Friedman, S., Maru, B.T., Tracy, B.P., 2020. Recent advances in single cell protein use as a feed ingredient in aquaculture. Curr. Opin. Biotechnol. 61, 189–197. Justino, C.I., Duarte, K., Loureiro, F., Pereira, R., Antunes, S.C., Marques, S.M., Goncalves, F., Rocha-Santos, T.A.P., Freitas, A.C., 2009. Toxicity and organic content characterization of olive oil mill wastewater undergoing a sequential treatment with fungi and photo-Fenton oxidation. J. Hazard. Mater. 172, 1560–1572. Kapoor, A., Viraraghavan, T., Cullimore, D.R., 1999. Removal of heavy metals using the fungus Aspergillus niger. Bioresour. Technol. 70, 95–104. Karimi, S., Soofiani, N.M., Mahboubi, A., Taherzadeh, M.J., 2018. Use of organic wastes and industrial by-products to produce filamentous Fungi with potential as aqua-feed ingredients. Sustainability 10, 3296. Karimi, S., Mahboobi Soofiani, N., Lundh, T., Mahboubi, A., Kiessling, A., Taherzadeh, M.J., 2019. Evaluation of filamentous fungal biomass cultivated on vinasse as an alternative nutrient source of fish feed: protein, lipid, and mineral composition. Fermentation 5, 99. Kats, L., Nelssen, J., Tokach, M., Goodband, R., Hansen, J., Laurin, J., 1994. The effect of spray-dried porcine plasma on growth performance in the early weaned pig. J. Anim. Sci. 72, 2075–2081. Kendrick, B., 2017. The Fifth Kingdom. Hackett Publishing Company, Incorporated, MA. Kim, J., Kim, Y., Kim, Y., Park, Y., 2016. Conjugated linoleic acid: potential health benefits as a functional food ingredient. Annu. Rev. Food Sci. Technol. 7, 221–244. Kinsella, J.E., German, B., Shetty, J., 1985. Uricase from fish liver—isolation and some properties. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 82, 621–624. Koven, W., Barr, Y., Lutzky, S., Ben-Atia, I., Weiss, R., Harel, M., Behrens, P., Tandler, A., 2001. The effect of dietary arachidonic acid (20:4n-6) on growth, survival and resistance to handling stress in gilthead seabream (Sparus aurata) larvae. Aquaculture 193, 107–122. Kris-Etherton, P.M., Harris, W.S., Appel, L.J., American Heart Association, Nutrition Committee, 2002. Fish consumption, fish oil, omega-3 fatty acids, and cardiovascular disease. Circulation 106, 2747–2757. Krogdahl, A., Penn, M., Thorsen, J., Refstie, S., Bakke, A.M., 2010. Important antinutrients in plant feedstuffs for aquaculture: an update on recent findings regarding responses in salmonids. Aquac. Res. 41, 333–344. Kus-Yamashita, M., Filho, J., McDonald, B., Ravacci, G., Rogero, M., Santos, R., Waitzberg, D., Reyes, M., Yehuda, S., Gierke, J., Cori, H., Pires, T., Lajolo, F., 2016. Polyunsaturated fatty acids: health impacts. Eur. J. Nutr. Food Saf. 6, 111–131.

430

Current Developments in Biotechnology and Bioengineering

KyungWoo, L., Lee, S., Lee, B., 2006. Aspergillus oryzae as probiotic in poultry—a review. Int. J. Poult. Sci. 5, 1–3. Langeland, M., Vidakovic, A., Vielma, J., Lindberg, J., Kiessling, A., Lundh, T., 2014. Digestibility of microbial and mussel meal for Arctic charr (Salvelinus alpinus) and Eurasian perch (Perca fluviatilis). Aquac. Nutr. 22, 485–495. Lee, C.S., 2015. The effect of vitamin C on fish health. In: Dietary Nutrients, Additives, and Fish Health. Wiley. Lee, C.-S., Lim, C., Gatlin, D., Webster, C.D., 2015. The effect of vitamin C on fish health. In: Dietary Nutrients, Additives, and Fish Health. John Wiley & Sons. Lennartsson, P.R., 2012. Zygomycetes and Cellulose Residuals: Hydrolysis, Cultivation and Applications. € gskola, Go € teborg. Diss. (sammanfattning), 2012 Chalmers tekniska ho Li, P., Gatlin, D., 2006. Nucleotide nutrition in fish: current knowledge and future applications. Aquaculture 251, 141–152. Li, P., Lewis, D., Gatlin, D., 2004. Dietary oligonucleotides from yeast RNA influence immune responses and resistance of hybrid striped bass (Morone chrysops X Morone saxatilis) to streptococcus iniae infection. Fish Shellfish Immunol. 16, 561–569. Liang, Y., Zhao, X.F., Strait, M., Wen, Z.Y., 2012. Use of dry-milling derived thin stillage for producing eicosapentaenoic acid (EPA) by the fungus Pythium irregulare. Bioresour. Technol. 111, 404–409. Lopez-Huertas, E., 2010. Health effects of oleic acid and long chain omega-3 fatty acids (EPA and DHA) enriched milks. A review of intervention studies. Pharmacol. Res. 61, 200–207. Lopez-Romero, E., Ruiz-Herrera, J., 1986. The role of chitin in fungal growth and morphogenesis. In: Muzzarelli, R., Jeuniaux, C., Gooday, G.W. (Eds.), Chitin in Nature and Technology. Springer US, Boston, MA. Mahboubi, A., Ferreira, J.A., Taherzadeh, M.J., Lennartsson, P.R., 2017. Value-added products from dairy waste using edible fungi. Waste Manag. 59, 518–525. Marijana, S., Petrujkic, B., Nikola, D., Djeli
c, N., Stevanovic, J., Stanimirovic, Z., 2012. Dietary conjugated linoleic acid influences the content of stearinic acid in porcine adipose tissue. Vet. Med. 57, 92–100. McGowan, M., Eisenberg, B., Lewis, L., Froehlich, H., Wells, W., Eastman, A., Kuemmerle, N., Rosenkrantz, K., Barth, R., Schwartz, G., Li, Z., Tosteson, T., Beaulieu, B., Kinlaw, W., 2013. A proof of principle clinical trial to determine whether conjugated linoleic acid modulates the lipogenic pathway in human breast cancer tissue. Breast Cancer Res. Treat. 138, 175–183. Miao, Z., Zhao, W., Guo, L., Wang, S., Zhang, J., 2019. Effects of dietary supplementation of chitosan on immune function in growing Huoyan geese. Poult. Sci. 99, 95–100. Mitra, D., Rasmussen, M.L., Chand, P., Chintareddy, V.R., Yao, L.X., Grewell, D., Verkade, J.G., Wang, T., Van Leeuwen, J., 2012. Value-added oil and animal feed production from corn-ethanol stillage using the oleaginous fungus Mucor circinelloides. Bioresour. Technol. 107, 368–375. Morenga, L., Montez, J., 2017. Health effects of saturated and trans-fatty acid intake in children and adolescents: systematic review and meta-analysis. PLoS One 12, e0186672. Murugesan, G.S., Sathishkumar, M., Swaminathan, K., 2005. Supplementation of waste tea fungal biomass as a dietary ingredient for broiler chicks. Bioresour. Technol. 96, 1743–1748. Nair, R.B., 2017. Integration of First and Second Generation Bioethanol Processes: Using Edible Filamen€ gskolan i Bora˚s, Bora˚s, p. 2017. tous Fungus Neuspora Intermedia. Diss. (sammanfattning), Ho Nalage, D., Khedkar, G., Kalyankar, A., Sarkate, A.P., Ghodke, S., Bedre, V.B., Khedkar, C., 2016. Single cell proteins. In: The Encyclopedia of Food and Health, first ed. Oxford Academic Press, London UK. Nitayavardhana, S., Issarapayup, K., Pavasant, P., Khanal, S.K., 2013. Production of protein-rich fungal biomass in an airlift bioreactor using vinasse as substrate. Bioresour. Technol. 133, 301–306.

Chapter 13 • Filamentous fungi as animal and fish feed ingredients

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NRC, 2011. Nutrient Requirements of Fish and Shrimp. The National Academies Press, Washington, DC. Olsen, R., Hasan, M., 2012. A limited supply of fishmeal: impact on future increases in global aquaculture production. Trends Food Sci. Technol. 27, 120–128. Pascual, M., Hualde, J., Bianchi, V., Moreno, P., Castro, J., Luquet, C., 2018. Wheat grains fermented by fungal mycelia (Pleurotus ostreatus or Lentinus edodes) as alternative feed ingredients for juvenile rainbow trout (Oncorhynchus mykiss). Aquac. Int. 26, 1339–1352. Passoth, V., 2017. Lipids of yeasts and filamentous fungi and their importance for biotechnology. In: Sibirny, A.A. (Ed.), Biotechnology of Yeasts and Filamentous Fungi. Springer International Publishing, Cham. Paul, I., Isore, D.P., Joardar, S., Samanta, I., Biswas, U., Maiti, T., Ganguly, S., Mukhopadhayay, S., 2012. Orally administered β-glucan of edible mushroom (Pleuratus florida) origin upregulates immune response in broiler. Indian J. Anim. Sci. 82, 745–748. Paulino, R.R., Pereira, R.T., Fontes, T.V., Oliva-Teles, A., Peres, H., Carneiro, D.J., Rosa, P.V., 2018. Optimal dietary linoleic acid to linolenic acid ratio improved fatty acid profile of the juvenile tambaqui (Colossoma macropomum). Aquaculture 488, 9–16. Quintero, J.C., Lu-Chau, T.A., Moreira, M.T., Feijoo, G., Lema, J.M., 2007. Bioremediation of HCH present in soil by the white-rot fungus Bjerkandera adusta in a slurry batch bioreactor. Int. Biodeterior. Biodegradation 60, 319–326. Quintin, J., 2018. Fungal mediated innate immune memory, what have we learned? Semin. Cell Dev. Biol. 89, 71–77. Ramaiah, N., 2006. A review on fungal diseases of algae, marine fishes, shrimps and corals. Indian J. Mar. Sci. 35, 380–387. Rasmussen, M.L., Khanal, S.K., Pometto, A.L., Van Leeuwen, J., 2014. Water reclamation and value-added animal feed from corn-ethanol stillage by fungal processing. Bioresour. Technol. 151, 284–290. Rezaei, M., Wall, H., Tarshan, M., Ivarsson, E., 2019. Evaluation of broiler chickens’ digestibility of Neurospora intermedia biomass. Poult. Sci. 98, 5017–5022.
zes, M., 2020. Review: practical use of n-3 fatty acids to improve reproduction Roszkos, R., To´th, T., Me parameters in the context of modern sow nutrition. Animals 10, 1141. Rumsey, G.L., Winfree, R.A., Hughes, S.G., 1992. Nutritional-value of dietary nucleic-acids and purinebases to rainbow-trout (Oncorhynchus-Mykiss). Aquaculture 108, 97–110. Sakai, M., 1999. Current research status of fish immunostimulants. Aquaculture 172, 63–92. Sakai, M., Taniguchi, K., Mamoto, K., Ogawa, H., Tabata, M., 2008. Immunostimulant effect of nucleotide isolated from yeast RNA on carp, Cyprinus carpio L. J. Fish Dis. 24, 433–438. Saleh, A., Eid, Y., Ebeid, T., Amber, K., Kamizono, T., Ohtsuka, A., Hayashi, K., 2011. Aspergillus Awamori as Probiotic in Broiler Chickens. € gberg, A., Neil, M., 2010. Fatty acid transfer from sow to piglet differs for difSampels, S., Pickova, J., Ho ferent polyunsaturated fatty acids (PUFA). Physiol. Res. 60, 113–124.
rez-Castan˜eda, R., Blanco, Z., Benavides-Gonza´lez, F., Sa´nchez-Martı´nez, J., Ra´bago, J., Vazquez, M., Pe 2017. Effect of β glucan dietary levels on immune response and hematology of channel catfish Ictalurus punctatus juveniles. Lat. Am. J. Aquat. Res. 45, 690–698. Sanchez-Muros, M.J., Barroso, F.G., Manzano-Agugliaro, F., 2014. Insect meal as renewable source of food for animal feeding: a review. J. Clean. Prod. 65, 16–27. Sangma, T., Kamilya, D., 2015. In vitro and dietary effects of chitin on cellular and humoral immune parameters of Catla, Catla catla (Hamilton). J. World Aquacult. Soc. 46, 617–623. Sankaran, S., Khanal, S.K., Jasti, N., Jin, B., Pometto, A.L., Van Leeuwen, J., 2010. Use of filamentous fungi for wastewater treatment and production of high value fungal byproducts: a review. Crit. Rev. Environ. Sci. Technol. 40, 400–449.

432

Current Developments in Biotechnology and Bioengineering

Seah, J., Gay, G., Su, J., Tai, E.S., Yuan, J.-M., Koh, W.-P., Ong, C., Van Dam, R., 2017. Consumption of red meat, but not cooking oils high in polyunsaturated fat, is associated with higher arachidonic acid status in Singapore Chinese adults. Nutrients 9, 101. Shiau, S.-Y., Gabaudan, J., Lin, Y.-H., 2015. Dietary nucleotide supplementation enhances immune responses and survival to Streptococcus iniae in hybrid tilapia fed diet containing low fish meal. Aquac. Rep. 2, 77–81. Shrivastava, B., Thakur, S., Khasa, Y.P., Gupte, A., Puniya, A.K., Kuhad, R.C., 2011. White-rot fungal conversion of wheat straw to energy rich cattle feed. Biodegradation 22, 823–831. Siddiquee, S., Kobun, R., Azad, S., Saallah, S., 2015. Heavy metal contaminants removal from wastewater using the potential filamentous fungi biomass: a review. J. Microb. Biochem. Technol. 7, 6. Siqueira, V., 2015. Fungal Biomolecules: Sources, Applications and Recent Developments. Wiley. Snarr, B.D., Qureshi, S.T., Sheppard, D.C., 2017. Immune recognition of fungal polysaccharides. J. Fungi 3, 47. Stuart, K., Johnson, R., Armbruster, L., Drawbridge, M., 2017. Arachidonic acid in the diet of captive California yellowtail Seriola dorsalis and its effects on egg quality. N. Am. J. Aquac. 80, 97–106. Tacon, A., 2004. Use of fish meal and fish oil in aquaculture: a global perspective. Aquat. Resour. Cult. Dev. 1, 3–14. Tacon, A., Hasan, M., 2007. Global synthesis of feeds and nutrients for sustainable aquaculture development. In: Study and Analysis of Feeds and Fertilizers for Sustainable Aquaculture Development. vol. 497. FAO, pp. 3–17. Tacon, A., Metian, M., 2015. Feed matters: satisfying the feed demand of aquaculture. Rev. Fish. Sci. Aquac. 23, 1–10. Takeda, E., Yamamoto, H., Yamanaka-Okumura, H., Taketani, Y., 2012. Dietary phosphorus in bone health and quality of life. Nutr. Rev. 70, 311–321. Tisˇma, M., Zeli
c, B., Vasic-Racki, D., 2010. White-rot fungi in phenols, dyes and other xenobiotics treatment—a brief review. Croat. J. Food Sci. Technol. 2 (2), 2. € hlha €usler, B., James, M., Stone, D., Gibson, R., 2012. Dietary alpha-linolenic acid does not Tu, W.-C., Mu enhance accumulation of omega-3 long-chain polyunsaturated fatty acids in Barramundi (Lates calcarifer). Comp. Biochem. Physiol. B Biochem. Mol. Biol. 164, 29–37. Vahedi, G., Ghodratizadeh, S., 2011. Effect of chitin supplemented diet on innate immune response of rainbow trout. World J. Fish Marine Sci. 3, 509–513. Wagner, L., Go´mez-Requeni, P., Moazzami, A.A., Lundh, T., Vidakovic, A., Langeland, M., Kiessling, A., Pickova, J., 2019. 1H NMR-based metabolomics and lipid analyses revealed the effect of dietary replacement of microbial extracts or mussel meal with fish meal to Arctic Charr (Salvelinus alpinus). Aust. Fish. 4, 46. Wakai, S., Arazoe, T., Ogino, C., Kondo, A., 2017. Future insights in fungal metabolic engineering. Bioresour. Technol. 245, 1314–1326. Wang, S.-H., Chen, J.-C., 2005. The protective effect of chitin and chitosan against Vibrio alginolyticus in white shrimp Litopenaeus vannamei. Fish Shellfish Immunol. 19, 191–204. Wei, W., Sun, J., Liu, C., Xue, Z., 2016. Application of immunostimulants in aquaculture: current knowledge and future perspectives. Aquac. Res. 48, 1–23. Wikandari, R., Millati, R., Lennartsson, P.R., Harmayani, E., Taherzadeh, M.J., 2012. Isolation and characterization of zygomycetes fungi from tempe for ethanol production and biomass applications. Appl. Biochem. Biotechnol. 167, 1501–1512. Wina, E., Tangendjaja, B., Pasaribu, T., Purwadaria, T., 2010. Broiler performance fed Jatropha curcas seed meal detoxified by fermentation, physic and chemical treatments. Indonesian J. Anim. Vet. Sci. 15, 174–181.

Chapter 13 • Filamentous fungi as animal and fish feed ingredients

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Wu, G., 2010. Functional amino acids in growth, reproduction, and health. Adv. Nutr. 1, 31–37. Wu, G., 2016. Dietary protein intake and human health. Food Funct. 7, 1251–1265. Yamauchi, M., Anderson, J.J.B., Garner, S.C., 1996. Calcium and Phosphorus in Health and Disease. CRC Press, New York. Yang, Y.X., Kim, Y.G., Lohakare, J., Yun, J.H., Lee, J.-K., Kwon, M.S., Park, J.I., Choi, J., Chae, B.J., 2007. Comparative efficacy of different soy protein sources on growth performance, nutrient digestibility and intestinal morphology in weaned pigs. Asian Australas. J. Anim. Sci. 20, 775–783. Yunus, F.U.N., Nadeem, M., Rashid, F., 2015. Single-cell protein production through microbial conversion of lignocellulosic residue (wheat bran) for animal feed. J. Inst. Brew. 121, 553–557. Zaragoza, O., Fajer-Avila, E., Almaza´n-Rueda, P., 2011. Influence of β-glucan on innate immunity and resistance of Lutjanus guttatus to an experimental infection of dactylogyrid monogeneans. Parasite Immunol. 33, 483–494.

14 Production of alcohols by filamentous fungi Behzad Sataria and Hamid Amirib,c a

DEPARTMENT OF FOOD TECHNOLOGY, COLLEGE OF ABURAIHAN, UNIVERSITY O F T EHRAN, TEHRAN, IRAN b DEPARTMENT OF BIOTECHNOLOGY, FACULTY OF BIOL OGICAL SCIENCE AND TECHNOLOGY, UNIVERSITY O F I SFAHAN, ISFAHAN, IRAN c E NV IR ONMENT AL RES EARCH I N S T I T U T E , UN I VERSITY OF ISFAHAN, I SFAHAN, IRAN

1. Introduction Ethanol is a colorless, flammable, and volatile alcohol with the chemical formula CH3CH2OH, often abbreviated as EtOH. Being the only nontoxic alcohol, ethanol has been used in alcoholic drinks for a long time. With the spread of coronavirus in early 2020, the use of ethanol as antiseptic agent and hand sanitizer gels becomes overspreading. A solution of 70% ethanol (in water) has the highest ability in dissolving the membrane lipid layer of the virus and deactivates it. Ethanol is used in different industries as a solvent because of its unique structure, capable of dissolving both hydrophilic and hydrophobic compounds. As a solvent, it is used in paints, tinctures, markers, perfumes, and deodorants. Many water-insoluble medications, e.g., cough and cold medications, uses ethanol as solvent media with concentrations of up to 25%. Besides, ethanol is used as an antimicrobial preservative in the preparation of many liquid medicines. Having a high vapor pressure, ethanol can be easily moved away from solutions, making it a suitable solvent for extraction purposes. Because of low toxicity and low freezing point (
114.14°C), it is used as a coolant to keep the temperature below the freezing point of water, when needed (Rosillo-Calle and Walter, 2006). However, the major application of ethanol is for transportation fuel. Ethanol is blended with gasoline with different volumes to use in spark-ignition engines. Depending on the percentage of ethanol and gasoline, the obtained fuel is coded as E(n) (n is the percentage of ethanol in the blend) (Fig. 1). To address the weakness of ethanol, e.g., relatively high volatility, low energy density, and high solubility in water, the production of n-butanol fuel by reviving the old acetone-butanol-ethanol (ABE) fermentation has been suggested by different researchers. The market for biofuels, especially ethanol as the major contributing fuel in transportation, is highly influenced by the oil market. The Brent crude oil price was $22.58 (£18.19) per barrel on March 30, 2020, which reached to its lowest price since November 2002. Declining stock market index and global economy in the long term and plummeting Current Developments in Biotechnology and Bioengineering. https://doi.org/10.1016/B978-0-323-91872-5.00016-8 Copyright © 2023 Elsevier Inc. All rights reserved.

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E5 5% anhydrous ethanol

95% gasoline

E10 10% anhydrous ethanol

90% gasoline

E15 15% anhydrous ethanol

85% gasoline

E25

E85

E100

25% anhydrous ethanol

75% gasoline

85% anhydrous ethanol

Brazilian hydrous ethanol (contains ca. 5% water)

15% gasoline FIG. 1 Ethanol blends for use is spark-ignition cars.

demand for fuel as a result of the global spreading of the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (commonly referred to as coronavirus disease 2019 (COVID-19)), were the major contributors. More than 80% of crude oil is processed for the production of gasoline, diesel, and jet fuel. Travel restrictions for preventing the virus outbreaks (Wilson and Chen, 2020) make grounded airlines and fewer cars on roads and consequently lower demands for fuels. During April 2020, oil took a historic nosedive when its price turned to a negative value for the first time on record. Consequently, many oil tankers floated on the sea without knowing where they are going to unload the fuel. With an average cost of holding oil at $0.2 per barrel per day, oil tankers have to spend $6.0 per barrel per month waiting for oil unloading. In May 2020, oil prices began to rise. On May 19, the WTI was trading at $32.36 while Brent was trading at $34.51 (oilprice.com). Gradual reopening of the economies and returned people to commute to work, preferring their own vehicles to public transportation, has increased the demand. Low oil price was another reason for increasing the demand, e.g., the China National Petroleum Corporation (CNPC) set an increase in crude oil imports by 2% in 2020. On the other hand, the oil supply has decreased and this helps oil prices come to life. An example of this decrease is falling oil production in the US from 13.1 million bpd on March 2020 to 11.6 million bpd in May, according to the Energy Information Administration. On the other hand, Iraq, the OPEC’s second-largest oil producer, did not comply with production cuts and according to the OPEC+ deal in early May (reported by Monthly Oil Market Report (MOMR)), Iraq needed to cut ca. 1 million bpd of its production. Fig. 2 shows the global ethanol production from 2007 to 2019. Global ethanol production grew from 13 billion gallons in 2007 to up to 29 billion gallons in 2019. The United States and Brazil are the major ethanol producers in the world, dominating up to 83% of total production in 2019. For a long time, Brazil has been the top producer of ethanol;

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35 USA

Billions of Gallons

30

Brazil European Union China Canada Rest of World

25 20 15 10 5 0 2007

2008

2009

2010

2011

2012

2013

2014

2015

2016

2017

2018

2019

Last updated: May 2020

FIG. 2 Global ethanol production by country or region. Renewable fuel association (https://ethanolrfa.org/statistics/ annual-ethanol-production/).

but recently, surpassed by the United States. However, sugar and ethanol industries in Brazil are responsible for providing 2.3 of the country’s domestic gross product and this country is the main exporter of ethanol in the world (Basso et al., 2011). Among countries, China is the third-largest ethanol production; however, it only accounts for the production of ca. 4% of the total production (Wu et al., 2021). Nowadays, ethanol is mainly produced via fermentation routes using plant-derived substrates. Therefore, the term “bioethanol” which is used to apply, is not very common in the current literature.

2. Feedstocks for fermentative production of alcohols The carbon source for fermentative alcohols production is generally obtained from plants. Feedstock cost is reported as a major contributor to final alcohols price. A European Commission estimated that 48%–60% of the cost of ethanol is due to feedstocks used (Moscoviz et al., 2021). Depending on its origin and structure, different generations of feedstocks have been developed. Sugar- and starch-based substrates are considered as the firstgeneration feedstocks and have the most direct bioconversion process to alcohols. Simple sugars, e.g., glucose, can be easily fermented to alcohols; however, in order to have an economically viable process, cheaper carbohydrates are envisaged (Rosales-Calderon and Arantes, 2019). A major by-product of sugar industries that is widely used for alcohols production is molasses. Molasses is a dark brown and viscous liquid obtained after crystallization of sucrose derived from sugar cane and sugar beet. In sugar industries, an average of 0.38-ton molasses is generated by the production of 1 ton of sugar, and the annual production of molasses reaches up to 55 million tons. It is characterized by having less than 20% water, 45%–60% sucrose, 2%–20% glucose and fructose, and small amounts of phosphorus, potassium, magnesium, sulfur, copper, and zinc. Even a traditional use of molasses has been cattle feeding, nowadays, most ethanol-producing distilleries in Brazil rely on molasses as the raw material, and almost 90% of molasses is used for

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manufacturing alcohol (Basso et al., 2011; Jamir et al., 2021; Zhang et al., 2021). After simple sugars, starch is the most readily digestible renewable carbon source for bioconversion purposes. However, an extra process of enzymatic- or acid-based hydrolysis is required in order to obtain fermentable sugars from starch (Torabi et al., 2020). The corn- and wheatderived starch are used for the production of ethanol in the United States and Europe, respectively. Notably, first-generation ethanol currently dominates the market, as more than 97% of ethanol is produced using these feedstocks (Moscoviz et al., 2021). Considering lignocellulosic substrates as the second-generation feedstocks for alcohol production has several advantages over the first-generation feedstocks, e.g., availability, low cost, high abundance, and no competition with human food. Lignocelluloses contain a matrix of cellulose (30%–50%), hemicellulose (10%–30%), and lignin (15%–30%) as the major carbohydrates and small amounts of inorganic matter, oils, and proteins. Potential sources of lignocelluloses include agricultural residues (corn stover, wheat straw, rice straw, and rye straw), energy crops (sorghum, switch grass), forestry residues, and a fraction of municipal solid waste. However, releasing fermentable sugars dumped in their complex structure is not as straightforward as starch-based substrates. A “pretreatment” step is required in order to open up the complex structure of lignocelluloses and make them amenable for hydrolysis. Pretreatment methods are categorized as “physical,” “chemical,” “physio-chemical,” and “biological” processes (Schubert, 2020). The changes that occurred in lignocellulosic structure during pretreatment are dependent on the pretreatment and lignocellulose types. In general, lowering cellulose crystallinity, partial hydrolysis of cellulose and hemicellulose, and removal of lignin, are the main effects of pretreatment on lignocellulosic structure (Satari and Jaiswal, 2021). This extra step along with the downstream processes for detoxification and high price of hydrolytic enzymes, make the process of second-generation alcohols production infeasible and research studies are on the way for its commercialization (Satari et al., 2019a). Algae are third-generation feedstocks for ethanol production, and depending on their size, they are categorized as micro- and macroalgae. The high carbohydrate content of some algal species make them suitable feedstocks for alcohols production; however, the production of simple sugars from algal biomass requires cell cultivation, harvest, fractionation, and finally hydrolysis of carbohydrate polymers. The extra processes make alcohols production from algae more challenging than that of lignocelluloses (da Maia et al., 2020; Satari and Jaiswal, 2021).

3. Production of ethanol by filamentous fungi Fermentative ethanol is obtained by the following simple reactions. C6 H12 O6 5C5 H10 O5

microorganisms

)

microorganisms

)

2C2 H5 OH + 2CO2 5C2 H5 OH + 5CO2

Chapter 14 • Production of alcohols by filamentous fungi

439

C6H12O6 represents a hexose, e.g., glucose, and C5H10O5 is a pentose, e.g., xylose. Based on the stoichiometry of these reactions, a maximum 0.51 g ethanol is obtainable from each gram of sugars. In the production of ethanol from lignocellulose-derived glucose, the yield is usually calculated according to the following formula. Ethanol yield ð%Þ ¼

½EtOH  100 ½Biomass  f  1:111  0:51

In this equation, [EtOH] is ethanol concentration at the end of fermentation period (g/L), [Biomass] is the biomass concentration (g/L) (DWB), 1.111 is the hydration factor of glucan to glucose, and f is the glucan fraction in substrate (Satari et al., 2018). A general process for the production of different generations of ethanol is shown in Fig. 3. Enzymatic hydrolysis and fermentation of starch and the next-generation feedstocks can be performed separately or via an integrated process called simultaneous saccharification and fermentation (SSF). In the SSF process, the microorganisms and hydrolytic enzymes are working simultaneously and fermentation of sugars occurs as the sugars are produced. Generally, integrated processes have been developed in order to increase the overall yield by eliminating the negative effect of initial high sugar concentration. In developing second-generation ethanol (and butanol) production, pretreatment, enzymatic hydrolysis, and fermentation, can be consolidated in a single process, i.e., consolidated bioprocessing (CBP) (Salehi Jouzani and Taherzadeh, 2015).

First-generation (sugars and starch) Hydrolysis (amylase)

Second-generation (lignocelluloses)

Third-generation (microalgae)

Pretreatment

Cell fractionation (milling, enzymatic hydrolysis, ...)

(physical, chemical, physico-chemical)

Hydrolysis

Hydrolysis

(dilute-acid, cellulase)

(amylase, cellulase)

(distillation, pervaporation, dehydration)

FIG. 3 Ethanol production process from different generations of feedstock.

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Current Developments in Biotechnology and Bioengineering

In developing a successful ethanol distillery, finding a suitable fermentative microorganism has great importance. In second-generation ethanol production, the microorganism must be able to ferment a variety of hexoses and pentoses in the lignocellulose-derived hydrolysates. Besides, as inhibitory by-products are usually generated during pretreatment of lignocelluloses, the microorganism should have tolerance to a reasonable concentration of them. Moreover, tolerance to a high ethanol titer and metabolic intermediates, high yield and productivity, and easy production and handling are other merits of a suitable microorganism. Saccharomyces cerevisiae, Escherichia coli, and Zymomonas mobilis possess some of these characteristics, which were extensively used in ethanolic fermentation (Adegboye et al., 2021; He et al., 2014).

3.1 Production of ethanol by zygomycetes Within the Zygomycetes fungi, which is a group of Zygomycota, some species in the order Mucorales are known to ferment sugars to ethanol with a high yield and productivity. Ethanol producing Mucorales are different in terms of growth requirements, e.g., carbon type assimilation, oxygen requirement, and optimal growth temperature. Among the Mucorales, Mucor indicus, Mucor circinelloides, Rhizopus oryzae, some species of Absidia and Rhizomucor have received great attention because of their ability to produce ethanol from a variety of substrates (Ferreira et al., 2013; Karimi and Zamani, 2013; Rodrigues Reis et al., 2019; Satari and Karimi, 2018). Table 1 summarized some results of ethanol production from different carbon sources by Mucorales. Different ethanol-producing Mucorales have high potential in ethanol production from first- and second-generation feedstocks, as shown in this table. The process involves the cultivation of fungal cells in agar plates, containing agar, peptone, and glucose, in order to propagate fungal hyphae and spores. Afterward, the generated cells were aseptically transferred to fermentation media containing carbon sources as well as nutrients, e.g., nitrogen, phosphorous, magnesium, and calcium sources, and some other elements. The pH of media is adjusted to ca. 5.5, and the temperature is kept at around 32°C (Satari and Karimi, 2020). During the fermentation, the fungal shape, mass, or size, increase, and the carbon sources are converted to fungal biomass and ethanol. Ethanol-producing Mucorales are dimorphic, and depending on fermentation conditions, e.g., aeration, and spore number inoculation, their morphology can switch between yeast-like and filamentous form (Lennartsson et al., 2009; Satari et al., 2016). Fungal filaments can grow as mycelial clumps or form spherical pellets (Fig. 4). Pellets restrict the mass transfer from fermentation media to the cells, and the formation of mycelia is associated with problems such as clogging the probes and wrapping around the impellers. However, collecting and reusing the filaments is more facilitated in comparison with the yeasts in the fermentation broth. The fungal biomass is a valuable by-product of fermentation. This valuable by-product can be directly consumed as fodder or used to extract valuable chemicals, e.g., chitosan, fatty acids, and mycoproteins (Edebo, 2008; Satari et al., 2016). Besides, the potential of

Chapter 14 • Production of alcohols by filamentous fungi

441

Table 1 Ethanol production by ethanol-producing Mucorales from different substrates. Zygomycetes fungi Substrate

Ethanol yield or Fermentation condition concentration

Mucor circinelloides

Glucose

R. oryzae M. indicus

Glucose Xylose Glucose

Absidia spp.

Glucose

Rhizomucor pusillus Rhizopus sp.

Xylose

Submerged batch cultivations, aerobic growth Batch cultivation, aerobic condition Batch cultivation, aerobic condition Submerge fermentation, aerobic Aerobic Anaerobic

M. indicus M. indicus

M. indicus a

Hydrolysates of wheat straw Mixed sugars derived from corn stover Glucose

Hydrolysates of rice straw

References

Up to 0.34 g/g sugar

€bbehu €sen et al. (2004) Lu

0.41 g/g sugar 0.07 g/g sugar 0.40 g/g sugar

Millati et al. (2005)

383 mg/g

Wikandari et al. (2012)

0.18 g/g

Komeda et al. (2015)

0.40 g/g sugar

FazeliNejad et al. (2016)

Aerobic cultivation, batch 0.38 g/g sugar mode Aerobic Up to 0.45 g/g sugar Anaerobic Up to 0.46 g/g sugar 99.4 g/L and SSSFa yield of 89.5%

Sues et al. (2005)

Shafiei Alavijeh et al. (2020) Abasian et al. (2020)

Molaverdi et al. (2019)

Solid-state simultaneous saccharification and fermentation (solid-state fermentation: fermentation at low moisture content, i.e., 80% efficiency in submerged cultivations. So, we might get a though, how the fungus grown in the natural ecosystem has such a high efficiency of organic acid production? May be the organic acid Current Developments in Biotechnology and Bioengineering. https://doi.org/10.1016/B978-0-323-91872-5.00005-3 Copyright © 2023 Elsevier Inc. All rights reserved.

455

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Current Developments in Biotechnology and Bioengineering

biosynthesis of fungus is not regulated in an organized manner, hence placed in the fermentation media with high substrate concentrations, the flux of the carbon will be toward acid synthesis. But there are advantages for the fungus in producing and adapting to change in the external environment because of these acids, first, these organic acids have chelating properties, which would help in chelating of metal compounds in the environment and increase solubility. Second, with acidic pH environment the bacterial contamination can be avoided (Alonso et al., 2015; Karaffa and Kubicek, 2019). Considering the global population, industrialization, environmental protection, food security, and meeting the needs, the bio-based production of these organic acids through the concept of biorefinery wherein renewable and sustainable lignocellulosic residues will be used as feedstock is inevitable. As filamentous fungi are known to grow on multiple feedstocks, they are considered as suitable candidates for developing bioprocesses for organic acid biosynthesis in commercial scales. This chapter discusses the aspects of fungal organic acid production, the biochemistry, genetics, metabolic, and process engineering approaches carried out to improve the end product titers to attain the commercial potential. The organic acids considered are itaconic, gluconic, citric, and oxalic acid (OA).

2. Itaconic acid IA also known as 2-methylidenebutanedioic acid, is an unsaturated dicarbonic acid with two pKa values, pKa1
3.84, and pKa2
5.55 at 25°C (Krull et al., 2017). IA has significant commercial interest as monomer or additive in the manufacturing of fiber, resins, lattices, plastic, detergents, rubber, paint, surfactants, lubricants, and bioactive compounds. Due to the presence of an unsaturated and highly reactive dicarboxylic acid functional group, the acid can be involved in various complex organic reactions like esterification, polymerization and anhydride formation (Saha et al., 2017). IA occurs in non-dissociated form in solution with pH 7.0 and in between pH 2.0–7.0, a mixture of dissociated and undissociated forms exists. The global IA production was over 41,400 tonnes worth 74.5 million USD in 2011 and is expected to improve 5.5% and worth 204.6 million USD by 2023 (Cunha da Cruz et al., 2018). In traditional chemical process, IA can be synthesized by pyrolysis of CA and subsequent hydrolysis of the resulting anhydride. Other approaches include oxidation of mesityl oxide and isomerization of the intermediate CA to IA. However, in the chemical process, the feedstocks catalysts and the process conditions used for IA production were not found to be economical and environmental friendly compared to the biological processes (Bafana and Pandey, 2018).

2.1 Microorganisms, metabolism, and physiology of itaconic acid biosynthesis Various fungal strains like Aspergillus terreus, Ustilago maydis, Candida sp., and Pseudozyma antarctica are reported IA producers. A. terreus and U. maydis, are potent strains and

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457

Table 1 Summary of organic acids production from various carbon sources by various fungal strains. Feedstock/ substrate

Cultivation conditions (pH, Temp °C)

Titers (g/L)

Yield (g/g)

Productivity (g/L h)

References

Glucose Food waste Glucose Glucose

3.4, 35 2.3, 45 2.3, 45 6.5, 30

162 41.1 44.7 75.7

0.46 0.27 0.3 0.54

0.99 0.19 0.20 0,53

Krull et al. (2017) Narisetty et al. (2021) Narisetty et al. (2021 Becker et al. (2021)

Glucose Glucose

6, 28 6, 28

56.25 39.69

0.46 0.33

0.39 0.27

Ahmed et al. (2015) Ahmed et al. (2015)

Pomegranate peel wastes Sugar beet molasses

8, 25

351

NG

1.79

6, 30

68.8

NG

0.4

Roukas and Kotzekidou (2020) Ozdal and Kurbanoglu (2019)

A. niger

Lactose

6.5, 30

26.62

0.26

0.18

A. niger

Cashew apple juice

6, 30

106.75 0.53

Microorganism Itaconic acid A. terreus DSM 23081 A. terreus BD A. terreus BD Ustilago maydis MB215 Gluconic acid Penicillium puberulum Penicillium frequentans Citric acid A. niger B60 A. niger Oxalic acid

NG

Mandal and Banerjee (2005) Betiku et al. (2016)

the model organisms evaluated for investigating the biosynthetic pathways and process conditions (Table 1; Bafana et al., 2017; Bafana and Pandey, 2018). IA is synthesized from cis-aconitic acid, the intermediate of tricarboxylic acid cycle (TCA) cycle and the pathway was proposed by Bentley and Thiessen in 1957. In the central carbon metabolism, glucose or other carbon source is assimilated through glycolysis, and pyruvate is generated, followed by dehydrogenation to produce acetyl-CoA. Later in mitochondria, acetyl-CoA and oxaloacetic acid form citrate via citrate synthase. In the subsequent reaction, citrate is dehydrated to cis-aconitic acid, which is transported to cytosol through putative mitochondrial tricarboxylic acid transporter (MTTA). In the cytosol, cis-aconitic acid in the present of cis-aconitic acid decarboxylase (CAD) [EC 4.1.16] is converted to IA. From the cytosol, IA is transported through major facilitator superfamily (MFSA) transporter into the extracellular environment. In addition to the cadA gene, few other regulatory genes were observed as cluster, which transcribe to mitochondrial TCA transporter (mtt1), a membrane permease and a transcription factor, that could regulate the pathway expression (Kuenz and Krull, 2018; Zhao et al., 2018). In U. maydis, trans-form of aconitic acid was observed to be the precursor to produce IA. cis-Aconitic acid is transported into the cytosol and converted into transform before decarboxylation into IA. Hence in the biosynthesis of IA from glucose or

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Current Developments in Biotechnology and Bioengineering

other carbon sources the key enzyme is cis-aconitate decarboxylase (CAD) encoded by cadA gene (Wierckx et al., 2020).

