Microbial Diversity, Interventions and Scope [1st ed.] 9789811540981, 9789811540998

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Shiwani Guleria Sharma Neeta Raj Sharma Mohit Sharma  Editors

Microbial Diversity, Interventions and Scope

Microbial Diversity, Interventions and Scope

Shiwani Guleria Sharma • Neeta Raj Sharma • Mohit Sharma Editors

Microbial Diversity, Interventions and Scope

Editors Shiwani Guleria Sharma School of Bioengineering and Biosciences Lovely Professional Univeristy Phagwara, Punjab, India

Neeta Raj Sharma School of Bioengineering and Biosciences Lovely Professional Univeristy Phagwara, Punjab, India

Mohit Sharma Molecular Genetics Laboratory Dayanand Medical College and Hospital Ludhiana, Punjab, India

ISBN 978-981-15-4098-1 ISBN 978-981-15-4099-8 https://doi.org/10.1007/978-981-15-4099-8

(eBook)

# Springer Nature Singapore Pte Ltd. 2020 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors, and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Springer imprint is published by the registered company Springer Nature Singapore Pte Ltd. The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore

Dedicated to budding microbiologists

Preface

The book is a comprehensive reference book containing information on relationships of microbes with different fields of science. Main concern of scientific society is to understand how microorganisms effect environment. Recycling of natural resources and development of recombinant DNA technology, nanotechnology, bioremediation, and industries bring microbiology in limelight. The chapters of this book focus on microbial ecosystem and exploitation of microbes and their activity for human benefit. Each portion of this book emphasizes on new fields with essays highlighting introduction and important discoveries and developments in microbiology. The book contains contributions from many experts and will be a valuable resource for undergraduate and graduate students, doctoral scholars, scientists, and researchers associated with microbiology. This book will be beneficial for academicians as many universities throughout world have microbiology as a subject that cannot be completed without understanding diversity, interventions, and scope of microbes. The book will be beneficial for graduate students to understand the relationship of microbes in various fields, that is, agriculture, nanotechnology, genetic engineering, medical science, forensic science, and space. The book will also be beneficial to researchers and scientists as they can understand the impact of and explore new opportunities in this field. Phagwara, Punjab, India Phagwara, Punjab, India Ludhiana, Punjab, India

Shiwani Guleria Sharma Neeta Raj Sharma Mohit Sharma

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Contents

1

Microbial Ecosystem and Anthropogenic Impacts . . . . . . . . . . . . . . Lalita Vithal Baragi, Dhiraj Dhondiram Narale, Sangeeta Mahableshwar Naik, and K. M. Rajaneesh

Part I

1

Microbes in Agriculture

2

Recent Advances in Plant-Microbe Interaction . . . . . . . . . . . . . . . . Jayakumar Pathma, Gurusamy Raman, Rajendiran Kamaraj Kennedy, and Laxman Sonawane Bhushan

23

3

Microbes in Crop Production: Formulation and Application . . . . . Pankaj Prakash Verma, Rahul Mahadev Shelake, Parul Sharma, Jae-Yean Kim, Suvendu Das, and Mohinder Kaur

51

4

Microorganisms Improving Food Quality and Safety . . . . . . . . . . . Manpreet Kaur and Vijay Kumar

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5

Microbes in Soil and Their Metagenomics . . . . . . . . . . . . . . . . . . . . Suruchi Jindal

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Part II

Microbes in Nanotechnology

6

Microbial Cell Factories in Nanotechnology . . . . . . . . . . . . . . . . . . Deepak Sharma, Reena Sharma, and Abhishek Chaudhary

7

Nanotechnology and Food Microbiology . . . . . . . . . . . . . . . . . . . . . 109 Gagandeep Kaur and Shivani Sharma

Part III

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Microbes in Genetic Engineering

8

Bioengineered Microbes in Disease Therapy . . . . . . . . . . . . . . . . . . 117 Rahul Mehta

9

Benefits and Biohazards of Microbial Recombinants . . . . . . . . . . . . 123 Alla Singh, Mehak Sethi, Diksha Verma, Ritu Naliath, and D. P. Chaudhary

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Contents

Part IV

Microbial Enzymes & Applications

10

Extremophile Microorganisms and Their Industrial Applications . . . 137 Kamla Malik, Nisha Kumari, Sushil Ahlawat, Upendra Kumar, and Meena Sindhu

11

Innovative Techniques for Improving Microbial Enzyme Production . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157 Abhishek Thakur, Chayanika Putatunda, Rashmi Sharma, Rahul Mehta, Preeti Solanki, and Kavita Bhatia

12

Microbial Enzymes from In Vitro to Market . . . . . . . . . . . . . . . . . . 185 Ashish Vyas and Abdulhadi Yakubu

Part V

Microbes in Bioremediation

13

Microbial Clean Up Strategy for Polluted Water . . . . . . . . . . . . . . 219 Amaninder Kaur Riat

14

Microbial Clean-Up Strategy for Eating Garbage . . . . . . . . . . . . . . 231 Sheetal Rana, Abha Sharma, and Ranbir Singh Rana

