Advanced Microbial Techniques in Agriculture, Environment, and Health Management: Impact and Disposal Strategies 0323916430, 9780323916431

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Advanced Microbial Techniques in Agriculture, Environment, and Health Management

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Developments in Applied Microbiology and Biotechnology

Advanced Microbial Techniques in Agriculture, Environment, and Health Management Edited by

Satish Chandra Pandey Center for Advanced Biotechnology Research, Absolute, Gurugram, Haryana, India Cell & Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University Campus, Almora, Uttarakhand, India

Veni Pande Cell & Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University Campus, Almora, Uttarakhand, India Department of Biotechnology, Sir J.C. Bose Technical Campus, Bhimtal, Kumaun University, Nainital, Uttarakhand, India

Diksha Sati Cell & Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University Campus, Almora, Uttarakhand, India Department of Zoology, Kumaun University, Nainital, Uttarakhand, India

Mukesh Samant Cell & Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University Campus, Almora, Uttarakhand, India

Academic Press is an imprint of Elsevier 125 London Wall, London EC2Y 5AS, United Kingdom 525 B Street, Suite 1650, San Diego, CA 92101, United States 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom 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: 978-0-323-91643-1 For Information on all Academic Press publications visit our website at https://www.elsevier.com/books-and-journals

Publisher: Stacy Masucci Acquisitions Editor: Kattie Washington Editorial Project Manager: Billie Jean Fernandez Production Project Manager: Omer Mukthar Cover Designer: Greg Harris Typeset by MPS Limited, Chennai, India

Contents List of contributors .............................................................................................................................. xv

CHAPTER 1 Beneficial microbes for sustainable agroecosystem .......................... 1 1.1 1.2 1.3 1.4

1.5

Sandhya Bind, Sudha Bind and Dinesh Chandra Introduction ................................................................................................................ 1 Beneficial microbes in agriculture............................................................................. 2 Beneficial microbes: a key element for sustainable agricultural system.................. 3 Rhizosphere: a hot spot of beneficial microbes ........................................................ 4 1.4.1 Beneficial microbes ......................................................................................... 4 1.4.2 Nutrient management by beneficial microbes................................................. 8 1.4.3 Role of beneficial microbes in production of plant growth regulators ........ 10 1.4.4 Beneficial microorganisms as biofertilizers and biopesticides ..................... 11 1.4.5 Role of beneficial microbes in abiotic stress ................................................ 11 1.4.6 Role of beneficial microbes as a biocontrol agent........................................ 11 Conclusion ................................................................................................................ 12 Reference .................................................................................................................. 12

CHAPTER 2 Strategies and implications of plant growth promoting rhizobacteria in sustainable agriculture ........................................... 21 2.1 2.2 2.3

2.4 2.5 2.6 2.7 2.8

Damini Maithani, Anita Sharma and S.T.M. Aravindharajan Introduction .............................................................................................................. 21 Plant growth promoting rhizobacteria and plant interaction................................... 22 Plant growth promoting rhizobacteria: mechanisms of action................................ 24 2.3.1 Biological nitrogen fixation ........................................................................... 25 2.3.2 Phosphorous solubilization ............................................................................ 28 2.3.3 Zinc solubilizing bacteria .............................................................................. 30 2.3.4 ACC deaminase production ........................................................................... 31 2.3.5 Phytohormone production.............................................................................. 32 2.3.6 Siderophore production for iron acquisition ................................................. 35 2.3.7 Antibiotic production ..................................................................................... 36 2.3.8 Biosurfactant production................................................................................ 38 Plant growth promoting rhizobacteria in abiotic stress remediation ...................... 38 Plant growth promoting rhizobacteria in biotic stress remediation ........................ 39 Induced systemic resistance ..................................................................................... 41 Commercialization of plant growth promoting rhizobacteria-based bioproducts ............................................................................................................... 43 Conclusion and future prospects.............................................................................. 44

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Acknowledgment ...................................................................................................... 44 References................................................................................................................. 44

CHAPTER 3 Role of quorum sensing in plant
microbe interactions................... 57 3.1 3.2 3.3 3.4 3.5 3.6

Prasenjit Debbarma, Chandra Mohan Kumar, Manshi Kumari, Poornima, Govind Makarana, Saurabh Gangola and Saurabh Kumar Introduction .............................................................................................................. 57 Quorum sensing in rhizobacterial community colonization ................................... 59 Quorum sensing and plant disease protection ......................................................... 60 Quorum sensing in nitrogen-fixing rhizobia ........................................................... 61 Quorum sensing in rhizosphere engineering ........................................................... 62 Conclusion ................................................................................................................ 62 References................................................................................................................. 63