2.2 Production and process conditions Although diverse microorganisms were identified and genetically constructed for IA production, A. terreus has been the organism of choice for industrial-scale production, mainly due to its tolerance to low pH, and the ability to accumulate higher IA titers and yield. In 1931, Kinoshita first reported the accumulation of IA in sucrose fermentation using Aspergillus sp., and later named the strain as A. itaconicus. Later in 1960 Lockwood and Reeves at the National Center for Agricultural Utilization Research (NRRL) isolated, identified and named A. terreus NRRL 1960, which is still considered as one of the most potent strains available for IA production from glucose. The A. terreus strain was observed to accumulate >120 g/L IA based on the feed concentration. During IA biosynthesis process parameters like physiological pH, temperature, aeration or oxygen concentration, and nutrient components play a significant role. For A. terreus, the optimal pH for IA production is between 1.8 and 2.2, but in an interesting approach, Hevekerl and associates, adjusted the pH to 3.0, after 2.1 days of cultivation, which resulted in 146 g/L IA, with 0.48 and 0.81 mol/mol productivity and yield, respectively (Hevekerl et al., 2014). A shift in the pH from 1.8 to 3.0 has posed a positive impact on the product titers. The pH < pKa2 resulted in cessation of growth and metabolite production, due to permeation of undissociated IA into the microbial cell changing the intracellular pH by acidifying the cytosol (Wierckx et al., 2020). Even the undissociated form of IA could enter the microbial cell by passive diffusion and was observed to inhibit isocitrate lyase, disrupting the anaplerotic glyoxylate cycle. Dissolved oxygen (DO) plays an important role in mycelial growth and IA accumulation. IA biosynthesis is a strict aerobic process, which requires 1.5 mol of O2 per mole of IA produced from glucose. It was also observed that interrupting the aeration for 10 min resulted in cessation of IA production and later the production re-commenced after 24 h of incubation. During reduced or low concentrations of oxygen available for the microbial cells, the NADH cannot be oxidized and accumulated intracellularly, which also results in the depletion of ATP levels, inhibiting fungal growth and metabolism. More contrary situation was the inhibition of citrate synthase and phosphofructokinase enzymes by accumulated NADH. Hence uninterrupted aeration and agitation is required for adequate IA biosynthesis and accumulation (Bafana et al., 2019; Bafana and Pandey, 2018; Hosseinpour Tehrani et al., 2019; Saha et al., 2019). Apart from process parameters, various media components like carbon source, nitrogen and phosphorous concentrations, and micronutrients were observed to affect IA accumulation. Kuenz and associates developed a simple media (g/L) with glucose (180), KH2PO4 (0.1), NH4NO3 (3.0), and CaCl2 (5.0) that provided high IA titers, yield and productivity (Kuenz et al., 2012). It was reported that a nitrogen and phosphate limitation triggered IA accumulation. During phosphate limitation, the levels of ATP drop,

Chapter 15 • Organic acids by filamentous fungi

459

impairing oxidative phosphorylation and increasing the carbon flux toward glycolysis and TCA cycle. This enhances substrate level phosphorylation, and NAD(P)H regeneration, as the carbon flux is more toward TCA than respiration, promoting IA accumulation. Whereas in nitrogen rich conditions, ammonium ions was observed to inhibit phosphofructokinase (fructose-6-phosphate + ATP ! fructose 1,6- bisphosphate + ADP), which may alter the carbon flux through Embden-Meyerhof-Parnas (EMP) pathway. A similar phenomenon was observed in all the IA producers like U. maydis, P. antarctica, and € chs, 2013; Saha et al., 2019). Furthermore, IA production is A. terreus (Klement and Bu influenced by other micronutrients like calcium, iron, manganese, and copper production in the absence of manganese ions growth was in the form of pellets, whereas in the presence of manganese the culture grew in the form of long hyphae with branching filaments (Kuenz and Krull, 2018; Saha, 2017).

2.3 Strain engineering and process modifications Several eukaryotic microorganisms, such as Yarrowia lipolytica, Saccharomyces cerevisiae, and Aspergillus niger, were developed for IA production. The titers produced by these recombinant strains were not in comparison with the commercially viable A. terreus strains. But the metabolic engineering has unlocked the innovative pathway of integrating the saccharification and fermentation in fungal strains, which could reduce the fermentation time, and prevent the inhibitors generated during high temperature and pressure pretreatment procedures. In U. maydis, by the overexpression of transcriptional regulator (ria 1), deletion of itaconate oxidase (cyp 3) and by optimizing the process conditions, the strain was able to accumulate 80 g/L IA in 16 L bioreactor in a fed-batch mode of fermentation (Demir et al., 2021). Currently, the utilization of second-generation lignocellulosic feedstocks as the carbon sources is of primary interest. The fungal strains have an ability to digest the polymeric cellulose to fermentable sugars, but these strains are sensitive to inhibitors like furfurals, phenols and fufuryl alcohols produced during the initial chemical pretreatment and enzymatic hydrolysis (Saha et al., 2019). Hence, strain development toward utilization of these renewable cost-effective feedstocks would be beneficial in the industrial perspective. A strain of A. terreus AFYSZ-38 was developed by protoplast fusion between the IA hyper producing strain and the strain resistant to fermentation inhibitors from the hydrolysates. The mutant strain was able to produce 41.5 g/L IA in an fed-batch mode and 22.43 g/L in simultaneous saccharification and fermentation strategy utilizing bamboo shoot feedstock (Yang et al., 2020). Starch-based feedstocks are also significant industrially based on the geographic locations and source availability. A new strain A. niveus MG183809, was able to utilize corn starch and produce 15.65 g/L IA, but further strain engineering and process modifications can be carried out to improve the IA titers (Gnanasekaran et al., 2018). Despite the high titers of IA by A. terreus, the strain still has limitations due to product mediated growth inhibition, lower carbon flux toward IA and improved excretion of IA into

460

Current Developments in Biotechnology and Bioengineering

the extracellular space. With the developed omics tools and techniques, the underlying mechanisms can be further investigated to address these limitations and construct an industrially economical strain.

3. Gluconic acid Gluconic acid (GA) or pentahydroxy hexanoic acid (C6H12O7) is a non-volatile, noncorrosive, and non-toxic mild organic acid with pKa of 3.86. It imparts sour taste in foods like wine and fruit juices (Zhang et al., 2016; Zhou et al., 2019). GA and its salts find wide application in food industry, pharmaceuticals, textile, and leather industry due to its unique properties like low toxicity, and corrosiveness, its metal ions sequestering capability, and biodegradability (Pal et al., 2016). GA is used in meat and dairy products as a leavening agent. It is also used as a flavoring agent and in formulation of various food products. Hence, in a due course of 20 years, the increasing demand for this organic acid summed to production capacity of more than 60,000 tonnes per year with a global market value of $ 1 billion USD in 2020 and expected to increase with CAGR of 5% to $ 1.9 billion USD by 2028. Commercially GA can be produced by three different approaches, namely, (a) chemical oxidation of glucose with a hypochlorite solution (b) electrolytic oxidation of glucose solution in the presence of gold catalysts (c) fermentation process with specific microorganisms. However, the microbial fermentation process is a more advantageous technique for GA production since the inevitable side reactions stemming during the chemical production processes may be avoided.

3.1 Microorganisms, metabolism, and physiology of gluconic acid biosynthesis A wide group of filamentous fungi have the ability to produce GA on a large-scale. The industrial production process is carried out in batch cultivation using several fungal species belonging to different fungal genera like Aspergillus, Penicillium, Fusarium, Mucor, and Geliocladium. Conventional screening protocols, like plate assay for acidification, were employed to isolate potential indigenous fungal strain for commercial production of GA. The biological process involves dehydrogenation of glucose catalyzed by glucose oxidase [EC 1.1.3.4] to produce GA. The metabolism involves oxidation of aldehyde group on the C1 of glucose to a carboxyl group resulting in the production of glucono-delta-lactone (GDL) (C6H10O6) and hydrogen peroxide (H2O2). The glucose oxidase is a FAD-dependent flavoprotein and a high concentration of glucose and oxygen at pH 5.5 favor this reaction. Further, spontaneous hydrolysis results in GA, mediated by lactone hydrolysing enzyme glucose dehydrogenase, and peroxidase (Pal et al., 2016).

Chapter 15 • Organic acids by filamentous fungi

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3.2 Production and process conditions Production of GA through biological process is impacted by physiological conditions and media parameters like aeration (KLa), agitation, pH, substrate (glucose), and nitrogen concentrations. The optimal conditions for GA production were observed as follows: glucose (110–250 g/L); nitrogen and phosphorous (20 mM); pH (4.5–7.0); and very high aeration rate at elevated pressure (4 bar), that could increase the DO concentration in the aqueous phase. Along with the glucose, oxygen is also considered as the key substrate in GA biosynthesis, as glucose oxidase uses molecular oxygen for the conversion of glucose. Hence the availability of oxygen in the external medium, its concentration and the oxygen transfer coefficient are of high importance. As the reaction progresses 0.5 mol of O2 is required per mole of glucose, for producing 1 mole of GA. This suggests that the process is highly oxygen consuming that can be supplemented by atmospheric compressed air or pure oxygen (Pal et al., 2016). In A. niger, GA accumulation depends on the pH and the optimal pH is between 4.5 and 7.0. If the pH drops below 3.5, CA production is triggered, and the carbon flux is diverted toward the TCA cycle. It was observed that at pH 5.6, glucose oxidase has 100% activity, whereas at pH 2.0 and 3.0 its activity dropped to 5 and 35% (Zhang et al., 2016; Zhou et al., 2019). A wide range of carbon sources like sugarcane molasses, grape, banana must, whey permeates, breadfruit, agro-residual biomass, which are rich in glucose were used for the production of GA through biochemical process. In a study, a perishable fruit from Nigeria, breadfruit hydrolysate with 120 g/L glucose was used for production of 109.9 g/L GA with 0.96 g/g yield using A. niger (Ajala et al., 2017). Similarly using corn stover hydrolysate 76.67 g/L of GA was produced with 0.94 g/g yield (Zhang et al., 2016).

3.3 Strain engineering and process modifications A wild type of strain can perform according to its metabolic efficiency, and all the strains cannot provide the theoretical maximum yields. However, the strain or the process can be improved by metabolic engineering techniques and process optimizations. Glucose oxidase is the rate limiting enzyme for the production of GA. Considering this an industrially feasible host Pichia pastoris, was used for heterologous expression of glucose oxidase, with increased thermostability. The resulted enzyme was able to convert 324 g/L glucose to GA (Mu et al., 2019). A cell-free enzymatic process with glucose oxidase and catalase derived from the filamentous fungus can perform better in comparison to cell mediated bioconversions. Nearly 100% glucose is converted to GA under the appropriate conditions by employing the enzymatic process. This method is also approved by the FDA as no product purification steps are required for the recovery of GA (Mu et al., 2019). As the fungal enzymes or cells produced GA in accordance with the maximum theoretical yields, most of the research was concentrated on process improvements and the use of sustainable feedstocks. Immobilized cells of A. niger in polyurethane foam produced 92 g/L of GA from 1 L of whey permeate consisting of 0.5% glucose, and 9.5% lactose (Mukhopadhyay et al., 2005). Hence with the available genetic tools for fungal engineering,

462

Current Developments in Biotechnology and Bioengineering

and the whole genome sequences, either the homologous overexpression of rate limiting enzymes, and deletion of by-product pathways could improve the GA titers and yield.

4. Citric acid CA or 2-hydroxy-propane-1,2,3-tricarboxylic acid (C6H8O7) is a natural, nontoxic, tricarboxylic organic acid formed in the metabolism of aerobic organisms (Amato et al., 2020). Naturally, it is found in citrus fruits like oranges, lime, lemon, berries, grapes, etc. (Papagianni, 2007). Due to its remarkable physico-chemical properties and environmentally benign nature, it is a widely used industrial acid with numerous applications in the food and beverage, pharmaceutical, personal care, detergent industry, and others (Ciriminna et al., 2017). In 2025 its global market is estimated to be US$ 3.6 billion, with a CAGR of 5.24% (Mores et al., 2021). In the food industry, it is used as an acidulant to prevent oxidative deterioration of food products such as sweets and soft drinks (Berovic and Legisa, 2007). In the pharmaceutical industry, it is used as a flavoring agent to enhance palatability and is also used as a cross-linking agent in films for controlled release of drugs (Dhillon et al., 2011). CA in the form of sodium citrate is also used as an anticoagulant in blood transfusions. Due to its low pH, in the cosmetic industry, CA is also used in astringent lotions. In addition, in the chemical industry, it is used to remove metal oxides from surfaces, tanning of leather, electroplating, etc. (Soccol et al., 2006). CA has also been widely employed in other applications like biodegradable packaging materials, as a disinfectant, extracting agent and in environmental remediation.

4.1 Microorganisms, metabolism, and physiology of citric acid biosynthesis Numerous fungi have been utilized for the production of CA using a variety of substrates. Various species of Aspergillus such as A. niger, A. awamori, A. foetidus, A. wentii, A. fenicis, A. fumaricus, A. fonsecalus, A. luchensis, A. usumii, A. aculeatus, A. phoenicis, A. saitoi, A. carbonaries and Trichoderma viride and Mucor pyriformis have been reported to produce significant amounts of CA (Show et al., 2015). Among these strains, A. niger is the preferred choice of microorganism for CA production at the industrial scale (Table 1). This is mainly because of the versatility of the organism to use multiple substrates, ease of handling and high product yields (Behera, 2020). The phenomenon of CA production by A. niger has been proposed via many theories, however no concrete explanation is available. It is assumed that accumulation of CA occurs due to an induced abnormality in (CA cycle of A. niger) (Angumeenal and Venkappayya, 2013). TCA cycle is a multienzyme catalyzed cyclic series of reactions in which the acetyl group of acetyl-Co enzyme is utilized to yield CO2 and protons. Carbohydrates are converted to pyruvate via the glycolytic pathway, which is then converted to acetyl-CoA and CO2 (Behera et al., 2021). Then, acetyl-CoA is condensed with oxaloacetate via citrate synthase enzyme to form citrate and CoA is

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released. In this pathway O2 is consumed to regenerate NADH formed during glycolysis to NAD+, thus generating ATP. Under specific environmental conditions, CA is overproduced mainly due to the enzymatic reactions in the TCA cycle and its production is also dependent on the co-factors associated with the enzymes (Show et al., 2015). In fungi, citrate biosynthesis occurs in the cytosol as well as in the mitochondria (Karaffa and Kubicek, 2003). After two molecules of pyruvate are formed via the conversion of D-glucose in the cytosolic glycolytic pathway, one molecule is transported into the mitochondria while the other enters the reverse TCA (rTCA) pathway. In the mitochondria, it is converted to acetyl-CoA and the malate in rTCA again enters the mitochondria via a malate-citrate antiporter (CTP) and is further converted into citrate through the TCA cycle. Citrate is then transported out of the mitochondria via counter transport of malate, thus leading to the accumulation of citrate (Karaffa and Kubicek, 2003). Through this pathway, maximum theoretical yield of citrate is 1 mol per mol glucose, if pyruvate originates from glycolysis.

4.2 Production and processing conditions The type of fermentation technique used can also have a significant influence on the yield of CA. Production of CA using fungi can be carried out through three different fermentation conditions, which include surface, submerged, and solid-state fermentation (Soccol et al., 2006). Surface fermentation was initially used to produce CA at the industrial level. However, over the past few years submerged fermentation has gained more popularity (Show et al., 2015). Surface fermentation is usually carried in two phases, wherein in the first phase, the fungus is grown as a mycelia mat on the surface of the media followed by the formation of CA via utilization of carbohydrates present in the media (Show et al., 2015). The CA formed is then extracted by washing the mycelia mats. Surface fermentation requires lower installation and energy costs but is labor intensive, sensitive to alterations in the media composition and often prone to contaminations (Soccol et al., 2006). Solidstate fermentation offers advantages of using lower water and energy, less wastewater generation and enables the use of diverse renewable feedstocks for the production of CA. However, the use of intense labor during loading, unloading, and cleaning stages might incur high operational costs and longer fermentation times (Mores et al., 2021). Submerged fermentation on the other hand mandates the use of complex equipment, which can increase the initial installation costs and in addition foaming occurs during fermentation (Mores et al., 2021). Nevertheless, it offers higher productivity and yields; it is less sensitive to changes in the medium composition, providing scope for utilizing wider range of substrates. Automation of the process can help in lowering the costs, standardization of the procedure, reduce labor and prevent contamination. Considering these advantages, submerged fermentation is extensively being used at the industrial scale for CA production. More recent studies indicate that innovations in CA fermentation can also be achieved by fungal immobilization methods, multi-step processes and the utilization of renewable feedstocks such as waste in place of conventional sugars.

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Current Developments in Biotechnology and Bioengineering

CA production was discovered more than 100 years ago and since then many studies have been carried out to enhance its fermentation process (Papagianni, 2007). Fermentation conditions for CA were established during the 1930s and 1940s, wherein various critical factors were evaluated. The accumulation of CA is predominantly influenced by the medium composition, particularly in submerged type of fermentation (Mores et al., 2021). In addition, the type of carbon source and its concentration, nitrogen and phosphate limitation, pH, aeration, trace metals concentrations and morphology of the microorganisms also play a significant role in CA fermentation (Hu et al., 2019). It has been reported that certain nutrients such as carbon source, oxygen or protons should be in excess, while nitrates and phosphates should be in limiting levels and trace elements such as manganese should be well below threshold levels. Several studies have been carried out using different carbon sources, and it was shown that CA yield is directly affected by carbon source (Dhillon et al., 2011). Monosaccharides and disaccharides are usually preferred since they can be rapidly utilized by the fungus in comparison to polysaccharides, which take more time to decompose. Sugars such as glucose, sucrose, fructose, maltose, and mannose were very effectively utilized by A. niger for CA production (Amato et al., 2020; Karaffa and Kubicek, 2019). This strain was able to utilize these sugars at a concentration range of 120–180 g/L. The yield of CA is higher when sucrose is utilized as a substrate in comparison to glucose, fructose, and lactose (Angumeenal and Venkappayya, 2013). The higher yield obtained with sucrose can be attributed to the strong extracellular mycelium-bound invertase of A. niger that effectively hydrolyzes sucrose at low pH (Karaffa and Kubicek, 2003). High sugar concentrations favor CA production since it inhibits the activity of α-ketoglutarate dehydrogenase enzyme, while low concentrations of carbon reduce the size of the mycelium affecting its shape. In industrial fermentations, glucose from starch hydrolysis, sugar cane by-products, sugar beet molasses, agro industrial wastes such as fruits, vegetables, lignocellulosic biomass, etc. are the most widely used carbon sources. Nevertheless, certain bottlenecks exist due to the need for pretreatment or difficulty in scale-up in the case of solid-state fermentation. The limitation of nitrogen and phosphorous is another crucial factor, since concentration of nitrogen greater than 0.25%, favors OA accumulation and decreases CA production. The type of nitrogen source also plays a role in CA synthesis and growth of the fungus. While ammonium nitrate reduces the duration of vegetative growth, ammonium sulfate promotes a longer period of vegetative growth (Papagianni, 2007). Supplementing salts of ammonia such as ammonium sulfate/nitrate, urea, etc. to the medium help in lowering the pH of the system, thus favoring CA production (Mores et al., 2021). Heavy metals such as Zn, Mn, Fe, and Cu are also added to liquid cultures during CA production. Metal ions can act as co-factors for the enzymes and hence controlling trace element concentration can regulate the enzyme activities for CA production (Angumeenal and Venkappayya, 2013). However, the concentration of these ions should be maintained below 1 mg/L as they tend to inhibit the activity of certain enzymes and might affect the cell morphology. Due to the accumulation of organic acids, the pH of the medium changes continuously. For inhibiting the formation of by-products such as oxalic and GAs, the pH of the medium should be

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maintained at 3.0 (Behera, 2020). At such low pH conditions, the chances of contamination are also much lower, and recovery of CA becomes easier. At the beginning of fermentation, the pH of the system should be above 5.0 to favor the formation of mycelium. As the biomass growth occurs during the first 48 h the pH of the system drops to 3.0 and CA production begins. Furthermore, DO also plays an important role during CA production. High DO can be regulated through agitation, aeration and culture time during fermentation. Addition of alcohols such as methanol or ethanol also has a positive effect on CA production due to its inhibitory effect. The concentration of the alcohol used is dependent on the type of the organism used and the media composition. Addition of alcohols causes a change in the lipid composition of the cell membrane of the fungi, thus affecting growth and sporulation. The concentration of the alcohols in the range of 1–5% neutralize the negative effect of the metals ions during CA production (Amato et al., 2020).

4.3 Genetic and process engineering strategies Apart from synthesis of CA using naturally producing strains, inducing mutations in these natural producers using physical and chemical agents has been extensively studied (Chroumpi et al., 2020). The commonly used method is to induce mutations in the parental strains, using mutagens such as gamma radiation, ultraviolet (UV), and chemical mutagens. Chemicals such as diethyl sulfonate (DES), N-methyl-N-nitrosoguanidine, ethidium bromide, etc., are well-known chemical mutagens. For the identification of mutated/improved strains enzyme diffusion zone analysis is usually performed and for the selection of improved strains single spore technique and passaging are the two widely employed techniques. Often for hyperproduction, hybrid methods involving UV and chemical mutagens are used. In addition, other techniques such as genome editing, metabolic engineering to reduce the formation of by-products and generating mutants with an ability to overproduce CA has been explored (Chroumpi et al., 2020). Systems metabolic engineering is another tool for developing a new synthetic pathway and introduce it into A. niger to enhance CA synthesis (Tong et al., 2019). It was reported that deletion of genes that are responsible for ATP-citrate lyase synthesis enhanced CA production while deletion of two cytosolic ATP citrate lyase subunits reduced CA production, growth pigmentation and conidial germination in A. niger (Chen and Nielsen, 2016; Meijnen et al., 2009). Conversion of fructose 6-phosphate into fructose 1,6-bisphosphate is considered a crucial controlling step for glycolysis metabolic flux via the allosteric inhibition or activation. This is carried out by the essential enzyme PFK which uses magnesium as a co-factor. It has been observed that single site mutations in this enzyme depicted 70% more CA production than the control strain. It was also observed that deleting glucose oxidase (goxC) and oxaloacetate acetyl hydrolase (OAH) (prtF) genes could lower the production of OA in the medium at pH 5.0 and in the absence of Mn2+ (Behera, 2020). Despite these strategies, metabolic engineering still presents several challenges due to the complexity of the regulation metabolism for CA accumulation and the inability to use a common metabolism engineering operating tool.

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Current Developments in Biotechnology and Bioengineering

5. Oxalic acid OA or ethanedioic acid (C2H2O4) is a strong organic acid with two pKa values, pKa1: 1.27; pKa2: 4.27. OA has major applications in pharmaceutical, textile and leather, metal processing, agriculture and commodity chemical industries. OA has been reported in mineral weathering, nutrients acquisition, wood degradation, and metal tolerance (Schmalenberger et al., 2015; Xing et al., 2020). Due to the increased demand of OA in hydrometallurgy and as a commodity chemical, diverse fungal strains have been investigated for improved production and commercialization. Due to its low molecular weight, OA has significant role in metals speciation and mobility (Etteieb et al., 2021). Besides, it has a low solubility and forms metal complexes. It stimulates metal precipitation by lowering pH value of the medium (Gadd et al., 2014). It profoundly regulates the biogeochemical cycles and nutrient cycling for microorganisms and plants. In 2017, the global OA market size reached $616.3 million USD and was projected to increase with CAGR of 3.4% by 2025. In comparison to the other metabolites, the production of OA has always been considered ineffective during CA fermentation. Like CA and its potential use in lipid production (Magdouli et al., 2018, 2020), recent attention has been paid to the fungal production of OA and process optimization. OA plays a catalytic role during pretreatment of lignocellulosics and can efficiently hydrolyze hemicellulose (Saini et al., 2020). Traditional chemical synthesis of OA involves heating of sodium formate followed by acidification through H2SO4.

5.1 Microorganisms, metabolism, and physiology of oxalic acid biosynthesis Several species such as Aspergillus niger, Fomes annosus, Amyloporia xantha, Acremoniun sp., Tyromyces palustris, Phanerochaete chrysosporium, Coriolus versicolor, Sclerotium rolfsii, Fusarium sp., Puxillus involutus, Coniophora puteana, Coniophora marmorata, and Poria vaporaria have been employed for OA production. Most of these fungal strains are not able to produce commercially acceptable volumes of OA. A. niger has been considered as a potent strain for commercial production because it produces higher levels of OA as compared to other strains (Amato et al., 2020; Han et al., 2007). The fungal strains are reported to use lactose, sucrose and glucose for OA production (Table 1; Kobayashi et al., 2014). OA can be synthesized via three metabolic pathways in fungi (a) the cytoplasmic pathway; (b) the TCA pathway; and (c) the glyoxylate pathway. In the case of the cytoplasmic pathway, oxaloacetate produced as an end product of the EMP pathway, undergoes hydrolysis into oxalate and acetate catalyzed by cytosolic oxaloacetase [EC 3.7.1.1] in the glyoxylate pathway (Han et al., 2007). Prior to entering into the TCA cycle, pyruvate is first oxidized into acetyl-CoA by the pyruvate dehydrogenase multienzyme complex (PDC) €kela € et al., 2010), followed by cleavage of oxaloacetate and then enters to mitochondria (Ma

Chapter 15 • Organic acids by filamentous fungi

467

by the oxaloacetate hydrolase (OAH) [EC 3.1.1.44] into OA. In the case of the glyoxylate pathway, OA is synthesized through the hydrolysis of citrate mediated by glyoxylate dehy€kela € et al., 2010). drogenase [EC 1.2.1.17]. This process occurs in the glyoxysomes (Ma Once produced, OA is excreted into extracellular medium via oxalate transporters. In F. palustris, a well-known producer of higher titers of OA, specific ATP-dependent FpOAR transporter, characterized as membrane protein with six transmembrane domains is present (Watanabe et al., 2010).

5.2 Production and process conditions OA production is affected by numerous factors including temperature, pH, inoculum size, minerals and medium type containing carbon, nitrogen, and phosphorous components. Various research studies have been carried out to optimize the abovementioned process parameters for improving OA yields (Table 1). Although, temperature has no direct effect on OA production, unsuitable incubation temperatures delay the process performance. For instance, if the temperature is 6% Chitin 92.8%, DAc 54.7% Protein 3.8% Mw 4.7  105 Da Chitin DAc 63.4%–79.8% CI 63%

Farinha et al. (2015)

Chitin purity 97.9 DAc 77.7% Mw 2.01  105 Da CGC, CI: 58.4 Ash: 3% Chitin DAc 89.8% Mw 2.7  106 Da

Ferreira et al. (2020) Sun et al. (2018a)

Hassainia et al. (2018) Liao and Huang (2019) Boureghda et al. (2021) Gachhi and Hungund (2018)

from two sources, Pleurotus ostreatus (oyster mushroom) fruiting body and Aspergillus niger cell walls. As a result, they obtained a range of products like chitooligosaccharides, water-soluble chitosan and CM-chitosan. Another company is Beijing Be-Better Technology Co. (http://be-bettertech.com/products), an 11-year-old company from China. They produce chitosan products from the same sources as the former company but also from crustacean ones. Finally, ChitosanLab has its production facilities in China, but their selling offices are in France. This company produces fungal chitosan from Agaricus bisporus and Pleurotus ostreatus mushrooms and A. niger fungal cell wall. Chitin and chitosan from other sources are also available. In all cases, the fungal chitosan production know-how is protected by patents or industrial secrets. It is expected that industrial production of chitinous materials will increase in the future, considering growing raw material availability and people’s habit changes worldwide toward a vegetarian lifestyle and non-animal-derived products used in cosmetics, nutraceuticals, and organic farming. Some characteristics from CGC and chitin isolated from fungal species in last 6 years are summarized in Table 2.

Chapter 17 • Production of fungal biopolymers and their advanced applications

511

5.2 Fungal chitosan Chitosan is a family of copolymers of β-1-4-linked D-glucosamine and N-acetyl-Dglucosamine in different ratios. They are traditionally obtained by thermochemical treatment of chitin isolated from the crustacean shell wastes. However, this process has some drawbacks such as: (1) environmental issues due to a high amount of pollutant chemicals used and high energy consumption, (2) limited availability of raw material (crustaceous shells), depending on the seasonal year, (3) heterogeneity of physicochemical characteristics in the end-chitosan products: degree of deacetylation (DD), degree of polymerization, protein content, among others, and (4) high-production cost (Singh et al., 2020). Fungi are an alternative source of chitosan and chitin; both are constituents of the fungal cell wall during their life cycle. Chitin is directly synthesized by fungal species, whereas chitosan is generated naturally by the deacetylase enzyme or alkali treatment that converts chitin to chitosan. Zygomycetes fungi are the only group in which chitosan is a natural component of the cell wall. Deacetylase enzymes have been isolated from fungi belong to the order of Mucorales and Saccharomycetales to convert the fungal chitin to chitosan in vitro. However, the activity of these enzymes is inhibited by the insolubility and crystallinity of the chitin (Ghormade et al., 2017). Recent advances in biotechnological tools offer promising possibilities for fungal chitosan production, with tailored properties, at an industrial scale. The Zygomycetes fungi have a huge potential for chitosan commercial production due to higher amounts of chitin and chitosan in their cell walls than other fungi classes. Several Zygomycetes strains are suitable for chitosan production such as Absidia coerulea, Absidia glauca, Benjaminiella poitrasii, Cunnighamella bertholletiae, Cunnighamella elegans, Gongronella butleri, Mucor rouxii, Mucor racemosus, Rhizopus arrhizus, and Rhizopus oryzae. These strains can produce 30–140 g of chitosan/kg dry biomass with a degree of deacetylation (DD) of 70%–90% (Ghormade et al., 2017). In addition to the strain selection, other relevant parameters to improve the quality and quantity of extracted fungal chitosan include: nature of the mycelia in solid or submerged fermentation; nutritional requirements for maximum growth; incubation time and conditions used; and chitosan extraction procedure (Kaur and Dhillon, 2014; Namboodiri and Pakshirajan, 2020). Usually, the chitosan extraction from fungal mycelia involves five steps: biomass extraction, alkali treatment, acid treatment, pH adjustment, and drying (Ghormade et al., 2017). The mild alkali treatment using 1 M NaOH at 120°C for 15–20 min is carried out to separate chitin/chitosan from the other carbohydrates, lipids and proteins available in fungal biomass. The insoluble material (chitin/chitosan is subjected to an acid treatment using, 2% (v/v) acetic acid at 90°C for 6–7 h for separation chitosan from chitin. Chitosan is soluble in acid solutions and can be recovered by increasing the pH to 8.0–9.0. The pretreatments of fungal biomass are also applied to improve the chitosan yield. Ma et al. (2021) investigated different pretreatment methods such as ionic liquid, steam explosion, and its combination to mycelium residues from citric acid fermentation. Steam explosion pretreatment (2.5 MPa for 1 min) of Aspergillus niger mycelium residues, combined with

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Current Developments in Biotechnology and Bioengineering

an ionic liquid extraction, increased the fungal chitosan enzymatic deacetylation using a Rhodococcus equi CGMCC14861 chitin deacetylase. The DD of chitosan was 1.2-fold higher than that produced from unpretreated mycelium residues. In another study (Yang et al., 2017), dilute acid-assisted steam explosion pretreatment of corn stover was effective for chitosan production from Rhizopus oryzae. Chitosan extraction was performed through subsequent alkali and acid treatments of fungal biomass, where cell-wall material was obtained by alkali treatment and chitosan was separated from the cell wall by dissolution in acetic acid. Pure chitosan was recovered by precipitation at alkaline pH. At the industrial scale, the utilization of fungal mycelium wastes resulting from biotechnological and food industries, and the improvement of chitosan yield within the fungal cell using the metabolic and process engineering strategies are two attractive approaches for the development of a cost-effective fermentation process of chitosan production (Ghormade et al., 2017; Singh et al., 2020). Both strategies are environmentally friendly due to reducing fungal waste harvest pollution and eliminating the expensive chemical deacetylation step. In last 5 years, the use of alternate inexpensive carbon sources such as cassava wastewater, steep corn liquor, and paper mill wastewater, for scaling-up fungal chitosan production have been of particular interest. Table 3 shows a summary of the current studies used waste material as a substrate for production of fungal chitosan. In conclusion, the use of low-cost fungal biomass is an unlimited economic source to fungal chitosan production. In addition, it will help to alleviate environmental pollution. The physicochemical properties of the fungal chitosan are consistent and can be controlled by changing the different fermentation variables. However, techno-economic studies of scaling up fungal cultivation and chitosan purification for industrial production must be performed to determine the economic feasibility and critical techno-economic variables that affect the profitability of fungal chitosan production.

6. Applications of fungal biopolymers The ability of the fungi for the growth on low cost substrates such as food waste, not only opens up opportunities for waste valorization but also set the stage for development of different products from the obtained fungal biopolymers (Svensson et al., 2021a). Here, different applications of fungal biopolymers will be discussed.

6.1 Bioemulsifiers and biosurfactants Bioemulsifiers and biosurfactants are surface active amphiphilic coumponds, produced by microorganisms, containing both hydrophilic and liphophilic functional groups (Alizadeh-Sani et al., 2018). Bioemulsifiers are polyphilic polymers that are effective in stabilizing oil–water emulsions and have wide applications in food industry. Biosurfactants efficiently reduce the surface tension between the air/water or oil/water interfaces and are used for several applications such as dispersion systems, personal hygiene, detergents,

Table 3

Fungal chitosan form alternative biowaste resources.

Fungal species

Culture medium

Extraction method

Yield

Physic-chemical attributes of chitosan

Mild alkali treatment using 1 M NaOH at 120 °C for 20 min

138 g/kg of dry fungal biomass

DD ¼ 81% Mw ¼ 300 kDa

Mild alkali treatment using 1 M NaOH (30 mL, v/v) at 121°C for 15 min

44.91 mg/g by L. hyalospora

DD ¼ 80%–84%

Mixture of cashew apple juice and cheese whey

Mild alkali treatment using 1 M NaOH (1:40 w/v) at 121°C for 15 min

65–55 mg Chitosan /g of mycelial dry mass

DD ¼ 75%

Deuterated glycerol and d7-glucose

Alkali treatment 2 N NaOH solution (1 g biomass: 100 mL solution) at 121°C for 30 min

1–7 wt% Free chitosan weight yield

Aspergillus niger and Fusarium culmorum

Mill potato suspension

Mild alkali treatment using 1 M NaOH (30 mL/g solid) at 121°C for 30 min

19%

Rhizopus oryzae AS 3.819

Xylose rich of corn stover prehydrolysate

Steam explotion biomass treatment Milk alkali treatment 1 N NaOH (1:40 w/v) at 121°C for 15 min

0.09 g/g biomass.

Penicillium citrinum IITG-KP1

Mucor subtilissimus UCP 1262 Lichtheimia hyalospora UCP 1266 Cunninghamella phaeospora UCP 1303 and Cunninghamella elegans UCP 1306 Yeast Pichia pastoris and Rhizopus oryzae

Paper mill wastewater (lignin compounds and pentose sugars) supplemented with N-source, minerals and acetic acid Mixture of corn steep liquor and cassava wastewater

a

DD ¼ 66%–83% Mw ¼ 90–27 kDa for A. niger, Mw ¼ 146–112 kDa for F. culmorum DD ¼ 91%

Application

Reference

Treatment of paper mill wastewater and simultaneous chitosan production

Namboodiri and Pakshirajan (2019)

de Souza et al. (2020)

Antimicrobial activity against Scytalidium lignicola and Fusarium. solani

Berger et al. (2020)

Chitosan film useful for enzyme immobilization and future neutron scattering experiments. Remotion of metallic contaminant and pesticide from water

Yuan et al. (2021)

CabreraBarjas et al. (2020)

Yang et al. (2017)

Continued

Table 3

Fungal chitosan form alternative biowaste resources—cont’d

Fungal species

Culture medium

Extraction method

Yield

Cunninghamella elegans SIS 41

Mixture of corn steep liquor and papaya peel juice

2% (w/v) NaOH (1:30 w/v at 90°C for 2 h/10% acetic acid (1:40 w/v) at 60°C for 6 h

37.2 mg/g

Fresh cut mushrooms strain A15

Mushroom stipe offcuts

2 M NaOH at 100°C for 2 h/1% w/v oxalic acid at 100°C for 1 h

105 mg/g

Rhizopus oryzae

Whey salt medium and molasses salt medium

Mild alkali treatment using 1 M NaOH (1:40 w/v) at 121°C for 15 min/0.05 N H2SO4 (1:100, w/v) at room temperature/ 2% acetic acid (v/v) for 24 h at 95°C

10.0%– 11.5%

a

Degree of deacetylation.

Physic-chemical attributes of chitosan DD ¼ 86% Mw ¼ 40.8 kDa

DD ¼ 87%–82% Mw ¼ 120–178 kDa

Application

Reference

Antibacterial effects against different phytopathogenic Colletotrichum species Active edible coatings for inhibition of Saccharomyces cerevisiae yeast and Escherichia coli

Ramos Berger et al. (2018)

Poverenov et al. (2018)

Chatterjee et al. (2019)

Chapter 17 • Production of fungal biopolymers and their advanced applications

515

and agriculture (Sena et al., 2018; Luft et al., 2020). While biosurfactants and bioemulsifiers are mainly produced by bacteria and yeast, recently filamentous fungi have shown high capacity for production of these materials (Sena et al., 2018; Sanches et al., 2021). Different type of extracellular biosurfactants is reported to be produced by fungi, among which glycolipids (containing a carbohydrate part which is linked to fatty acids) and lipopeptides (containing a hydrophobic tail of fatty acids linked to a hydrophilic head of amino acids), and complexes of carbohydrates with proteins and lipids can be mentioned (Luft et al., 2020; Sanches et al., 2021). Furthermore, yeast and filamentous fungi have shown the capacity for production of different types of bioemulsifiers. Mannoproteins are one of the most important type of fungal bioemulsifiers that are available in the cell wall of yeast (Saccharomyces spp. and Kluyveromyces marxianus) and can be released by treatment of the yeast biomass with aqueous solutions under pressure in autoclave (Dikit et al., 2010; Alizadeh-Sani et al., 2018). By optimization of the fermentation conditions, using low costs substates, and more efficient methods for biopolymers recovery, it is expected that production of fungal bioemulsifiers and biosurfactants becomes more economically feasible in the future (Luft et al., 2020). Furthermore, fungal bioemulsifiers and biosurfactants can be extracted from by-products of other industries where yeast/filamentous fungi are used for production of other products such as wine (Dikit et al., 2010). Moreover, recently fungal biopolymers that are released from the fungal biomass in the process of edible mycoproteins production, Quorn™, have shown promising foaming and emonsidying properties for using in the food industry (Lonchamp et al., 2019).

6.2 Wound healing materials Application of fungal-based materials for wound healing goes back to ancient times where fungi was used to stop bleeding (Jones et al., 2020a). In 1994, Chung et al. (1994) tested effect of alkali insoluble material of A. oryzae, M. mucedo, and P. blakesleeanus on rate of proliferation of human fibroblasts and observed proproliferant activity over 13 days. These fungi belong to the division of ascomycota, zygomycota, and mucoromycota, respectively. This means their cell wall contains mainly chitin-glucan, chitin-chitosan, and chitin-chitosan, respectively. In that study, a correlation was reported between the proproliferant effect of fungal alkali insoluble material and their chitin content where P. blakesleeanus with highest chitin content (91%) resulted in highest enhancement in cell proliferation. Since 1997, most of the research studies conducted on wound healing properties of the fungal chitin have used fungal species that have chitin-glucan in their cell wall. In 1997, Su et al. (1997) used fruiting body of Ganoderma tsugae to make a membrane called Sacchachitin which was tested as a skin replacement. Ganoderma tsugae is a mushroom that belongs to the division of Basidiomycota, which contain chitin-glucan in their cell wall. The alkali insoluble material of this mushroom, containing 60% glucans and 40% chitin, was suspended in water and subjected to a wet laying process to form a membrane which was then freeze dried. The dried membrane, Sacchachitin, improved the wound healing process in rat skin compared to the control experiment where cotton gauge

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Current Developments in Biotechnology and Bioengineering

was used to cover the wound. Later, in 2004, effect of Sacchachitin membrane was investigated on the rate of wound heling process and the resulted indicated that Sacchachitin may increase the wound healing rate by earlier expression of proliferating cell nuclear antigen and type I collagen compared to the control experiments. Furthermore, Sacchachitin led to later expression of tissue-transglutaminase which is an indicator for apoptosis and maybe a sign for longer period of blood supply to the wound area which facilitates the wound healing (Chao et al., 2020).

6.3 Tissue engineering Biopolymers play an important role in the development of scaffolds that can induce the regenerative processes in the body. Nwe et al. (2009) extracted chitosan from cell wall of Gongronella butleri and developed a scaffold by dissolution of chitosan in acetic acid solution followed by freeze drying. The obtained scaffold exhibited an interconnected porous structure and showed high mechanical strength, and promoted proliferation of fibroblast cells which are necessary properties for material used in tissue engineering (Nwe et al., 2009). Narayanan et al. (2020) developed a 3D scaffolds containing chitin-glucan by growing of Aspergillus sp. on potato dextrose broth under static conditions to form a fungal mat, followed by dehydration of fungal mat using ethanol, and freeze drying. The surface associated proteins of obtained fungal-scaffolds were then solubilized through reaction with a reducing agent. Human keratinocytes were seeded on the fungal-scaffold and the results indicated deposition of extra cellular matrix components and formation of cell sheets in 14 day. This indicates the potential of the fungal-scaffold for tissue engineering applications.