Part VI

Microbes in Industries

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Microbes in Food and Beverage Industry . . . . . . . . . . . . . . . . . . . . 249 Neegam Nain, Katoch Gunjan Kumari, Hridya Haridasan, and Shiwani Guleria Sharma

16

Microbes in Pharmaceutical Industry . . . . . . . . . . . . . . . . . . . . . . . 259 Divya Kapoor, Pankaj Sharma, Mayur Mukut Murlidhar Sharma, Anju Kumari, and Rakesh Kumar

17

Industrial Potential of Microbial Enzymes . . . . . . . . . . . . . . . . . . . 301 Sonali and Richa Arora

Part VII

Microbes in Medicine

18

Living Medicines for Health and Disease Management . . . . . . . . . . 321 Surender Jangra and Ramesh Pothuraju

19

Fighting Microbes with Microbes . . . . . . . . . . . . . . . . . . . . . . . . . . 335 Boopathi Seenivasan, Chiranth M. Prakash, and Vani Janakiraman

20

Impact of Human Microbiome on Health . . . . . . . . . . . . . . . . . . . . 349 Sujata Das, Charu Khanna, Shalini Singh, Shilpa Nandi, and Reema Verma

Contents

Part VIII

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Microbes in Forensic Science

21

An Introduction to Microbial Forensics . . . . . . . . . . . . . . . . . . . . . . 377 Richa Aeri, Jasbir Arora, Priyanka Kapoor, and Arun Dev Sharma

22

Microbial Forensics: A New Boon to Legal Justice . . . . . . . . . . . . . 399 Jaskaran Singh, Shikha, and Ekampreet Kaur

Part IX 23

Microbes in Space

Microbes Supporting Life Off-Planet . . . . . . . . . . . . . . . . . . . . . . . 411 Shiwani Guleria Sharma and Mohit Sharma

About the Editors

Shiwani Guleria Sharma is an Assistant Professor at the School of Bioengineering and Biosciences at Lovely Professional University, Punjab, India. She holds a PhD in Microbiology from DR Yashwant Singh Parmar University of Horticulture and Forestry, Himachal Pradesh. Her research interests include agricultural microbiology, microbial enzymology and molecular biology. She has published articles in national and international, peer-reviewed journals. She has received various awards, including INSPIRE fellowship by DST-GOI, Gold Medal for doctorate from DR YSP UHF, H.P., state merit scholarships and a best research award from the Society for Advancement of Human and Nature, H.P. Neeta Raj Sharma holds a Ph.D. in Biochemistry from Jiwaji University Gwalior, and heads the School of Bioengineering and Biosciences as Additional Dean at Lovely Professional University, Punjab. She has experience in multidisciplinary areas such as microbial biochemistry and biotechnology, and waste management. She has been instrumental in conducting various international funded research projects. Dr. Sharma is a member of a number of societies, including the Association of Biotechnology and Pharmacy, Indian Science Congress, Association of Microbiologists of India, Indo-US Collaboration of Engineering Education, International Science Congress Association, and the Indian Society of Agricultural Biochemists. She has published over 55 articles in respected journals and book chapters, and holds 20 patents. Mohit Sharma is an Associate Biotechnologist at the Molecular Genetics Laboratory at Dayanand Medical College and Hospital, Ludhiana, Punjab. His interests include human genetics and cytogenetics, molecular plant microbial interactions, vector cloning, bioinformatics, molecular biology, and cell biology. He holds a Ph.D. in Biotechnology from Shoolini University of Biotechnology and Management Sciences, Himachal Pradesh, India. He has also worked on the isolation and characterization of hypovirulence-associated mycovirus from Fusarium species from apple orchards in Himachal Pradesh. He has published research articles in various national and international, peer-reviewed journals.

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Abbreviations

AMF BOD CAED CDC COD DGGE FBI FMT GEMS HMP ISR ISS ITS MPS MS NAATs NSG PMA PNAS SCFAs SDM SOM SRB STDs

Arbuscular mycorrhizal fungi Biological oxygen demand Computer Aided Enzyme Design Centre for Disease Control Chemical oxygen demand Denaturing gradient gel electrophoresis Federal Bureau of Investigation Fecal microbial transplantation Genetically Engineered Microorganisms Human Microbiome Project Induced systemic resistance International Space Station Internal transcribed spacer Massive parallel sequencing Mass spectrometry Nucleic acid amplification tests Next generation sequencing Propidium monoazide Proceedings of National Academies of Science Short chain fatty acids Site-directed mutagenesis Soil organic matter Sulfates reducing bacteria Sexually transmitted diseases

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1

Microbial Ecosystem and Anthropogenic Impacts Lalita Vithal Baragi, Dhiraj Dhondiram Narale, Sangeeta Mahableshwar Naik, and K. M. Rajaneesh

Abstract

Oceans are the most vulnerable sites for anthropogenic waste from domestic as well as industrial origin. Usually, marine ecosystems are exposed to most anthropogenic stressors ranging from sewage disposal to nuclear waste contaminants. Most recent threats to marine ecosystems are ocean warming and ocean acidification (related to anthropogenic emission of CO2), oil (tarball), and (micro) plastic contamination, which is proved to have a devastating impact on the marine ecosystem. Microbes are abundantly present in marine ecosystems playing essential roles in ecosystem productivity and biogeochemistry. Generally, microbial communities are the initial responders of these stressors. Altered microbial communities in response to these stressors can, in turn, have adverse impact on the marine ecosystem and later on humans. In this review, we highlight the effect of oil pollution, microplastics, and increased CO2 on the marine microbial ecosystem. The information on the impacts of such stressors on microbial communities will be valuable to formulate appropriate remediation approaches for future use.