CHAPTER 4 Microbial services for mitigation of biotic and abiotic stresses in plants................................................................................ 67 4.1 4.2

4.3

4.4 4.5 4.6

Viabhav Kumar Upadhayay, Damini Maithani, Hemant Dasila, Gohar Taj and Ajay Veer Singh Introduction .............................................................................................................. 67 Different types of stresses........................................................................................ 68 4.2.1 Abiotic stress.................................................................................................. 68 4.2.2 Biotic stress .................................................................................................... 68 Microbial resources for alleviation of stress in plant.............................................. 68 4.3.1 Bacterial-assisted drought mitigation in plants ............................................. 69 4.3.2 Bacterial-assisted salinity mitigation in plant ............................................... 69 4.3.3 Bacterial-assisted heavy metal stress mitigation........................................... 70 4.3.4 Bacterial-assisted cold stress mitigation........................................................ 71 4.3.5 Bacterial-assisted biotic stress mitigation ..................................................... 71 Microbial effects on crop productivity under stress conditions.............................. 72 Agricultural application of stress-tolerant microorganisms .................................... 73 Conclusion ................................................................................................................ 74 References................................................................................................................. 75

CHAPTER 5 Prospects of biotechnology for productive and sustainable agro-environmental growth ............................................ 83 Madhvi Sharma, Amanpreet K. Sidhu and Diksha Sati 5.1 Introduction .............................................................................................................. 83 5.2 Genetic engineering and sustainable agriculture..................................................... 83 5.3 Role of microorganisms in agriculture .................................................................... 84 5.3.1 Biofertilizers in agroecosystem ..................................................................... 85 5.3.2 Biopesticides, biofungicides, and bioinsecticides in agroecosystem............ 86

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5.3.3 Plant
microbial interaction: mycorrhiza and plant growth-promoting rhizobacteria .................................................................... 88 5.4 Nanotechnology in agriculture................................................................................. 89 5.4.1 Nanofertilizers................................................................................................ 89 5.4.2 Nanopesticides ............................................................................................... 90 5.4.3 Nanotechnology for improved soil quality.................................................... 91 5.4.4 Nanotechnology in food industry .................................................................. 91 5.5 Conclusion and future prospects.............................................................................. 91 References................................................................................................................. 92

CHAPTER 6 Biofertilizers: a microbial-assisted strategy to improve plant growth and soil health .............................................................. 97 6.1 6.2 6.3 6.4 6.5

6.6

6.7

6.8

Amir Khan, Divyansh Panthari, Raj Shekhar Sharma, Arjita Punetha, Ajay Veer Singh and Viabhav Kumar Upadhayay Introduction .............................................................................................................. 97 What is a biofertilizer?............................................................................................. 98 Need for biofertilizers at higher altitudes................................................................ 99 Preparation of biofertilizer: steps and standards ................................................... 100 Types of bioformulations ....................................................................................... 102 6.5.1 Solid bioformulation .................................................................................... 102 6.5.2 Liquid bioformulation .................................................................................. 104 6.5.3 Encapsulated bioformulations...................................................................... 105 Types of biofertilizers ............................................................................................ 105 6.6.1 Nitrogen-fixing biofertilizers ....................................................................... 105 6.6.2 Phosphate solubilizing biofertilizers............................................................ 106 6.6.3 Phosphate-mobilizing biofertilizers ............................................................. 107 6.6.4 Potassium-solubilizing biofertilizers ........................................................... 107 6.6.5 Iron-solubilizing biofertilizers ..................................................................... 108 6.6.6 Zinc-solubilizing biofertilizer ...................................................................... 108 Mode of biofertilizer application ........................................................................... 109 6.7.1 Foliar application ......................................................................................... 109 6.7.2 Seed treatment.............................................................................................. 110 6.7.3 Soil treatment ............................................................................................... 110 Challenges of biofertilizer commercialization ...................................................... 110 6.8.1 Biological constraints................................................................................... 112 6.8.2 Technical constraints ................................................................................... 112 6.8.3 Regulatory constraints ................................................................................. 112 6.8.4 Marketing constraints................................................................................... 112 6.8.5 Field-level constraints .................................................................................. 113 6.8.6 Biofertilizer carrier....................................................................................... 113

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6.9 Conclusion .............................................................................................................. 113 Acknowledgment .................................................................................................... 113 References............................................................................................................... 114

CHAPTER 7 Biocontrol: an efficient solution for sustainable agriculture and food production ...................................................... 119 7.1 7.2 7.3