6.4 Antimicrobial and preserving agent From the last two decades, the antimicrobial effect of chitosan and its derivatives has fascinated lot of attention in agriculture, pharmaceutics, medical, and food industry (Brasselet et al., 2019). Chitosan was demonstrated to be efficient inhibitor of the growth of many microbials species such as yeast, bacteria and fungi among them spoilage, phytopathogens, and pathogens species (Kisko´ et al., 2005; Raafat and Sahl, 2009; Hosseinnejad and Jafari, 2016; Hu et al., 2019). By comparison with other biomolecules such as phenolic compounds, chitosan presents 30%–50% higher antimicrobial activity and a large antiseptic spectrum (Raafat and Sahl, 2009; Brasselet et al., 2019) not only on Gram-positive bacteria (Staphylococcus aureus or Bacillus subtilis) but also to Gramnegative bacteria (Pseudomonas aeruginosa or Escherichia coli). Therefore, chitosan and its derivatives have been mainly described for their ability to eliminate microorganism in biofilm and planktonic form and to reduce the adhesion and growth of microorganism: (i) on specific surface of antiseptic material (Costa et al., 2017; Campana et al., 2018) and (ii) in liquid food such as fruit juices or wine (Kisko´ et al., 2005; Paulin et al., 2020). The last years in winemakers industries, fungal chitosan have been approved by European Union and International Organization of Vine and Wine

Chapter 17 • Production of fungal biopolymers and their advanced applications

517

(International Code of Oenological Practices) as non-allergenic, non-toxic, and renewable natural antiseptic biomolecules for wine treatment to reduce Brettanomyces microorganisms by sedimentation process (Taillandier et al., 2015; Paulin et al., 2020). In this context, recently the antiseptic effect of fungal chitosan on Brettanomyces bruxellensis strains which are yeast and well-known as the main spoilage microbial agent in red wines has been confirmed (Paulin et al., 2020). In this study on a collection of 53 strains of B. bruxellensis, such as 13 diploid strains belong to the CBS2499 genetic group, 13 triploid strains belong to the genetic group AWRI1499, 14 triploid strains belong to the genetic group AWRI1608, and 13 strains distributed into the L14165, L0308, and CBS5512 genetic clusters were investigated. The authors particularly showed that two types of fungal chitosan (a high molecular weight fraction of 400 kDa and a low molecular weight fraction of 32 kDa) could specifically disturb and significantly decrease the cultivable Brettanomyces bruxellensis strains by flocculation/sedimentation step (Paulin et al., 2020). Concerning the real antimicrobial effect from chitosan and derivatives, lot of studies proposed diverse mechanistic approaches due to the specific interaction between the cationic charge of chitosan (R-NH3+) and the negatives charges of the bacterial surface (No et al., 2002; Raafat and Sahl, 2009; Younes et al., 2014b). As observed in Fig. 4, some antimicrobial mechanisms largely described in literature could be suggested. All the main described mechanisms could be summarized as: (i) coating of the cell wall (negatively charged) or directly the cell membrane leading to the establishment of an oxygen/nutrient barrier; (ii) alteration of membrane cell permeability and energy generating pathways leading to cellular morphological change; (iii) low molecular weight chitosan such as chitooligosaccharides (COSs) induce cell aggregation and insoluble fractions act as fining agents; (iv) COS may cross the walls and membranes to interact with

Cells with external wall/polysaccharides iii. COS induce cell agregation and insoluble fractions act as fining agents

ii. Alteration of membrane permeability and energy generating pathways

Cells with external membrane

iv. COS may cross the walls and membranes

v. Damage to DNA, RNA, proteins; stress, autolysis

vi. Wall and membrane disruption

iii.

vi. Collapse of internal membrane or total disruption of the two membranes; internal material leakage

v.

ii i.

i. Coating the cell wall (negatively charged) or directly the cell membrane

vii. Negatively charged nutrient sequestration

+++++++++

++++

++

Positively charged chitosan FIG. 4 Schematic representation of the proposed antimicrobial mechanisms of chitosan. Adapted from Brasselet, C., Pierre, G., Dubessay, P., Dols-Lafargue, M., Coulon, J., Maupeu, J., Vallet-Courbin, A., de Baynast, H., Doco, T., Michaud, P., Delattre, C., 2019. Modification of chitosan for the generation of functional derivatives. Appl. Sci. 9(7), 1321.

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DNA; (v) damage to DNA transcription (supposed interaction between chitosan and 30S ribosomal subunit), RNA, proteins, stress, autolysis; (vi) wall and membrane disruption and finally, (vii) negatively charged nutrient sequestration. Mostly, studies indicated that the main ionic interactions between chitosan and microorganisms disturb the cell surface leading to contents leakage in bacterial growth inhibition (Raafat and Sahl, 2009; Brasselet et al., 2019). Nevertheless, other structural parameters of chitosan have also been widely described in the modulation and increasing of antimicrobial effect such as the molecular weight (Mw) and the degrees of deacetylation (DD) which are well known to control the water solubility of chitosan and derivatives (Qin et al., 2006; Brasselet et al., 2019). Therefore, many publications reported the physicochemical or enzymatic production of efficient antimicrobial chitosan derivatives with low molecular weight (such as chitooligosaccharides) and high degree of deacetylation to increase antimicrobial activities against fungi and bacteria (No et al., 2002; Qin et al., 2006; Raafat and Sahl, 2009; Younes et al., 2014b; Brasselet et al., 2019). Finally, it is important to mention that in chitosan aqueous solutions, the antimicrobial effect is strongly affected by the pH solution (range of pH 4–6) with increased effect at lower pH and decreased effect at pH near to pH 7 due to insolubility and deprotonation of chitosan (RNH3+ ! R-NH2) (No et al., 2002; Younes et al., 2014a). In this context, some chemical modification of chitosan such as carboxymethylation, and N-trimethylation have been investigated to increase antibacterial activity at pH higher than 7 (Meng et al., 2012; Shariatinia, 2018). The last decades, lots of antimicrobial studies have been reported using fungal PSs (chitin, chitosan, glucan, and their derivatives). For example, chitin and chitosan extracted from Pleurotus spp. using alkaline method gave antimicrobial effect (Johney et al., 2016). In fact, authors demonstrated that chitin and chitosan from P. florida and P. eous have: (1) antibacterial effect against Bacillus subtilis, Staphylococcus aureus, and Escherichia coli and, (2) antifungal effect against Fusarium solani, Aspergillus flavus, and Aspergillus niger. In another study, Jeihanipour et al. (2007) investigated the antimicrobial properties of chitosan extracted from the cell wall of filamentous zygomycetes fungus Rhizopus oryzae. Authors observed the reduction of bacteria viability for Staphylococcus aureus, Klebsiella pneumoniae, and E. coli higher than 60% when they used a fungal chitosan concentration of 200 ppm. More, in this study (Jeihanipour et al., 2007) analyzed the minimum bactericidal concentration (MBC) of the fungal chitosan from R. oryzae and MBC was estimated at 700, 500, and 300 ppm for K. pneumoniae, E. coli, and S. aureus, respectively. Recently, an interesting approach was proposed to improve the antibacterial effect of fungal chitin-glucan complex by grafting of gallic acid using a free radical mediated method (Singh et al., 2019). Chitin-glucan complex was firstly extracted from the mushroom Agaricus bisporus and secondly gallic acid was covalently grafted into chitin-glucan complex with a degree of derivatization of 40% employing ascorbic acid/hydrogen peroxide reactive system. Interestingly, compared to chitin-glucan complex, gallic acid grafted chitin-glucan complex was more efficient on growth inhibition of Escherichia coli and Bacillus subtilis.

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In the same strategy, Wan-Mohtar et al. (2016) chemically sulfated a β-D-(1,3)-Glucan extracted from the mushroom Ganoderma lucidum in order to obtain effective watersoluble antimicrobial agent against a panel of several bacteria well-known in human health and food topics. Therefore, β-D-(1,3)-Glucan was sulfated using dimethyl sulfoxide/urea/sulfuric acid media in order to produce a soluble sulfated β-D-(1,3)-Glucan (GS) with a degree of sulfation (DS) of 0.90 (i.e., 90 sulfate residues for 100 glucose units in the main glucan backbone). As observed, this GS showed antimicrobial effect with minimum inhibiting concentration (MIC) of 1, 2, and 5 mg/mL for Escherichia coli, Staphylococcus aureus and Staphylococcus epidermis, respectively. Furthermore, the MBC was estimated at 2, 5, and 10 mg/mL for E. coli, S. aureus and S. epidermis, respectively. Finally, it is worth mentioning that very interesting recent reviews described the high potential of antimicrobial activity of chitin, chitosan, and glucan extracted from several fungal organ´ jo et al. 2020b). isms (Lehtovaara and Gu, 2011; Arau

6.5 Textiles (textile fibers, nonwoven textiles, and leather like materials) and paper like materials from fungi Due to the unsustainable cultivation of cotton, the environmental concerns regarding use of synthetic textiles, and struggling issues in natural leather productions, sustainable textile alternatives are highly demanded. In recent years fungal polymers have been introduced as promising resources for the textile production and the fungal materials have been processed to form leather like materials, paper like materials, and textile fibers (Jones et al., 2021). Liquid state and solid state fermentations are used for production of fungal biomass and development of textiles and paper like materials. When using liquid-state fermentation, the filamentous fungi grow on liquid media in shake flasks or bioreactors and pure fungal microfibers are separated from the media at the end of cultivation. Different substrates have been used for fungal cultivation, including (semi)synthetic media (Appels et al., 2020; Attias et al., 2021). However, using byproducts and waste streams is preferred since it will contribute to a lower production cost and more sustainable process. Jones et al. (2019a, b) used molasses which is a byproduct obtained in the sugar production process for growth of filamentous fungi and development of paper € hnlein (Ko € hnlein, 2020), Wijayarathna like materials. Recently, Svensson et al. (2021b), Ko (2021), and Mohammadkhani (2021) used a suspension of bread waste in water for cultivation of filamentous fungi and development of fungal based textiles and paper like materials. SSF can also be used for cultivation of filamentous fungi using lignocellulosic materials as the substrate. However, in this method separation of the fungal microfibers from the substrate residues is not possible and the obtained fungal material has foam like properties (C.f. Section 6.6). The fruiting body of the mushrooms can also be processed to develop textile and paper like materials. The fungal textiles and paper like materials are either developed using the whole fungal biomass or just its cell wall material containing PSs, namely chitin-chitosan or chitinglucan. Fungal leather like materials is produced by processing the whole fungal biomass.

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There are already some commercialized leather alternatives from fungi. MycoTech which is an Indonesian biotechnology-based company has released several products such as wallet, watch strap, and card tags based on their mushroom leather. MyloTM is another example which is a leather alternative produced from fungal mycelium grown on sawdust. Muskin is another fungal-based leather produced from the caps of the mushroom, Phellinus ellipsoideus, through non-toxic tanning treatments (Bustillos et al., 2020). However, details of those processed are not available and on the other hand, the properties of the available fungal leather like materials still need to be improved to replace the natural leather. Therefore, research is still ongoing in order to improve the process using more sustainable materials, to enhance the properties of the fungal leather alternatives, a replacement for the fossil-based polyester textile support which is nowadays used in the in formulation of leather alternatives (Meyer et al., 2021). Appels et al. (2020)) applied a post treatment, with different concentration of glycerol, to the films of the whole mycelium of the fungus Schizophyllum and developed films with different properties from polymer to elastomer like materials. (Wijayarathna, 2021) developed leather like materials from the fungus Rhizopus delemar grown on bread waste, through tanning of the fungal microfibers, wet laying of the microfibers, and post-treatment of the fungal films using glycerol and a bio-binder. Paper-like materials can be produced from the cell wall fraction of the filamentous fungi. Alkali treatment (for example, by sodium hydroxide solution) is usually used to remove the alkali soluble materials from the fungal biomass, leaving the cell wall fraction (i.e., alkali insoluble material). The fungal cell wall material have a fibrous structure containing micro (when mycelium is used) or nano-sized (when fruiting bodies are used) fibers of chitin together with glucans or chitosan. Often the paper like materials are produced from edible fruiting body of fungi, i.e., white champignon mushroom Agaricus biporus (Nawawi, 2016). Among different fungi, alkali insoluble materials of microfibers of A. arbuscula, M. genevensis (Jones et al. (2019a, b)), T. versicolor (Jones et al. (2019a, € hnlein, 2020) have been used for production of wet laid paper-like b)), and R. delemar (Ko materials. Moreover, chitin-glucan nanofibers extracted from fruiting bodies of A. bisporus and D. confragosa have been use for development of nanopapers with high tensile strength (more than 200 MPa) which are more hydrophobic than nanopapers made using crustacean chitin (Nawawi et al., 2019, 2020b). Generally, the papers made using nanofibers exhibit higher tensile strength compared to the one made using microfibers. During the alkali treatment a significant fraction (More than 70%) of the fungal biomass is dis€ hnlein (2020) developed an enzymatic treatsolved in alkali solution and discarded. Ko ment process using protease to extract the fungal cell wall and developed wet laid materials from the enzyme treated microfibers. The enzymatic approach set the stage for recovery of the soluble fraction of fungal biomass (namely proteins) for other applications. The fungal wet laid materials usually exhibit a yellow to brownish color and heat treatments during the drying process results in darkening of the color. Bleaching of the fungal micro and nanofibers results in formation of transparent films after wet laying and drying steps. The highest tensile strength of the fungal wet laid microfibers was

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€ hnlein (2020) which was 71.5 MPa. For the nanopapers derived from mushreported by Ko room higher tensile strength up to 204 MPa (Nawawi et al., 2020a) has been reported. Biocomposite nonwoven textiles have also been developed using fungal microfibers and cellulosic fibers such as flax (Nawawi, 2016), hemp (Irbe et al., 2021), and viscose € hnlein, 2020) fibers. In the biocomposites, fungal microfibers act as a binder for the (Ko cellulosic fibers. Fungal leather and paper-like materials are made by random distribution of fungal micro and nanofibers. Recently, Svensson et al. (2021b) reported alignment of the fungal microfibers of the zygomycetes fungus R. delemar (grown on bread waste) along one axis and developed fungal monofilament yarns. This was done through wet spinning of a hydrogel containing fungal cell wall into a coagulation bath containing ethanol. This opens up opportunities for development of the woven fungal textiles for different applications. Mohammadkhani (Mohammadkhani, 2021) reported that the fungal wet spun filaments exhibit antibacterial properties and therefore can be a good candidate for medical textile applications.

6.6 Biocomposites for construction and packaging applications Another innovative feature of usage of fungal biopolymers is their introduction for packaging and construction applications as alternatives for traditional materials (Jones et al., 2020b). Fungal biocomposite materials are produced through SSF of the filamentous fungi on lignocellulosic materials, namely agricultural and forestry byproducts (Jones et al., 2017). Therefore, usually fungal species with the ability for synthesizing the enzymes needed for degradation of the lignocellulosic materials such as white rot fungi are used for development of fungal biocomposites (Jones et al., 2017). During the growth, fungal microfibers are formed as a binder which holds the lignocellulosic material together resulting in a biocomposite structure. Therefore, the whole fungal biomass is used in the structure of fungal biocomposite materials. The obtained biocomposite material is dried to stop the fungal growth and usually subjected to a hot/cold pressing to reduce the porosity, increase the density, and therefore enhance the mechanical properties of the biocomposite material (Jones et al., 2017; Appels et al., 2019). The fungal mycelium usually makes around 5% of the obtained biocomposites while the rest is the residues of the lignocellulosic substrates used for cultivation of the fungi (Jones et al. (2019a, b)). The properties of the obtained biocomposites depend on the type of the substrate (Elsacker et al., 2019). Using low-cost agricultural residues and wastes, such as straw, results in formation of biocomposite materials with foam-like properties. These foam like biocomposite materials are suitable for packaging applications (Jones et al., 2020b). For example IKEA (the world’s largest furniture retailer since 2008)a uses the fungal biocomposite materials as a replacement for polystyrene in their packaging.b Furthermore, getting benefit of the low density and low thermal conductivity of the lignocellulosic substrates, fungal a

https://en.wikipedia.org/wiki/IKEA#cite_note-6.

b

https://www.intelligentliving.co/ikea-mushroom-based-packaging/.

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biocomposites are good candidates for insulation applications with properties comparable to commercial thermal insulation materials such as glass wool and polystyrene (Xing et al., 2018). Furthermore, due to presence of lignin and silica in the lignocellulosic substrates, the fungal biocomposite materials exhibit fire-retardant properties (Jones et al., 2018). Highwater absorption properties of the fungal-based biocomposites limit their use for indoor applications. There are some prototypes and few commercial products of fungal biocomposites already available. For example, furnishing items such as chairs have been prepared using the fungal biocomposites and a prototype house with 10 m height using fungal bricks has been made (Jones et al., 2020b). There are also some companies in the USA (Ecovative design), Italy (Mogu), Indonesia (Mycotech), and the Netherlands (Officina Corpuscoli), which have released fungal-based biocomposites to the market for packaging and construction applications. However, the mechanical properties of the fungal-based biocomposites still needs to be improved before the materials can be used for commercial construction applications.

6.7 Other applications of fungal biopolymers The application of the fungal biopolymers is not only limited to the area mentioned in Sections 6.1–6.6 and other applications have also been suggested. European Food Safety Authority (ESFA) has confirmed the safety of chitin-glucan to be used as a food ingredient with the purpose to increase the daily intake of fibers (EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA), 2010). Chitin-glucan has also been recognized as safe (GRAS) by the Food and Drug Administration (FDA, USA) as a novel food ingredient (EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA), 2010). This material is available in weight losing tablets provided by KitoZyme (Belgium). Chitin-glucan can be consumed as a dietary supplement with an intended 2–5 g/day intake. Recently, an in vivo study in rats was conducted (Alessandri et al., 2019) and concluded that chitin-glucan is a valuable novel prebiotic molecule, which could be introduced to the human diet to re-establish/ reinforce bifidobacteria colonization in the mammalian gut. On the other side, fungal chitin, chitosan, chitin-glucan, or its hydrolysate are a valuable product for wine limpidity prevention (Bornet and Teissedre, 2008). Their use improved wine safety by reducing heavy metals (Fe, Pb, Cd), and mycotoxins (ochratoxin A) levels. Fungal cell wall biopolymers, in pure form as well as their complex in the cell wall, have shown high potential for removal of heavy metals from aqueous solutions (Rouhollahi et al., 2014; Behnam et al., 2015). Several authors reported the potential applications of fungal chitin and chitin-glucan in agriculture as pathogen control agents. For example, Sun et al. (2018a) studied the influence of the postharvest treatment with fungal chitin from Saccharomise cerevisae on disease resistance against Botrytis cinerea infection in tomato fruit. The results showed that fungal chitin dipping treatment effectively produces strong resistance to B. cinerea in tomato fruit. The fruit protection occurred by eliciting several plant defense responses such as proteins (β-1-3-glucanase, chitinase, PAL, SOD, CAT), and callose accumulation in tomato peels. This finding agrees with the previous one using chitin-glucan containing

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cell wall preparation from Rhodosporidium paludigenum yeast to protect pear fruits (Sun et al., 2018b). It created disease resistance against blue mold rot caused by Penicillium expansum in pear fruit and reduced the fungal germination fruit wounds. Fungal chitin and chitosan can be used in nearly all applications where the shellfish chitin and chitosan are used. For example superabsorbent materials have been developed from cell wall of zygomycetes fungi and purified fungal chitosan (Zamani, 2010; Zamani and Taherzadeh, 2012). Furthermore, hydrogels have been produced from the chitosan extracted from the cell wall of the fungus Aspergillus niger for application in controlled drug release (Mun˜oz et al., 2015). Recently, fungal chitosan has been successfully tested to be used as blood-clotting agent (Radwan-Pragłowska et al., 2021). Biocompatible hydrogels have also been produced from chitin-glucan extracted from the cell wall of yeast Komagataella pastoris (DSM 70877) ´ jo et al., 2020). for potential medical applications such as drug delivery (Arau

7. Conclusions and perspectives Fungal cell wall displays a unique biocomposite structure which is composed of different PSs. Chitin, glucans, and chitosan are major components of the fungal cell wall. Composition of the fungal cell wall can be controlled by selection of the substrate and controlling the cultivation conditions. Liquid-state submerged cultivation give the possibility for production of pure fungal microfibers while the solid state cultivation results in formation of a composite structure where fungal microfibers act as a binder for the residues of the substrate. Fungal biopolymers exhibit antimicrobial properties and are biocompatible. Those properties make them good candidates for biomedical applications. The whole fungal biomass, its cell wall, or its purified biopolymers have been used for development of novel sustainable textile fibers, leather alternatives, paper-like materials, and construction materials. Fungal biopolymers are also a promising source for bioemulsifiers and biosurfactants, for application in food and agriculture industries. With the inspiration of the recycling of the materials in the nature, fungi can be key elements for bioconversion of different waste materials and side streams to functional biopolymers. Using low-cost substrates is necessary in order to have an economically feasible process for production of fungal biopolymers. Cultivation parameters should be optimized to enhance the yield of fungal biopolymers and more efficient purification steps will improve the process economy. Furthermore, a multi-product process, where nearly all fractions of fungal biomass are recovered and used for development of new products, in a biorefinery approach, will enhance the process feasibility. Fungal biopolymers are undoubtedly a promising resource for development of different products from commodity products to advanced products required for health care and medical applications.

References Alessandri, G., Milani, C., Duranti, S., Mancabelli, L., Ranjanoro, T., Modica, S., Carnevali, L., Statello, R., Bottacini, F., Turroni, F., Ossiprandi, M.C., Sgoifo, A., Van Sinderen, D., Ventura, M., 2019. Ability of bifidobacteria to metabolize chitin-glucan and its impact on the gut microbiota. Sci. Rep. 9, 5755.

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Current Developments in Biotechnology and Bioengineering

Alizadeh-Sani, M., Hamishehkar, H., Khezerlou, A., Azizi-Lalabadi, M., Azadi, Y., Nattagh-Eshtivani, E., Fasihi, M., Ghavami, A., Aynehchi, A., Ehsani, A., 2018. Bioemulsifiers derived from microorganisms: applications in the drug and food industry. Adv. Pharm. Bull. 8 (2), 191–199. € sten, Appels, F.V.W., Camere, S., Montalti, M., Karana, E., Jansen, K.M.B., Dijksterhuis, J., Krijgsheld, P., Wo H.A.B., 2019. Fabrication factors influencing mechanical, moisture- and water-related properties of mycelium-based composites. Mater. Des. 161, 64–71. € sten, H.A.B., 2020. Fungal myceAppels, F.V.W., van den Brandhof, J.G., Dijksterhuis, J., de Kort, G.W., Wo lium classified in different material families based on glycerol treatment. Commun. Biol. 3 (1), 334. Araujo, D., Ferreira, I.C., Torres, C.A.V., Neves, L., Freitas, F., 2020. Chitinous polymers: extraction from fungal sources, characterization and processing towards value-added applications. J. Chem. Technol. Biotechnol. 95 (5), 1277–1289. Arau´jo, D., Alves, V.D., Lima, S.A.C., Reis, S., Freitas, F., Reis, M.A.M., 2020. Novel hydrogels based on yeast chitin-glucan complex: characterization and safety assessment. Int. J. Biol. Macromol. 156, 1104–1111. Attias, N., Reid, M., Mijowska, S.C., Dobryden, I., Isaksson, M., Pokroy, B., Grobman, Y.J., Abitbol, T., 2021. Biofabrication of nanocellulose–mycelium hybrid materials. Adv. Sustain. Syst. 5 (2), 2000196. Bartnicki-Garcia, S., 1968. Cell Wall chemistry, morphogenesis, and taxonomy of Fungi. Annu. Rev. Microbiol. 22 (1), 87–108. Bartnicki-Garcia, S., Nickerson, W.J., 1962. Isolation, composition, and structure of cell walls of filamentous and yeast-like forms of Mucor rouxii. Biochim. Biophys. Acta 58, 102–119.
, J.-P., 2018. Special issue: fungal cell wall. J. Fungi 4 (3), 91. Beauvais, A., Latge Behnam, S., Zamani, A., Karimi, K., Mehrabani-Zeinabad, A., 2015. Copper removal using different fungalbased adsorbents: a comparative and detailed study. J. Dispers. Sci. Technol. 36 (6), 866–876. Berbee, M.L., Strullu-Derrien, C., Delaux, P.-M., Strother, P.K., Kenrick, P., Selosse, M.-A., Taylor, J.W., 2020. Genomic and fossil windows into the secret lives of the most ancient fungi. Nat. Rev. Microbiol. 18 (12), 717–730. Berger, L.R.R., de Arau´jo, M.B., da Costa, D.P., de Lima, M.A.B., de Almeida, J.W.L., de Medeiros, E.V., 2020. Agroindustrial waste as ecofriendly and low-cost alternative to production of chitosan from Mucorales fungi and antagonist effect against fusarium solani (Mart.) Sacco and Scytalidium lignicola Pesante. Int. J. Biol. Macromol. 161, 101–108. Berovic, M., Habijanic, J., Zore, I., Wraber, B., Hodzar, D., Boh, B., Pohleven, F., 2003. Submerged cultivation of Ganoderma lucidum biomass and immunostimulatory effects of fungal polysaccharides. J. Biotechnol. 103 (1), 77–86. Bleackley, M.R., Dawson, C.S., Payne, J.A.E., Harvey, P.J., Rosengren, K.J., Quimbar, P., Garcia-Ceron, D., Lowe, R., Bulone, V., van der Weerden, N.L., Craik, D.J., Anderson, M.A., 2019. The interaction with fungal cell wall polysaccharides determines the salt tolerance of antifungal plant defensins. Cell Surf. 5, 100026. Bornet, A., Teissedre, P.L., 2008. Chitosan, chitin-glucan and chitin effects on minerals (iron, lead, cadmium) and organic (ochratoxin A) contaminants in wines. Eur. Food Res. Technol. 226 (4), 681–689. Boureghda, Y., Satha, H., Bendebane, F., 2021. Chitin–glucan complex from Pleurotus ostreatus mushroom: physicochemical characterization and comparison of extraction methods. Waste Biomass Valoriz. 12, 6139–6153. Bowman, S.M., Free, S.J., 2006. The structure and synthesis of the fungal cell wall. BioEssays 28 (8), 799–808. Brasselet, C., Pierre, G., Dubessay, P., Dols-Lafargue, M., Coulon, J., Maupeu, J., Vallet-Courbin, A., de Baynast, H., Doco, T., Michaud, P., Delattre, C., 2019. Modification of chitosan for the generation of functional derivatives. Appl. Sci. 9 (7), 1321.

Chapter 17 • Production of fungal biopolymers and their advanced applications

525

Bustillos, J., Loganathan, A., Agrawal, R., Gonzalez, B.A., Perez, M.G., Ramaswamy, S., Boesl, B., Agarwal, A., 2020. Uncovering the mechanical, thermal, and chemical characteristics of biodegradable mushroom leather with intrinsic antifungal and antibacterial properties. ACS Appl. Biomater. 3 (5), 3145–3156. Bzducha-Wrobel, A., Pobiega, K., Blazejak, S., Kieliszek, M., 2018. The scale-up cultivation of Candida utilis in waste potato juice water with glycerol affects biomass and beta(1,3)/(1,6)-glucan characteristic and yield. Appl. Microbiol. Biotechnol. 102 (21), 9131–9145. Cabrera-Barjas, G., Gallardo, F., Nesic, A., Taboada, E., Marican, A., Mirabal-Gallardo, Y., Avila-Salas, F., Delgado, N., de Armas-Ricard, M., Valdes, O., 2020. Utilization of industrial by-product fungal biomass from Aspergillus niger and Fusarium culmorum to obtain biosorbents for removal of pesticide and metal ions from aqueous solutions. J. Environ. Chem. Eng. 8 (5), 104355. Campana, R., Biondo, F., Mastrotto, F., Baffone, W., Casettari, L., 2018. Chitosans as new tools against biofilms formation on the surface of silicone urinary catheters. Int. J. Biol. Macromol. 118 (Pt B), 2193–2200. Chao, F.-C., Wu, M.-H., Chen, L.-C., Lin, H.-L., Liu, D.-Z., Ho, H.-O., Sheu, M.-T., 2020. Preparation and characterization of chemically TEMPO-oxidized and mechanically disintegrated sacchachitin nanofibers (SCNF) for enhanced diabetic wound healing. Carbohydr. Polym. 229, 115507. Chatterjee, S., Guha, A.K., Chatterjee, B.P., 2019. Evaluation of quantity and quality of chitosan produce from Rhizopus oryzae by utilizing food product processing waste whey and molasses. J. Environ. Manag. 251, 109565. Chen, X., Wu, J.Y., Gui, X.T., 2016. Production and characterization of exopolysaccharides in mycelial culture of Cordyceps sinensis fungus Cs-HK1 with different carbon sources. Chin. J. Chem. Eng. 24 (1), 158–162.
ska, M., Siwulski, M., Wiater, A., 2018. Chemical Choma, A., Nowak, K., Komaniecka, I., Wa
sko, A., Pleszczyn characterization of alkali-soluble polysaccharides isolated from a boletus edulis (bull.) fruiting body and their potential for heavy metal biosorption. Food Chem. 266, 329–334. Chung, L.Y., Schmidt, R.J., Hamlyn, P.F., Sagar, B.F., Andrews, A.M., Turner, T.D., 1994. Biocompatibility of potential wound management products: fungal mycelia as a source of chitin/chitosan and their effect on the proliferation of human F1000 fibroblasts in culture. J. Biomed. Mater. Res. 28 (4), 463–469. Costa, E.M., Silva, S., Tavaria, F.K., Pintado, M.M., 2017. Insights into chitosan antibiofilm activity against methicillin-resistant Staphylococcus aureus. J. Appl. Microbiol. 122 (6), 1547–1557. Costachel, C., Coddeville, B., Latg
e, J.P., Fontaine, T., 2005. Glycosylphosphatidylinositol-anchored fungal polysaccharide in aspergillus fumigatus. J. Biol. Chem. 280 (48), 39835–39842. De Ruiter, G.A., Van Bruggen-Van der Lugt, A.W., Mischnick, P., Smid, P., Van Boom, J.H., Notermans, S.H., Rombouts, F.M., 1994. 2-O-methyl-D-mannose residues are immunodominant in extracellular polysaccharides of Mucor racemosus and related molds. J. Biol. Chem. 269 (6), 4299–4306. de Souza, A.F., Galindo, H.M., de Lima, M.A.B., Ribeaux, D.R., Rodrı´guez, D.M., da Silva Andrade, R.F., Gusma˜o, N.B., de Campos-Takaki, G.M., 2020. Biotechnological strategies for chitosan production by Mucoralean strains and dimorphism using renewable substrates. Int. J. Mol. Sci. 21 (12), 4286. Dikit, P., Maneerat, S., Musikasang, H., H-kittikun, A., 2010. Emulsifier properties of the mannoprotein extract from yeast isolated from sugar palm wine. ScienceAsia 36, 312–318. Dow, J.M., Darnall, D.W., Villa, V.D., 1983. Two distinct classes of polyuronide from the cell walls of a dimorphic fungus, Mucor rouxii. J. Bacteriol. 155 (3), 1088–1093. EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA), 2010. Scientific opinion on the safety of ‘chitin-glucan’ as a novel food ingredient. EFSA J. 8 (7), 1687. https://doi.org/10.2903/j.efsa.2010.1687. Elboutachfaiti, R., Delattre, C., Petit, E., Michaud, P., 2011. Polyglucuronic acids: structures, functions and degrading enzymes. Carbohydr. Polym. 84 (1), 1–13.

526

Current Developments in Biotechnology and Bioengineering

Elsacker, E., Vandelook, S., Brancart, J., Peeters, E., De Laet, L., 2019. Mechanical, physical and chemical characterisation of mycelium-based composites with different types of lignocellulosic substrates. PLoS One 14 (7), e0213954. Erwig, L.P., Gow, N.A.R., 2016. Interactions of fungal pathogens with phagocytes. Nat. Rev. Microbiol. 14 (3), 163–176. Farinha, I., Duarte, P., Pimentel, A., Plotnikova, E., Chagas, B., Mafra, L., Grandfils, C., Freitas, F., Fortunato, E., Reis, M.A.M., 2015. Chitin-glucan complex production by Komagataella pastoris: downstream optimization and product characterization. Carbohydr. Polym. 130, 455–464. Farinha, I., Araujo, D., Freitas, F., 2019. Optimization of medium composition for production of chitinglucan complex and mannose-containing polysaccharides by the yeast Komagataella pastoris. J. Biotechnol. 303, 30–36. Ferreira, I.C., Arau´jo, D., Voisin, P., Alves, V.D., Rosatella, A.A., Afonso, C.A.M., Freitas, F., Neves, L.A., 2020. Chitin-glucan complex-based biopolymeric structures using biocompatible ionic liquids. Carbohydr. Polym. 247, 116679. Fontaine, T., Simenel, C., Dubreucq, G., Adam, O., Delepierre, M., Lemoine, J., Vorgias, C.E., Diaquin, M., Latg
e, J.P., 2000. Molecular organization of the alkali-insoluble fraction of aspergillus fumigatus cell wall. J. Biol. Chem. 275 (36), 27594–27607. Fontaine, T., Beauvais, A., Loussert, C., Thevenard, B., Fulgsang, C.C., Ohno, N., Clavaud, C., Prevost, M.C., Latg
e, J.P., 2010. Cell wall alpha1-3glucans induce the aggregation of germinating conidia of Aspergillus fumigatus. Fungal Genet. Biol. 47 (8), 707–712. Fontaine, T., Delangle, A., Simenel, C., Coddeville, B., van Vliet, S.J., van Kooyk, Y., Bozza, S., Moretti, S.,
, J.-P., 2011. GalactosamiSchwarz, F., Trichot, C., Aebi, M., Delepierre, M., Elbim, C., Romani, L., Latge nogalactan, a new immunosuppressive polysaccharide of aspergillus fumigatus. PLoS Pathog. 7 (11), e1002372. Free, S.J., 2013. Fungal cell wall organization and biosynthesis. Adv. Genet. 81, 33–82. Fu, Y., Huang, X., Zhou, Z., 2020. Insight into the assembling mechanism of Cryptococcus capsular glucuronoxylomannan based on molecular dynamics simulations. ACS Omega 5 (45), 29351–29356. Gachhi, D.B., Hungund, B.S., 2018. Two phase extraction, characterization and biological evaluation of chitin and chitosan from Rhizopus oryzae. J. Appl. Pharm. Sci. 8 (11), 116–122. Garcia-Rubio, R., de Oliveira, H.C., Rivera, J., Trevijano-Contador, N., 2020. The fungal cell wall: Candida, Cryptococcus, and aspergillus species. Front. Microbiol. 10, 2993. Ghormade, V., Pathan, E.K., Deshpande, M.V., 2017. Can fungi compete with marine sources for chitosan production? Int. J. Biol. Macromol. 104, 1415–1421. Giavasis, I., Seviour, R., Hudman, P., McNeil, B., 2019. Fungal Bioproducts for Use in Food: Polysaccharides, Organic Acids, and Mycoprotein. CRC Press, pp. 511–547. Goldman, G.H., Delneste, Y., Papon, N., 2021. Fungal polysaccharides promote protective immunity. Trends Microbiol. 29 (5), 379–381. Gooday, G.W., 1995. Cell walls. In: Gow, N.A.R., Gadd, G.M. (Eds.), The Growing Fungus. Dordrecht, Springer, Netherlands, pp. 43–62. Gow, N.A.R., Latge, J.P., Munro, C.A., 2017. The fungal cell wall: structure, biosynthesis, and function. Microbiol. Spectr. 5 (3). https://doi.org/10.1128/microbiolspec.FUNK-0035-2016. € n, C.H., Hochstenbach, F., Humbel, B.M., Verkleij, A.J., Sietsma, J.H., Klis, F.M., Kamerling, J.P., Gru Vliegenthart, J.F.G., 2004. The structure of cell wall α-glucan from fission yeast. Glycobiology 15 (3), 245–257. € n, C.H., Hochstenbach, F., Humbel, B.M., Verkleij, A.J., Sietsma, J.H., Klis, F.M., Kamerling, J.P., Gru Vliegenthart, J.F., 2005. The structure of cell wall alpha-glucan from fission yeast. Glycobiology 15 (3), 245–257.

Chapter 17 • Production of fungal biopolymers and their advanced applications

527

Hassainia, A., Satha, H., Boufi, S., 2018. Chitin from Agaricus bisporus: extraction and characterization. Int. J. Biol. Macromol. 117, 1334–1342. He, X., Li, S., Kaminskyj, S., 2017. An amylase-like protein, AmyD, is the major negative regulator for α-glucan synthesis in aspergillus nidulans during the asexual life cycle. Int. J. Mol. Sci. 18 (4), 695. ˜ o-Vega, G.A., Mora-Montes, H.M., 2017. Fungal strategies Herna´ndez-Cha´vez, M.J., P
erez-Garcı´a, L.A., Nin to evade the host immune recognition. J. Fungi 3 (4), 51. Hosseinnejad, M., Jafari, S.M., 2016. Evaluation of different factors affecting antimicrobial properties of chitosan. Int. J. Biol. Macromol. 85, 467–475. €nzle, M.G., 2019. Effect of chitosan, and bacteriocin – proHu, Z.Y., Balay, D., Hu, Y., McMullen, L.M., Ga ducing Carnobacterium maltaromaticum on survival of Escherichia coli and salmonella typhimurium on beef. Int. J. Food Microbiol. 290, 68–75. Hyde, K.D., Xu, J., Rapior, S., Jeewon, R., Lumyong, S., Niego, A.G.T., Abeywickrama, P.D., Aluthmuhandiram, J.V.S., Brahamanage, R.S., Brooks, S., Chaiyasen, A., Chethana, K.W.T., Chomnunti, P., Chepkirui, C., Chuankid, B., de Silva, N.I., Doilom, M., Faulds, C., Gentekaki, E., Gopalan, V., Kakumyan, P., Harishchandra, D., Hemachandran, H., Hongsanan, S., Karunarathna, A., Karunarathna, S.C., Khan, S., Kumla, J., Jayawardena, R.S., Liu, J.-K., Liu, N., Luangharn, T., Macabeo, A.P.G., Marasinghe, D.S., Meeks, D., Mortimer, P.E., Mueller, P., Nadir, S., Nataraja, K.N., Nontachaiyapoom, S., O’Brien, M., Penkhrue, W., Phukhamsakda, C., Ramanan, U.S., Rathnayaka, A.R., Sadaba, R.B., Sandargo, B., Samarakoon, B.C., Tennakoon, D.S., Siva, R., Sriprom, W., Suryanarayanan, T.S., Sujarit, K., Suwannarach, N., Suwunwong, T., Thongbai, B., Thongklang, N., Wei, D., Wijesinghe, S.N., Winiski, J., Yan, J., Yasanthika, E., Stadler, M., 2019. The amazing potential of fungi: 50 ways we can exploit fungi industrially. Fungal Divers. 97 (1), 1–136. Irbe, I., Filipova, I., Skute, M., Zajakina, A., Spunde, K., Juhna, T., 2021. Characterization of novel biopolymer blend Mycocel from plant cellulose and fungal fibers. Polymers 13 (7), 1086. Jeihanipour, A., Karimi, K., Taherzadeh, M., 2007. Antimicrobial properties of fungal chitosan. Res. J. Biol. Sci. 2, 1874–1880. Johney, J., Eagappan, K., Ragunathan, R., 2016. Microbial extraction of chitin and chitosan from PLEUROTUS SPP, its characterization and antimicrobial activity. Int. J. Curr. Pharm. Res. 9, 88–93. Jones, M., Huynh, T., Dekiwadia, C., Daver, F., John, S., 2017. Mycelium composites: a review of engineering characteristics and growth kinetics. J. Bionanoscience 11 (4), 241–257. Jones, M., Bhat, T., Huynh, T., Kandare, E., Yuen, R., Wang, C.H., John, S., 2018. Waste-derived low-cost mycelium composite construction materials with improved fire safety. Fire Mater. 42 (7), 816–825. Jones, M.P., Lawrie, A.C., Huynh, T.T., Morrison, P.D., Mautner, A., Bismarck, A., John, S., 2019a. Agricultural by-product suitability for the production of chitinous composites and nanofibers utilising Trametes versicolor and Polyporus brumalis mycelial growth. Process Biochem. 80, 95–102. €hlig, H., Kontturi, E., John, S., Bismarck, A., Jones, M., Weiland, K., Kujundzic, M., Theiner, J., Ka Mautner, A., 2019b. Waste-derived low-cost mycelium nanopapers with tunable mechanical and surface properties. Biomacromolecules 20 (9), 3513–3523. Jones, M., Kujundzic, M., John, S., Bismarck, A., 2020a. Crab vs. mushroom: a review of crustacean and fungal chitin in wound treatment. Mar. Drugs 18 (1), 64. Jones, M., Mautner, A., Luenco, S., Bismarck, A., John, S., 2020b. Engineered mycelium composite construction materials from fungal biorefineries: a critical review. Mater. Des. 187, 108397. Jones, M., Gandia, A., John, S., Bismarck, A., 2021. Leather-like material biofabrication using fungi. Nat. Sustain. 4 (1), 9–16. Joseph, S.M., Krishnamoorthy, S., Paranthaman, R., Moses, J.A., Anandharamakrishnan, C., 2021. A review on source-specific chemistry, functionality, and applications of chitin and chitosan. Carbohydr. Polym. Technol. Appl. 2, 100036.