L. V. Baragi (*) Applied and Environmental Biotechnology Laboratory, Department of Biological Sciences, BITS, Pilani, KK Birla Goa Campus, Sancoale, Goa, India e-mail: [email protected] D. D. Narale CSIR-National Institute of Oceanography, Dona Paula, Goa, India S. M. Naik National Center for Coastal Research, Government of India, Ministry of Earth Science, Chennai, India K. M. Rajaneesh King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia # Springer Nature Singapore Pte Ltd. 2020 S. G. Sharma et al. (eds.), Microbial Diversity, Interventions and Scope, https://doi.org/10.1007/978-981-15-4099-8_1

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L. V. Baragi et al.

Keywords

Microbial ecosystem · Anthropogenic stressors · Oil pollution · Microplastics · Ocean warming · Ocean acidification

1.1

Introduction

It is well known that two-thirds of planet Earth is covered by marine waters (Charette and Smith 2010). These waters have a significant role in the global biogeochemical cycles, which sustains the life in the ocean (Schlesinger 1997; Sarmiento and Gruber 2006). Even though the standing crop of marine ecosystems represents 1% of the terrestrial biomass, it contributes to approximately half of the biomass produced on Earth (Gruber et al. 2009; Hader et al. 2011). Among the marine ecosystems, one-half of global primary production occurs in the oceans (Falkowski et al. 1998; Field et al. 1998). Oceans also control the climate and weather pattern. Therefore, the ocean has a significant effect on the biosphere and much of life on Earth. In recent years, exploitation of the ocean by human-derived activities such as fishing, tourism, oil exploration, maritime transport, and industrial activities has a substantial impact on the marine ecosystem (Nogales et al. 2011; Halpern et al. 2007, 2008). These activities affect different trophic levels of marine food web, which comprises microorganisms to animal predators. According to a recent study, the vast region of the world ocean is forecasted to have medium to high impact from these stressors (Halpern et al. 2008). Most recent stressors to these ecosystems are ocean warming and ocean acidification and oil (tarball) and microplastic contamination, which are proved to have a devastating impact on the marine ecosystem, mainly biology of the ecosystem. Ocean warming and ocean acidification are the result of increasing concentration of atmospheric CO2 (Caldeira and Wickett 2003; Orr et al. 2005) and are now being recognized as a major responsible factor for change in the biological system of the oceans (Lovejoy and Hannah 2005). Presently, the concentration of atmospheric CO2 has reached 400 ppm from 280 ppm from preindustrial revolution (NOAA/ ESRL; Stocker et al. 2013) with ~0.5% year 1 rising rate (Forster et al. 2007). Approximately one-third of the anthropogenic CO2 generated is absorbed by the oceans and will help moderate future climate change (Sabine et al. 2004). This resulted in a decrease in pH by 0.1 unit (referred to as ocean acidification) and rise in temperature by 0.85  C (referred to as ocean warming) (Raven et al. 2005). By the end of this century, the concentration of atmospheric CO2 is predicted to reach 800–1000 μatm by the “business as usual” CO2 emission scenario climate models, which will further decrease the pH (0.3–0.4 units) and increase the temperature (1–4  C) (Stocker et al. 2013; Caldeira and Wickett 2003). Elevated CO2 concentration will result in an increase in H+ concentration (100–150%), which will negatively affect the marine organisms, especially calcifying organisms (Haugan and Drange 1996; Brewer 1997).

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Microbial Ecosystem and Anthropogenic Impacts

3

Oil pollution is another threat to the marine environment presently. Oil spills mainly arise from either accidents or oily discharges from ships (Solberg 2012). Operational discharges from tankers cause the majority of the oil pollution cases. The effect of the spills on the marine ecosystem depends on several factors such as the quantity and quality of spilled oil, the sensitivity of the organisms exposed to the oil, location, depth, season, and meteorological and oceanic conditions (Fukuyama et al. 1998). These oil spills mainly have negative consequences on the ecology of the marine ecosystem (Fukuyama et al. 1998). To some extent, oceans are also used as dumping sites for debris from human activities. Marine debris comprised of manufactured solid material, of which 60–80% consists of plastic (Gregory and Ryan 1997). According to a study, an estimated 1.3 plastic items can be found for every m2 of shoreline worldwide, which is believed to be a significant threat to the marine ecosystem (Bravo et al. 2009). More than 267 species worldwide are impacted by this debris either by ingestion or entanglement (Gall and Thompson 2015). Plastics having size range between 333 μm and 5 mm are called microplastics. Smaller particles (