528

Current Developments in Biotechnology and Bioengineering

Kajiwara, K., M. T., 2005. Progress in structural characterization of functional polysaccharides. In: Dumitriu, S. (Ed.), Polysaccharides – Structural Diversity and Functional Versatility. Marcel Dekker, New York.
ski, A., Widanage, M.C.D., Chen, A., Azadi, P., Wang, P., Mentink-Vigier, F., Kang, X., Kirui, A., Muszyn Wang, T., 2018. Molecular architecture of fungal cell walls revealed by solid-state NMR. Nat. Commun. 9 (1), 2747. Kaur, S., Dhillon, G.S., 2014. The versatile biopolymer chitosan: potential sources, evaluation of extraction methods and applications. Crit. Rev. Microbiol. 40 (2), 155–175. Khora, S.S., 2016. Seafood-associated shellfish allergy: a comprehensive review. Immunol. Investig. 45 (6), 504–530. Kisko´, G., Sharp, R., Roller, S., 2005. Chitosan inactivates spoilage yeasts but enhances survival of Escherichia coli O157:H7 in apple juice. J. Appl. Microbiol. 98 (4), 872–880. € hnlein, M., 2020. Preparation of Films and Nonwoven Composites from Fungal Microfibers Grown in Ko Bread Waste (Master of engineering). University of Bora˚s. Krylov, V.B., Nifantiev, N.E., 2020a. Synthetic oligosaccharides mimicking fungal cell wall polysaccharides.
, J.-P. (Ed.), The Fungal Cell Wall : An Armour and a Weapon for Human Fungal Pathogens. In: Latge Springer International Publishing, Cham, pp. 1–16. Krylov, V.B., Nifantiev, N.E., 2020b. Synthetic oligosaccharides mimicking fungal cell wall polysaccharides. Curr. Top. Microbiol. Immunol. 425, 1–16. Laroche, C., Michaud, P., 2007. New developments and prospective applications for beta (1,3) glucans. Recent Pat. Biotechnol. 1 (1), 59–73. Latg
e, J.-P., 2007. The cell wall: a carbohydrate Armour for the fungal cell. Mol. Microbiol. 66 (2), 279–290. Latge, J.P., Beauvais, A., 2014. Functional duality of the cell wall. Curr. Opin. Microbiol. 20, 111–117. Lecointe, K., Cornu, M., Leroy, J., Coulon, P., Sendid, B., 2019. Polysaccharides cell wall architecture of mucorales. Front. Microbiol. 10, 469. Lehtovaara, B.C., Gu, F.X., 2011. Pharmacological, structural, and drug delivery properties and applications of 1,3-β-glucans. J. Agric. Food Chem. 59 (13), 6813–6828. Liao, J., Huang, H., 2019. Extraction of a novel fungal chitin from Hericium erinaceus residue using multistep mild procedures. Int. J. Biol. Macromol. 156, 1279–1286. Lima, S.L., Colombo, A.L., de Almeida Junior, J.N., 2019. Fungal cell wall: emerging antifungals and drug resistance. Front. Microbiol. 10, 2573. Lonchamp, J., Clegg, P.S., Euston, S.R., 2019. Foaming, emulsifying and rheological properties of extracts from a co-product of the Quorn fermentation process. Eur. Food Res. Technol. 245 (9), 1825–1839. Louise, A.W., Neil, A.R.G., Carol, A.M., 2013. Elevated chitin content reduces the susceptibility of Candida species to Caspofungin. Antimicrob. Agents Chemother. 57 (1), 146–154. Luft, L., Confortin, T.C., Todero, I., Zabot, G.L., Mazutti, M.A., 2020. An overview of fungal biopolymers: bioemulsifiers and biosurfactants compounds production. Crit. Rev. Biotechnol. 40 (8), 1059–1080. Luo, Z., Liu, S., Du, G., Zhou, J., Chen, J., 2017. Identification of a polysaccharide produced by the pyruvate overproducer Candida glabrata CCTCC M202019. Appl. Microbiol. Biotechnol. 101 (11), 4447–4458. Ma, L., Chen, Z., Huang, D.W., Kutty, G., Ishihara, M., Wang, H., Abouelleil, A., Bishop, L., Davey, E., Deng, R., Deng, X., Fan, L., Fantoni, G., Fitzgerald, M., Gogineni, E., Goldberg, J.M., Handley, G., Hu, X., Huber, C., Jiao, X., Jones, K., Levin, J.Z., Liu, Y., Macdonald, P., Melnikov, A., Raley, C., Sassi, M., Sherman, B.T., Song, X., Sykes, S., Tran, B., Walsh, L., Xia, Y., Yang, J., Young, S., Zeng, Q., Zheng, X., Stephens, R., Nusbaum, C., Birren, B.W., Azadi, P., Lempicki, R.A., Cuomo, C.A., Kovacs, J.A., 2016. Genome analysis of three pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts. Nat. Commun. 7 (1), 10740.

Chapter 17 • Production of fungal biopolymers and their advanced applications

529

Ma, Q., Gao, X., Bi, X., Xia, M., Han, Q., Peng, M., Tu, L., Yang, Y., Shen, Y., Wang, M., 2021. Combination of steam explosion and ionic liquid pretreatments for efficient utilization of fungal chitin from citric acid fermentation residue. Biomass Bioenergy 145, 105967. Mahapatra, S., Banerjee, D., 2013. Fungal exopolysaccharide: production, composition and applications. Microbiol. Insights 6, 1–16. Meng, X., Xing, R., Liu, S., Yu, H., Li, K., Qin, Y., Li, P., 2012. Molecular weight and pH effects of aminoethyl modified chitosan on antibacterial activity in vitro. Int. J. Biol. Macromol. 50 (4), 918–924. Meyer, M., Dietrich, S., Schulz, H., Mondschein, A., 2021. Comparison of the technical performance of leather, artificial leather, and trendy alternatives. Coatings 11 (2), 226. Mohammadi, M., Zamani, A., Karimi, K., 2013. Effect of phosphate on glucosamine production by ethanolic fungus Mucor indicus. Appl. Biochem. Biotechnol. 171 (6), 1465–1472. Mohammadkhani, G., 2021. Evaluation of Wet Spinnig of Fungal and Shellfish Chitosan for Medical Applications. Master of Engineering, University of Bora˚s. ˜ oz, G., Valencia, C., Valderruten, N.E., Ruiz-Dura´ntez, E., Zuluaga, F., 2015. Extraction of chitosan from Mun aspergillus Niger mycelium and synthesis of hydrogels for controlled release of betahistine. React. Funct. Polym. 91-92, 1–10. Namboodiri, M.M.T., Pakshirajan, K., 2019. Sustainable and green approach of chitosan production from Penicillium citrinum biomass using industrial wastewater as a cheap substrate. J. Environ. Manag. 240, 431–440. Namboodiri, M.M.T., Pakshirajan, K., 2020. Valorization of waste biomass for chitin and chitosan production. In: Bhaskar, T., Pandey, A., Rene, E.R., Tsang, D.C.W. (Eds.), Waste Biorefinery. Elsevier, pp. 241–266 (Chapter 10). Naranjo-Ortiz, M.A., Gabaldo´n, T., 2019. Fungal evolution: diversity, taxonomy and phylogeny of the fungi. Biol. Rev. 94 (6), 2101–2137. Narayanan, K.B., Zo, S.M., Han, S.S., 2020. Novel biomimetic chitin-glucan polysaccharide nano/microfibrous fungal-scaffolds for tissue engineering applications. Int. J. Biol. Macromol. 149, 724–731. Nawawi, W., 2016. Renewable Chitin Based Nanomaterials from Fungi. Nawawi, W., Lee, K.-Y., Kontturi, E., Murphy, R.J., Bismarck, A., 2019. Chitin nanopaper from mushroom extract: natural composite of nanofibers and glucan from a single biobased source. ACS Sustain. Chem. Eng. 7 (7), 6492–6496. Nawawi, W., Jones, M., Kontturi, E., Mautner, A., Bismarck, A., 2020a. Plastic to elastic: fungi-derived composite nanopapers with tunable tensile properties. Compos. Sci. Technol. 198, 108327. Nawawi, W., Lee, K.-Y., Kontturi, E., Bismarck, A., Mautner, A., 2020b. Surface properties of chitin-glucan nanopapers from Agaricus bisporus. Int. J. Biol. Macromol. 148, 677–687. Netea, M.G., Gow, N.A., Munro, C.A., Bates, S., Collins, C., Ferwerda, G., Hobson, R.P., Bertram, G., Hughes, H.B., Jansen, T., Jacobs, L., Buurman, E.T., Gijzen, K., Williams, D.L., Torensma, R., McKinnon, A., MacCallum, D.M., Odds, F.C., Van der Meer, J.W., Brown, A.J., Kullberg, B.J., 2006. Immune sensing of Candida albicans requires cooperative recognition of mannans and glucans by lectin and toll-like receptors. J. Clin. Invest. 116 (6), 1642–1650. No, H.K., Young Park, N., Ho Lee, S., Meyers, S.P., 2002. Antibacterial activity of chitosans and chitosan oligomers with different molecular weights. Int. J. Food Microbiol. 74 (1), 65–72. Nwe, N., Furuike, T., Tamura, H., 2009. The mechanical and biological properties of chitosan scaffolds for tissue regeneration templates are significantly enhanced by chitosan from Gongronella butleri. Materials 2 (2), 374–398. Ohno, N., 2007. Yeast and fungal polysaccharides. In: Comprehensive Glycoscience. 2. Elsevier, pp. 559–577.

530

Current Developments in Biotechnology and Bioengineering


ska-Jaroszuk, M., Sulej, J., Jaszek, M., Jaroszuk-S´ciseł, J., 2020. Applications of fungal polysaccharides. Osin In: Reference Module in Life Sciences. Elsevier. Paulin, M., Miot-Sertier, C., Dutilh, L., Brasselet, C., Delattre, C., Pierre, G., Dubessay, P., Michaud, P., Doco, T., Ballestra, P., Albertin, W., Masneuf-Pomare`de, I., Moine, V., Coulon, J., Vallet-Courbin, A., Maupeu, J., Dols-Lafargue, M., 2020. Brettanomyces bruxellensis displays variable susceptibility to chitosan treatment in wine. Front. Microbiol. 11, 571067. Pinto, M.R., Barreto-Bergter, E., Taborda, C.P., 2008. Glycoconjugates and polysaccharides of fungal cell wall and activation of immune system. Braz. J. Microbiol. 39 (2), 195–208. Poverenov, E., Arnon-Rips, H., Zaitsev, Y., Bar, V., Danay, O., Horev, B., Bilbao-Sainz, C., McHugh, T., Rodov, V., 2018. Potential of chitosan from mushroom waste to enhance quality and storability of fresh-cut melons. Food Chem. 268, 233–241. Qin, C., Li, H., Xiao, Q., Liu, Y., Zhu, J., Du, Y., 2006. Water-solubility of chitosan and its antimicrobial activity. Carbohydr. Polym. 63 (3), 367–374. Raafat, D., Sahl, H.-G., 2009. Chitosan and its antimicrobial potential—a critical literature survey. Microb. Biotechnol. 2 (2), 186–201. Radwan-Pragłowska, J., Janus, Ł., Pia˛tkowski, M., Sierakowska, A., Galek, T., Szajna, E., Bogdał, D., Tupaj, M., 2021. Fungal chitosan-derived biomaterials modified with Kalanchoe pinnata as potential hemostatic agents—development and characterization. Polymers 13 (8), 1300. Ragavan, M.L., Das, N., 2019. Optimization of exopolysaccharide production by probiotic yeast Lipomyces starkeyi VIT-MN03 using response surface methodology and its applications. Ann. Microbiol. 69 (5), 515–530. ´ .R., de Miranda Pereira de Pessoa, A., de Ramos Berger, L.R., Montenegro Stamford, T.C., de Oliveira, K.A ^mara, M.P., de Oliveira Franco, L., Magnani, M., de Lima, M.A.B., Estevez Pintado, M.M., Saraiva Ca Souza, E.L., 2018. Chitosan produced from Mucorales fungi using agroindustrial by-products and its efficacy to inhibit Colletotrichum species. Int. J. Biol. Macromol. 108, 635–641. Robison, R.A., Crick, R.E., 2021. Paleozoic era. In: Encyclopedia Britannica. Britannica. https://www. britannica.com/science/Paleozoic-Era. (Accessed 27 October 2022). Roeder, A., Kirschning, C.J., Rupec, R.A., Schaller, M., Weindl, G., Korting, H.C., 2004. Toll-like receptors as key mediators in innate antifungal immunity. Med. Mycol. 42 (6), 485–498. Rouhollahi, F., Zamani, A., Karimi, K., Etesami, N., 2014. Enhancement of nickel biosorption on fungal biomass by enzymatic and alkali pretreatments. Int. J. Environ. Sci. Technol. 11 (7), 1911–1918. Ruiz-Herrera, J., 2012. Fungal Cell Wall; Structure, Synthesis, and Assembly, 2nd. CRC, Boca Raton, FL, pp. 5–22. Ruiz-Herrera, J., Ortiz-Castellanos, L., 2019. Cell wall glucans of fungi. A review. Cell Surf. 5, 100022. Ruiz-Herrera, J., Victoria Elorza, M., Valentı´n, E., Sentandreu, R., 2006. Molecular organization of the cell wall of Candida albicans and its relation to pathogenicity. FEMS Yeast Res. 6 (1), 14–29. Safaei, Z., Karimi, K., Golkar, P., Zamani, A., 2015. Effects of plant growth hormones on Mucor indicus growth and chitosan and ethanol production. Int. J. Mol. Sci. 16 (7), 16683–16694. Salehinik, F., Behzad, T., Zamani, A., Bahrami, B., 2021. Extraction and characterization of fungal chitin nanofibers from Mucor indicus cultured in optimized medium conditions. Int. J. Biol. Macromol. 167, 1126–1134.
Albuquerque, P.M., Chopra, H.K., Sanches, M.A., Luzeiro, I.G., Alves Cortez, A.C., Simplı´cio de Souza, E., Braga de Souza, J.V., 2021. Production of biosurfactants by ascomycetes. Int. J. Microbiol. 2021, 6669263.
Sena, H.H., Sanches, M.A., Rocha, D.F.S., Segundo, W.O.P.F., de Souza, E.S., de Souza, J.V.B., 2018. Production of biosurfactants by soil Fungi isolated from the Amazon Forest. Int. J. Microbiol. 2018, 5684261. Shariatinia, Z., 2018. Carboxymethyl chitosan: properties and biomedical applications. Int. J. Biol. Macromol. 120 (Pt B), 1406–1419.

Chapter 17 • Production of fungal biopolymers and their advanced applications

531

Shibata, N., Kobayashi, H., Suzuki, S., 2012. Immunochemistry of pathogenic yeast, Candida species, focusing on mannan. Proc. Jpn. Acad. Ser. B Phys. Biol. Sci. 88 (6), 250–265. Singh, A., Dutta, P., Kumar, H., Kureel, A.K., Rai, A., 2019. Improved antibacterial and antioxidant activities of gallic acid grafted chitin-glucan complex. J. Polym. Res. 26, 234. Singh, R., Upadhyay, S., Singh, M., Sharma, I., Sharma, P., Kamboj, P., Saini, A., Voraha, R., Sharma, A., Upadhyay, T., Khan, F., 2020. Chitin, Chitinases and chitin derivatives in biopharmaceutical, agricultural and environmental perspective. Biointerface Res. Appl. Chem. 11, 9985–10005. Smiderle, F.R., Olsen, L.M., Ruthes, A.C., Czelusniak, P.A., Santana, A.P., Sassaki, G.L., Gorin, P.A.J., Iacomini, M., 2012. Exopolysaccharides, proteins and lipids in Pleurotus pulmonarius submerged culture using different carbon sources. Carbohydr. Polym. 87 (1), 368–376. Su, C.H., Sun, C.S., Juan, S.W., Hu, C.H., Ke, W.T., Sheu, M.T., 1997. Fungal mycelia as the source of chitin and polysaccharides and their applications as skin substitutes. Biomaterials 18 (17), 1169–1174. Sun, C., Fu, D., Jin, L.F., Chen, M.Y., Zheng, X.D., Yu, T., 2018a. Chitin isolated from yeast cell wall induces the resistance of tomato fruit to Botrytis cinerea. Carbohydr. Polym. 199, 341–352. Sun, C., Lin, M., Fu, D., Yang, J., Huang, Y.N., Zheng, X.D., Yu, T., 2018b. Yeast cell wall induces disease resistance against Penicillium expansum in pear fruit and the possible mechanisms involved. Food Chem. 241, 301–307. Svensson, S.E., Bucuricova, L., Ferreira, J.A., Souza Filho, P.F., Taherzadeh, M.J., Zamani, A., 2021a. Valorization of bread waste to a fiber- and protein-rich fungal biomass. Fermentation 7 (2), 91. Svensson, S.E., Ferreira, J.A., Hakkarainen, M., Adolfsson, K.H., Zamani, A., 2021b. Fungal textiles: wet spinning of fungal microfibers to produce monofilament yarns. Sustain. Mater. Technol. 28, e00256. Taillandier, P., Joannis-Cassan, C., Jentzer, J.B., Gautier, S., Sieczkowski, N., Granes, D., Brandam, C., 2015. Effect of a fungal chitosan preparation on Brettanomyces bruxellensis, a wine contaminant. J. Appl. Microbiol. 118 (1), 123–131. Tsuchihashi, H., Yadomae, T., Miyazaki, T., 1983. Structural analysis of the cell-wall d-glucuronans from the fungi Absidia cylindrospora, Mucor mucedo, and Rhizopus nigricans. Carbohydr. Res. 111 (2), 330–335. Wang, Q., Wang, F., Xu, Z.H., Ding, Z.Y., 2017. Bioactive mushroom polysaccharides: a review on monosaccharide composition, biosynthesis and regulation. Molecules 22 (6). Wan-Mohtar, W.A.A.Q.I., Young, L., Abbott, G.M., Clements, C., Harvey, L.M., Mcneil, B., 2016. Antimicrobial properties and cytotoxicity of sulfated (1,3)-β-D-glucan from the mycelium of the mushroom Ganoderma lucidum. J. Microbiol. Biotechnol. 26 (6), 999–1010. Warnock, D.W., 1999. Cryptococcus neoformans. J. Antimicrob. Chemother. 44 (1), 139. Wijayarathna, K., 2021. Development of Fungal Leather-Like Material from Bread Waste. Master of Engineering, University of Bora˚s. Wu, Z.W., Yang, Z.J., Gan, D., Fan, J.L., Dai, Z.Q., Wang, X.Q., Hu, B., Ye, H., Abid, M., Zeng, X.X., 2014. Influences of carbon sources on the biomass, production and compositions of exopolysaccharides from Paecilomyces hepiali HN1. Biomass Bioenergy 67, 260–269. Xiao, Z., Zhou, W., Zhang, Y., 2020a. Fungal polysaccharides. In: Du, G. (Ed.), Advances in Pharmacology. 87. Academic Press, pp. 277–299 (Chapter 10). Xiao, Z., Zhou, W., Zhang, Y., 2020b. Fungal polysaccharides. Adv. Pharmacol. 87, 277–299. Xing, Y., Brewer, M., El-Gharabawy, H., Griffith, G., Jones, P., 2018. Growing and testing mycelium bricks as building insulation materials. IOP Conf. Ser.: Earth Environ. Sci. 121, 022032. Xu, L., Wang, F., Zhang, Z.C., Terry, N., 2019. Optimization of polysaccharide production from Cordyceps militaris by solid-state fermentation on Rice and its antioxidant activities. Foods 8 (11), 590.

532

Current Developments in Biotechnology and Bioengineering

Yang, L., Li, X., Lai, C., Fan, Y., Ouyang, J., Yong, Q., 2017. Fungal chitosan production using xylose rich of corn Stover prehydrolysate by Rhizopus oryzae. Biotechnol. Biotechnol. Equip. 31 (6), 1160–1166. Yarden, O., Osherov, N., 2010. The Cell Wall of Filamentous Fungi. Cellular and Molecular Biology of Filamentous Fungi. K. A. Borkovich and D. J. Ebbole, American Society of Microbiology, pp. 224–237. Yoshimi, A., Miyazawa, K., Abe, K., 2017. Function and biosynthesis of cell wall α-1,3-glucan in Fungi. J. Fungi 3 (4). Younes, I., Hajji, S., Frachet, V., Rinaudo, M., Jellouli, K., Nasri, M., 2014a. Chitin extraction from shrimp shell using enzymatic treatment. Antitumor, antioxidant and antimicrobial activities of chitosan. Int. J. Biol. Macromol. 69, 489–498. Younes, I., Sellimi, S., Rinaudo, M., Jellouli, K., Nasri, M., 2014b. Influence of acetylation degree and molecular weight of homogeneous chitosans on antibacterial and antifungal activities. Int. J. Food Microbiol. 185, 57–63.
, J.L., Weiss, K.L., Pingali, S.V., Hong, K., Urban, V.Yuan, Y., Li, H., Leite, W., Zhang, Q., Bonnesen, P.V., Labbe S., Salmon, S., O’Neill, H., 2021. Biosynthesis and characterization of deuterated chitosan in filamentous fungus and yeast. Carbohydr. Polym. 257, 117637. Zamani, A., 2010. Superabsorbent Polymers from the Cell Wall of Zygomycetes Fungi (23 Doctoral thesis, monograph). Chalmers University of Technology. Zamani, A., Taherzadeh, M.J., 2012. Production of superabsorbents from fungal chitosan. Iran. Polym. J. 21 (12), 845–853. Zaragoza, O., Rodrigues, M.L., De Jesus, M., Frases, S., Dadachova, E., Casadevall, A., 2009. The capsule of the fungal pathogen Cryptococcus neoformans. Adv. Appl. Microbiol. 68, 133–216. Zeng, Y.J., Yang, H.R., Wu, X.L., Peng, F., Huang, Z., Pu, L., Zong, M.H., Yang, J.G., Lou, W.Y., 2019. Structure and immunomodulatory activity of polysaccharides from fusarium solani DO7 by solid-state fermentation. Int. J. Biol. Macromol. 137, 568–575. Zhao, W., Chai, D.D., Li, H.M., Chen, T., Tang, Y.J., 2014. Significance of metal ion supplementation in the fermentation medium on the structure and anti-tumor activity of tuber polysaccharides produced by submerged culture of tuber melanosporum. Process Biochem. 49 (12), 2030–2038.
ska, M., Paduch, R., Jaroszuk-S´ciseł, J., Bieganowski, A., 2019. Złotko, K., Wiater, A., Wa
sko, A., Pleszczyn A report on fungal (1!3)-α-d-glucans: properties, functions and application. Molecules 24 (21), 3972.

18 Versatility of filamentous fungi in novel processes € lru Bulkan, Jorge A. Ferreira, and Mohsen Parchami, Taner Sar, Gu Mohammad J. Taherzadeh ˚ S , SW EDEN SWE DISH C ENTRE FOR RE SOUR CE R ECOVE RY, UNIVERS ITY O F BORA˚ S, BOR A

1. Introduction Establishing a harmony between population growth and its impact on the environment is humankind’s one of the most demanding challenges. Human activity has an immensely negative effect on the natural resources cycle through over-usage of the resources and rapid waste generation. A vital tool for mitigating these adverse effects is sustainable development. Sustainability is attainable by maximizing resource utilization efficiency and minimizing waste generation (Clark and Deswarte, 2008). Bioeconomy, as sustainable development of products and processes from the utilization of renewable resources, has become the center of attention over the past years. For instance, it is one of the main sections in the Horizon 2020 framework (European Union research and innovation program). Currently, the bioeconomy’s annual turnover is 2.3 trillion euros, with 22 million people employed. The bioeconomy focus on the production of €s et al., food, feed, biofuels, and bioproducts from renewable biological resources (Tera 2014; Hassan et al., 2019). For instance, the EU goal for renewable energy share was 20% by 2020, and it has been set to 32% by 2030. The share of renewable energy in 2016 was 17% at the EU level. (Popp et al., 2021). Waste biorefinery corresponds to the concept of sustainable development, as various value-added products such as chemicals, fuels, and biomaterials are produced from different wastes. Several strategies have been developed for waste valorization via the biorefinery concept, among which using microorganisms is a prominent method (Ferreira et al., 2016). Filamentous fungi are cell factories that can produce a wide range of value-added products. Historically, filamentous fungi had a significant impact on our life. For centuries, they have been used for the production of food and beverage. In the early twentieth century, the production of penicillin, the first true antibiotic by Penicillium rubens, made a breakthrough for the development of biological production of antibiotics, € sten, 2019; Hu € ttner et al., 2020). Moreover, filamentous enzymes, and control agents (Wo fungi have been used on an industrial scale to produce different enzymes, organic acids,

Current Developments in Biotechnology and Bioengineering. https://doi.org/10.1016/B978-0-323-91872-5.00009-0 Copyright © 2023 Elsevier Inc. All rights reserved.

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€ sten, 2019). A few examples pharmaceuticals, and food products (Ferreira et al., 2016; Wo of fungal products and producing companies are listed below – – – –

Food products (Marlow Foods, United Kingdom) Citric acid (Citrique Belge, Belgium) Malic acid (Novozymes, Denmark) Industrial-grade enzymes (Aumenzymes, India)

Additionally, filamentous fungi are capable of utilizing a versatile types of materials. These characteristics, versatile substrates, and products have put the filamentous fungi in the spotlight for establishing the biorefineries. Over the past years, fungi have exclusively been explored as a core element for establishing biorefinery by utilizing various industrial wastes and returning these wastes to the production and consumption cycle as valueadded resources (Ferreira et al., 2016). Fig. 1 shows the potential of filamentous fungi in utilizing various wastes and producing different products. In this chapter, the generation and composition of eight different agro-industrial process waste were studied. Furthermore, valorizing these wastes with filamentous fungi and establishing fungal biorefinery based on those processes were evaluated.

2. Brewery waste The brewing industry is one of the main sections of the food industry, which holds a considerable market value. Global production of beer in 2018 was around 188 billion liters (beer from the malt with alcohol >0.5% v/v), with a market value of 504 billion Euros. The main by-product of a brewery is brewer’s spent grain (BSG), with the average generation of 15–20 kg wet BSG per 100 L of beer. Thus, the generated BSG in 2018 could be estimated at around 38 million metric tons (Qiu et al., 2019; Parchami et al., 2021a). BSG is the lignocellulosic solid fraction separated after filtration of wort and is rich in various nutrients such as cellulose, starch, arabinoxylans, phenolic compounds, vitamins, lignin, fatty acids, and proteins (Meneses et al., 2013; Terrasan and Carmona, 2015; Parchami et al., 2021a). Table 1 presents the typical composition of BSG. Since BSG has a high moisture nutrient-rich content, it can biologically deteriorate in a matter of few days, changing from a valuable source of nutrients to waste, posing different environmental problems. Traditionally, BSG is used as low-quality animal feed or ends up in landfills as the generation often exceeds the demand. Numerous efforts have been made to improve the utilization of BSG by producing value-added products from it through different valorization techniques. One of these techniques that have attracted considerable attention for years is BSG valorization by using filamentous fungi. Fungal products from BSG ranging from food and feed-grade products, medical products, hormones to enzymes, biopesticides, and bioethanol. There have been different studies on the production of food and feed-grade products by filamentous fungi from BSG, since BSG is considered a food-grade by-product. Edible biomass is one of the products that has been produced from BSG using filamentous fungi.

Chapter 18 • Versatility of filamentous fungi in novel processes

Waste streams •Wheat straw •Wheat bran •Corn straw •Rice hulls •Sugarcane bagasse •Tee waste •Brewer spent grain •Empty fruit bunches

•Cheese whey •Cream •Crème fraiche •Ice cream

•Whole stillage •Thin stillage

•Oil waste •Meat waste •Fish waste

•Wastewater

Metabolites •Citric acid •Gluconic acid •Itaconic acid •Kojic acid •Oxalic acid •Malic acid •Pigments •Ethanol

•Orange peel •Banana peel •Pineapple peel •Onion peel •Potato peel •Corn cobs •Carrot peel •Apple pomace

•Empty fruit bunches •Coir pith •Thatch grass •Paper waste

535

•

Biomass Filamentous fungi cultivation

•Food and feed •Chitin •Amino acids •Lipids •Fatty acids •Sterols

Enzymes •Amylase •Cellulase •Xylanase •Protease •Lipases •Phytases •Laccase •Catalase •Keratinase

FIG. 1 Substrates and products prospect in a fungal biorefinery. Modified from Ferreira, J.A., Mahboubi, A., Lennartsson, P.R., Taherzadeh, M.J. 2016. Waste biorefineries using filamentous ascomycetes fungi: present status and future prospects. Bioresour. Technol. 215, 334–345.

Filamentous fungi have traditionally been used to produce Asian cuisines for hundreds of years, and these strains have been classified as Generally Regarded as Safe (GRAS) such as Aspergillus oryzae, Rhizopus oryzae, Rhizopus oligosporus, Neurospora intermedia. GRAS is a designation by the United States Food and Drug Administration (FDA) that a substance considered safe and can be added to the food. The safety of the substance is determined through the scientific procedure. There are two key terms, “general recognition”

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Table 1

Brewer spent grain (BSG) chemical composition.

Componentsa (%)

BSGb

BSGc

BSGd

BSGe

Cellulose Hemicellulose Total Lignin Starch Protein Ash

17.5 25.3 16.74 20.9 22.7 n.d. f

16.5 26.3 20.4 n.d.f n.d. f 2.1

18.5 23 45.2 8.7 14.8 3.3

17.9 35.7 17.8 n.d.f 19.2 3.9

a

Percentage of dry weight. From Parchami et al. (2021b). c From Michelin and Teixeira (2016). d From Gmoser et al. (2020). e From Torres-Mayanga et al. (2019). f Not determined. b

and “qualified expert,” in this designation considered for safety evaluation of a substance. The process of approving new microorganisms is costly, strict, and time-consuming; thus, using the GRAS microorganisms is preferred in industrial processes (Waites et al., 2009; Sewalt et al., 2016). Therefore, these fungi have been used in various studies to produce biomass with applications as food and feed products. In a study by Serba et al. (2020), A. oryzae has been used to produce fungal biomass as a food source rich in protein and carbohydrates. In another work, Parchami et al. (2021a) produced protein and fiber-rich fungal biomass from BSG as a food and feed source. They used three different filamentous fungi, namely A. oryzae, R. delemar, and N. intermedia. They have reported that submerged cultivation with Aspergillus oryzae resulted in the highest increase in protein content (34.6% w/w) compared to the initial protein content of BSG. R. oryzae is another filamentous fungus that has been used for the production of biomass from BSG. Ibarruri et al. (2019) have obtained protein-rich biomass (32% (w/w) protein content) by solid-state fermentation (SSF). Wolters et al. (2016) have produced medicinal biomass from BSG using Hericium erinaceus. For centuries, H. erinaceus has been used in Chinese traditional medicine. Additionally, various filamentous fungi species are capable of secreting lignocellulose degrading enzymes, and several studies have focused on producing cellulolytic and xylanolytic enzymes from BSG (Table 2), primarily by Aspergillus sp., Rhizopus sp., and Penicillium sp. (Terrasan et al., 2010; Knob et al., 2013; Izidoro and Knob, 2014; Terrasan and Carmona, 2015; Leite et al., 2019). Leite et al. (2019) have evaluated the capacity of six Aspergillus sp., and Rhizopus sp. for lignocellulolytic enzyme production from agroindustrial wastes, including the BSG. They have reported that the BSG was the most suitable substrate for enzyme production by SSF, and Aspergillus ibericus strains were the best enzyme producers. Besides, as these fungi are cable of breaking down the structure of BSG, different phenolic compounds in BSG such as ferulic acid and p-coumaric acid could be extracted by fungal cultivation. These phenolic compounds have antioxidant and

Chapter 18 • Versatility of filamentous fungi in novel processes

Table 2

Production of various cellulolytic and xylanolytic enzymes from BSG.

Enzyme

Fungus strain

Fermentation mode

Operation temperature (°C)

Enzyme activitya

β-Xylosidase

P. janczewskii

SSF

28

0.18–0.25

P. janczewskii

SmF

28

0.07–0.16

B. spectabilis

SmF

25

0.47

P. janczewskii A. niger CECT2915 A. niger CECT2088 A. ibericus MUM 03.49 A. ibericus MUM 04.86 R. oryzae MUM 10.260 P. glabrum A.niger

SSF SSF

28 25

169–370 290

SSF

25

246

SSF

25

313

SSF

25

300

SSF

25

106

SmF SmF

25 30

34 3

P. janczewskii

SmF

28

5.14–13.6

P. brasilianum

SSF

26.5

709

H. grisea var. thermoidea T. stipitatus A. niger J4

SmF

45

8.19–16.9

SmF SmF

37 28

2.33 9.8

Mucor sp. AB1

SSF

30

67

B. spectabilis

SmF

25

8.88

N. crassa A.niger CECT2915 A.niger CECT2088 A. ibericus MUM 03.49 A. ibericus MUM 04.86 R. oryzae MUM 10.260

SSF SSF

30 25

200 57

SSF

25

51

SSF

25

51

SSF

25

62

SSF

25

18

Xylanase

Cellulase

537

References Terrasan and Carmona (2015) Terrasan et al. (2010) Galanopoulou et al. (2021) Terrasan and Carmona (2015)

Knob et al. (2013) Izidoro and Knob (2014) Terrasan et al. (2010) Panagiotou et al. (2006) Mandalari et al. (2008) Stroparo et al. (2012) Hassan et al. (2020) Galanopoulou et al. (2021) Xiros et al. (2008) Leite et al. (2019)

Continued

538

Current Developments in Biotechnology and Bioengineering

Table 2

Production of various cellulolytic and xylanolytic enzymes from BSG—cont’d Fungus strain

Fermentation mode

Operation temperature (°C)

Enzyme activity

M. thermophila

SmF

47

0.11

A. fumigatus A. fumigatus Penicillium sp. Penicillium sp. A. fumigatus

SmF SSF SmF SSF SSF

30 30 30 30 30

0.35 7.5 0.23 8.3 5.03

N. crassa A. niger CECT2915 A. niger CECT2088 A. ibericus MUM 03.49 A. ibericus MUM 04.86 R. oryzae MUM 10.260 P. janczewskii

SSF SSF

30 25

40 3

SSF

25

93

SSF

25

4

SSF

25

9

SSF

25

1

SSF

28

0.22–0.60

P. janczewskii

SmF

28

0.05–0.64

P. brasilianum

SSF

26.5

0.004

Feruloyl esterase

P. brasilianum

SSF

26.5

0.002

SmF

45

0.17–0.47

Pectinase

H. grisea var. thermoidea T. stipitatus Mucor sp. AB1

SmF SSF

37 30

0.14 137

Enzyme

β-Glucosidase

α-Larabinofuranosidase

a

References Matsakas et al. (2015) Casas-Godoy et al. (2020)

Grigorevski-Lima et al. (2009) Xiros et al. (2008) Leite et al. (2019)

Terrasan and Carmona (2015) Terrasan et al. (2010) Panagiotou et al. (2006) Panagiotou et al. (2006) Mandalari et al. (2008) Hassan et al. (2020)

Reported as U/g for SSF and U/mL for SmF.

antimicrobial activity and are conventionally extracted by using organic solvents. Using fungi remove the need for organic solvents and the possible final product contaminations with the solvents. Moreover, as a cleaner technology, it could eliminate environmental problems associated with using solvent and improve the process economy (Leite et al., 2019; da Costa Maia et al., 2020). Gibberellic acid, a plant hormone, is another fungus metabolite that affects plant growth and has a significant role and value in agriculture. Currently, gibberellic acid is produced by Fusarium fujikuroi submerged cultivation on a commercial scale (da Silva et al.,

Chapter 18 • Versatility of filamentous fungi in novel processes

539

2021). da Silva et al. (2021) reported that solid-state cultivation of Fusarium fujikuroi on BSG is a viable alternative way for Gibberellic acid production. Lastly, filamentous fungi could be used for ethanol production from BSG. For bioethanol production from lignocellulosic material, the primary industrial ethanol producers such as Escherichia coli and Saccharomyces cerevisiae cannot utilize this material, and a pretreatment step is required to improve the hydrolysis. This pretreatment step is a costly and energy-intensive process that has hindered bioethanol’s industrial production from lignocellulosic wastes. A strategy to bypass this technical difficulty is using filamentous fungi. As mentioned before, different filamentous species are capable of degrading lignocellulosic material, which can deconstruct the structure of BSG and release monomeric sugars in the system. The released sugar can be converted to ethanol by well-known ethanol producers such as E. coli and S. cerevisiae. Therefore, many research studies have been done on consolidated bioprocesses (CBPs) using lignocellulose degrading fungi such as Aspergillus niger, Aspergillus oryzae, Trichoderma reesei, and Humicola insolens (Wilkinson et al., 2017). Wilkinson et al. (2017) have tested bioethanol production from BSG using different filamentous fungi paired with yeast strains. They have reported that the A. oryzae and S. cerevisiae CBP system was the best consortia for ethanol production with the yield of 94 kg pure ethanol per 1 t dry BSG. The other strategy for ethanol production is using filamentous fungi to produce ethanol directly. Xiros et al. (2008) have reported 74 kg ethanol production per 1 t dry BSG by fungal fermentation with Neurospora crassa on BSG. Above all, filamentous fungi can produce a wide range of value-added products from BSG ranging from food and feed to fuels, making it possible to establish a circular economy based on the valorization of BSG. Although, the production of food and feed-grade products seems to be more favorable as the by-products from the food industry end up back to the food production cycle. Fig. 2 presents an overview of the integration of filamentous fungi to a brewing process for valorization BSG.

FIG. 2 Brewery biorefinery based on filamentous fungi products.

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Current Developments in Biotechnology and Bioengineering

3. Fruit industry waste The fruit processing sector is one of the biggest sectors in the food industry and is responsible for generating enormous agro-industrial waste (Dhillon et al., 2013). In 2019, the global production of fruits was around 917 million metric tons. Apple, orange, and grapes were among the top five most-produced fruits, with 87.24, 78.7, and 77.14 million metric tons, respectively (FAO, 2021). Approximately 20%–30% of produced apple and orange was used in the juice industry, while grape mostly (ca. 57%) used for wine production (Kantifedaki et al., 2018; Molinuevo-Salces et al., 2020; Filippi et al., 2021). One of the main waste after processing the fruit is the pomace. Fruit pomace is the solids generated after extracting the juice, including the pulp, peel, seeds, etc. Pomace is accounting for up to 50% of the fruit’s weight for apple and orange juice production (Kantifedaki et al., 2018; Molinuevo-Salces et al., 2020), while for the wine, pomace weight is 20% of the grape weight (Filippi et al., 2021). Moreover, the peel and seeds from other products such as canned, dried, and frozen fruits are added to this amount resulting in the annual generation of million tons of solid waste, which causes various environmental problems. Since fruits (apple, orange, and grape) pomace is rich in various nutrients, the valorization of fruits pomace by microorganisms has caught attention as a strategy for handling this enormous amount of waste. The main compounds in fruits pomace are cellulose, hemicellulose, lignin, pectin, protein, minerals, and phenolic compounds (Kantifedaki et al., 2018; Awasthi et al., 2021; Balli et al., 2021). The proximate compositional analysis of fruit pomace is reported in Table 3. As microorganisms capable of degrading lignocellulosic material, filamentous fungi have been the center of attention for the production of products such as protein-rich biomass, organic acids, enzymes, pigments, antioxidants, Table 3

Compositional analysis of apple, orange, and grape pomace.

Composition

Apple pomacea

Orange pomaceb

Grape pomacec

Moisture (%) Fat (%) Protein (%) Ash (%) Carbohydrate (%) TDF (%) Pectin (%) Fructose (%) Calcium Potassium Magnesium Zinc Iron

9.00 2.27 2.37 1.60 84.76 30.15 N/A N/A 126.50a 253.10a 12.60a 0.17a 0.84a

10.55 1.88 6.00 3.68 77.78 40.47 N/A N/A 411.20a 411.2a 57.00a 0.23a 0.98a

3.33 8.16 8.49 4.65 29.2 46.17 3.92 8.91 440d 1400d 130d 980d 1800d

a

Reported as mg/100 mL. From O’Shea et al. (2015). c From Sousa et al. (2014). d Reported as mg/100 mg. b

Chapter 18 • Versatility of filamentous fungi in novel processes

541

and biofuels from fruit pomace (Dhillon et al., 2012; Ucuncu et al., 2013). Filamentous fungi are known for the high production of extracellular enzymes, and they have been extensively researched for enzyme production. Aspergillus sp. have been vastly researched for enzyme production among different fungi, especially pectin degrading enzymes. Dı´az et al. (2012) have evaluated the enzyme production by SSF of Aspergillus awamori on grape pomace. A higher pectinase production has been reported for fermentation with a mixture of grape pomace and orange peels than only grape pomace as substrate. Pyc et al. (2003) have studied the condition of enzyme production by Aspergillus niger fermentation on apple pomace. In another study, Martin et al. (2010) isolated 34 fungal strains from soil and evaluated pectinase production in SSF. About 50% of the isolated fungi belonged to Aspergillus, Scopulariopsis, Thermomucor, Chaetomium, Thermomyces, Neosartoria, and Monascus sp.. Pectinase with the highest enzymatic activity was obtained for the SSF with Thermomucor indica-eseudaticae N31 on mixture of orange peel and wheat bran. Pathania et al. (2018) have reported the production of pectinase among other enzymes from apple pomace by solid state fermentation of Rhizopus delemar F2. Cellulase and hemicellulase are other groups of enzyme that have been produced by filamentous fungi. Table 4 shows the production of various enzyme from apple, orange, and grape pomace. Organic acids are other highly demanded commodities that filamentous fungi can produce. In fact, industrial production of organic acids such as citric acid and gluconic acid by fungi is a well-established process. For instance, the fungal production of citric acid is the Table 4 Production of various enzymes with different filamentous fungi from apple, orange, and grape pomace. Enzyme

Fungus strain

Fermentation mode

References

Apple pomace β-Glucosidase Xylanase

Amylase Endoglucanase Laccase Manganese peroxidase Chitinase Chitosanase Pectin methylesterase (PME) Pectinase Polygalacturonase

M. phaseolina M. phaseolina R. delemar F2 A. niger M. phaseolina R. delemar F2 A. niger M. phaseolina P. chrysosporium P. chrysosporium A. niger A. niger A. niger A. foetidus R. delemar F2 A. niger A. niger

SSF SSF SSF SSF SSF SSF SSF SSF SSF SSF SSF SSF/SmF SSF SSF SSF SSF

Kaur et al. (2012) Pathania et al. (2018) Pyc et al. (2003) Kaur et al. (2012) Pathania et al. (2018) Dhillon et al. (2012) Kaur et al. (2012) Gassara et al. (2010) Dhillon et al. (2011) Joshi et al. (2006) Hours et al. (1988) Pathania et al. (2018) Kiran et al. (2010) Berovic and Ostroversˇnik (1997) Continued

542

Current Developments in Biotechnology and Bioengineering

Table 4 Production of various enzymes with different filamentous fungi from apple, orange, and grape pomace—cont’d Enzyme

Fungus strain

Fermentation mode

A. versicolor A. awamori A. awamori A. awamori P. atrovenetum A. flavus A. oryzae T. hirsuta P. atrovenetum A. flavus A. oryzae A. giganteus A. sojae

SSF SSF SSF SSF SSF SSF SSF SSF SSF SSF SSF SmF SmF

A. awamori A. awamori A. awamori

SSF SSF SSF

References

Orange pomace Cellulase Exo-polygalacturonase Xylanase Endoglucanase

Laccase Polygalacturonase

Exo-polygalacturonase

Srivastava et al. (2017) Dı´az et al. (2012)

Adeleke et al. (2012)

€hmer et al. (2011) Bo Adeleke et al. (2012)

Pedrolli et al. (2008) Buyukkileci et al. (2015)

Grape pomace Exo-polygalacturonase Xylanase Endoglucanase

Dı´az et al. (2012)

oldest and most studied process. Aspergillus and Rhizopus are the most studied genus for different organic acid production. Most of these industrial processes use glucose or sucrose as the substrates. Using agro-industrial waste as a low-cost substrate for fungal production of organic acids improves the economics of the process. It could help the fungal process of less demanded acids such as oxalic, fumaric, and itaconic acid compete with chemical production routes (Magnuson and Lasure, 2004). In a study Papadaki and Mantzouridou (2019), citric acid production from grape pomace by A. niger is reported. Ousmanova and Parker (2007) evaluated the SSF production of organic acids by three different Aspergillus strains from agro-industrial wastes. They have reported that the fungi could produce multiple acids from each substrate; however, the fungal strain and substrate type affect the produced acids. After 8 days of SSF cultivation with A. niger NRRL 2001 on the apple pomace, about 800 mg/L oxalic acid and 400 mg/L citric acid were produced while no level of citric acid was reported for the cultivation on corn cob. Ousmanova and Parker (2007) showed that the produced acids by fungi could be used for extraction of lead from contaminated soil. Additionally, pigments can be produced by filamentous fungi. Pigments have been used in many different industries for adding color to different products, especially food products (Lopes and Ligabue-Braun, 2021). Initially, pigments were extracted from natural sources such as vegetables, fruits, and insects. Although, high production costs and color instability led to the development of synthetic pigments. However, due to the

Chapter 18 • Versatility of filamentous fungi in novel processes

543

harmful effect of synthetic pigments on human health, there was a growing demand for natural pigments, resulting in the development of the natural color industry. With recent advances in biotechnology, microbial production of pigments as alternative ways for production of natural pigments has captured lots of attention (de Oliveira et al., 2020; Kalra et al., 2020). Filamentous fungi are microorganisms that produce a good level of pigment with high color variation. For instance, the fungus genus Monascus is reported as one of the best fungal pigment producers. Penicillium, Trichoderma, Talaromyces, and Fusarium are other species that have been vastly researched for pigment production. Kantifedaki et al. (2018) have evaluated the production of yellow, orange, and red pigment by M. purpureus and P. purpurogenum using orange pomace. They have reported significant production of red pigment by P. purpurogenum. Fungi can produce pigments with different colors and eliminate seasonal limitations associated with natural pigment production from vegetables and fruits. However, mycotoxins produced by fungi are the critical drawback of fungal pigment production. Lopes et al. (2013) have studied the effect of substrate on pigment and mycotoxins production. They have studied the pigment production capacity of 24 different fungi, out of these 24 only four fungi, namely P. chrysogenum IFL1 and IFL2, F. graminearum IFL3, M. purpureus NRRL 1992, were capable of pigment production on different agroindustrial wastes, including grape pomace. They have reported production of pigment on grape pomace only for cultivation with P. chrysogenum IFL1. Different fungi, different levels of mycotoxins such as diacetoxyscirpenol, citrinin, and fusarenone X, were obtained for cultivation with other waste. They have reported that avoiding the mycotoxin generation is possible by adjusting the culture media and condition. de Oliveira et al. (2020) have studied the application biofilm produced from T. amestolkiae submerged cultivation. They have reported the biofilm produced from fermentation broth containing the pigments showed good antioxidant activity and could be used for food packaging. Hormones, phenolic compounds, fatty acids, protein-rich biomass, and biofuels are other valuable products produced from fruits pomace by fungal cultivation. Table 5 shows the other products that have been produced by the fungal cultivation of fruits pomace. Table 5 strain.

Valorization of fruits pomace by fungal cultivation, products types, and fungi

Product

Fungus strain

Fermentation mode

R. miehei P. chrysosporium C. fimbriata R. oryzae T. harzianum P. chrysosporium

SSF SSF SSF SSF SSF SSF

Reference

Apple pomace Phenolic compounds Fruity aroma Volatile compounds Protein-rich biomass

Zambrano et al. (2018) Ajila et al. (2012) Bramorski et al. (1998) Christen et al. (2000) Ortiz-Tovar et al. (2007)

Continued

544

Current Developments in Biotechnology and Bioengineering

Table 5 Valorization of fruits pomace by fungal cultivation, products types, and fungi strain—cont’d Fermentation mode

Reference

T. harzianum Co-culture of T. harzianum, A. sojae, and Saccharomyces cerevisiae

SmF SmF

Ucuncu et al. (2013) Evcan and Tari (2015)

F. moniliforme G. fujikuroi Rhizopus sp. A. niger M. isabellina NRRL 1757 T. harzianum

SSF/SmF

De Oliveira et al. (2017)

SmF SSF SmF SmF

Ibarruri and Herna´ndez (2019) Alemu (2013) Carota et al. (2018) Ucuncu et al. (2013)

SSF

Dulf et al. (2020)

SSF

Zambrano et al. (2018)

Product

Fungus strain

Bioethanol

Orange pomace Plant hormone Protein-rich biomass Microbial oil Bioethanol Grape pomace Fatty acid Phenolic compounds

A. elegans U. isabellina R. miehei

The previous research shows the possibility of producing multiple products from fruits pomace by various filamentous fungi, which fits the biorefinery concept. Thus, it can be hypothesized that a biorefinery can be established by integrating fungal processing into the fruit processing industry (Fig. 3).

4. Bioethanol industry wastes The bioethanol industry has a global production of 114 billion L ethanol in 2019, and it is the most produced liquid biofuel in the transportation sector (REN21, 2020). Bioethanol can be produced from different raw materials. First-generation ethanol is produced from sugar- or starch-based crops, while second-generation ethanol is produced from nonedible lignocellulosic sources such as agricultural residuals. This section focuses on valorizing first-generation ethanol wastes as the most industrially established bioethanol process. Dry-grind bioethanol plant is the most popular ethanol process in the world. In this process, the hexose sugars are converted into ethanol and CO2 in a fermenter. Then, the ethanol is separated from the fermentation residuals in the distillation column (Lennartsson et al., 2014; Ferreira, 2015). This residual stream is called whole stillage. The whole stillage is sent to a decanter, and the solid fraction, wet distillers grain (WDG), separated from the liquid fraction, thin stillage. The latter is concentrated in evaporators and mixed with WDG before being sent to a drier to produce dried distillers grains with solubles (DDGS). WDG and DDGS are commonly used as animal feed due to their nutrient content, such as carbohydrates, lipids, and proteins (Ferreira, 2015). WDG has

Chapter 18 • Versatility of filamentous fungi in novel processes

545

FIG. 3 Fungal biorefinery for the valorization of apple, orange, and grape pomace.

a short shelf life due to its high moisture content, limiting the application as a product and otherwise requiring treatment to avoid a negative impact on the environment. Therefore, the dried product DDGS more common, although it requires an energy- and costintensive process. On the other hand, animal feed ingredients’ production rate and demand are another concern that produces more demand resulting in waste. In order to produce 1 L of ethanol, ca 20 L stillage is produced (Ferreira, 2015; Rocha-Meneses et al., 2017). It means that for an ethanol plant producing 200 million L ethanol/year, 4 billion L stillage/year is produced. This nutrient-rich material contains fibers, proteins, carbohydrates. The content of stillage from an ethanol plant using wheat grains as raw material is shown in Table 6 (Ba´tori et al., 2015). Rocha-Meneses et al. (2017) stated that the bioethanol production wastes create an environmental concern with its BOD level ranging from 10 to 100 g O2 L
1. There have been numerous research studies about the valorization of bioethanol industry waste, and microbial conversion via filamentous fungi is one alternative way. Filamentous fungi can grow on various materials and produce a wide range of products (Ferreira, 2015; Nair, 2017). Unlike the common bakery yeast used in ethanol fermentation, filamentous fungi are capable of consuming xylose sugars. The reactions for glucose and xylose conversion to ethanol are shown in Eq. (1) (Smith et al., 2006) and Eq. (2) (McMillan, 1993):

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Current Developments in Biotechnology and Bioengineering

Table 6 Composition of wheat-based whole stillage (Ba´tori et al., 2015). Parameter

Value

pH Total solids (% w/w) Suspended solids (% w/w) Sieved solids (% w/v) Crude protein (% w/w)a Crude protein (% w/w)b

4.3  0.0 15.6  0.1 8.8  0.0 3.2  0.2 32.0  0.6 15.1  3.9

Dissolved monomers (g/L) 0.4  0.1 1.6  0.1 0.7  0.0 1.4  0.1 12.0  0.1 1.7  0.0 0.6  0.1 0.7  0.1

Acetic acid Arabinose Ethanol Glucose Glycerol Lactic acid Xylitol Xylose Dissolved saccharides (g/L)c

6.3  0.1 1.7  0.0 12.0  0.3 2.4  0.1 9.7  0.1

Arabinose Galactose Glucose Mannose Xylose Sugar polymers (g/L)d

1.8  0.1 0.3  0.0 4.7  0.1 0.6  0.0 3.6  0.1

Arabinan Galactan Glucan Mannan Xylan a

Based on dry total solids. Based on dry sieved solids. c Dissolved monomers included. d From dry sieved solids. b

C6 H12 O6 ƒƒƒƒƒ! 2CH2 H5 OH + 2CO2

(1)

3C5 H10 O5 ƒƒƒƒƒ! 5CH2 H5 OH + 5CO2

(2)

Hence, they have been an interest of research in the valorization of fermentation residuals (Ferreira, 2015). Ferreira et al. (2014) stated that protein-rich biomass was produced from thin stillage using five different food-grade fungi. Among these five strains (Neurospora intermedia, Aspergillus oryzae, Fusarium venenatum, Monascus purpureus, and Rhizopus sp.), N. intermedia and A. oryzae provided the best result in terms of bioethanol (5 g/L) and biomass production (19 g/L), respectively. This indicates the importance of fungus strain toward the

Chapter 18 • Versatility of filamentous fungi in novel processes

547

value-added product. Besides, filamentous fungi growth reduced the total solids in the remaining liquid, as well as lactic acid and glycerol. The total solids content of the medium decrease as the fungi convert polymeric sugars and other components of thin stillage into metabolites and fungal biomass. Besides, the fungal cultivation results in biomass which is entangled with the solids in the medium. Therefore, after biomass separation, the remaining liquid has less total solids concentration (Ferreira et al., 2014). In a similar study, it was stated that N. intermedia growth on thin stillage in airlift reactor (26 L) resulted in biomass which comprises 50% (w/w) protein (including essential amino acids) and 12% lipids (i.e., omega-3 and -6 fatty acids) (Ferreira et al., 2015). Fungal biomass produced on thin stillage can be used as animal feed or fish feed ingredient as protein content is up to 50% (Ferreira et al., 2015). In another study, the whole stillage was valorized by N. intermedia cultivation, where the ethanol production was higher than S. cerevisiae. A two-stage process was implemented using two different fungi strains, resulting in 7.6 g/L ethanol and 5.8 g/L biomass with 42% protein content (Ba´tori et al., 2015). The techno-economic perspective of filamentous fungi integration to 1st generation ethanol plant was investigated by Rajendran et al. (2016). The energy consumption of the process decreased by filamentous fungi integration, particularly in evaporator units. In a similar process, (Bulkan et al., 2020) emphasized that the filamentous fungi integrated process has the potential to provide protein-rich food and feed ingredients such as fish feed, resulting in an improved and robust economy toward raw material/product price fluctuations in comparison to conventional bioethanol plant. Downstream processing of the fungal biomass can be carried out in different ways. Sieving and the following drying process are assumed in previous experimental studies (Ferreira, 2015), while centrifugation replaced sieving in some studies (Rasmussen et al., 2014; Rajendran et al., 2016; Bulkan et al., 2020). Koza et al. (2017) studied different dewatering strategies for the fungal biomass separation, including “gravity and centrifugal sedimentation, gravity screening, a belt filter, a filter press, and centrifuge filtration.” Gravity screening coupled with a filter centrifuge is reported to result in biomass with maximum 30% solids, due to the internal water content of the fungi cell. A following thermal drying carries up the solid concentration to 90%. Metabolites produced by fungi can be recovered from the liquid remaining after fungal biomass separation. The liquid fraction is proposed to be re-used in the liquefaction unit of the process (Lennartsson et al., 2014). In some studies, it is considered to be used as backset water partially, while the rest is re-used following a multi-evaporation step (Ferreira et al., 2015; Rajendran et al., 2016; Bulkan et al., 2020). The re-use of the liquid as process water allows the ethanol produced by filamentous fungi to mix to fresh feed for bakery yeast and end up in the distillation column with the ethanol produced by bakery yeast (Rajendran et al., 2016; Bulkan et al., 2020). The economy of the bioethanol plant has the potential to be improved by enzyme production using thin stillage as raw material, according to Shahryari et al. (2019). Amylase and xylanase were produced by N. intermedia on wheat-based thin stillage. Apart from Ascomycetes and Zygomycetes, Basidiomycetes were also used for stillage valorization. Pena et al. (2012) utilized white-rot fungi in order to valorize DDGS and whole stillage

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Current Developments in Biotechnology and Bioengineering

while producing ligninolytic enzymes. Co-cultures of microorganisms are studied in order to reach the target product, i.e., feed with balanced nutrients or improved wastewater remediation of the bioethanol process (Rodrigues Reis et al., 2018). Pietrzak and KawaRygielska (2019) reported that utilization of co-cultures of edible filamentous fungi and fodder yeast Candida utilis on corn thin stillage valorization resulted in biomass comprised essential amino acids. In addition to biomass, a potential feed ingredient, ethanol, and amylase enzyme were produced. Additionally, ethanol production in yeast fermenters was improved when the liquid left after co-culture cultivation used as backset water in the primary ethanol process. There have been several studies about the production of polyunsaturated fatty acids by filamentous fungi grown on thin stillage reported by Reis et al. (2017). Liang et al. (2012) studied eicosapentaenoic acid (EPA) production from corn thin stillage and obtained 243 g/L day EPA yield at the 9th day of Pythium irregulare cultivation. The produced oil can be further utilized in feed/food supplements (Liang et al., 2012; Reis et al., 2017). Production of biocrude is another application for fungal biomass produced from thin stillage. Suesse et al. (2016) stated that similar yield and quality of biocrude could be obtained by using Rhizopus oligosporus as feedstock compared to biocrude from microalgae. Among the various studies, bioethanol industry wastewater can be converted into various valueadded products, while the bioconversion of nutrients results in naturally treated postcultivation wastewater, which has the potential to be recycled as process water.

5. Fish processing industry waste Fish processing products are an essential source of commercial products in countries such as China, India, Thailand, Indonesia, Canada, United States of America. Although the types of fish processed/consumed vary depending on the geographical location of the countries, fish species such as salmon, herring, tuna, and shellfish can be given as examples in the world. The fish processing process may differ depending on the fish type and product type in the facilities. Standard processes in industry are filleting, freezing, drying, fermenting, canning and smoking. In fish fillets and similar production processes, solid components (head, internal organs, etc.), liquids (e.g., blood), and processing water (salt brine, filleting water, etc.) could be released. The biochemical compositions of the fish processing wastes vary according to fish species, fishing season, and process type (additives, processing water source) (Aidos et al., 2002). These wastewaters having a high content of solids which are mainly nitrogen (0.5–8.4 g/kg), phosphorus, oil (up to 43 g/kg), and have high BOD5 (up to 6000 mg/L) and COD (up to104,000 mg/L) levels (Sathivel et al., 2003; Sar et al., 2020a, 2021). The salt content of fish waste could be high due to the salting process in the fish filleting process. However, this salt content (1.2%) in fish waste is much less than in fish fillets (2.4%) (Aidos et al., 2002). Fish processing wastes are an important source of pollution for the environment, and the wastewaters are directed to waste management. Except that, offal disposals (head and internal organs) can be considered as feed because of having high-protein content. Since total mercury and selenium can accumulate in the kidneys and liver in general, fish internal organs can be expressed as non-edible according to the heavy metal content

Chapter 18 • Versatility of filamentous fungi in novel processes

549

(Julshamn et al., 1987). Therefore, elemental analysis is of great importance in the evaluation of internal organs as feed. Biodiesel or biogas can be produced using the fish industry wastes rich in nitrogen and carbon sources. Typically, the fish waste having high total solids is converted to biogas/methane production through anaerobic digestion. Herein, methanogenesis can be performed through fungi (Eurotiales, Sordariales, Saccharomycetales, Sporidiales, Capnodiales, Microascales, Wallemiales, and Tremellales), bacteria (Clostridia, € cker et al., 2020). Oil extracted from disSynergistia), and archaea (Methanomicrobia) (Bu carded parts of fish or fish waste can be evaluated for biodiesel production (Yahyaee et al., 2013; Garcı´a-Moreno et al., 2014; Madhu et al., 2014; Ching-Velasquez et al., 2020). Herein, ultrasound or microwave-assisted extraction, supercritical fluid extraction, and enzymatic hydrolysis methods can be used for oil extraction from fish waste (Ivanovs and Blumberga, 2017). In addition, natural pigments can be recovered from seafood (such as shrimp, lobster, crab, crayfish, trout, and salmon) having carotenoids (Shahidi and Brown, 1998; Simpson, 2007). As an alternative to conducted processes, value-added products by filamentous fungi have been investigated from the fish industry wastes (Fig. 4). Protein-rich edible biomass can be produced through some filamentous fungi and evaluated as high-value animal feed. For this purpose, it was reported that biomass, containing 35%–65% protein produced from fish processing wastes through Aspergillus oryzae and Rhizopus oryzae, can be an alternative to biogas production and waste treatment with fungal culture process integration (Sar et al., 2020a, 2021). Some fungal species can naturally produce pigments. Lopes et al. (2013) screened the 24 different fungal strains and determined four pigment producer fungal strains (Penicillium chrysogenum, P. vasconiae, Fusarium graminearum, Monascus purpureus) using agro-industrial waste, including fish meal. Natural pigments can be potentially used in textile, food, and pharmacy industries. White-rot fungi have the ability to degrade some environmental pollutants (Moredo et al., 2003). Among them, Phanerochaete chrysosporium can grow rapidly and produce ligninolytic enzymes such as manganese peroxidase (MnP), lignin peroxidase (LiP), and laccase (Barclay et al., 1993; Hatakka, 1994). Gassara et al. (2010) evaluated the ligninolytic enzyme production using industrial wastes by P. chrysosporium. Ligninolytic enzymes can be produced in pomace, brewery wastes, fishery, and pulp and paper industry sludge, while their activities were found to be low in fish wastes (Gassara et al., 2010).

FIG. 4 Valorization of fish industry waste by filamentous fungi.

550

Current Developments in Biotechnology and Bioengineering

Filamentous fungi (Trichoderma and Penicillium) can also be used in the hydrolysis of fish wastewaters rich in keratin and collagen due to their proteolytic activity (Martins et al., 2014). Similarly, significant reductions in the total solids, COD, and nitrogen amounts were achieved by Aspergillus oryzae and Rhizopus oryzae strains when cultivated for fungal biomass production (Sar et al., 2020a, 2021). Therefore, fish processing wastes for fungal biomass and pigment production can be transferred to fungal culture processes, providing biological treatment of the wastes. Fish waste from the fish processing industry, rich in lipids and proteins, has been generally evaluated for low-value animal feed products and methane production (Cirne et al., 2007; Nges et al., 2012; Cadavid-Rodrı´guez et al., 2019). As an alternative to these productions, fish processing wastes can be directed to fungal culture processes for fungal biomass and pigment production.

6. Oil processing industry waste Vegetable oils are generally obtained from seeds or beans via pressing or extraction methods. Soybean, rapeseed, sunflower, groundnut, cottonseed, coconut, palm, olive, corn have been traditionally consumed and commercially traded in many countries. Among them, olive and palm oil productions have been turned into automated systems instead of the traditional pressing process, and plenty of oily wastewater has been generated during the newly generated systems.

6.1 Olive oil processing industry Olive oil products as an essential vegetable oil play a significant role in the Mediterranean Basin market (Italy, Greece, Syria, Tunisia, Turkey, Morocco, Algeria, Portugal, and Argentina) (Lopez-Villalta, 1998). Olive oil is obtained by processing olive fruit in processes called discontinuous (pressing) or continuous (centrifugation) (Dermeche et al., 2013; Sar et al., 2020b). The oldest and most basic method for olive oil production is a discontinuous pressing process. In this process, a small amount of water is required to separate the oil from other components. Olive pomace consisting of olive fruits and seeds and less amount of olive oil mill water (OOMW; 40–60 L/100 kg of olives) are released along with the production of olive oil by the traditional method. Although a small amount of waste is generated, it has a higher COD amount. It also has some disadvantages, such as non-continuous processes and required manpower. Due to the disadvantages of the traditional olive oil production method, many facilities have been switched to two- or three-stage continuous processes. More hot water is used in continuous processes, and then three different fractions (olive oil, OOMW, and olive pomace) are released by following centrifugation processes. Because of the high amount of water used, a greater amount of wastewater (80–120 L/100 kg olives) is released. The three-phase system is the most widely used method because more olive oil can be produced in a short time, despite the high water consumption. OOMW is slightly acidic, contains sugars, nitrogenous compounds, fatty acids with residual oil, tannins, lignins, organic and phenolic compounds, and has high BOD and COD concentrations (Sayadi and Ellouz, 1995; Rinaldi et al., 2003; Hentati et al., 2016;

Chapter 18 • Versatility of filamentous fungi in novel processes

551

Sar et al., 2020b). Similarly, olive pomace is also rich in sugars, polyphenols, and oil (Alburquerque et al., 2004; Sec¸meler et al., 2018). The mainly phenolic compounds in OOMW are phenyl acids (vanillic acid, caffeic acid, p-cumaric acid, ferulic acid), phenyl alcohols (hydroxytyrosol and tyrosol), flavonoids (luteolin), and oleuropein which are potential inhibitory materials (Romeo et al., 2019). Phenolic compounds containing these wastes are important environmental pollutant sources regarding their management and disposal (Paulo and Santos, 2021). For waste minimization, various extraction methods for the recovery of phenolic compounds have been investigated, and their potential for use in areas such as food, pharmacology, and health have been researched (Torrecilla and Cancilla, 2021). In addition, both various metabolite productions and waste treatments by microorganisms have been conducted. OMW can be viewed as a suitable growth medium for lipase production because it contains olive oil residuals and simple and complex sugars. Fungal lipase production has been extensively investigated by the genera Geotrichum, Penicillium, and Fusarium (Salgado et al., 2020). Some lipolytic fungal/yeast species such as Aspergillus oryzae, Aspergillus niger, Candida cylindracea, Geotrichum candidum, Penicillium citrinum, Rhizopus arrhizus, Rhizopus oryzae, and Yarrowia lipolytica have been generally screened and cultivated in the olive waste by-products for lipase production (Lotti et al., 1998; D’Annibale et al., 2006; Gonc¸alves et al., 2009; Lopes et al., 2009; Abrunhosa et al., 2013). Among them, C. cylindracea (0.46 U/mL) and G. candidum (0.52 U/mL) had high volumetric lipase activities, while P. citrinum strains (4.58–5.42 U/L/h) also had high enzyme productivity (D’Annibale et al., 2006). Lipase production can be affected by growth conditions and media components such as pH, initial COD levels, supplementations (such as nitrogen, oil), and cultivation types (submerged, bioreactors) (reviewed in Table 7). D’Annibale et al. (2006) suggested that supplementation of NH4Cl (2.4 g/L) and olive oil (3 g/L)

Table 7 Lipase production by filamentous fungi from olive oil processing wastes and comparison of lipase activity with COD. Strain

COD levels

Lipase production

References

C. cylindracea NRRL Y-17506 C. cylindracea NRRL Y-17506

43 g/L 50 g/L

D’Annibale et al. (2006) Brozzoli et al. (2009)

C. cylindracea CBS 7869 C. cylindracea CBS 7869 G. candidum NRRL Y-553 P. citrinum ISRIM 118 A. ibericus MUM 03.49 A. ibericus MUM 03.49 Y. lipolytica W29-N6 Magnusiomyces capitatus JT5 Magnusiomyces capitatus JT5

115 g/L 179 g/L 43 g/L 43 g/L 97 g/L 97 g/L 19 g/L 55 g/L 55 g/L

0.46 IU/mL 18.7a 20.4a 2200 U/L 877 U/L 0.52 IU/mL 0.38 IU/mL 2927  54 U/L 8319  33 U/L 78 U/L 1.4 3.96 a

a

Lipase activity was obtained in bioreactors.

a

Gonc¸alves et al. (2009) Gonc¸alves et al. (2009) D’Annibale et al. (2006) D’Annibale et al. (2006) Abrunhosa et al. (2013) Abrunhosa et al. (2013) Lopes et al. (2009) Salgado et al. (2020) Salgado et al. (2020)

552

Current Developments in Biotechnology and Bioengineering

improved the enzyme activity of C. cylindracea NRRL Y-17506 strain. Further studies showed that besides the addition of nitrogen and oil, lipase activity of the same strain increased from 1.8 U/mL to 18.7 U/mL and 20.4 U/mL with uncontrolled pH or pH control (below 6.5), respectively (Brozzoli et al., 2009). Geotrichum candidum can be easily produced in an OMW-based medium and produce lignin-modifying enzymes concomitantly lipase enzyme (Assas et al., 2000; Gopinath et al., 2003; D’Annibale et al., 2006; Asses et al., 2009). Aspergillus species are also promising microorganism for lipase and proteinase production (Abrunhosa et al., 2013; Oliveira et al., 2016; Salgado et al., 2016). These enzymes are important in the laundry as they are the main enzymes of the detergent formulation for removing oily and proteinaceous food stains (Grbav ci  c et al., 2011). Salgado et al. (2016) determined that high lipase (1253 U/L) and protease (3700  124.3 U/L) activities were achieved by the combination of Aspergillus species (A. ibericus, A. uvarum, and A. niger) when cultivated in olive mills and wineries effluents (1:1). Olive oil mill water (OOMW) can be considered as a potential substrate for microbial fermentation processes because of its high COD and composition regarding sugars and oil content. For this purpose, Sar et al. (2020b) examined the efficiency of fungal biomass production from OOMW through various filamentous fungi (Aspergillus oryzae, Rhizopus delemar, and Neurospora intermedia) and determined that the high biomass production (8.4 g/L), which contains 15%–49% protein, was realized by A. oryzae. The compositional of fungal biomass produced by different fungi (A. niger, Paecilomyces variotii, Pleurotus floridae, P. eryngii, P. ostreatus, P. sajor-caju) contains 13%–14% protein, 6% fiber, vitamin A, vitamin E, nicotinic acid, calcium, potassium, iron, and unsaturated fatty acids. Although microbial biomass can be produced from OMWW, additional studies are needed before it can be used as animal feed due to its unknown beneficial health effects. The total amount of phenolic compounds, organic loads, and COD have been successfully reduced and decolorized using olive oil wastewater via microbial processes (D’Annibale et al., 2004; Abrunhosa et al., 2013). Thus, biological waste treatment/ improvement has also been achieved along with microbial culture studies. Usually, there has not been a specific regulation regarding olive oil mill wastewater discharge in Mediterranean countries. OOMW is generally treated using a slow rate land treatment system (Erses Yay et al., 2012). OOMW is a rich substrate source having metal ions (K, Ca, Na, Fe, Cu, Zn, Mn) and inorganic anions (Cl
, H2PO4
, F
, SO42
and NO3
) (Arienzo and Capasso, 2000). Although macro and microelements are nutrient sources for agriculture or microorganisms, extensive metal ions with inorganic ions related to phenols and pollutants need purification. For this purpose, a filtration system needs to develop for removing and recovering metal ions. Alternatively, another way could be conceivable that olive oil industry by-products can be diverted to microbial production systems. In this way, it could be ensured that OOMW can be evaluated as a raw material for enzyme (mainly lipase) and fungal biomass production, and its negative effect on the environment can be reduced.

Chapter 18 • Versatility of filamentous fungi in novel processes

553

6.2 Palm oil processing industry Palm oil is extracted from the ripened mesocarp of the fruits of the oil palm tree (Elaeis guineensis). The oil palm fruit is a drupe formed in tight spiky bunches (Ngando-Ebongue et al., 2012). The five leading producing countries are Indonesia, Malaysia, Thailand, Colombia, and Nigeria. Among them, Indonesia and Malaysia produce about 80% of the world’s palm oil and export more than 90% of their palm oil production (Tan and Lim, 2019). Similar to the olive oil process, the processing of palm oil releases excessive amounts of palm oil industry wastes which are palm oil mill effluent (POME), empty fruit bunches (EFBs), oil palm trunks (OPTs), and oil palm fronds (OPFs) (Mohammad et al., 2012). POME, containing some sugars, fat, and lignocellulosic waste, has high COD and BOD values (Oswal et al., 2002). The POME is an important source of phenolic compounds such as gallic acid, protocatechuic acid, p-hydroxybenzoic acid, caffeic acid, syringic acid, vanillic acid, p-coumaric acid, and ferulic acid (Chantho et al., 2016). Various filamentous fungi (Aspergillus, Penicillium, Rhizopus, Mucor, Phanerochaete, Trichoderma, Myrothecium, and Sporotrichum) grown in POME can produce industrial enzymes (cellulase and lipase) (Prasertsan et al., 1992; Rashid et al., 2009; Suseela et al., 2014; Moya-Salazarm et al., 2019; Rachmadona et al., 2021). Concomitantly to enzyme production, fungal biomass containing 40% protein by Aspergillus oryzae can be grown in POME (Barker and Worgan, 1981). A. oryzae cultivation also contributes to significant reductions in BOD (85%) and COD (75%–80%) values (Barker and Worgan, 1981). Biovalorization in terms of decolorization and reduction of COD values can be performed by using fungal strains (Aspergillus fumigatus and Trichoderma viride) (Abdul Karim and Ahmad Kamil, 1989; Mohammad et al., 2012; Neoh et al., 2013). POME contains high levels of zinc, manganese, and iron (Shavandi et al., 2012), as well as high BOD and COD content. As POME can be evaluated for enzyme (mainly lipase) production, reduction of heavy metal values can also be evaluated in addition to BOD and COD removals after fungal cultivations.

7. Potato processing industry waste Starchy agricultural products such as corn, wheat, rice, potatoes, cassava are preferred in the food industry for various purposes such as the primary food source or obtaining refined products. Among these starchy products, potatoes are both widely grown worldwide and processed on a large scale in the food industry for various purposes, such as chips and starch. During the processing of potatoes in the food industry, different types of potato processing by-products (potato pulp, potato wastewater, potato liquor, potato peel) are generated. During the potato chips production process, an excessive amount of potato processing waste (PPW) is generated by cleaning, cutting, slicing, washing, frying, and salting steps (Kot et al., 2020). Potato liquor from the potato starch production process is heated at 110°C to remove proteins. The remaining potato peel liquor (PPL) € gerl, 1994; Bergthis rich in protein and contains a high percentage of solid material (Schu aller et al., 1999). The potato wastes contain starch, cellulose, hemicellulose, lignin,

554

Current Developments in Biotechnology and Bioengineering

fermentable sugars, proteins with a high COD, BOD, and solids (Malladi and Ingham, 1993; Ga´spa´r et al., 2007; Ahokas et al., 2014). Mainly starch and other biocompounds such as damaged starch, protein, and amylose can be recovered from PPWs (Devereux et al., 2011). The chemical composition of PPWs provides a good carbon and nitrogen source for microbial processes (Fig. 5, Table 8). For this purpose, many researchers have focused on microbial productions such as ethanol, organic acid, and fungal biomass (Jin et al., 2005; Abanoz et al., 2012; Sumer et al., 2015; Souza Filho et al., 2017b, 2019; Palakawong Na Ayudthaya et al., 2018) using various potato wastes. Microorganisms that can

FIG. 5 Evaluation of potato processing wastes in fungal production processes.

Table 8 fungi.

Production of biometabolites from starchy products through filamentous

Metabolite

Bioproduct

Fungal strain

Enzyme

amylase

Aspergillus niger Aspergillus niger Rhizopus oryzae Rhizopus arrhizus Rhizopus oryzae Aspergillus oryzae

cellulase Organic acid

Fungal biomass

Lactic acid

References Abouzied and Reddy (1986) Jin et al. (1998), Izmirlioglu and Demirci (2016a,b) Julia et al. (2016), Verma and Kumar (2019) Rosenberg and Krisˇofı´kova´ (1995), Huang et al. (2003), Huang et al. (2005), Jin et al. (2005)

Jin et al. (1998), Jin et al. (1999), Jin et al. (2005), Souza Filho et al. (2017b)

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synthesize several enzymes, such as amylase and cellulase, should be included in microbial processes since PPW contains starch and cellulose. Starch-degrading enzymes, which are α-amylase, glucoamylase, and α-glucosidase, are regulated by a pathway-specific transcription factor, AmyR (Kato et al., 2002). Cellulases are produced as a multicomponent enzyme system which are endocellulases (endoglucanases), exocellulases (exocellobiohydrolases or exoglucanases), and cellobiase (β-glucosidase) (Cao and Tan, 2002; Lockington et al., 2002). The xlnR gene is the gene encoding enzymes of the cellulolytic enzymes pathway and regulates the endo-cellulase genes eglA and eglB (Van Peij et al., 1998) and exocellulase genes cbhA and cbhB (Gielkens et al., 1999) in Aspergillus niger. S. cerevisiae, which is widely used in ethanol and single-cell protein production, can consume simple sugars such as glucose. Since S. cerevisiae cannot be naturally produced in PPW, it should not be used in starch and cellulose-containing systems. The inclusion of microorganisms such as S. cerevisiae and E. coli in the process involving PPW requires additional costincreasing processes such as hydrolysis. Instead, filamentous fungi, which can naturally hydrolyze starch and cellulose, can be integrated into potato waste-containing systems and used to produce microbial products. Ethanol production from potato starch or potato waste can be performed by amylolytic fungus, Aspergillus niger, and its co-culture with S. cerevisiae (Abouzied and Reddy, 1986; Izmirlioglu and Demirci, 2016a,b). The filamentous fungi can have different metabolite and enzyme activities to hydrolyze the starch and produce metabolites through simultaneous saccharification and fermentation (Jin et al., 1998, 2005; Richter and Berthold, 1998; Oda et al., 2002). Therefore, edible filamentous fungi mainly were studied for the determination of their capacities for organic acid productions. Lactic acid is a valuable industrial organic acid used in the food, pharmaceutical, leather, and textile industries (Huang et al., 2005). Biological production of lactic acid has been widely carried out by some bacteria (e.g., Lactobacillus and Lactococcus) and fungi (e.g., Rhizopus) species (Huang et al., 2005; Li and Cui, 2010). Fungal cultivation is more advantageous than bacterial fermentation due to their ability to consume different types of raw/waste substrates, require no additional supplements, do not require pH adjustment, and easy harvest of fungal biomass (Soccol et al., 1994; Rosenberg and Krisˇofı´kova´, 1995; Huang et al., 2005). Fungal biomass can also be assessable as a valuable product due to its high protein content. For this purpose, Jin et al. (1999) evaluated 30 different microfungal strains for screening their amylolytic activities and biomass production capacities and selected Aspergillus oryzae, Rhizopus oligosporus, and R. arrhizus regarding the biomass production yield (4.3–5.6 g/L). Further studies showed that R. arrhizus and R. oryzae could be successfully lactic acid (0.94–0.97 g/g of starch) and fungal biomass (17–19 g/L) producers, respectively Jin et al. (2005). Similarly, many researchers suggested Rhizopus arrhizus strains to have a high capacity for starch saccharification and lactic acid synthesis (Rosenberg and Krisˇofı´kova´, 1995; Huang et al., 2003, 2005). Protein-rich fungal biomass can be produced from potato protein liquor (PPL), concentrated wastewater generated from the starch production process (Souza Filho et al., 2017b). It was determined that the fungal biomass produced by R. oryzae in an airlift

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bioreactor, as above 65 g/L of undiluted PPL, and its protein content was 70% under optimum conditions (Souza Filho et al., 2017b). Similarly, fungal biomass, having 35%–50% protein content, produced by Aspergillus and Rhizopus species can be evaluated as animal feed (Jin et al., 1998, 2005; Souza Filho et al., 2019). COD levels of the potato processing streams were successfully reduced via fungal cultivation concomitantly the metabolite production (Jin et al., 1998; Mishra et al., 2004; Souza Filho et al., 2017b, 2019). Therewith, filamentous fungi species (especially Aspergillus and Rhizopus) can be integrated into the potato waste processes. Souza Filho et al. (Souza Filho et al., 2017a) evaluated different scenarios to analyze the techno-economic and life-cycle assessments of potato peel liquor and suggested that fungal cultivation was economically preferable.

8. Sugar processing industry waste Sugar is one of the most important food products obtained by sugarcane (Saccharum officinarum L.) and sugar beet (Beta vulgaris L. ssp. saccharata) through various processes. During the process, 1 kg sugar production results in by-products such as 0.3–0.4 kg of molasses and a high amount of fibrous residue (Fig. 6) (Ramjeawon, 2004; Botha and von Blottnitz, 2006; Mashoko et al., 2010). Molasses contains fermentable sugars (mainly sucrose and less amount of glucose and fructose) and organic substances (betaine, amino acids, minerals, vitamins, trace elements) (Valli et al., 2012; Nakata et al., 2014). Molasses containing high organic matter is generally preferred as a raw material for various biochemical processes such as ethanol (Akbas et al., 2014; Reis et al., 2020), butanol (Zetty-Arenas et al., 2021), organic acid (Abdel-Rahman et al., 2020), single-cell (Nigam and Vogel, 1991), and miscellaneous productions (Oliveira et al., 2020; Zhang et al., 2021) in industry.

Sugar

Sugar beet

Washing & Cutting

Diffusion

Evaporation

Crystallisation

Molasses

Sugar cane

FIG. 6 A schematic diagram for sugar production and molasses generation from the processing of sugar cane and sugar beet.

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Biofuels, hydrotreated jet fuel (from lipids), and ethanol (from sugars) can be generated by using sugar processing products (Kumar et al., 2018). Molasses has become the primary raw material for ethanol production in Brazil, China, and European countries (Cardona and Sa´nchez, 2007; Tang et al., 2010). Ethanol production (Eqs. 3 and 4) is mainly carried out by the yeast Saccharomyces cerevisiae (Pattanakittivorakul et al., 2019; Wu et al., 2020), while other microorganisms are also used for ethanol production (Sharifia et al., 2008; Yilmaztekin et al., 2008; Akbas et al., 2014). Sucrose ðC12 H22 O11 Þ + H2 O ! Glucose ðC6 H12 O6 Þ + Fructose ðC6 H12 O6 Þ

(3)

Glucose or Fructose ðC6 H12 O6 Þ ! Ethanol ð2C2 H5 OHÞ + 2CO2

(4)

After ethanol production and distillation in such processes, what remains is called vinasse. An excessive amount of vinasse (15 kg) is released by distilling ethanol (1 kg) produced from molasses (Nair and Taherzadeh, 2016). This ethanol industry waste, which is acidic (pH 3.5–5.0), contains a high level of organic materials (50–150 g/L COD) and is a critical pollutant source for the environment (Christofoletti et al., 2013). Various filamentous fungi were included in the system for the valorization of vinasse, and their producibility was investigated (Nitayavardhana et al., 2013; Nair and Taherzadeh, 2016; Karimi et al., 2019). Accordingly, it was determined that Aspergillus oryzae and Neurospora intermedia strains can grow in vinasse, and protein-rich fungal biomass (40%–45% protein content) and extra bioethanol production were detected. Moreover, a significant amount of COD removal was also successful (Nair and Taherzadeh, 2016). Similar studies conducted with Rhizopus strains (R. oryzae and R. oligosporus), it has been reported that fungal biomass produced from vinasse contains high protein, and this fungal biomass can be considered as a commercial protein source for aquatic feeds (fishmeal and soybean meal) (Nitayavardhana et al., 2013; Karimi et al., 2019). According to these studies, ethanol production from molasses, as sugar industry byproduct, could be integrated by a second process to produce fungal biomass. Thus, integrated two processes can become more suitable for enhancing metabolite production yields and improving the valorization of sugar industry byproducts and wastes. Recently, high lipid-containing fungal biomass from sugar industry by-products has been investigated for biodiesel production (Fig. 7). Bento et al. (2020) suggested that fungal biomass production from sugarcane molasses by Mucor circinelloides could be used in biodiesel production depending on its lipid content (29%) and fatty acid composition. Reis et al. (2020) tried to grow Mucor circinelloides in a combination of molasses and vinasse media to assimilate sucrose, glucose, and fructose, and fungal biomass with 25% lipids. Fungal biomass yield and its lipid content (35%) could be enhanced via fungal (Aspergillus sp.) co-cultivation with microalgae (Chlorella sp.) in molasses wastewater (Yang et al., 2019). In addition to ethanol production, molasses can be used for various metabolites through filamentous fungi. The ligninolytic enzyme is a group of lignin peroxidases (LiP), manganese-dependent peroxidases (MnP), and laccase. Ligninolytic enzyme

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FIG. 7 A schematic representation for biodiesel production from lipid-containing fungal biomass.

production by fungi (Phylosticta, Aspergillus, Fusarium, and Penicillium) have been studied. Pant and Adholeya (2007) investigated some isolated fungi to screen their ligninolytic enzyme production activities and determined that Fusarium verticillioides, Aspergillus niger, and Aspergillus flavus had the highest LiP, MnP, and laccase activities, respectively. Similarly, it is widely common to investigate the production of enzymes such as dextranase by Aspergillus fumigatus (Fadel et al., 2020), invertase by A. niger (Veana et al., 2014), βfructofuranosidase by A. tubingensis (Xie et al., 2020), laccase by white-rot fungi (Coriolus versicolor and Funalia trogii) (Kahraman and Gurdal, 2002), phytase by Sporotrichum thermophile (Singh and Satyanarayana, 2008) from molasses. Similar to enzyme production, Pleurotus ostreatus, Flavodon flavus, Geotrichum candidum were reported to be effective in studies on the decolorization of molasses (Kim and Shoda, 1999; Raghukumar and Rivonkar, 2001; Pant and Adholeya, 2007). Sugar industry products can be evaluated as conventional sugar production, synthetic fertilizer, biogas, and alcohol production. The life-cycle assessment analyzes clearly demonstrate the advantage of producing alternative products (ethanol, biogas, animal feed, and fertilizers), with a comparative study for resource savings (Contreras et al., 2009). Alternatively, fungal products can be evaluated considering their high-lipid fungal biomass and enzyme production abilities. For this, filamentous fungi can be integrated into processes containing vinasse generated from ethanol fermentation of molasses and evaluated in microbiological production.

9. Dairy processing industry Cheese whey is an important industrial by-product of the dairy industry during the cheese production process. Approximately 9 L of whey are generated by processing each kg of cheese produced (Kosikowski, 1979). Whey containing 5%–6% lactose, 1% protein, fat, and minerals (especially nitrogen and phosphorus) has high organic load, COD, and €nzle et al., 2008; Prazeres et al., 2012). Since whey is a by-product of milk, BOD levels (Ga it is easily degradable and is challenging to store and transport as it is formed in excess.

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Whey powder having a high concentration of lactose is formed of dried and concentrated whey. Many researchers used cheese whey and whey powder for ethanol production (Eqs. 5 and 6) because of their high carbohydrate content. Typical ethanol producer strain, S. cerevisiae cannot assimilate lactose to ethanol due to the lack of lactose hydrolyzing enzymes. Kluyveromyces and E. coli were reported to produce ethanol from cheese whey and whey powder (Kargi and Ozmıhcı, 2006; Sar et al., 2017a,b, 2019; Alves et al., 2019). In addition, fungi such as Trichoderma reesei, Aspergillus niger, Neurospora crassa, and Fusarium graminearum can assimilate lactose and produce metabolites. Ethanol production from whey by various fungi (Fusarium, Monilia, Neurospora, Mucor, and Paecilomyces sp.) have also been studied, similar to fermentation of yeast and E. coli (Singh et al., 1992). Lactose ðC12 H22 O11 Þ + H2 O ! Glucose ðC6 H12 O6 Þ + Galactose ðC6 H12 O6 Þ

(5)

Glucose or Galactose ðC6 H12 O6 Þ ! Ethanol ð2C2 H5 OHÞ + 2CO2

(6)

Whereas fungal strains exhibited higher ethanol productivity and high sugar tolerance, bioconversion rate is slower than yeast cultivations. Nevertheless, fungal strains can be a potential candidate for ethanol production from lignocellulosic materials thanks to their enzyme (cellulases and xylanases) production capacities (Singh et al., 1992). Similarly, fungal strains can be used in lactose-containing media for ethanol production. Okamoto et al. (2019) investigated the ethanol production capacity of Neolentinus lepideus from cheese whey and expired milk. Enzyme complexes produced by Aspergillus niger for ethanol production can be used for hydrolysis for agroindustrial wastes (whey, sugarcane bagasse, and rice byproducts), and the hydrolysates can be evaluated by ethanol-producing organisms such as S. cereviase via separate hydrolysis and fermentation (SHF) (Rocha et al., 2013). Rocha et al. (2013) reported obtaining higher ethanol yield by enzyme cocktail of A. niger than Trichoderma reesei, and complex enzyme of A. niger was promising in the disposal of dairy industry wastes. Some yeast strains such as Kluyveromyces marxianus, K. fragilis, Candida pseudotropicalis, C. versatilis were able to produce microbial lipid (single cell oil, SCO) (Schultz et al., 2006; Vamvakaki et al., 2010). Similarly, some fungal species (Mortierella isabellina, Thamnidium elegans, Mucor sp., and Fusarium) can synthesize lipase and produce SCO (Mahadik et al., 2002; Vamvakaki et al., 2010; Akpinar-Bayizit et al., 2014; Chan et al., 2018; Roy et al., 2021). Herein, whey can be promising feedstocks for lipid accumulation in fungal biomass (Akpinar-Bayizit et al., 2014; Chan et al., 2018). Lipid and amino acid contents of fungal biomass can be reached up to 24% and 48%, respectively, at the optimum conditions (Chan et al., 2018; Ibarruri and Herna´ndez, 2019). This oily biomass can be suggested for biodiesel production as it contains oleic and palmitic, or in nutraceutical applications, as it contains linolenic acid (Chan et al., 2018). The stages of biodiesel production from biomass of an oleaginous fungus are generally as follows; oil extraction from biomass and obtaining fatty acid methyl esters (FAMEs) by acid-catalyzed transesterification and esterification at 65°C for 8 h (Vicente et al., 2009). Vicente et al. (2009)

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suggested that biodiesel production by direct transformation from fungal biomass without lipid extraction is technically possible and that this process needs to be developed on an industrial scale. Various dairy wastes (such as cheese whey, milk, yogurt, cream) can be converted into fungal biomass, ethanol, and glycerol through A. oryzae and N. intermedia cultivations (Mahboubi et al., 2017b). Dairy industry wastes can also contain high amounts of fat in addition to being rich in lactose and protein. It is even more important to evaluate dairy industry wastes containing high-fat content by microbial processes, but it also makes microbial bioconversion difficult. In order to overcome these difficulties, two-stage continuous cultivation was created using Aspergillus oryzae as fat degrader and Neurospora intermedia as lactose ` me fraiche media, which are fat-rich dairy products (Mahboubi consumer in cream and cre et al., 2017a). A similar application was examined with the same fungal strains in expired milk, and it was reported that A. oryzae produced 11 g/L biomass by degrading fat and proteins; after that N. intermedia produced 7 g/L biomass consuming the remaining lactose (Thunuguntla et al., 2018). The crude protein of A. oryzae and N. intermedia biomass from dairy industry byproducts was around 30%–40% on a dry weight basis, and these protein-rich fungal biomasses can be used as feed (Mahboubi et al., 2017b). An excessive amount of dairy industry waste (50%) has been discharged into the environment without any treatment (Kolev Slavov, 2017; Bosco et al., 2018). Traditionally treatment options, activated sludge processing, is not economically due to its having high organic load and low alkalinity (Asunis et al., 2020). Industry-integrated microbial production processes are insufficient. Therefore, dairy industry wastes/byproducts can be included in fungal growth processes, including fungal biomass production, lipase enzyme, enzyme-complex production for degradation of lignocellulose compounds, and microbial oil production.

10. Conclusions and perspectives Agro-industrial wastes are generated every year in significant quantities. These wastes mostly end up in landfills cause various environmental problems. However, recent studies on cultivation with filamentous fungi has resulted in various value-added products from these wastes. These fungal processes can be integrated into the already established industrial processes. With the integrated process, valuable products are produced by utilizing the agro-industrial wastes as low-cost substrates, which reduce the production cost while eliminating the waste management expenses. Additionally, the environmental problems thereof will be mitigated. Besides, the filamentous fungi integration simplifies the process, e.g., removing the pretreatment step in bioethanol production from lignocellulosic material. It is evident that fungal valorization paves the way for reaching the biorefinery. Although to have the biorefinery within our grasp, scaling-up these waste-based fungal processes to the industrial level is a crucial step. To do so, further studies are required, such as feedstock selection and process optimization, product development, life-cycle assessment, techno-economic analysis, and the role of involved stakeholders.

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Lastly, the main future objective of the fungal biorefinery based on agro-industrial waste could be food production. In the reviewed processes in this chapter, many of the used fungi for chemical production were edible filamentous fungi. By using edible fungi, it would be possible to have edible biomass in addition to produced chemicals. Moreover, since agro-industrial wastes are mainly generated from food production sectors, it has a higher possibility to produce biomass with food-grade quality. Thus, further research is required to develop the process that produces biomass with food-grade quality while producing other chemicals. This could provide an alternative source of food and feed, aiding with global food security.

Acknowledgments €xtverket (Tillva €xtverket) through a European Regional This work was supported by the Tillva Development Fund.

References Abanoz, K., Stark, B.C., Akbas, M.Y., 2012. Enhancement of ethanol production from potato-processing wastewater by engineering Escherichia coli using Vitreoscilla haemoglobin. Lett. Appl. Microbiol. 55 (6), 436–443. Abdel-Rahman, M.A., Hassan, S.E.D., El-Din, M.N., Azab, M.S., El-Belely, E.F., Alrefaey, H.M.A., Elsakhawy, T., 2020. One-factor-at-a-time and response surface statistical designs for improved lactic acid production from beet molasses by Enterococcus hirae ds10. SN Appl. Sci. 2 (4), 573. Abdul Karim, M.I., Ahmad Kamil, A.Q., 1989. Biological treatment of palm oil mill effluent using Trichoderma viride. Biol. Wastes 27 (2), 143–152. Abouzied, M.M., Reddy, C.A., 1986. Direct fermentation of potato starch to ethanol by cocultures of Aspergillus niger and Saccharomyces cerevisiae. Appl. Environ. Microbiol. 52 (5), 1055. Abrunhosa, L., Oliveira, F., Dantas, D., Gonc¸alves, C., Belo, I., 2013. Lipase production by Aspergillus ibericus using olive mill wastewater. Bioprocess Biosyst. Eng. 36 (3), 285–291. Adeleke, A.J., Odunfa, S.A., Olanbiwonninu, A., Owoseni, M.C., 2012. Production of cellulase and pectinase from orange peels by fungi. Nat. Sci. 10 (5), 107–112. €limaa, A.-L., Lo € tjo € nen, T., Kankaala, A., Taskila, S., Virtanen, E., 2014. Resource assessment Ahokas, M., Va for potato biorefinery: side stream potential in northern Ostrobothnia. Agron. Res. 12 (3), 695–704. Aidos, I., van der Padt, A., Luten, J.B., Boom, R.M., 2002. Seasonal changes in crude and lipid composition of herring fillets, byproducts, and respective produced oils. J. Agric. Food Chem. 50 (16), 4589–4599. Ajila, C.M., Gassara, F., Brar, S.K., Verma, M., Tyagi, R.D., Val ero, J.R., 2012. Polyphenolic antioxidant mobilization in apple pomace by different methods of solid-state fermentation and evaluation of its antioxidant activity. Food Bioprocess Technol. 5 (7), 2697–2707. Akbas, M.Y., Sar, T., Ozcelik, B., 2014. Improved ethanol production from cheese whey, whey powder, and sugar beet molasses by “Vitreoscilla hemoglobin expressing” Escherichia coli. Biosci. Biotechnol. Biochem. 78 (4), 687–694. Akpinar-Bayizit, A., Ozcan, T., Yilmaz-Ersan, L., Basoglu, F., 2014. Single cell oil (SCO) production by fusarium species using cheese whey as a substrate. Dairy 64 (2), 111–118. Alburquerque, J.A., Gonza´lvez, J., Garcı´a, D., Cegarra, J., 2004. Agrochemical characterisation of “alperujo”, a solid by-product of the two-phase centrifugation method for olive oil extraction. Bioresour. Technol. 91 (2), 195–200.

562

Current Developments in Biotechnology and Bioengineering

Alemu, T., 2013. Process of optimization and characterization of protein enrichment of orange wastes through solid state fermentation by Aspergillus niger isolate no.5. J. Biol. Sci. 13 (5), 341–348.  Alves, E.d.P., Morioka, L.R.I., Suguimoto, H.H., 2019. Comparison of bioethanol and beta-galactosidase production by Kluyveromyces and Saccharomyces strains grown in cheese whey. Int. J. Dairy Technol. 72 (3), 409–415. Arienzo, M., Capasso, R., 2000. Analysis of metal cations and inorganic anions in olive oil mill waste waters by atomic absorption spectroscopy and ion chromatography. Detection of metals bound mainly to the organic polymeric fraction. J. Agric. Food Chem. 48 (4), 1405–1410. Assas, N., Marouani, L., Hamdi, M., 2000. Scale down and optimization of olive mill wastewaters decolorization by Geotrichum candidum. Bioprocess Eng. 22 (6), 503–507. Asses, N., Ayed, L., Bouallagui, H., Ben Rejeb, I., Gargouri, M., Hamdi, M., 2009. Use of Geotrichum candidum for olive mill wastewater treatment in submerged and static culture. Bioresour. Technol. 100 (7), 2182–2188. Asunis, F., De Gioannis, G., Dessı`, P., Isipato, M., Lens, P.N.L., Muntoni, A., Polettini, A., Pomi, R., Rossi, A., Spiga, D., 2020. The dairy biorefinery: integrating treatment processes for cheese whey valorisation. J. Environ. Manag. 276, 111240. Awasthi, M.K., Ferreira, J.A., Sirohi, R., Sarsaiya, S., Khoshnevisan, B., Baladi, S., Sindhu, R., Binod, P., Pandey, A., Juneja, A., Kumar, D., Zhang, Z., Taherzadeh, M.J., 2021. A critical review on the development stage of biorefinery systems towards the management of apple processing-derived waste. Renew. Sust. Energ. Rev. 143, 110972. Balli, D., Cecchi, L., Innocenti, M., Bellumori, M., Mulinacci, N., 2021. Food by-products valorisation: grape ^te ) as sources of phenolic compounds and fiber for enrichment of tagliapomace and olive pomace (pa telle pasta. Food Chem. 355, 129642. Barclay, C.D., Legge, R.L., Farquhar, G.F., 1993. Modelling the growth kinetics of Phanerochaete chrysosporium in submerged static culture. Appl. Environ. Microbiol. 59 (6), 1887. Barker, T.W., Worgan, J.T., 1981. The utilisation of palm oil processing effluents as substrates for microbial protein production by the fungus Aspergillus oryzae. Eur. J. Appl. Microbiol. Biotechnol. 11 (4), 234–240. Ba´tori, V., Ferreira, J.A., Taherzadeh, M.J., Lennartsson, P.R., 2015. Ethanol and protein from ethanol plant by-products using edible fungi Neurospora intermedia and aspergillus oryzae. Biomed. Res. Int. 2015, 176371. Bento, H.B.S., Carvalho, A.K.F., Reis, C.E.R., De Castro, H.F., 2020. Single cell oil production and modification for fuel and food applications: assessing the potential of sugarcane molasses as culture medium for filamentous fungus. Ind. Crop. Prod. 145, 112141. Bergthaller, W., Witt, W., Goldau, H.-P., 1999. Potato starch technology. Starch-Starke 51 (7), 235–242. Berovic, M., Ostroversˇnik, H., 1997. Production of aspergillus Niger pectolytic enzymes by solid state bioprocessing of apple pomace. J. Biotechnol. 53 (1), 47–53. €hmer, U., Fro € mmel, S., Bley, T., Mu € ller, M., Frankenfeld, K., Miethe, P., 2011. Solid-state fermentation of Bo lignocellulotic materials for the production of enzymes by the white-rot fungus Trametes hirsuta in a modular bioreactor. Eng. Life Sci. 11 (4), 395–401. Bosco, F., Carletto, R., Marmo, L., 2018. An integrated cheese whey valorization process. Chem. Eng. Trans. 64, 379–384. Botha, T., von Blottnitz, H., 2006. A comparison of the environmental benefits of bagasse-derived electricity and fuel ethanol on a life-cycle basis. Energy Policy 34 (17), 2654–2661. Bramorski, A., Soccol, C.R., Christen, P., Revah, S., 1998. Fruity aroma production by Ceratocystis fimbriata in solid cultures from agro-industrial wastes. Rev. Microbiol. 29 (3), 208–212.

Chapter 18 • Versatility of filamentous fungi in novel processes

563

Brozzoli, V., Crognale, S., Sampedro, I., Federici, F., D’Annibale, A., Petruccioli, M., 2009. Assessment of olive-mill wastewater as a growth medium for lipase production by Candida cylindracea in benchtop reactor. Bioresour. Technol. 100 (13), 3395–3402. € cker, F., Marder, M., Peiter, M.R., Lehn, D.N., Esquerdo, V.M., Antonio de Almeida Pinto, L., Konrad, O., Bu 2020. Fish waste: an efficient alternative to biogas and methane production in an anaerobic monodigestion system. Renew. Energy 147, 798–805. Bulkan, G., Ferreira, J.A., Rajendran, K., Taherzadeh, M.J., 2020. Techno-economic analysis of bioethanol plant by-product valorization: exploring market opportunities with protein-rich fungal biomass production. Fermentation 6 (4), 99. Buyukkileci, A.O., Lahore, M.F., Tari, C., 2015. Utilization of orange peel, a food industrial waste, in the production of exo-polygalacturonase by pellet forming aspergillus sojae. Bioprocess Biosyst. Eng. 38 (4), 749–760. ˜ oz, M.A., Pla´cido, J., 2019. Biomethane from fish waste as a source of Cadavid-Rodrı´guez, L.S., Vargas-Mun renewable energy for artisanal fishing communities. Sustainable Energy Technol. Assess. 34, 110–115. Cao, Y., Tan, H., 2002. Effects of cellulase on the modification of cellulose. Carbohydr. Res. 337 (14), 1291–1296. ´ .J., 2007. Fuel ethanol production: process design trends and integration opporCardona, C.A., Sa´nchez, O tunities. Bioresour. Technol. 98 (12), 2415–2457. Carota, E., Crognale, S., D’Annibale, A., Petruccioli, M., 2018. Bioconversion of agro-industrial waste into microbial oils by filamentous fungi. Process Saf. Environ. Prot. 117, 143–151. Casas-Godoy, L., Gonza´lez-Escobar, J.L., Mathis, A.G., Barrera-Martı´nez, I., 2020. Revalorization of untreated Brewer’s spent grain: novel and versatile feedstock to produce cellulases, lipases, and yeast biomass in a biorefinery approach. Biomass Convers. Biorefinery, 1–12. Chan, L.G., Cohen, J.L., Ozturk, G., Hennebelle, M., Taha, A.Y., de Moura Bell, J.M.L.N., 2018. Bioconversion of cheese whey permeate into fungal oil by Mucor circinelloides. J. Biol. Eng. 12 (1), 25. Chantho, P., Musikavong, C., Suttinun, O., 2016. Removal of phenolic compounds from palm oil mill effluent by thermophilic Bacillus thermoleovorans strain A2 and their effect on anaerobic digestion. Int. Biodeterior. Biodegradation 115, 293–301. Ching-Velasquez, J., Ferna´ndez-Lafuente, R., Rodrigues, R.C., Plata, V., Rosales-Quintero, A., TorrestianaSa´nchez, B., Tacias-Pascacio, V.G., 2020. Production and characterization of biodiesel from oil of fish waste by enzymatic catalysis. Renew. Energy 153, 1346–1354. Christen, P., Bramorski, A., Revah, S., Soccol, C.R., 2000. Characterization of volatile compounds produced by Rhizopus strains grown on agro-industrial solid wastes. Bioresour. Technol. 71 (3), 211–215. Christofoletti, C.A., Escher, J.P., Correia, J.E., Marinho, J.F.U., Fontanetti, C.S., 2013. Sugarcane vinasse: environmental implications of its use. Waste Manag. 33 (12), 2752–2761. € rnsson, L., Alves, M.M., Mattiasson, B., 2007. Anaerobic digestion of lipid-rich Cirne, D.G., Paloumet, X., Bjo waste—effects of lipid concentration. Renew. Energy 32 (6), 965–975. Clark, J.H., Deswarte, F.E.I., 2008. The biorefinery concept—an integrated approach. In: Introduction to Chemicals from Biomass. vol. 1. Wiley, pp. 1–20. rez, M., Van Langenhove, H., Dewulf, J., 2009. Comparative life cycle assessContreras, A.M., Rosa, E., Pe ment of four alternatives for using by-products of cane sugar production. J. Clean. Prod. 17 (8), 772–779. D’Annibale, A., Sermanni, G.G., Federici, F., Petruccioli, M., 2006. Olive-mill wastewaters: a promising substrate for microbial lipase production. Bioresour. Technol. 97 (15), 1828–1833. da Costa Maia, I., Thomaz dos Santos D’Almeida, C., Guimara˜es Freire, D.M., d’Avila Costa Cavalcanti, E., Cameron, L.C., Furtado Dias, J., Simo˜es Larraz Ferreira, M., 2020. Effect of solid-state fermentation

564

Current Developments in Biotechnology and Bioengineering

over the release of phenolic compounds from brewer’s spent grain revealed by UPLC-MSE. LWT 133, 110136. da Silva, L.R.I., de Andrade, C.J., de Oliveira, D., Lerin, L.A., 2021. Solid-state fermentation in brewer’s spent grains by fusarium fujikuroi for gibberellic acid production. Biointerface Res. Appl. Chem. 11 (5), 13042–13052. D’Annibale, A., Ricci, M., Quaratino, D., Federici, F., Fenice, M., 2004. Panus tigrinus efficiently removes phenols, color and organic load from olive-mill wastewater. Res. Microbiol. 155 (7), 596–603. ^mara, M.C., Libardi, N., Soccol, C.R., 2017. GibberDe Oliveira, J., Rodrigues, C., Vandenberghe, L.P.S., Ca ellic acid production by different fermentation systems using citric pulp as substrate/support. Biomed. Res. Int. 2017, 5191046. de Oliveira, F., Lima, C.d.A., Lopes, A.M., Marques, D.d.A.V., Druzian, J.I., Pessoa Ju´nior, A., SantosEbinuma, V.C., 2020. Microbial colorants production in stirred-tank bioreactor and their incorporation in an alternative food packaging biomaterial. J. Fungi 6 (4), 264. Dermeche, S., Nadour, M., Larroche, C., Moulti-Mati, F., Michaud, P., 2013. Olive mill wastes: biochemical characterizations and valorization strategies. Process Biochem. 48 (10), 1532–1552. Devereux, S., Shuttleworth, P.S., Macquarrie, D.J., Paradisi, F., 2011. Isolation and characterization of recovered starch from industrial wastewater. J. Polym. Environ. 19 (4), 971–979. Dhillon, G.S., Brar, S.K., Kaur, S., Valero, J.R., Verma, M., 2011. Chitinolytic and chitosanolytic activities from crude cellulase extract produced by A. niger grown on apple pomace through koji fermentation. J. Microbiol. Biotechnol. 21 (12), 1312–1321. Dhillon, G.S., Kaur, S., Brar, S.K., Verma, M., 2012. Potential of apple pomace as a solid substrate for fungal cellulase and hemicellulase bioproduction through solid-state fermentation. Ind. Crop. Prod. 38, 6–13. Dhillon, G.S., Kaur, S., Brar, S.K., 2013. Perspective of apple processing wastes as low-cost substrates for bioproduction of high value products: a review. Renew. Sust. Energ. Rev. 27, 789–805. Dı´az, A.B., de Ory, I., Caro, I., Blandino, A., 2012. Enhance hydrolytic enzymes production by aspergillus awamori on supplemented grape pomace. Food Bioprod. Process. 90 (1), 72–78. Dulf, F.V., Vodnar, D.C., Tos¸ a, M.I., Dulf, E.-H., 2020. Simultaneous enrichment of grape pomace with γ-linolenic acid and carotenoids by solid-state fermentation with Zygomycetes fungi and antioxidant potential of the bioprocessed substrates. Food Chem. 310, 125927. € n, O., 2012. A study on olive oil mill wastewater management in Erses Yay, A.S., Oral, H.V., Onay, T.T., Yenigu Turkey: a questionnaire and experimental approach. Resour. Conserv. Recycl. 60, 64–71. Evcan, E., Tari, C., 2015. Production of bioethanol from apple pomace by using cocultures: conversion of agro-industrial waste to value added product. Energy 88, 775–782. Fadel, M., Motawe, F.H., Roshdy, A.M., 2020. Production of dextranase by aspergillus fumigatus NRC-F103 and its application in cane juice treatment and enhancing ethanol production from sugarcane molasses. Egypt. Pharm. J. 19 (3), 283. FAO, 2021. Global fruit production in 2019, by selected variety (in million metric tons). https://www. statista.com/statistics/264001/worldwide-production-of-fruit-by-variety/. (Accessed 22 May 2022). € gskolan i Bora˚s. Ferreira, J., 2015. Integration of Filamentous fungi in Ethanol Dry-Mill Biorefinery. Ho Ferreira, J.A., Lennartsson, P.R., Taherzadeh, M.J., 2014. Production of ethanol and biomass from thin stillage using food-grade zygomycetes and ascomycetes filamentous fungi. Energies 7 (6), 3872–3885. Ferreira, J.A., Lennartsson, P.R., Taherzadeh, M.J., 2015. Production of ethanol and biomass from thin stillage by Neurospora intermedia: a pilot study for process diversification. Eng. Life Sci. 15 (8), 751–759. Ferreira, J.A., Mahboubi, A., Lennartsson, P.R., Taherzadeh, M.J., 2016. Waste biorefineries using filamentous ascomycetes fungi: present status and future prospects. Bioresour. Technol. 215, 334–345.

Chapter 18 • Versatility of filamentous fungi in novel processes

565

Filippi, K., Georgaka, N., Alexandri, M., Papapostolou, H., Koutinas, A., 2021. Valorisation of grape stalks and pomace for the production of bio-based succinic acid by Actinobacillus succinogenes. Ind. Crop. Prod. 168, 113578. Galanopoulou, A.P., Haimala, I., Georgiadou, D.N., Mamma, D., Hatzinikolaou, D.G., 2021. Characterization of the highly efficient acid-stable xylanase and β-xylosidase system from the fungus Byssochlamys spectabilis ATHUM 8891 (Paecilomyces variotii ATHUM 8891). J. Fungi 7 (6), 430. €nzle, M.G., Haase, G., Jelen, P., 2008. Lactose: crystallization, hydrolysis and value-added derivatives. Ga Int. Dairy J. 18 (7), 685–694. Garcı´a-Moreno, P.J., Khanum, M., Guadix, A., Guadix, E.M., 2014. Optimization of biodiesel production from waste fish oil. Renew. Energy 68, 618–624. Ga´spa´r, M., Ka´lma´n, G., R eczey, K., 2007. Corn fiber as a raw material for hemicellulose and ethanol production. Process Biochem. 42 (7), 1135–1139. Gassara, F., Brar, S.K., Tyagi, R.D., Verma, M., Surampalli, R.Y., 2010. Screening of agro-industrial wastes to produce ligninolytic enzymes by Phanerochaete chrysosporium. Biochem. Eng. J. 49 (3), 388–394. Gielkens, M.M., Dekkers, E., Visser, J., de Graaff, L.H., 1999. Two cellobiohydrolase-encoding genes from aspergillus Niger require D-xylose and the xylanolytic transcriptional activator XlnR for their expression. Appl. Environ. Microbiol. 65 (10), 4340–4345. Gmoser, R., Fristedt, R., Larsson, K., Undeland, I., Taherzadeh, M.J., Lennartsson, P.R., 2020. From stale bread and brewers spent grain to a new food source using edible filamentous fungi. Bioengineered 11 (1), 582–598. Gonc¸alves, C., Lopes, M., Ferreira, J.P., Belo, I., 2009. Biological treatment of olive mill wastewater by nonconventional yeasts. Bioresour. Technol. 100 (15), 3759–3763. Gopinath, S., Hilda, A., Annadurai, G., Anbu, P., 2003. Purification of lipase from Geotrichum candidum: conditions optimized for enzyme production using box–Behnken design. World J. Microbiol. Biotechnol. 19 (7), 681–689. Grbavcic, S., Bezbradica, D., Izrael-Zˇivkovi c, L., Avramovi c, N., Milosavi c, N., Karadzˇi c, I., Knezˇevi cJugovic, Z., 2011. Production of lipase and protease from an indigenous Pseudomonas aeruginosa strain and their evaluation as detergent additives: compatibility study with detergent ingredients and washing performance. Bioresour. Technol. 102 (24), 11226–11233. Grigorevski-Lima, A.L., Da Vinha, F.N.M., Souza, D.T., Bispo, A.S.R., Bon, E.P.S., Coelho, R.R.R., Nascimento, R.P., 2009. Aspergillus fumigatus thermophilic and acidophilic endoglucanases. Appl. Biochem. Biotechnol. 155 (1), 18–26. Hassan, S.S., Williams, G.A., Jaiswal, A.K., 2019. Moving towards the second generation of lignocellulosic biorefineries in the EU: drivers, challenges, and opportunities. Renew. Sust. Energ. Rev. 101, 590–599. Hassan, S.S., Tiwari, B.K., Williams, G.A., Jaiswal, A.K., 2020. Bioprocessing of brewers’ spent grain for production of xylanopectinolytic enzymes by Mucor sp. Bioresour. Technol. Rep. 9, 100371. Hatakka, A., 1994. Lignin-modifying enzymes from selected white-rot fungi: production and role from in lignin degradation. FEMS Microbiol. Rev. 13 (2–3), 125–135. Hentati, O., Oliveira, V., Sena, C., Bouji, M.S.M., Wali, A., Ksibi, M., 2016. Soil contamination with olive mill wastes negatively affects microbial communities, invertebrates and plants. Ecotoxicology 25 (8), 1500–1513. Hours, R.A., Voget, C.E., Ertola, R.J., 1988. Apple pomace as raw material for pectinases production in solid state culture. Biol. Wastes 23 (3), 221–228. Huang, L.P., Jin, B., Lant, P., Zhou, J., 2003. Biotechnological production of lactic acid integrated with potato wastewater treatment by Rhizopus arrhizus. J. Chem. Technol. Biotechnol. 78 (8), 899–906.

566

Current Developments in Biotechnology and Bioengineering

Huang, L.P., Jin, B., Lant, P., Zhou, J., 2005. Simultaneous saccharification and fermentation of potato starch wastewater to lactic acid by Rhizopus oryzae and Rhizopus arrhizus. Biochem. Eng. J. 23 (3), 265–276. € ttner, S., Johansson, A., Gonc¸alves Teixeira, P., Achterberg, P., Nair, R.B., 2020. Recent advances in the Hu intellectual property landscape of filamentous fungi. Fungal Biol. Biotechnol. 7 (1), 16. Ibarruri, J., Herna´ndez, I., 2019. Valorization of cheese whey and orange molasses for fungal biomass production by submerged fermentation with Rhizopus sp. Bioprocess Biosyst. Eng. 42 (8), 1285–1300. Ibarruri, J., Cebria´n, M., Herna´ndez, I., 2019. Solid state fermentation of Brewer’s spent grain using Rhizopus sp. to enhance nutritional value. Waste Biomass Valoriz. 10 (12), 3687–3700. Ivanovs, K., Blumberga, D., 2017. Extraction of fish oil using green extraction methods: a short review. Energy Procedia 128, 477–483. Izidoro, S.C., Knob, A., 2014. Production of xylanases by an Aspergillus niger strain in wastes grain. Acta Sci. Biol. Sci. 36 (3), 313–319. Izmirlioglu, G., Demirci, A., 2016a. Improved simultaneous saccharification and fermentation of bioethanol from industrial potato waste with co-cultures of Aspergillus niger and Saccharomyces cerevisiae by medium optimization. Fuel 185, 684–691. Izmirlioglu, G., Demirci, A., 2016b. Strain selection and medium optimization for glucoamylase production from industrial potato waste by aspergillus Niger. J. Sci. Food Agric. 96 (8), 2788–2795. Jin, B., van Leeuwen, H.J., Patel, B., Yu, Q., 1998. Utilisation of starch processing wastewater for production of microbial biomass protein and fungal α-amylase by aspergillus oryzae. Bioresour. Technol. 66 (3), 201–206. Jin, B., van Leeuwen, J., Yu, Q., Patel, B., 1999. Screening and selection of microfungi for microbial biomass protein production and water reclamation from starch processing wastewater. J. Chem. Technol. Biotechnol. 74 (2), 106–110. Jin, B., Yin, P., Ma, Y., Zhao, L., 2005. Production of lactic acid and fungal biomass by Rhizopus fungi from food processing waste streams. J. Ind. Microbiol. Biotechnol. 32 (11), 678–686. Joshi, V.K., Parmar, M., Rana, N.S., 2006. Pectin esterase production from apple pomace in solid-state and submerged fermentations. Food Technol. Biotechnol. 44 (2), 253–256. n, A.M., Georgina, B., Beatriz, F., 2016. Potential use of soybean hulls and waste paper as Julia, B.M., Bele supports in SSF for cellulase production by aspergillus Niger. Biocatal. Agric. Biotechnol. 6, 1–8. Julshamn, K., Andersen, A., Ringdal, O., Mørkøre, J., 1987. Trace elements intake in the Faroe Islands I. Element levels in edible parts of pilot whales (Globicephalus meleanus). Sci. Total Environ. 65, 53–62. Kahraman, S.S., Gurdal, I.H., 2002. Effect of synthetic and natural culture media on laccase production by white rot fungi. Bioresour. Technol. 82 (3), 215–217. Kalra, R., Conlan, X.A., Goel, M., 2020. Fungi as a potential source of pigments: harnessing filamentous fungi. Front. Chem. 8, 369. Kantifedaki, A., Kachrimanidou, V., Mallouchos, A., Papanikolaou, S., Koutinas, A.A., 2018. Orange processing waste valorisation for the production of bio-based pigments using the fungal strains Monascus purpureus and Penicillium purpurogenum. J. Clean. Prod. 185, 882–890. Kargi, F., Ozmıhcı, S., 2006. Utilization of cheese whey powder (CWP) for ethanol fermentations: effects of operating parameters. Enzym. Microb. Technol. 38 (5), 711–718. Karimi, S., Mahboobi Soofiani, N., Lundh, T., Mahboubi, A., Kiessling, A., Taherzadeh, M.J., 2019. Evaluation of filamentous fungal biomass cultivated on vinasse as an alternative nutrient source of fish feed: protein, lipid, and mineral composition. Fermentation 5 (4), 99. Kato, N., Murakoshi, Y., Kato, M., Kobayashi, T., Tsukagoshi, N., 2002. Isomaltose formed by α-glucosidases triggers amylase induction in Aspergillus nidulans. Curr. Genet. 42 (1), 43–50.

Chapter 18 • Versatility of filamentous fungi in novel processes

567

Kaur, S., Dhillon, G.S., Brar, S.K., Chauhan, V.B., 2012. Carbohydrate degrading enzyme production by plant pathogenic mycelia and microsclerotia isolates of Macrophomina phaseolina through koji fermentation. Ind. Crop. Prod. 36 (1), 140–148. Kim, S.J., Shoda, M., 1999. Decolorization of molasses and a dye by a newly isolated strain of the fungus Geotrichum candidum Dec 1. Biotechnol. Bioeng. 62 (1), 114–119. Kiran, R.R.S., Konduri, R., Rao, G.H., Madhu, G.M., 2010. Statistical optimization of endopolygalacturonase production by overproducing mutants of Aspergillus niger in solid-state fermentation. J. Biochem. Technol. 2 (2), 154–157. Knob, A., Beitel, S.M., Fortkamp, D., Terrasan, C.R.F., Almeida, A.F.d., 2013. Production, purification, and characterization of a major Penicillium glabrum xylanase using Brewer’s spent grain as substrate. Biomed. Res. Int. 2013, 728735. Kolev Slavov, A., 2017. General characteristics and treatment possibilities of dairy wastewater–a review. Food Technol. Biotechnol. 55 (1), 14–28. Kosikowski, F.V., 1979. Whey utilization and whey products1. J. Dairy Sci. 62 (7), 1149–1160.  ska, E., 2020. BiotechKot, A.M., Pobiega, K., Piwowarek, K., Kieliszek, M., Błazejak, S., Gniewosz, M., Lipin nological methods of management and utilization of potato industry waste—a review. Potato Res. 63, 1–17. 

Koza, C.R., Norton, G.A., van Leeuwen, J.H., 2017. Dewatering investigations on fungal biomass grown in thin stillage from a dry-mill corn ethanol plant. Biomass Bioenergy 97, 65–69. Kumar, D., Long, S.P., Singh, V., 2018. Biorefinery for combined production of jet fuel and ethanol from lipid-producing sugarcane: a techno-economic evaluation. GCB Bioenergy 10 (2), 92–107. Leite, P., Silva, C., Salgado, J.M., Belo, I., 2019. Simultaneous production of lignocellulolytic enzymes and extraction of antioxidant compounds by solid-state fermentation of agro-industrial wastes. Ind. Crop. Prod. 137, 315–322. Lennartsson, P.R., Erlandsson, P., Taherzadeh, M.J., 2014. Integration of the first and second generation bioethanol processes and the importance of by-products. Bioresour. Technol. 165, 3–8. Li, Y., Cui, F., 2010. Microbial lactic acid production from renewable resources. In: Singh, O.V., Harvey, S.P. (Eds.), Sustainable Biotechnology: Sources of Renewable Energy. Springer Netherlands, Dordrecht, pp. 211–228. Liang, Y., Zhao, X., Strait, M., Wen, Z., 2012. Use of dry-milling derived thin stillage for producing eicosapentaenoic acid (EPA) by the fungus Pythium irregulare. Bioresour. Technol. 111, 404–409. Lockington, R.A., Rodbourn, L., Barnett, S., Carter, C.J., Kelly, J.M., 2002. Regulation by carbon and nitrogen sources of a family of cellulases in Aspergillus nidulans. Fungal Genet. Biol. 37 (2), 190–196. Lopes, F.C., Ligabue-Braun, R., 2021. Agro-industrial residues: eco-friendly and inexpensive substrates for microbial pigments production. Front. Sustain. Food Syst. 5 (65), 589414. Lopes, M., Arau´jo, C., Aguedo, M., Gomes, N., Gonc¸alves, C., Teixeira, J.A., Belo, I., 2009. The use of olive mill wastewater by wild type Yarrowia lipolytica strains: medium supplementation and surfactant presence effect. J. Chem. Technol. Biotechnol. 84 (4), 533–537. Lopes, F.C., Tichota, D.M., Pereira, J.Q., Segalin, J., de Oliveira Rios, A., Brandelli, A., 2013. Pigment production by filamentous fungi on agro-industrial byproducts: an eco-friendly alternative. Appl. Biochem. Biotechnol. 171 (3), 616–625. Lopez-Villalta, L., 1998. The Olive Tree, the Oil, the Olive. International Olive Oil Council Publications, Madrid, Spain. Lotti, M., Monticelli, S., Luis Montesinos, J., Brocca, S., Valero, F., Lafuente, J., 1998. Physiological control on the expression and secretion of Candida rugosa lipase. Chem. Phys. Lipids 93 (1), 143–148. Madhu, D., Singh, B., Sharma, Y.C., 2014. Studies on application of fish waste for synthesis of high quality biodiesel. RSC Adv. 4 (59), 31462–31468.

568

Current Developments in Biotechnology and Bioengineering

Magnuson, J.K., Lasure, L.L., 2004. Organic acid production by filamentous fungi. In: Advances in Fungal Biotechnology for Industry, Agriculture, and Medicine. Springer, pp. 307–340. Mahadik, N.D., Puntambekar, U.S., Bastawde, K.B., Khire, J.M., Gokhale, D.V., 2002. Production of acidic lipase by Aspergillus niger in solid state fermentation. Process Biochem. 38 (5), 715–721. Mahboubi, A., Ferreira, J.A., Taherzadeh, M.J., Lennartsson, P.R., 2017a. Production of fungal biomass for feed, fatty acids, and glycerol by aspergillus oryzae from fat-rich dairy substrates. Fermentation 3 (4), 48. Mahboubi, A., Ferreira, J.A., Taherzadeh, M.J., Lennartsson, P.R., 2017b. Value-added products from dairy waste using edible fungi. Waste Manag. 59, 518–525. Malladi, B., Ingham, S.C., 1993. Thermophilic aerobic treatment of potato-processing wastewater. World J. Microbiol. Biotechnol. 9 (1), 45–49. Mandalari, G., Bisignano, G., Lo Curto, R.B., Waldron, K.W., Faulds, C.B., 2008. Production of feruloyl esterases and xylanases by Talaromyces stipitatus and Humicola grisea var. thermoidea on industrial food processing by-products. Bioresour. Technol. 99 (11), 5130–5133. Martin, N., Guez, M.A.U., Sette, L.D., Da Silva, R., Gomes, E., 2010. Pectinase production by a Brazilian thermophilic fungus Thermomucor indicae-seudaticae N31 in solid-state and submerged fermentation. Microbiology 79 (3), 306–313. Martins, V.G., Palezi, S.C., Costa, J.A.V., Prentice, C., 2014. Hydrolysis of insoluble fish protein residue from whitemouth croaker (Micropogonias furnieri) by fungi. Braz. Arch. Biol. Technol. 57 (1), 96–102. Mashoko, L., Mbohwa, C., Thomas, V.M., 2010. LCA of the south African sugar industry. J. Environ. Plan. Manag. 53 (6), 793–807. Matsakas, L., Antonopoulou, I., Christakopoulos, P., 2015. Evaluation of Myceliopthora thermophila as an enzyme factory for the production of thermophilic cellulolytic enzymes. Bioresources 10 (3), 5125–5139. McMillan, J.D., 1993. Xylose Fermentation to Ethanol. A Review. National Renewable Energy Lab, Golden, CO (United States). Meneses, N.G.T., Martins, S., Teixeira, J.A., Mussatto, S.I., 2013. Influence of extraction solvents on the recovery of antioxidant phenolic compounds from brewer’s spent grains. Sep. Purif. Technol. 108, 152–158. Michelin, M., Teixeira, J.A., 2016. Liquid hot water pretreatment of multi feedstocks and enzymatic hydrolysis of solids obtained thereof. Bioresour. Technol. 216, 862–869. Mishra, B.K., Arora, A., Lata, 2004. Optimization of a biological process for treating potato chips industry wastewater using a mixed culture of aspergillus foetidus and aspergillus Niger. Bioresour. Technol. 94 (1), 9–12. Mohammad, N., Alam, M.Z., Kabbashi, N.A., Ahsan, A., 2012. Effective composting of oil palm industrial waste by filamentous fungi: a review. Resour. Conserv. Recycl. 58, 69–78. Molinuevo-Salces, B., Rian˜o, B., Hijosa-Valsero, M., Gonza´lez-Garcı´a, I., Paniagua-Garcı´a, A.I., Herna´ndez, D., Garita-Cambronero, J., Dı´ez-Antolı´nez, R., Garcı´a-Gonza´lez, M.C., 2020. Valorization of apple pomaces for biofuel production: a biorefinery approach. Biomass Bioenergy 142, 105785. Moredo, N., Lorenzo, M., Domı´nguez, A., Moldes, D., Cameselle, C., Sanroman, A., 2003. Enhanced ligninolytic enzyme production and degrading capability of Phanerochaete chrysosporium and Trametes versicolor. World J. Microbiol. Biotechnol. 19 (7), 665–669. rtiz-Osores, J., Jibaja, S., 2019. Fungi lipases homology modeling and molecular Moya-Salazarm, J., Ve docking with fatty acids and tripalmitin of palm oil effluent. Arch. Org. Inorg. Chem. Sci. 4 (2), 493–500. Nair, R.B., 2017. Integration of First and Second Generation Bioethanol Processes Using Edible Filamen€ gskolan i Bora˚s. tous Fungus Neurospora Intermedia. Ho Nair, R.B., Taherzadeh, M.J., 2016. Valorization of sugar-to-ethanol process waste vinasse: a novel biorefinery approach using edible ascomycetes filamentous fungi. Bioresour. Technol. 221, 469–476.

Chapter 18 • Versatility of filamentous fungi in novel processes

569

Nakata, H., Tamura, M., Shintani, T., Gomi, K., 2014. Evaluation of baker’s yeast strains exhibiting significant growth on Japanese beet molasses and compound analysis of the molasses types. J. Biosci. Bioeng. 117 (6), 715–719. Neoh, C.H., Yahya, A., Adnan, R., Abdul Majid, Z., Ibrahim, Z., 2013. Optimization of decolorization of palm oil mill effluent (POME) by growing cultures of aspergillus fumigatus using response surface methodology. Environ. Sci. Pollut. Res. 20 (5), 2912–2923. Ngando-Ebongue, G.F., Ajambang, W.N., Koona, P., Firman, B.L., Arondel, V., 2012. Oil palm. In: Gupta, S.K. (Ed.), Technological Innovations in Major World Oil Crops, Volume 1: Breeding. Springer New York, New York, NY, pp. 165–200. € rnsson, L., 2012. Improved utilization of fish waste by anaerobic digestion folNges, I.A., Mbatia, B., Bjo lowing omega-3 fatty acids extraction. J. Environ. Manag. 110, 159–165. Nigam, P., Vogel, M., 1991. Bioconversion of sugar industry by-products—molasses and sugar beet pulp for single cell protein production by yeasts. Biomass Bioenergy 1 (6), 339–345. Nitayavardhana, S., Issarapayup, K., Pavasant, P., Khanal, S.K., 2013. Production of protein-rich fungal biomass in an airlift bioreactor using vinasse as substrate. Bioresour. Technol. 133, 301–306. O’Shea, N., Ktenioudaki, A., Smyth, T.P., McLoughlin, P., Doran, L., Auty, M.A.E., Arendt, E., Gallagher, E., 2015. Physicochemical assessment of two fruit by-products as functional ingredients: apple and orange pomace. J. Food Eng. 153, 89–95. Oda, Y., Saito, K., Yamauchi, H., Mori, M., 2002. Lactic acid fermentation of potato pulp by the fungus Rhizopus oryzae. Curr. Microbiol. 45 (1), 1–4. Okamoto, K., Nakagawa, S., Kanawaku, R., Kawamura, S., 2019. Ethanol production from cheese whey and expired Milk by the Brown rot fungus Neolentinus lepideus. Fermentation 5 (2), 49. ^ncio, A., Belo, I., 2016. Olive pomace valorization by Oliveira, F., Moreira, C., Salgado, J.M., Abrunhosa, L., Vena aspergillus species: lipase production using solid-state fermentation. J. Sci. Food Agric. 96 (10), 3583–3589. Oliveira, C.A., Fuess, L.T., Soares, L.A., Damianovic, M.H.R.Z., 2020. Thermophilic biohydrogen production from sugarcane molasses under low pH: metabolic and microbial aspects. Int. J. Hydrog. Energy 45 (7), 4182–4192. Ortiz-Tovar, G., Lo´pez-Miranda, J., Cerrillo-Soto, M.A., Jua´rez-Reyes, A., Favela-Torres, E., Soto-Cruz, O., 2007. Effect of solid substrate fermentation on the nutritional quality of agro-industrial residues. Interciencia 32 (5), 339–343. Oswal, N., Sarma, P.M., Zinjarde, S.S., Pant, A., 2002. Palm oil mill effluent treatment by a tropical marine yeast. Bioresour. Technol. 85 (1), 35–37. Ousmanova, D., Parker, W., 2007. Fungal generation of organic acids for removal of lead from contaminated soil. Water Air Soil Pollut. 179 (1–4), 365–380. Palakawong Na Ayudthaya, S., van de Weijer, A.H.P., van Gelder, A.H., Stams, A.J.M., de Vos, W.M., Plugge, C.M., 2018. Organic acid production from potato starch waste fermentation by rumen microbial communities from Dutch and Thai dairy cows. Biotechnol. Biofuels 11 (1), 13. Panagiotou, G., Granouillet, P., Olsson, L., 2006. Production and partial characterization of arabinoxylandegrading enzymes by Penicillium brasilianum under solid-state fermentation. Appl. Microbiol. Biotechnol. 72 (6), 1117–1124. Pant, D., Adholeya, A., 2007. Enhanced production of ligninolytic enzymes and decolorization of molasses distillery wastewater by fungi under solid state fermentation. Biodegradation 18 (5), 647–659. Papadaki, E., Mantzouridou, F.T., 2019. Citric acid production from the integration of Spanish-style green olive processing wastewaters with white grape pomace by aspergillus Niger. Bioresour. Technol. 280, 59–69. Parchami, M., Ferreira, J.A., Taherzadeh, M.J., 2021a. Brewing process development by integration of edible filamentous Fungi to upgrade the quality of Brewer’s spent grain (BSG). Bioresources 16 (1), 1686–1701.

570

Current Developments in Biotechnology and Bioengineering

Parchami, M., Ferreira, J.A., Taherzadeh, M.J., 2021b. Starch and protein recovery from brewer’s spent grain using hydrothermal pretreatment and their conversion to edible filamentous fungi – a brewery biorefinery concept. Bioresour. Technol. 337, 125409. Pathania, S., Sharma, N., Handa, S., 2018. Utilization of horticultural waste (apple pomace) for multiple carbohydrase production from Rhizopus delemar F2 under solid state fermentation. J. Genet. Eng. Biotechnol. 16 (1), 181–189. Pattanakittivorakul, S., Lertwattanasakul, N., Yamada, M., Limtong, S., 2019. Selection of thermotolerant Saccharomyces cerevisiae for high temperature ethanol production from molasses and increasing ethanol production by strain improvement. Antonie Van Leeuwenhoek 112 (7), 975–990. Paulo, F., Santos, L., 2021. Deriving valorization of phenolic compounds from olive oil by-products for food applications through microencapsulation approaches: a comprehensive review. Crit. Rev. Food Sci. Nutr. 61 (6), 920–945. Pedrolli, D.B., Gomes, E., Monti, R., Carmona, E.C., 2008. Studies on productivity and characterization of polygalacturonase from aspergillus giganteus submerged culture using citrus pectin and orange waste. Appl. Biochem. Biotechnol. 144 (2), 191–200. ´ -Chau, T.A., Lema, J.M., 2012. Use of white-rot fungi for valorization of stillage from bioethanol Pena, R., Lu production. Waste Biomass Valoriz. 3 (3), 295–303. Pietrzak, W., Kawa-Rygielska, J., 2019. Backset valorization in dry-grind ethanol process by co-culture of edible filamentous fungi and fodder yeast. J. Clean. Prod. 220, 376–385. ki, Z., Bala´zs, E., 2021. Bioeconomy: biomass and biomass-based energy Popp, J., Kova´cs, S., Ola´h, J., Dive supply and demand. New Biotechnol. 60, 76–84. Prasertsan, P., H-kittikul, A., Chitmanee, B., 1992. Isolation and selection of cellulolytic fungi from palm oil mill effluent. World J. Microbiol. Biotechnol. 8 (6), 614–617. Prazeres, A.R., Carvalho, F., Rivas, J., 2012. Cheese whey management: a review. J. Environ. Manag. 110, 48–68. Pyc, R., So´jka-Ledakowicz, J., Bratkowska, H., 2003. Biosynthesis of enzymes by aspergillus niger IBT-90 and an evaluation of their application in textile technologies. Fibres Text. East. Eur. 11 (4), 71–77. Qiu, L., Li, J.J., Li, Z., Wang, J.J., 2019. Production and characterization of biocontrol fertilizer from brewer’s spent grain via solid-state fermentation. Sci. Rep. 9 (1), 480. Rachmadona, N., Quayson, E., Amoah, J., Alfaro-Sayes, D.A., Hama, S., Aznury, M., Kondo, A., Ogino, C., 2021. Utilizing palm oil mill effluent (POME) for the immobilization of aspergillus oryzae whole-cell lipase strains for biodiesel synthesis. Biofuels Bioprod. Biorefin. 15 (3), 804–814. Raghukumar, C., Rivonkar, G., 2001. Decolorization of molasses spent wash by the white-rot fungus Flavodon flavus, isolated from a marine habitat. Appl. Microbiol. Biotechnol. 55 (4), 510–514. Rajendran, K., Rajoli, S., Taherzadeh, M.J., 2016. Techno-economic analysis of integrating first and secondgeneration ethanol production using filamentous fungi: an industrial case study. Energies 9 (5), 359. Ramjeawon, T., 2004. Life cycle assessment of cane-sugar on the island of Mauritius. Int. J. Life Cycle Assess. 9 (4), 254–260. Rashid, S.S., Alam, M.Z., Karim, M.I.A., Salleh, M.H., 2009. Management of palm oil mill effluent through production of cellulases by filamentous fungi. World J. Microbiol. Biotechnol. 25 (12), 2219–2226. Rasmussen, M.L., Khanal, S.K., Pometto, A.L., van Leeuwen, J., 2014. Water reclamation and value-added animal feed from corn-ethanol stillage by fungal processing. Bioresour. Technol. 151, 284–290. Reis, C.E.R., Rajendran, A., Hu, B., 2017. New technologies in value addition to the thin stillage from cornto-ethanol process. Rev. Environ. Sci. Biotechnol. 16 (1), 175–206. Reis, C.E.R., Valle, G.F., Bento, H.B.S., Carvalho, A.K.F., Alves, T.M., de Castro, H.F., 2020. Sugarcane by-products within the biodiesel production chain: vinasse and molasses as feedstock for oleaginous fungi and conversion to ethyl esters. Fuel 277, 118064.

Chapter 18 • Versatility of filamentous fungi in novel processes

571

REN21, 2020. Renewables 2020 Global Status Report. Richter, K., Berthold, C., 1998. Biotechnological conversion of sugar and starchy crops into lactic acid. J. Agric. Eng. Res. 71 (2), 181–191. Rinaldi, M., Rana, G., Introna, M., 2003. Olive-mill wastewater spreading in southern Italy: effects on a durum wheat crop. Field Crop Res. 84 (3), 319–326. Rocha, N.R.d.A.F., Barros, M.A., Fischer, J., Coutinho Filho, U., Cardoso, V.L., 2013. Ethanol production from agroindustrial biomass using a crude enzyme complex produced by aspergillus Niger. Renew. Energy 57, 432–435. Rocha-Meneses, L., Raud, M., Orupo˜ld, K., Kikas, T., 2017. Second-generation bioethanol production: a review of strategies for waste valorisation. Agron. Res. 15 (3), 830–847. Rodrigues Reis, C.E., Ogero D’Otaviano, L., Rajendran, A., Hu, B., 2018. Co-culture of filamentous feedgrade Fungi and microalgae as an alternative to increase feeding value of ethanol coproducts. Fermentation 4 (4), 86. Romeo, R., De Bruno, A., Imeneo, V., Piscopo, A., Poiana, M., 2019. Evaluation of enrichment with antioxidants from olive oil mill wastes in hydrophilic model system. J. Food Process. Preserv. 43 (11), e14211. Rosenberg, M., Krisˇofı´kova´, L., 1995. Physiological restriction of the L-lactic acid production by Rhizopus arrhizus. Acta Biotechnol. 15 (4), 367–374. Roy, M., Kumar, R., Ramteke, A., Sit, N., 2021. Identification of lipase producing fungus isolated from dairy waste contaminated soil and optimization of culture conditions for lipase production by the isolated fungus. J. Microbiol. Biotechnol. Food Sci. 2021, 698–704. ^ncio, A., Domı´nguez, J.M., Belo, I., 2016. Combined bioremediation and Salgado, J.M., Abrunhosa, L., Vena enzyme production by aspergillus sp. in olive mill and winery wastewaters. Int. Biodeterior. Biodegradation 110, 16–23. bio, A., 2020. Isolation and identification of Salgado, V., Fonseca, C., Lopes da Silva, T., Roseiro, J.C., Euse Magnusiomyces capitatus as a lipase-producing yeast from olive mill wastewater. Waste Biomass Valoriz. 11 (7), 3207–3221. Sar, T., Seker, G., Erman, A.G., Stark, B.C., Yesilcimen Akbas, M., 2017a. Repeated batch fermentation of immobilized E. coli expressing Vitreoscilla hemoglobin for long-term use. Bioengineered 8 (5), 651–660. Sar, T., Stark, B.C., Yesilcimen Akbas, M., 2017b. Effective ethanol production from whey powder through immobilized E. coli expressing Vitreoscilla hemoglobin. Bioengineered 8 (2), 171–181. Sar, T., Stark, B.C., Akbas, M.Y., 2019. Bioethanol production from whey powder by immobilized E. coli expressing Vitreoscilla hemoglobin: optimization of sugar concentration and inoculum size. Biofuels 12 (9), 1–6. Sar, T., Ferreira, J.A., Taherzadeh, M.J., 2020a. Bioprocessing strategies to increase the protein fraction of Rhizopus oryzae biomass using fish industry sidestreams. Waste Manag. 113, 261–269. Sar, T., Ozturk, M., Taherzadeh, M.J., Ferreira, J.A., 2020b. New insights on protein recovery from olive oil mill wastewater through bioconversion with edible filamentous fungi. Processes 8 (10), 1210. Sar, T., Ferreira, J.A., Taherzadeh, M.J., 2021. Conversion of fish processing wastewater into fish feed ingredients through submerged cultivation of aspergillus oryzae. Syst. Microbiol. Biomanuf. 1 (1), 100–110. Sathivel, S., Bechtel, P.J., Babbitt, J., Smiley, S., Crapo, C., Reppond, K.D., Prinyawiwatkul, W., 2003. Biochemical and functional properties of herring (Clupea harengus) byproduct hydrolysates. J. Food Sci. 68 (7), 2196–2200. Sayadi, S., Ellouz, R., 1995. Roles of lignin peroxidase and manganese peroxidase from Phanerochaete chrysosporium in the decolorization of olive mill wastewaters. Appl. Environ. Microbiol. 61 (3), 1098. € gerl, K., 1994. Agriculture wastes. A source of bulk products? Chem. Eng. Technol. 17 (5), 291–300. Schu

572

Current Developments in Biotechnology and Bioengineering

Schultz, N., Chang, L., Hauck, A., Reuss, M., Syldatk, C., 2006. Microbial production of single-cell protein from deproteinized whey concentrates. Appl. Microbiol. Biotechnol. 69 (5), 515–520. € Gu € Ferna´ndez-Bolan˜os, J., Rodrı´guez-Gutie € u , O., € c¸lu € Ust € ndag rrez, G., 2018. Effect of subcritSec¸meler, O., ical water and steam explosion pretreatments on the recovery of sterols, phenols and oil from olive pomace. Food Chem. 265, 298–307. Serba, E., Pimenov, N., Mochalina, P., Overchenko, M., Borscheva, Y., Sharikov, A., Rimareva, L., 2020. Production of aspergillus oryzae RCAM 01133 biomass with increased protein and polysaccharides content using by-products of food industry. Agron. Res. 18 (1), 290–300. Sewalt, V., Shanahan, D., Gregg, L., La Marta, J., Carrillo, R., 2016. The generally recognized as safe (GRAS) process for industrial microbial enzymes. Ind. Biotechnol. 12 (5), 295–302. Shahidi, F., Brown, J.A., 1998. Carotenoid pigments in seafoods and aquaculture. Crit. Rev. Food Sci. Nutr. 38 (1), 1–67. Shahryari, Z., Fazaelipoor, M.H., Ghasemi, Y., Lennartsson, P.R., Taherzadeh, M.J., 2019. Amylase and xylanase from edible fungus neurospora intermedia: production and characterization. Molecules 24 (4), 721. Sharifia, M., Karimi, K., Taherzadeh, M.J., 2008. Production of ethanol by filamentous and yeast-like forms of Mucor indicus from fructose, glucose, sucrose, and molasses. J. Ind. Microbiol. Biotechnol. 35 (11), 1253–1259. Shavandi, M.A., Haddadian, Z., Ismail, M.H.S., Abdullah, N., Abidin, Z.Z., 2012. Removal of Fe(III), Mn(II) and Zn(II) from palm oil mill effluent (POME) by natural zeolite. J. Taiwan Inst. Chem. Eng. 43 (5), 750–759. Simpson, B.K., 2007. Pigments from by-products of seafood processing. In: Shahidi, F. (Ed.), Maximising the Value of Marine by-Products. Woodhead Publishing, pp. 413–432 (Chapter 19). Singh, B., Satyanarayana, T., 2008. Phytase production by Sporotrichum thermophile in a cost-effective cane molasses medium in submerged fermentation and its application in bread. J. Appl. Microbiol. 105 (6), 1858–1865. € gerl, K., 1992. Bioconversion of cellulosic materials to ethanol by filamentous Singh, A., Kumar, P.K.R., Schu fungi. In: Enzymes and Products from Bacteria Fungi and Plant Cells. Springer Berlin Heidelberg, Berlin, Heidelberg, pp. 29–55. Smith, T.C., Kindred, D.R., Brosnan, J.M., Weightman, R.M., Shepherd, M., Sylvester-Bradley, R., 2006. Wheat as a feedstock for alcohol production. HGCA Res. Rev. 61, 88. Soccol, C.R., Stonoga, V.I., Raimbault, M., 1994. Production of l-lactic acid by Rhizopus species. World J. Microbiol. Biotechnol. 10 (4), 433–435. ^ a-Thomaz, A.M.A., Carioca, J.O.B., Morais, S.M.d., Lima, A.d., Martins, C.G., Sousa, E.C., Ucho Alexandrino, C.D., Ferreira, P.A.T., Rodrigues, A.L.M., Rodrigues, S.P., 2014. Chemical composition and bioactive compounds of grape pomace (Vitis vinifera L.), Benitaka variety, grown in the semiarid region of Northeast Brazil. Food Sci. Technol. 34 (1), 135–142. Souza Filho, P.F., Brancoli, P., Bolton, K., Zamani, A., Taherzadeh, M.J., 2017a. Techno-economic and life cycle assessment of wastewater management from potato starch production: present status and alternative biotreatments. Fermentation 3 (4), 56. Souza Filho, P.F., Zamani, A., Taherzadeh, M.J., 2017b. Production of edible fungi from potato protein liquor (PPL) in airlift bioreactor. Fermentation 3 (1), 12. Souza Filho, P.F., Zamani, A., Taherzadeh, M.J., 2019. Edible protein production by filamentous fungi using starch plant wastewater. Waste Biomass Valoriz. 10 (9), 2487–2496. Srivastava, N., Srivastava, M., Manikanta, A., Singh, P., Ramteke, P.W., Mishra, P.K., Malhotra, B.D., 2017. Production and optimization of physicochemical parameters of cellulase using untreated orange waste by newly isolated Emericella variecolor NS3. Appl. Biochem. Biotechnol. 183 (2), 601–612.

Chapter 18 • Versatility of filamentous fungi in novel processes

573

Stroparo, E.C., Beitel, S.M., De Resende, J.T.V., Knob, A., 2012. Filamentous fungi and agro-industrial residues selection for enzyme production of biotechnological interest. Semina Cienc. Agrar. 33 (6), 2267–2278. Suesse, A.R., Norton, G.A., van Leeuwen, J., 2016. Pilot-scale continuous-flow hydrothermal liquefaction of filamentous Fungi. Energy Fuel 30 (9), 7379–7386. Sumer, F., Stark, B.C., Yesilcimen Akbas, M., 2015. Efficient ethanol production from potato and corn processing industry waste using E. coli engineered to express Vitreoscilla haemoglobin. Environ. Technol. 36 (18), 2319–2327. Suseela, L., Anupama, M., Prudhvilal, B., Narasaiah, T., Latha, J.N.L., 2014. Isolation & characterization of lipase producing fungi from palm oil mill effluent obtained from Pedavegi, AP, India. Int. J. Biol. Pharm. Res. 5 (7), 559–565. Tan, Y.D., Lim, J.S., 2019. Feasibility of palm oil mill effluent elimination towards sustainable Malaysian palm oil industry. Renew. Sust. Energ. Rev. 111, 507–522. Tang, Y.-Q., An, M.-Z., Zhong, Y.-L., Shigeru, M., Wu, X.-L., Kida, K., 2010. Continuous ethanol fermentation from non-sulfuric acid-washed molasses using traditional stirred tank reactors and the flocculating yeast strain KF-7. J. Biosci. Bioeng. 109 (1), 41–46. €s, J., Johnsen, I.H.G., Lindberg, G., Perjo, L., Giacometti, A., 2014. Bioeconomy in the Nordic Region: Tera Regional Case Studies. Terrasan, C.R.F., Carmona, E.C., 2015. Solid-state fermentation of brewer’s spent grain for xylanolytic enzymes production by penicillium janczewskii and analyses of the fermented substrate. Biosci. J. 31 (6), 1826–1836. Terrasan, C.R.F., Temer, B., Duarte, M.C.T., Carmona, E.C., 2010. Production of xylanolytic enzymes by Penicillium janczewskii. Bioresour. Technol. 101 (11), 4139–4143. Thunuguntla, R., Mahboubi, A., Ferreira, J.A., Taherzadeh, M.J., 2018. Integration of membrane bioreactors with edible filamentous fungi for valorization of expired milk. Sustainability 10 (6), 1940. Torrecilla, J.S., Cancilla, J.C., 2021. Phenolic compounds in olive oil mill wastewater. In: Preedy, V.R., Watson, R.R. (Eds.), Olives and Olive Oil in Health and Disease Prevention, second ed. Academic Press, San Diego, pp. 693–700 (Chapter 58). Torres-Mayanga, P.C., Azambuja, S.P.H., Tyufekchiev, M., Tompsett, G.A., Timko, M.T., Goldbeck, R., Rostagno, M.A., Forster-Carneiro, T., 2019. Subcritical water hydrolysis of brewer’s spent grains: selective production of hemicellulosic sugars (C-5 sugars). J. Supercrit. Fluids 145, 19–30. Ucuncu, C., Tari, C., Demir, H., Buyukkileci, A.O., Ozen, B., 2013. Dilute-acid hydrolysis of apple, orange, apricot and peach pomaces as potential candidates for bioethanol production. J. Biobased Mater. Bioenergy 7 (3), 376–389. Valli, V., Go´mez-Caravaca, A.M., Di Nunzio, M., Danesi, F., Caboni, M.F., Bordoni, A., 2012. Sugar cane and sugar beet molasses, antioxidant-rich alternatives to refined sugar. J. Agric. Food Chem. 60 (51), 12508–12515. Vamvakaki, A.-N., Kandarakis, I., Kaminarides, S., Komaitis, M., Papanikolaou, S., 2010. Cheese whey as a renewable substrate for microbial lipid and biomass production by zygomycetes. Eng. Life Sci. 10 (4), 348–360. Van Peij, N.N.M.E., Visser, J., De Graaff, L.H., 1998. Isolation and analysis of xlnR, encoding a transcriptional activator co-ordinating xylanolytic expression in Aspergillus niger. Mol. Microbiol. 27 (1), 131–142. Veana, F., Martı´nez-Herna´ndez, J., Aguilar, C., Rodrı´guez-Herrera, R., Michelena, G., 2014. Utilization of molasses and sugar cane bagasse for production of fungal invertase in solid state fermentation using Aspergillus niger GH1. Braz. J. Microbiol. 45 (2), 373–377. Verma, N., Kumar, V., 2019. Application of Box–Behnken design for the optimization of cellulase production under solid-state fermentation. SN Appl. Sci. 1 (12), 1733.

574

Current Developments in Biotechnology and Bioengineering

rrez, F.J., Sa´daba, I., Ruiz-Va´zquez, R.M., Torres-Martı´nez, S., Vicente, G., Bautista, L.F., Rodrı´guez, R., Gutie Garre, V., 2009. Biodiesel production from biomass of an oleaginous fungus. Biochem. Eng. J. 48 (1), 22–27. Waites, M.J., Morgan, N.L., Rockey, J.S., Higton, G., 2009. Industrial Microbiology: An Introduction. Wiley. Wilkinson, S., Smart, K.A., James, S., Cook, D.J., 2017. Bioethanol production from brewers spent grains using a fungal consolidated bioprocessing (CBP) approach. Bioenergy Res. 10 (1), 146–157. Wolters, N., Schabronath, C., Schembecker, G., Merz, J., 2016. Efficient conversion of pretreated brewer’s spent grain and wheat bran by submerged cultivation of Hericium erinaceus. Bioresour. Technol. 222, 123–129. € sten, H.A.B., 2019. Filamentous fungi for the production of enzymes, chemicals and materials. Curr. Wo Opin. Biotechnol. 59, 65–70. Wu, R., Chen, D., Cao, S., Lu, Z., Huang, J., Lu, Q., Chen, Y., Chen, X., Guan, N., Wei, Y., Huang, R., 2020. Enhanced ethanol production from sugarcane molasses by industrially engineered Saccharomyces cerevisiae via replacement of the PHO4 gene. RSC Adv. 10 (4), 2267–2276. Xie, B., Li, S., Chu, W., Liu, C., Hu, S., Jin, H., Zhou, F., 2020. Improving filtration and pulse-jet cleaning performance of metal web filter media by coating with polytetrafluoroethylene microporous membrane. Process Saf. Environ. Prot. 136, 105–114. Xiros, C., Topakas, E., Katapodis, P., Christakopoulos, P., 2008. Hydrolysis and fermentation of brewer’s spent grain by Neurospora crassa. Bioresour. Technol. 99 (13), 5427–5435. Yahyaee, R., Ghobadian, B., Najafi, G., 2013. Waste fish oil biodiesel as a source of renewable fuel in Iran. Renew. Sust. Energ. Rev. 17, 312–319. Yang, L., Li, H., Wang, Q., 2019. A novel one-step method for oil-rich biomass production and harvesting by co-cultivating microalgae with filamentous fungi in molasses wastewater. Bioresour. Technol. 275, 35–43. Yilmaztekin, M., Erten, H., Cabaroglu, T., 2008. Production of Isoamyl acetate from sugar beet molasses by Williopsis saturnus var. saturnus. J. Inst. Brew. 114 (1), 34–38. € lgyi, C., Mondal, K.C., Krisch, J., Tako´, M., 2018. Zambrano, C., Kotoga´n, A., Bencsik, O., Papp, T., Va´gvo Mobilization of phenolic antioxidants from grape, apple and pitahaya residues via solid state fungal fermentation and carbohydrase treatment. LWT 89, 457–465. Zetty-Arenas, A.M., Tovar, L.P., Alves, R.F., Mariano, A.P., van Gulik, W., Maciel Filho, R., Freitas, S., 2021. Co-fermentation of sugarcane bagasse hydrolysate and molasses by clostridium saccharoperbutylacetonicum: effect on sugar consumption and butanol production. Ind. Crop. Prod. 167, 113512. Zhang, S., Wang, J., Jiang, H., 2021. Microbial production of value-added bioproducts and enzymes from molasses, a by-product of sugar industry. Food Chem. 346, 128860.

Index Note: Page numbers followed by f indicate figures, and t indicate tables. A Acetylation, 135 Acetyl-CoA, 456–457 Acremonium chrysogenum, 68t Activated charcoal, 134 Adenosine triphosphate (ATP) measurement, 173 Aeration, 222–223 in solid-state fermentation, 261–262 Aflatoxins, 105, 124, 376–378 economic impact, 108t exposure of, 107 health effect, 106t occurrence of, 125–127t structure, producing fungi and stability of, 109–123t worldwide regulation limit of, 129t AFTOL project, 78 Agar disc diffusion method, 480 Agaricus bisporus, 68t Agar overlay bioassay, 482 Agar plug diffusion method, 482 Agar well diffusion method, 482 AGF. See Anaerobic gut fungi (AGF) AGF CAZyome, 87–88 AGF protein domains, 84f, 86 Agitation, 152–153 power consumed for, 221–222 in solid-state fermentation, 262 Agriculture industry, fungi in, 43–44, 43f Agrocybe cylindracea, 40–41 Agro-industrial residues, 299, 300t Air-lift reactors, 39, 40f, 204, 224–225t, 229 configuration, 226f effect on fungal morphology, 241 Alcohols ethanol (see Ethanol)

fermentative production butanol, 445–447 feedstocks for, 437–438 production process, filamentous fungi in, 448f Algae, 337–338, 438 Allomyces macrogynus, 88 Allopolyploidy, 78 α-zearalenol (α-ZEL), 377 Alpha linolenic acid (ALA), 410, 412–413 Alternaria toxins, 109–123t American Type Culture Collection (ATCC), 165 Amylases, 198–199 Anaerobic fungi, 18 in biogas production, 47 Anaerobic gut fungi (AGF), 86 Anamorph, 153–154 Anamorphic fungi, 1 Aneuploidy, 78 Animal and fish feed ingredients, filamentous fungi as compound feed fishmeal (see Fishmeal) plant protein meals, 402–404 terrestrial animal by-product meals, 404 economic and environmental aspects, 424–425 fermented soybean and soybean meal piglets fed, 421–422 in poultry, 421 fungal biomass amino acid profile, 406–408, 408t, 409f antioxidant agents, 418 broiler chicken, 421–422 cell wall components, 413–416 fat and fatty acid content, 408–413 fish fed, application in, 422–424

575

576

Index

Animal and fish feed ingredients, filamentous fungi as (Continued) mammalian food, application in, 423 minerals, 416–417 nucleotides, 419–420 pigments, 417–418 prebiotics, 420–421 protein, 406–408, 407t vitamins, 419 waste streams, 423–424 fungi kingdom, 405–406 protein source ingredients, 399–400 ruminants, fermented feed application in, 421 single-cell proteins (SCPs), 404–405 Animal-pathogenic fungi, 6–7 Animal protein consumption of, 348, 348f greenhouse gas (GHG) emissions of, 343, 348–349, 349t health concerns, 343 protein content, quality, fat, and antinutrient compounds, 345, 346t sources, 344–345 world demand for, 343 Ankaflavin, 329, 330f Antarctic fungi, 16–17 Anthraquinone fungal, 334, 335f Natural Red™, 332–334 Antibiotics, 105 industrial applications, 205–206t solid-state fermentation produced, 276t, 277–278 Antibiotics production, filamentous fungi antimicrobial assay, 480–483 ascochlorinis, 491 asperchondols, 489–490 aspergillin, 490 aspochalasin, 490 carbon source, antibiotic synthesis, 477–478 cell membrane function, inhibitors of, 486 cell wall synthesis, inhibitors of, 485 cephalosporins, 477, 487–488

claviformin, 490 dihydrogeodin, 491 diketopiperazine, 479 fermentation process extraction and purification, 484 quality control, 485 refining, 484–485 solid-state fermentation, 483–484 submerged fermentation, 483 fumagillin, 490 fusidane, 488–489 fusidanes, 479 gigantic acid, 491 glucose, 477–478 heterologous expression, 477–478 history, 478 β-lactam antibiotics, 477 marine ecosystem, 479 metabolic engineering, 491–492 metabolic processes, inhibitors of, 486 microbes, isolation and screening of, 480 microorganisms, 477 nucleic acid synthesis, inhibitors of, 486 penicillins, 477, 479, 486–487 perspectives, 492 primary use of, 477 protein synthesis, inhibitors of, 486 schematic representation of, 481f tropolone derivative, 490 Antioxidant agents, 418 Aphelids, 79 morphological characters, 80t Aquatic fungi, 15–16 α-Arabino furanosidase, 210–211t Arachidonic acid, 366, 375, 410–412 Aroma compounds, 281 Arpink red™. See Natural Red™ Ascogonium, 74–75 Ascoma, 74–75 Ascomycetes biomass in animal feed, 55 in human food, 54–55 ethanol production by, 442–443, 443t metabolites production, 50

Index 577

citric acid, 51 ethanol, 50 gluconic acid, 51 itaconic acid, 51 for solid-state fermentation, 254 Ascomycetes dikaryons, 75 Ascomycota, 67–69 characteristic features of, 96 classification of, 95 reproduction, 74–75 Ascospores, 74–75 Asexual reproduction in Ascomycota, 74 in Entomophthoromycotina, 91 in Kickxellomycotina, 92 in Mucoromycota, 93–94 in Mucoromycotina, 94 in Zoopagomycotina, 91 in Zygomycota, 73 Asexual spore formation, 153–154 Ashbya gossypii, 68t, 242, 419 Asperchondols, 489–490 Aspergillin, 490 Aspergillus niger, 366, 422–423 agitation and, 152–153 citric acid production, 464–465 gluconic acid production, 461–462 oxalic acid production, 467–468 pelleted mass of, 152–153 Aspergillus sp., 68t A. awamori, 422 A. oryzae, 421–422 A. parasiticus, 377–378 A. terreus, 457t, 458–460 for citric acid production, 47, 51, 462–463 cultivation pH, 41–42 enzyme production, 197, 295, 297–298t for ethanol production, 50 for gluconic acid production, 47, 51 hydroxyanthraquinoid (HAQN) pigments, 332 for itaconic acid production, 51 lovastatin production, 45 in marine habitats, 336–337 morphology/factors affecting, 202t

mycotoxins, 108–124 pigment production, 54 value-added products by, 182–183 xylanase and lignin peroxidase by, 208 Aspochalasin, 490 Assembling the Fungal Tree of Life (AFTOL) project, 67 Autopolyploidy, 78 Axial pumping impellers, 227 Azaphilone pigments mycotoxin-free Monascus red, 328–329 non-toxigenic fungal strains, Monascus pigments from, 329–331 B Bacillomycin D, 135 Ballistoconidiogenesis, 3 Basidiobolus sp., 91 Basidiomycetes, 53 biomass, 57 ethanol production from, 53–54 reproduction, 72 Basidiomycota, 67–69 characteristic features of, 96–97 classification of, 96 reproduction, 75 Basidiomycotina, 97 Batch culture, 222–223 Batch fermentation, 38 phases in, 39f systems, 308–309, 309f Batrachochytrium dendrobatidis, 6, 84–85 Beauveria bassiana, 278 Beauvericins, 109–123t Beta-glucan, 414 Bioactive compounds, 276 Bioactive pigment production, by filamentous fungi anthraquinones, 334, 335f Natural Red™, 332–334 azaphilone pigments mycotoxin-free Monascus red, 328–329 non-toxigenic fungal strains, Monascus pigments from, 329–331 food colorants

578

Index

Bioactive pigment production, by filamentous fungi (Continued) hydroxyanthraquinoid (HAQN) pigments as, 326, 331–332 polyketide-Monascus-like pigments as, 326–328 marine fungi, 326, 334–338 microbial cell factories, 325–326, 326f Biobleaching, 208–209 Biochemical, 47–48 Biocomposites, construction and packaging applications, 521–522 Bio-debarking, 204–206 Biodegradation, 190 Biodiesel, 278–279 Bioethanol, 209 industry wastes, 544–548 solid-state fermentation, 279 Bio-fabrication, 47 Biofilms, 70 Biofuels, 47–48, 209–211, 272 Biogenic amines (BAs), 377–378 Bioluminescent methods, 483 Biomass evaluation direct methods for cell count, 169–170 fluorescence techniques, 172 gravimetric technique, 169 imaging and microscopy, 170–171 impedance and capacitance techniques, 171–172 near-infrared spectroscopy, 172–173 optical density, 170 indirect methods for adenosine triphosphate measurement, 173 calorimetry, 174 chitin measurement, 173–174 CO2 production and oxygen uptake rate, 174–175 Biomass, fungal, 54–57, 151 Biomaterial, 47–48 Biopesticides, 278, 278t Bio-pitching, 206–207 Biopolymers, 280–281

Bioprocess, with filamentous fungi, 198–200 factors affecting, 200 morphology, 201–203, 201f, 202t rheology, 203–204 strain screening and inoculum, 200 Biopulping, 207–208 Bioreactor(s), 37, 219 for solid-state fermentation, 38f for submerged fermentation, 40f Bioreactor design air-lift reactor, 229 bubble columns, 228 configurations, 224, 224–225t engineering fundamentals in, 220 medium aeration and kLa, 222–223 medium viscosity and rheology, 220–221 power consumed for agitation, 221–222 shear forces and shear stress, 223–224 filamentous fungi morphology and, 236 effect of, 239–241 life cycle, 237 macromorphology in submerged fermentations, 237–238 productivity, 238–239 tailoring, 241–242 fluidized-bed bioreactors, 233–234, 233f packed-bed bioreactors, 231–232, 232f rotating-bed bioreactors, 234–235, 234f stirred-tank reactors, 226–227 trickle-bed bioreactors, 229–231, 230f Biorefineries, fungal applications, 18 industries, 42–48, 43f investment and productivity improvement strategies, 48–50 value addition to organic wastes, 48 Bioremediation, 189–190 Bio-retting, 207 Biosafety level 3 (BSL-3), 162 Biosurfactants, 279–280 Blakeslea trispora, 68t Blastocladiella emersonii, 88 Blastocladiomycota, 88–89 characteristic features of, 88 Bleaching, 208–209

Index 579

Botrytis cinerea, 522–523 Brachyallomyces life cycle, 88 Branched-chain amino acids (BCAAs), 408 Brewer’s spent grain (BSG), 258, 534–538, 536t cellulolytic and xylanolytic enzymes, 537–538t fermentation with Rhizopus sp., 265, 266f Brewery waste, 534–539 Bubble column bioreactors, 39, 40f, 224–225t, 226f, 228, 299, 302f Budding, 3, 72 Burkholderia, 77 Burkholderia gladioli, 379 Butanol, fermentative production of, 445–447 C Calorimetry, 174 Candida albicans, 2 Candida famata, 68t Cantharellus cibarius, 68t Capacitance measurement, 171–172 Carbon, role of, 257 Carbon to nitrogen (C:N) ratio, 35, 257 β-Carotene, 325–326 Carotenoids, 325 Cell count method, 169–170 Cellobiohydrolase, 210–211t Cellulases, 210 Cell wall, fungal, 3 components of, 3t Cell wall, of filamentous fungi, 413 chitin, 414–415 chitosan, 415 glucans, 414 mannose, 415–416 Cephalosporin, 487–488 mode of action, 488 structure of, 488f Cereals, mycotoxins in, 124–128 Chaetoglobosin, 109–123t Chemical methods, for mycotoxins reduction, 135–136 Chemical mutagens, 465 Chitin, 414–415 Chitinases, 198–199

Chitin assay, 173–174 Chitin-glucan complex (CGC), 508–510, 510t Chitooligosaccharides (COSs), 517–518 Chitosan, 186–187, 415 extraction and purification of, 511–512, 513–514t in zygomycetes, 56–57 3-Chloropropane-1,2-diol (3-MCPD), 378 Chytridiomycetes, 83–85 Chytridiomycota (chytrids), 67–69, 81–85 morphological features of, 82–83 parasitic roles, 83 reproduction, 73 Citric acid (CA), 275, 366 applications, 462 from ascomycetes, 51 biochemical pathway, 470f biosynthesis, microorganisms, metabolism, and physiology of, 462–463 chemical structure of, 468f definition, 462 genetic and process engineering strategies, 465 global market, 462 production and processing conditions, 463–465 Citrinin, 108–124, 109–123t, 327–329, 330f Claviformin, 490 Clostridium botulinum, 378 Clustered regularly interspaced short palindromic repeats/CRISPRassociated protein 9 (CRISPR/Cas9) genome editing, 18, 444 Coagulative pellets, 237–238 Co-cultivation, 49 Codex Alimentarius, 131 CODEX set, 128–129 Coemansia, 92 Coenocytic hyphae, 1–2 CO2 evolution rate (CER), 174 Compound feed fishmeal (see Fishmeal) plant protein meals, 402–404 terrestrial animal by-product meals, 404 Concentration of dissolved oxygen, 222

580

Index

Conidia, 73 Conidiobolus, 91 Conidiophores, 73 Consolidated bioprocessing (CBP), 49, 439, 539 Continuous culture, 38 Continuous fermentation systems, 308–309, 309f Cornmeal agar, 152 Cross-streak method, 482 Cryopreservation, of filamentous fungi, 160–166 factors influencing, 163–164 freezing temperatures, 164–165 protocols for, 165, 166t steps in, 165f Cryoprotectants, 163, 164t Cryptic species, 14 Culture media, 33–35, 152 design and preparation of, 35 growth chemical requirements, 33–35 macro-nutrients, 34t for isolation and enumeration of mycobiota from fermented products, 159t types of, 33 Cycloleucomelone, 334–336 Cystogenes life cycle, 88 Cytochalasins, 109–123t Cytoplasmic waves, 70–71 Czapek-Dox Agar, 159t Czapek yeast extract agar, 159t D Daedaleopsis flavida, 45 Dairy processing industry, 558–560 Deacetylases, 210–211t Degassed power number, 222 Denaturing gradient gel electrophoresis (DGGE), 156 Deoxynivalenol economic impact, 108t health effect, 106t occurrence of, 125–127t structure, producing fungi and stability of, 109–123t worldwide regulation limit of, 129t

Dermocybe sanguinea, 332 Dew retting, 207 Dichloran 18% glycerol agar, 159t Dihydrosterimagtocystin, 109–123t Dikarya, 95–97, 149–150 Dimethyl sulfoxide (DMSO), as cryoprotectant, 163, 164t Dimorphic fungi, 2, 72 Dinomyces arenysensis, 83 Direct bioautography, 482 Dispersed filamentous growth, 238 Dispersed mycelia, 200–201 Dissolved oxygen, 303, 458, 464–465 concentration of, 222 Distillation, of ethanol, 444–445, 445f Diversity, fungal, 13–14 Docosahexaenoic acid (DHA), 375, 410 Downcomer, 229 Dried distillers grains with solubles (DDGS), 544–545 Dry-grind bioethanol plant, 544–545 E EAA. See Essential amino acid (EAA) Ecosystems, fungal, 14–18 aquatic ecosystems, 15–16 extremophile environments, 16–18 terrestrial ecosystems, 15 Ectomycorrhizal Basidiomycota, 97 Eicosapentaenoic acid (EPA), 410 ELISA-spectrometric method, 136 Endo β 1,4 glucanase, 210–211t Endo β 1,4 mannanase, 210–211t Endo β 1,4 xylanase, 210–211t Endomycorrhizae, 7 Enniatins, 109–123t Entomopathogenic fungi, 278 Entomophthoromycotina, 91 Environments, for filamentous fungi isolation, 154–156 Enzymatic hydrolysis, 210 Enzymes. See also Industrial enzymes for biofuel production, 272 for food and feed applications, 272 production by SSF, 272–274, 273–274t

Index 581

Enzymes, fungal, 4, 54, 181–182 applications in biofuel industry, 210, 210–211t industrial, 204, 205–206t in food industry, 44–45 in pharma industry, 45 in pulp and paper industry, 46 Epicoccum nigrum, 327–328 Ergot alkaloids, 109–123t Essential amino acid (EAA), 345, 349, 373, 374t, 407, 408t, 409f Ethanedioic acid. See Oxalic acid Ethanol, 48 applications, 435, 436f from ascomycetes, 50 from basidomycetes, 53–54 definition, 435 global production, 436–437, 437f market for, 435–436 production, by filamentous fungi, 438–443, 439f ascomycetes, 442–443, 443t metabolic engineering strategies, 443–444 zygomycetes, 440–441, 441t recovery and concentration distillation, 444–445, 445f pervaporation (PV), 445, 446f from zygomycetes, 52 Euallomyces life cycle, 88 Eukaryotic protein expression systems, 311–313, 312t European Food Safety Authority (EFSA), 254, 522 Eurotium sp., 332 Exopolysaccharides (EPS), 280, 497–498 Expression system, 197 Extremophile fungi, 16–18 F Fat mimetics, 372 Fatty acids alpha linolenic acid, 410, 412–413 arachidonic acid, 410–412 docosahexaenoic acid, 410 eicosapentaenoic acid, 410

linoleic acid, 410, 412 lipids, 408–409 oleic acid, 413 saturated fatty acids, 410 unsaturated fatty acids, 410 Fed-batch fermentation, 38, 308–309, 309f Feed conversion ratios (FCR), 402, 403t Feed ingredients, filamentous fungi as. See Animal and fish feed ingredients, filamentous fungi as Fermentation, fungal, 31 factors influencing, 40–42 inoculum preparation, 36 types, 36–39, 38–40f Fermented food, filamentous fungi in, 343–344, 353–362t advantages, 351–352 flavor enhancer, 369–370 oncom, 364–366 protein. Protein, filamentous fungi safety issues harmful contaminants, 378 mycotoxins, 376–378 pathogenic bacteria, 378–379 soy sauce (see Soy sauce) tempe (see Tempe) Fermented products, filamentous fungi isolation, 156–158, 157–158t culture media, 159t Feruloylesterase, 210–211t Filamentous fungi, 1, 150 animal feed, application in (see Animal and fish feed ingredients, filamentous fungi as) applications, 150–151, 337–338, 338f biofilm production, 70 characteristics, 42 compounds in industrial application, 186, 186t cultivation (see Bioreactor design) diversity of, 184–185 enzyme production (see Industrial enzymes) growth monitoring of, 168–175 growth of, 69–70 identification of, 159–160

582

Index

Filamentous fungi (Continued) industrial applications, 204–211 industrial bioprocess with, 198–200 isolation and purification of, 151–158 single spore isolation, 154 spore isolation, 153–154 microbiology of, 183–184 in microplastics removal, 189–190 nutrient uptake in, 4 organic acid, biological production of (see Organic acid production, filamentous fungi) pigment production (see Bioactive pigment production, by filamentous fungi) in pollution reduction, 187–189, 187f, 189t preservation of, 160–168 sampling and isolation from environments, 154–156 from fermented products, 156–158, 157–158t sampling procedures for, 158 solid-state fermentation (see Solid-state fermentation (SSF)) vegetative reproduction in, 3 Fish feed, fungal biomass in. See Animal and fish feed ingredients, filamentous fungi as Fishmeal, 424 amino acid profile of, 400–401, 408, 409f consumption, status of, 401, 401f definition, 400 diets, inclusion rate in, 400 economic and environmental aspects, 401–402, 403t protein, 400 Fish processing industry waste, 548–550 Flammulina velutipes, 53 Flavor enhancer, 369–370 Flax dew retting, 207 Flow cytofluorometric assay, 483 Flow cytometry, 169 Fluid dynamics, 203–204 Fluidized-bed bioreactors, 39, 40f, 224–225t, 233–234, 233f, 241, 269, 269f characteristics and limitations, 271t

Fluorescence techniques, for biomass evaluation, 172 Fluorescent ELISA, 136 Fluorophores, 172 Food additives, 366–372 and feed industry, fungi in, 43f, 44–45 mycotoxins in, 124–130, 125–127t Food applications, filamentous fungi challenges, 385 enzymes, 370–372, 371–372t fermented food (see Fermented food, filamentous fungi in) flavor enhancer, 369–370 food additives, 366 food ingredients, 372 food products, 344, 344f fungal mycelium-based food, 372–373 health aspects/functional properties, 376 industrial production modern processes, 382–384 traditional methods, 379–382 lipid, 375 vs. mushrooms, 350–351 natural pigments, 366–369, 367t proteins (see Protein) vitamins, 375 Food colorants anthraquinone fungal, 334, 335f Natural Red™, 332–334 criteria for, 368 hydroxyanthraquinoid (HAQN) pigments as, 326, 331–332 polyketide-Monascus-like pigments as, 326–328 Food grade pigments, 325–326 Freeze-drying, 160–163, 166–167 Freshwater fungi, 16 Fruit industry waste, 540–544 Fumagillin, 490 Fumaric acid, 53 Fumonisin B1 (FB1), 377 Fumonisins economic impact, 108t

Index 583

health effect, 106t occurrence of, 125–127t structure, producing fungi and stability of, 109–123t worldwide regulation limit of, 129t Functional amino acids (FAAs), 407 Fungal antibiotics, production of ascochlorinis, 491 asperchondols, 489–490 aspergillin, 490 aspochalasin, 490 cell membrane function, inhibitors of, 486 cell wall synthesis, inhibitors of, 485 cephalosporin, 487–488 mode of action, 488 claviformin, 490 dihydrogeodin, 491 fumagillin, 490 fusidane, 488–489 mode of action, 489 gigantic acid, 491 metabolic engineering, 491–492 metabolic processes, inhibitors of, 486 nucleic acid synthesis, inhibitors of, 486 penicillin, 486–487 mode of action, 487 protein synthesis, inhibitors of, 486 tropolone derivative, 490 Fungal biomass, 54–57 Fungal biopolymers applications of antimicrobial and preserving agent, 516–519 biocomposites, for construction and packaging applications, 521–522 bioemulsifiers and biosurfactants, 512–515 textiles, 519–521 tissue engineering, 516 wound healing materials, 515–516 chitin, 498–499, 504 exopolysaccharides, 497–498 extraction and purification of chitin–glucan complex (CGC) and chitin, 508–510, 510t

chitosan, 511–512, 513–514t fungal cell wall, 499–500, 501t polysaccharides, 500–505 structural organization of, 503f heterotrophic eukaryotes, 497 macromolecular constituents, 497–498 mannan, 504–505 perspectives, 523 Fungal biorefineries agriculture industry, 43–44 biofuels, biochemical, and biomaterial production, 47–48 food and feed industry, 44–45 industries, 42, 43f investment and productivity improvement strategies, 48–50 pharmaceutical industry, 45 pulp and paper industry, 46 textile industry, 46–47 value addition to organic wastes, 48 Fungal biotechnology, 31, 32f biomass, 54–57 culture medium, 33–35 fermentation process, 36–39 metabolites, 50–54 Fungal culture medium, 33–35 design and preparation of, 35 growth chemical requirements, 33–35 macro-nutrients, 34t Fungal diversity, 13–14 Fungal ecosystems, 14–18 aquatic, 15–16 extremophile, 16–18 terrestrial, 15 Fungal enzymes in biofuel industry, 210, 210–211t industrial applications, 204, 205–206t Fungal metabolites, 50–54 Fungal morphology, 1–4 hyphae, 2f reproduction, 3 Fungal nutrition, 4 nutrient uptake, 4 Fungal one-step IsolatioN Device (FIND), 153–154

584

Index

Fungal reproduction, 71–75 Fungi, 1 applications, in biorefineries, 18 classification of, 78–97, 149–150 growth of, 69–70 lifestyles of, 4–8 metabolic and genetic complexity in, 76–77 nutrition and transport in, 70–71 roles of, 67 taxonomy of, 8–13 Hibbett classification, 9–10, 10f Tedersoo classification, 10–11, 11f Wijayawardene classification, 11–12, 12f toxigenic, 130–131 FUNGIpath, 76–77 Fusaproliferin, 109–123t Fusarin C, 109–123t Fusarium sp. biomass, 372–373 in enzymes production, 296, 297–298t for ethanol production, 50 F. oxysporum, 6, 442 F. solani, 241 F. venenatum, 44, 55, 68t, 405–406 mycotoxins, 108–124, 377 Fusidane-type antibiotics, 488–489 mode of action, 489 structure of, 489f G α-Galactosidase, 210–211t Gamma-ray irradiation, 135 Ganoderma lucidum, 68t Generally Recognized as Safe (GRAS), 197–198, 254, 405–406, 534–536 Genetically modified organisms (GMOs), 150–151 Genome, 77–78 Genome sequencing, 9 Geomyces destructans, 6 Gibberellic acid, 538–539 Gigantic acid, 491 Glomeromycota, 92–93 reproduction, 74 Glucans, 414

Gluconic acid (GA) applications, 460 from ascomycetes, 51 biochemical pathway, 469f biosynthesis, microorganisms, metabolism, and physiology of, 460 chemical structure of, 468f definition, 460 production and process conditions, 460–461 strain engineering and process modifications, 461–462 Glucosamine, 173–174 β-Glucosidase, 210–211t α-Glucuronidase, 210–211t Glucuronoyl esterase, 210–211t Glycosylation, 135 Gold NPs, 47–48 Good agricultural practice (GAP), 132–133 Good manufacturing practices (GMPs), 131 Granger causality test, 70 Gravimetric measurement technique, 169 Greenhouse gas (GHG) emissions, of protein sources, 348–349, 349t Groundnut dextrose broth, 40–41 Growth angle, fungi, 69–70 Growth monitoring, of filamentous fungi, 168–169 H Haploid mating, 72 HAQN pigments. See Hydroxyanthraquinoid (HAQN) pigments Hazard analysis and critical control point (HACCP), 131, 138 Heat flow, 174 Heat transfer, in solid-state fermentation, 262–265 Heavy metals, removal of, 188–189 Hemicellulose debranching enzymes, 210–211t Heterologous expression, 197 Hibbett classification, of fungi, 9–10, 10f High-throughput screening (HTS), 480 Homologous expression, 197 Horizontal gene transfer (HGT), 78

Index 585

Hortaea werneckii, 78 HPLC-fluorescence, 136–137 Hybrid genome, 77–78 Hydrodynamics, 203–204 in fluidized bed bioreactors, 233 Hydrogenosomes, 76 Hydrothermal method, 135 Hydroxyanthraquinoid (HAQN) pigments, 326, 331–332 2-Hydroxy-propane-1,2,3-tricarboxylic acid. See Citric acid (CA) Hyperparasitic fungi, 4–5, 7 Hyperparasitism, 7 Hyperspora aquatica, 81 Hyphae, 1–2, 2f, 72, 201f I Imleria badia, 68t Immobilized fermentation, 307–308, 308f Immunoaffinity column (IAC) cleans-up spectrometric method, 136 Impedance measurement, 171–172 Industrial bioprocess, with filamentous fungi, 198–200 factors affecting, 200 morphology, 201–203, 201f, 202t rheology, 203–204 strain screening and inoculum, 200 Industrial enzymes, 272 advantages, 294 applications, 294 production, by filamentous fungi, 297–298t advantages, 294–295 agitation, 307 Aspergillus, 295 batch, fed-batch, and continuous fermentation systems, 308–309, 309f cultivation media, 310 economic aspect, 313 engineering, 310–311, 311t food industry, application in, 370–372, 371–372t Fusarium, 296 future research, 313–314 immobilization strategies, 307–308, 308f

morphologies, 306–307, 306f Penicillium, 296 pH control strategy, 309–310 process engineering challenges, 303–305 protein expression systems, 311–313, 312t Rhizopus, 296 solid-state fermentation (SSF) platforms, 299, 300t, 301f submerged fermentation (SmF) platforms, 299, 301–303, 302f Trichoderma, 297–298 Industrial wastes, as fungal growth media, 181–182, 183f Infections, fungal, 6–7 Inhibition zone diameter (IZD), 480 Inoculum preparation, 200 Inoculum transfer, 36 Inonotus obliquus, 45 In-situ microscopy (ISM), 170–171 International Code of Botanical Nomenclature (ICBN), 67 International Nucleotide Sequence Database, 9 Iron oxide NPs, 47–48 Irradiation, 134 Isoflavone, 364 Isolation and purification, of filamentous fungi, 151–158 single spore isolation, 154 spore isolation, 153–154 Itaconic acid (IA) from ascomycetes, 51 biochemical pathway, 469f biosynthesis, microorganisms, metabolism, and physiology of, 456–458 chemical process, 456 chemical structure of, 468f definition, 456 global production, 456 production and process conditions, 458–459 strain engineering and process modifications, 459–460 J Joint FAO/WHO Expert Committee on Food Additives (JECFA), 333

586

Index

K Kappa number, 208 KEGG, 76–77 Kickxellomycotina, 92 Koji fermentation, 364, 380 L Lactic acid, 275 from zygomycetes, 52–53, 52t Laricifomes officinalis, 45 LC-MS-MS method, 137 Leather like materials, 519–521 Lentinula edodes, 68t Lentinus edodes, 423 Lichen compounds, 8 Life cycle of Aphelids, 79 of Batrachochytrium dendrobatidis, 84–85 of Blastocladiomycota, 88 of filamentous fungi, 237 Lignocellulose, 18, 438 Lignocellulose hydrolysis, 181–182 Lignocellulosic materials (LCMs), 221 Lignocellulosic substrates, 258 Linderina pennispora, 92 Linoleic acid (LA), 410, 412 Lipases, 198–199 for biodiesel production, 279 Lipids, 375, 408–409 Long-chain polyunsaturated fatty acids (LC-PUFAs), 410 Long-term preservation, of filamentous fungi, 162–167 Lovastatin, 45 Lycopene, 277 Lyophilization, 160–161, 166–167 Lyoprotectants, 167 Lytic polysaccharide monooxygenase (LPMO), 210–211t M Macromorphology, fungal, 237–238 Macronutrients, 33–34 physiological functions of, 34t Macroscale phenomena, during SSF, 263–264, 263f

Magneto-acoustic and photoacoustic spectroscopy (MA/PAS), 174 Malt extract agar, 159t Mangrove fungi, 16 Mannan, 504–505 Mannose, 415–416 β-Mannosidase, 210–211t Mann-Whitney test, 70 Marine fungi, 16 isolation of, 155 pigment production, 326, 334–338 Marteilia cochillia, 81 Masked mycotoxins, 105 Mass transfer, 223–224, 227–228, 234–235 in solid-state fermentation, 262–265 Melanin, 334–336 Membrane filtration, 155 Metabolic engineering, 491–492 metabolomics approaches, 492 targeted approaches, 491 untargeted approaches, 491 Metabolites, fungal, 45, 50, 366–372 of ascomycetes, 50–51 of basidiomycetes, 53–54 pigments and enzymes, 54 of zygomycetes, 51–53 MetaCyc, 76–77 Metarrhizium, 78 2-Methylidenebutanedioic acid. See Itaconic acid (IA) Microbiology, of filamentous fungi, 183–184 Microdilution method, 482 Micronutrients, 33–34 Microplastics, 189–190 removal using filamentous fungi, 189–190 Micropollutants, 190 Microscale phenomena, during SSF, 263–265, 265f Microsporidia, 13–14, 81 spores, 81, 82f Minerals, 416–417 Miso, 351–352, 376 Mitosomes, 81 Mixed agar plate culture (MAPC), 480 Mixing impellers, 227

Index 587

Modified mycotoxins, 105 Moisture content, 259–260 Molasses, 437–438 Molds, 105 Mollicutes-related endobacteria (MRE), 93 Monascorubrin, 329, 330f Monascus-like polyketide azaphilone (MPA) pigments, 327–328 Monascus pigments, 54, 277, 326–328 mycotoxin-free Monascus red, 328–329 from non-toxigenic fungal strains, 329–331 Moniliformin, 109–123t Monoblepharidomycetes, 85 Monomorphic fungi, 72 Morphology, fungal, 1–4 factors affecting, 201–203, 201f, 202t hyphae, 2f reproduction, 3 Mortierella sp. fatty acids production, 282 PUFA production, 282 Mortierellomycotina, 94 Mucorales, ethanol-producing, 440–441, 441t Mucor indicus, 254 chitin production, 506–508 chitosan in, 56–57 in ethanol production, 52 Mucoromycota, 93–95 Mucoromycotina, 94–95 Mushrooms, 347–348, 350–351 Myceliophthora thermophila, 444 Mycelium, 1–2 of Basidiomycota, 97 of Glomeromycotina, 93 of Kickxellomycotina, 92 Mycobiont, 8 Mycoloop mechanism, 83 Mycoprotein, 349–350, 405 on dry/wet basis, 373 essential PUFA content of, 373 health benefits, 373 Quorn, 373, 375 Mycoremediation, 187–188 Mycorrhizae, 7 Mycorrhiza helper bacteria, 190

Mycorrhizal symbiosis, 7–8 Mycotoxins, 376–378 chemistry and processing stability, 108–124, 109–123t classification, 105 definition of, 105 detection and determination by advanced technologies, 137 by chromatographic method, 136–137 by spectrometric method, 136 economic impact, 107, 108t exposure of, 107 factors affecting production, 130–131 extrinsic factors, 131 intrinsic factors, 130–131 health risk/clinical manifestation of, 106, 106t industrial applications, 205–206t lethal effect of, 106 naphtoquinone-type, 332 occurrence in food, 124, 125–127t, 128f cereals, 124–128 international regulation, 128–130, 129t spices, 128 prevention of good agricultural practices, 132–133 networking, 133–134 by storage condition, 133 production, 303–305, 304t reduction, 134–136 by biological methods, 135 by chemical methods, 135–136 by physical methods, 134–135 test procedures, 129–130 N Nanoparticles (NPs), 47–48 Naphtoquinones, 332 Natural culture media, 33 Natural Red™, 332–334 Near-infrared spectroscopy (NIR), 172–173 Neocalimastigomycota, 85–88 AGF protein domains and homologous genes, 87–88 characteristic features of, 86 Neocallimastigomycota, 76, 78, 86

588

Index

Neocallimastix frontalis, 86 Net protein utilization (NPU), 345 Networking, in mycotoxin prevention and control, 133–134 Neurospora spp. for ethanol production, 50 N. crassa, 97–98 N. intermedia, 55, 442–443 Neurospora tetrasperma, genome, 77–78 Next-generation sequencing (NGS), 175 Nicotinamide adenine dinucleotide (phosphate) (NADPH), 172 Nitrogen-fixing bacteria, 190 Nitrogen, role of, 257 Nivalenol, 108–124, 109–123t Nixtamalization, 135 Non-coagulative pellets, 237–238 Non-essential amino acid (NEAAs), 407, 408t, 409f Nonwoven textiles, 519–521 Novozymes, 197, 210 Nucleophaga, 79 Nucleotides, 419–420 Nutrients, for fungal growth, 187f, 189t wastes, residuals, and wastewaters as, 185–187 Nutrition, fungal, 4, 70–71 O oCelloScope, 171 Ochratoxins, 376–377 economic impact, 108t health effect, 106t occurrence of, 124, 125–127t structure, producing fungi and stability of, 109–123t worldwide regulation limit of, 129t Oil cakes, as substrates, 258 Oil processing industry waste, 550–553 olive oil, 550–552 palm oil, 553 Oleaginous fungi, lipids from, 47 Oleic acid, 413 Olive oil mill water (OOMW), 552 Olive oil processing industry, 550–552

Oncom, 353–362t, 364–368 Operational taxonomic units (OTUs), 13 Opisthosporidia, 78–79 Optical density (OD), 170 Organic acid, 47, 366 production by SSF, 274, 274t citric acid, 275 lactic acid, 275 succinic acid, 275 Organic acid production, filamentous fungi, 455–456, 457t citric acid applications, 462 biochemical pathway, 470f biosynthesis, microorganisms, metabolism, and physiology of, 462–463 chemical structure of, 468f definition, 462 genetic and process engineering strategies, 465 global market, 462 production and processing conditions, 463–465 gluconic acid applications, 460 biochemical pathway, 469f biosynthesis, microorganisms, metabolism, and physiology of, 460 chemical structure of, 468f definition, 460 production and process conditions, 460–461 strain engineering and process modifications, 461–462 itaconic acid biochemical pathway, 469f biosynthesis, microorganisms, metabolism, and physiology of, 456–458 chemical process, 456 chemical structure of, 468f definition, 456 global production, 456 production and process conditions, 458–459

Index 589

strain engineering and process modifications, 459–460 oxalic acid applications, 466 biochemical pathway, 470f biosynthesis, microorganisms, metabolism, and physiology of, 466–467 chemical structure of, 468f definition, 466 production and process conditions, 467 strain engineering and process modifications, 468 Oxalic acid applications, 466 biochemical pathway, 470f biosynthesis, microorganisms, metabolism, and physiology of, 466–467 chemical structure of, 468f definition, 466 production and process conditions, 467 strain engineering and process modifications, 468 Oxidative stress, 418 Oxidoreductases, 5 Oxygen availability, 222 Oxygen transfer, fermentation, 42 Oxygen uptake rate (OUR), 174–175 Oxypilins, 76 Oyster mushroom, optimal temperature for, 41 Ozonation, 135 P Packed-bed bioreactors, 37, 38f, 40f, 267–268, 268f, 299, 301f characteristics and limitations, 271t for filamentous fungi cultivation, 224–225t, 231–232, 232f Palm oil mill effluent (POME), 553 Palm oil processing industry, 553 Paper like materials, from fungi, 519–521 Paramicrosporidium, 79 genes of, 81 Parasexual cycle, 72 Parasitic fungi, 4–6 Particle size, 262

Paspalitrems, 109–123t Pathogenic bacteria, in fermented food, 378–379 Pathogenic fungi, 6 Patulin economic impact, 108t health effect, 106t occurrence of, 124, 125–127t structure, producing fungi and stability of, 109–123t worldwide regulation limit of, 129t Pectinases, 198–199 Pellets, 199, 201f in submerged fermentation, 237–238 Penicillin, 45, 277, 486–487 mode of action, 487, 488f Penicillium sp., 68t in enzymes production, 296, 297–298t hydroxyanthraquinoid (HAQN) pigments, 331–332 in marine habitats, 336–337 mycotoxins, 108–124 P. chrysogenum, 491 P. marneffei, 329, 330f P. oxalicum var, 332–333 P. simplicissimum, 188–189 Penitrems, 109–123t Pentahydroxy hexanoic acid. See Gluconic acid (GA) Peptidases, 305 Pervaporation (PV), 445, 446f pH fermentation, 41–42 solid-state fermentation, 261 Pharma industry, fungi in, 43f, 45 Phenolic compounds, solid-state fermentation, 276t, 277 Phlebia sp., 53 Photobionts, 8 Phytase, 198–199 Phytohormones, 281 Pichia pastoris, 72 Pigment production, by filamentous fungi, 366–368, 367t animal feed, 417–418

590

Index

Pigment production, by filamentous fungi (Continued) bioactive pigment production (see Bioactive pigment production, by filamentous fungi) carbon and nitrogen source, 369 challenges and limitations, 369 downstream process, 368 extracellular pigment production, 368 factors affecting, 369 intracellular pigment, 368 solid-state fermentation, 368 submerged fermentation, 368 Pigments fungal, 45, 54 solid-state fermentation, 276t, 277 PlaFractor process, 272 Plant proteins in aquaculture diets, 402–404 consumption of, 348, 348f greenhouse gas (GHG) emissions of, 349, 349t protein content, quality, fat, and antinutrient compounds, 345–347, 346t sources, 344–345 Plants, fungal infections in, 6–7 Pleurotus eryngii, 40–41 Pleurotus ostreatus, 40–41, 68t, 423 Poisoned food method, 482 Pollution reduction, filamentous fungi in, 187–189, 187f, 189t Polyhydroxyalkanoates (PHA), 280 Poly-3-hydroxybutyrate (PHB), 280 Polyketide-Monascus-like pigments, 326–328 Polyketide synthases (PKSs), 328–329 Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), 159–160 Polyphasic taxonomy, 159 Polyploidy, 78 Polyunsaturated fatty acids (PUFAs), 366, 373, 375, 400–401, 410, 413 solid-state fermentation produced, 281–282 Potato dextrose agar, 159t Potato processing industry waste, 553–556

Potato protein liquor (PPL), 56 Power draw, 221 Prebiotics, 420–421 Predictive modeling, of mycotoxins, 137 Preservation, of filamentous fungi, 160–168 long-term, 162–163 cryopreservation, 163–166, 164t, 165f, 166t freeze-drying, 166–167 quality control, 167–168 short-term, 161–162 Pretreatment methods, 438 Primary microplastics, 189–190 PR-imine, 109–123t Productivity, fungal morphology and, 238–239 Prokaryotic protein expression systems, 311–313, 312t Protease, 273–274t, 305 Protein(s) animal and fish feed ingredients, 399–400 fishmeal, 400 fungal biomass, 406–408, 407t plant protein meals, 402–404 single-cell proteins (SCPs), 404–405 terrestrial animal by-product meals, 404 animal protein sources (see Animal protein) filamentous fungi environmental concerns, 349, 349t essential amino acid (EAA) contents, 374–375, 374t protein content, quality, fat, and antinutrient compounds, 343–344, 346t, 347–348 smart proteins, 349–350 tempe, 343–344 insects greenhouse gas (GHG) emissions, 348–349, 349t protein content, quality, fat, and antinutrient compounds, 346t, 347 plant-based sources (see Plant proteins) recombinant heterologous, 205–206t Protein-degrading enzymes, 305 Protein digestibility-corrected amino acid score (PDCAAS), 345–347, 373 Protein-encoding genes, 159–160

Index 591

Protein expression systems, 311–313, 312t Proteobacteria, 190 Pseudomycelia, 3 Psychrophilic fungi, 155 Puccinia graminis, 97 Pulp and paper industry, fungi in, 43f, 46 Pulp industry biobleaching, 208–209 bio-debarking, 204–206 bio-pitching, 206–207 biopulping, 207–208 bio-retting, 207 PV. See Pervaporation (PV) Q Quorn, 44, 55, 327, 372–373, 405 fatty acid profile, 375 production of, 384, 384f protein content of, 346t, 347–348 R Radial pumping impellers, 227 Raimbault columns, 267–268 Reactive oxygen species (ROS), 76, 418 Recombinant deoxyribonucleic acid (rDNA), 197 Recombinant heterologous proteins, 205–206t Red pigment mycotoxin-free Monascus red, 328–329 Natural Red™, 332–334 Reproduction, fungal, 3, 71 Ascomycota, 74–75 Basidiomycota, 75 Chytridomycota, 73 Glomeromycota, 74 unicellular yeast form, 72 Zygomycota, 73–74 Respiratory quotient, 174 Retting, 207 Reverse TCA (rTCA) pathway, 462–463 Reynolds number, 222 Rhamnolipids, 280 Rheology, 203–204, 220–221 Rhizomorphs, 71 Rhizopus sp., 51

BSG fermentation with, 265, 266f chitosan in, 56–57 enzymes production, 296 fruit and vegetable discards fermented with, 264, 264f fumaric acid production from, 53 lactic acid production, 52–53, 52t R. microsporus, 77, 379 R. oligosporus, 68t, 254 R. oryzae, 405, 440, 442f, 444 Riboflavin, 419 Riser, 229 Roquefortines, 109–123t Rose Bengal agar, 159t Rotating-bed bioreactors, 234–235, 234f Rotating drum bioreactor (RDB), 37, 38f, 267f, 268–269 characteristics and limitations, 271t Rotating fibrous bed reactor (RFBR), 240–241 Rotating/stirred drum reactors, 236 Rozella sp., 79–81 Rozellidea, 79–81 Rubia tinctoria, 332 Rubratoxin, 109–123t S Sacchachitin, 515–516 Saccharomyces cerevisiae, 68t, 445–447 genome of, 77–78, 242 growth of, 69 Salmonella sp. S. paratyphi, 378 S. typhimurium, 378 Sambacide, 277–278 Sampling and isolation, of filamentous fungi from environments, 154–156 from fermented products, 156–158, 157–158t Sampling procedures, filamentous fungi, 158 Saprophytic fungi, 4–5 Saprotrophic fungi, 5 Satratoxins, 108–124, 109–123t Saturated fatty acids (SFAs), 410 Schizophyllum commune, 68t Schizosaccharomyces pombe, 3 Scleroglucan, 497–498

592

Index

Secondary metabolites, 76, 275 Secondary microplastics, 189–190 Sekelan, 107 Semi-synthetic medium, 33 Sepiolite, 134 Sexual reproduction, 3, 71 in Ascomycota, 74–75 in chytrids, 73 in Entomophthoromycotina, 91 in Kickxellomycotina, 92 in Mucoromycota, 93–94 in Mucoromycotina, 94 in Zoopagomycotina, 91 in zygomycetes, 73–74 Shear forces, 223–224 Shear stress, 223–224 Short-term preservation, of filamentous fungi, 161–162 Sigmoidal growth curve, 70 Simultaneous saccharification and fermentation (SSF), 439 Single-cell genomics method, 83 Single-cell protein (SCP), 44, 404–405 Single spore isolation, 154 SmF. See Submerged fermentation (SmF) Solid-phase extraction (SPE) cleanup-fluorometric method, 136 Solid-state fermentation (SSF), 36–37, 198–199, 219–220, 251, 505–506 advantages, 37, 252 aroma compounds, 281 bioactive compounds/secondary metabolites, 275–278, 276t antibiotics, 277–278 phenolic compounds, 277 pigments, 277 biofuels production by, 278–279, 279t biopesticide production by, 278, 278t biopolymers, 280–281 bioreactors, 37, 38f, 265–270 characteristics and limitations, 271t fluidized-bed, 269, 269f packed-bed, 267–268, 268f rotating drum, 267f, 268–269 scaling-up, 265–266

spouted-bed, 269–270 tray, 266–267, 267f biosurfactants, 279–280 enzyme production by, 272–274, 273–274t advantages, 300 agro-industrial residues, 299, 300t limitation, 300 tray and packed-bed bioreactor, 299, 301f Zymotis design, 301 filamentous fungi for, 253–258, 256f fungal pigment production, 368 heat and mass transfer in, 262–265, 263f organic acids production by, 274, 274t citric acid, 275 lactic acid, 275 succinic acid, 275 phytohormones, 281 polyunsaturated fatty acids, 281–282 process control parameters, 258–259 aeration, 261–262 agitation, 262 biological factors, 259 moisture content and water activity, 259–260 particle size, 262 pH, 261 temperature, 260–261 products and current industrial applications, 270–282 reactor designs in, 235 rotating/stirred drum, 236 tray-like bioreactors, 235–236 substrates for, 252–258, 256f value-added products of, 255f Sophorolipids, 280 Soybean meal (SBM), 402–404, 408, 409f, 421–422, 424 Soy sauce, 353–362t, 370 definition, 364 fermentation, 364 health aspects, 376 names, 364 safety issues, 378 taste of, 364 traditional production methods, 380

Index 593

filtration and cooking, 382 koji fermentation, 380 moromi fermentation, 382 sortation and boiling, 380 types of, 378 Spices, mycotoxins in, 128 € rper, 69 Spitzenko Spo11, 72 Sporangia, 73 Sporangiophore, 73 Spore isolation, 153–154 single spore technique, 154 stages in, 153–154 Spores, 200, 201f Spouted-bed bioreactors, 269–270 characteristics and limitations, 271t SSF. See Solid-state fermentation (SSF) Staphylococcus aureus, 378 Starch, 437–438 Starch-based ethanol facility, 49 Statoliths, 71 Sterigmatocystins, 108–124 occurrence of, 125–127t structure, producing fungi and stability of, 109–123t Stirred packed bed bioreactor, 37, 38f Stirred-tank reactor (STR), 39, 40f, 224–225t, 226–227, 299, 302f configuration, 226f effect on fungal morphology, 240–241 Streptomyces sp., 484 Subculturing (serial transfer), 161–162 Submerged fermentation (SmF), 36–37, 198–199, 219–220, 480 advantages and disadvantages, 37–38 aeration and agitation in, 42 antibiotic production, 483 bioreactors for, 40f for enzymes production, 368 bubble column bioreactor, 299, 302f disadvantages, 301–303 fungal species, 299 stirred-tank bioreactor (STR), 299, 302f fungal pigment production, 368 modes in, 38

pellets formation in, 237–238 vs. solid-state fermentation, 252 Succinic acid, 275 Sugar, 437–438 Sugar processing industry waste, 556–558 Suspension, 199 Swiss-Prot, 76–77 Symbiotic Basidiomycota, 97 Symbiotic fungi, 4–5, 7 Synthetic culture media, 33 Synthetic dyes, bioremediation of, 46 T Talaromyces sp., 327–328 T. aculeatus, 327–328 T. albobiverticillius, 329–331 T. atroroseus, 329–331, 331f T. purpurogenus, 327–331 Taxonomy, of fungi, 8–13 Hibbett classification, 9–10, 10f Tedersoo classification, 10–11, 11f Wijayawardene classification, 11–12, 12f Tedersoo classification, of fungi, 10–11, 11f Tempe, 351–352, 353–362t, 375 definition, 351–352 essential amino acid (EAA) contents, 374–375, 374t fermentation process, 352–364 food by-products, 352 food safety concerns, 378–379 functional properties of, 376 industrial production modern process, 382–384, 383f traditional methods, 379–380, 381f protein source, 343–344 consumption rate, 351 greenhouse gas (GHG) emissions of, 343 protein content, quality, fat, and antinutrient compounds, 346t raw materials, 352 vitamin, 375 Temperature fermentation, factors influencing, 41 in solid-state fermentation, 260–261 Termitomyces clypeatus, 68t

594

Index

Terrestrial animal by-product meals, 404 Terrestrial fungi, 15 Tetracycline antibiotics, 478 Tetrapolar breeding, 75 Textile fibers, 519–521 Textile industry, fungi in, 43f, 46–47 Thaumatin, 372 Thermal processing, 135 Thermomyces lanuginosus, cultivation pH, 41–42 Thermotelomyces thermophila, 68t Thin stillage, 544–545 1000 Fungal Genomes project, 9 Time-kill test, 482 Tissue engineering, 516 Toxigenic fungi, 130–131 Trametes versicolor, 53 Transport, fungal, 70–71 Tray bioreactors, 37, 38f, 235–236, 266–267, 267f, 299, 301f characteristics and limitations, 271t Tremorgen, 109–123t Tricarboxylic acid cycle (TCA) cycle, 456–457, 462–463, 466–467 Trichoderma sp. in agriculture, 44 in enzyme production, 54, 297–298, 297–298t Trichoderma asperellum, 188–189 Trichoderma harzianum, 7 as biopesticide, 278 lipase production, 272 Trichoderma reesei, agitation in, 152–153 Trichothecenes, 108–124, 109–123t, 377 Trickle-bed bioreactors, 224–225t, 229–231, 230f Tricoderma reesei, 68t Tropolones, 490 True fungi (Eumycota), 9 Tryptoquivalines, 109–123t T-2 tetraol, 109–123t 2G bioethanol, 209 U Ultraviolet (UV) mutagens, 465 Unfolded protein response (UPR), 197 UNITE, 9

Usar, 380, 381f Ustilago maydis, 2, 68t, 457–459, 457t V Valorization, 255–257 Value-added products, 48–49 by solid-state fermentation, 255f Vanillic acid, 281 Vegan-mycoprotein, 48 Vegetative reproduction, 3, 72 Versatility, filamentous fungi bioeconomy, 533 bioethanol industry wastes, 544–548 brewery waste, 534–539 dairy processing industry, 558–560 fish processing industry waste, 548–550 fruit industry waste, 540–544 oil processing industry waste, 550–553 olive oil, 550–552 palm oil, 553 perspectives, 560–561 potato processing industry waste, 553–556 sugar processing industry waste, 556–558 sustainable development, 533 waste biorefinery, 533–534 Versicolorins, 109–123t Versiconol acetate, 109–123t Viomellein, 109–123t Viscosity, 220–221 Vitamins, 375, 419 Viticolins, 490 Void space, 263 Volvariella volvacea, 68t W Waste Directive 2018/851, 255–257 Wastewater treatment, 187–189 Water activity, 259–260 Water distribution systems, filamentous fungi isolation, 155 Water retting, 207 Wet distillers grain (WDG), 544–545 White-rot fungi, 5 in pulp and paper industry, 46 in synthetic dye degradation, 46

Index 595

Whittaker classification, of fungi, 9 Whole stillage, 544–545 Wijayawardene classification, of fungi, 11–12, 12f Wine, 444–445 Wound healing materials, 515–516 X Xanthomegnin, 109–123t Xeromyces bisporus, 152 Xylanase, 198–199, 209 Xylitol, 45 Xyloglucanase, 210–211t β-Xylosidase, 210–211t Y Yarrowia, 2 Yeasts, 2 budding in, 3 genome, 77–78 reproduction, 72 for solid-state fermentation, 253–258 Z Zearalenone, 377 economic impact, 108t health effect, 106t

occurrence of, 125–127t structure, producing fungi and stability of, 109–123t worldwide regulation limit of, 129t Zinc-finger transcription factors, 70–71 Zoopagomycota, 89–92 Zoopagomycotina, 91 Zoosporangia, 73 Zoosporic fungi, 70–71 genomes, 77 Zygomycetes biomass, 55–56 chitosan in, 56–57 food and feed applications, 56 cell wall, 186–187 ethanol production by, 440–441, 441t metabolites production, 51 ethanol, 52 fumaric acid, 53 lactic acid, 52–53, 52t phylogenic classification of, 89, 90t sexual reproduction in, 73–74 Zygomycota, 67–69 reproduction, 73–74 for solid-state fermentation, 254 Zygosporangium, 73–74 Zymomonas mobilis, 444