7.4

7.5

Amrita Kumari, Ankita H. Tripathi, Priyanka H. Tripathi and Anupam Pandey Introduction ............................................................................................................ 119 Biological control: types ........................................................................................ 120 7.2.1 Types of biocontrol strategies...................................................................... 120 Biocontrol and biofertilization with microorganisms for sustainable agriculture............................................................................................................... 121 7.3.1 Plant growth-promoting rhizobacteria ......................................................... 121 7.3.2 Rhizobia ....................................................................................................... 123 7.3.3 Endophytic fungi.......................................................................................... 123 7.3.4 Mycorrhizal fungi ........................................................................................ 123 7.3.5 Rhizospheric fungi ....................................................................................... 124 7.3.6 Bacterial endosymbionts and endophytes ................................................... 125 7.3.7 Microbes of various environments .............................................................. 125 7.3.8 Viruses: biological control agents ............................................................... 126 Examples of biocontrol agents used in agriculture ............................................... 127 7.4.1 Biocontrol of sugarcane Pyrilla................................................................... 127 7.4.2 Biocontrol of cotton bollworm .................................................................... 127 7.4.3 Biocontrol of water hyacinth ....................................................................... 128 7.4.4 Biocontrol of woolly apple aphid................................................................ 128 7.4.5 Biocontrol of white woolly aphid................................................................ 128 Conclusion .............................................................................................................. 129 References............................................................................................................... 129

CHAPTER 8 Impact of environmental pollutants on agriculture and food system ....................................................................................... 133 Sofiya Anjum and Smita Rana 8.1 Introduction ............................................................................................................ 133 8.1.1 Metals and metalloids .................................................................................. 134 8.1.2 Electronic waste ........................................................................................... 137 8.1.3 Plastics.......................................................................................................... 138 8.1.4 Nanoparticles................................................................................................ 138 8.1.5 Radioactivity/nuclear reactors ..................................................................... 139 8.1.6 Pharmaceuticals and personal care products ............................................... 139

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8.1.7 Sewage wastewater and sludge.................................................................... 140 8.1.8 Particulate matter ......................................................................................... 141 8.1.9 Dyes from textile industries......................................................................... 142 8.2 Remediation for removal of chemical contaminants............................................. 142 8.3 Conclusion .............................................................................................................. 143 References............................................................................................................... 144

CHAPTER 9 Hazardous waste: impact and disposal strategies.......................... 153

9.1 9.2 9.3

9.4 9.5

9.6

9.7

Hemant Dasila, Divya Joshi, Shulbhi Verma, Damini Maithani, Sawan Kumar Rawat, Amit Kumar, Neha Suyal, Narendra Kumar and Deep Chandra Suyal Introduction ............................................................................................................ 153 Classification of hazardous wastes ........................................................................ 154 Impact of hazardous waste..................................................................................... 155 9.3.1 Environment ................................................................................................. 155 9.3.2 Humans......................................................................................................... 156 Methods for identification and monitoring of hazardous waste ........................... 158 9.4.1 Identification of hazardous waste: Indian scenario..................................... 159 Strategies for hazardous waste management ......................................................... 159 9.5.1 Physical strategies ........................................................................................ 159 9.5.2 Chemical strategies ...................................................................................... 161 9.5.3 Biological strategies..................................................................................... 162 9.5.4 Modern hybrid technology........................................................................... 163 Impact of mismanagement: illegal trafficking and poor transportation facility ...........164 9.6.1 Hazardous waste transportation ................................................................... 164 9.6.2 Illegal trafficking ......................................................................................... 164 Conclusion .............................................................................................................. 165 References............................................................................................................... 165

CHAPTER 10 Bioremediation of heavy metals by soil-dwelling microbes: an environment survival approach................................................... 167 Amir Khan, Raj Shekhar Sharma, Divyansh Panthari, Bharti Kukreti, Ajay Veer Singh and Viabhav Kumar Upadhayay 10.1 Introduction ............................................................................................................ 167 10.2 Sources of heavy metals ........................................................................................ 168 10.2.1 Industrial source of heavy metals.............................................................. 168 10.2.2 Natural source of heavy metals ................................................................. 169 10.2.3 Agricultural source of heavy metal ........................................................... 169 10.2.4 Domestic sources ....................................................................................... 170 10.2.5 Other sources of heavy metal effluence .................................................... 170 10.3 Consequences of heavy metal toxicity on human and plant health...................... 170

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10.4 Techniques for heavy metal removal .................................................................... 173 10.4.1 Physical methods........................................................................................ 173 10.4.2 Chemical remediation ................................................................................ 174 10.4.3 Phytoremediation ....................................................................................... 174 10.4.4 Microbial remediation of heavy metals..................................................... 175 10.5 Genes involved in determining resistance against different heavy metals in bacteria ................................................................................................... 178 10.5.1 Resistance to antimony and arsenic .......................................................... 179 10.5.2 Resistance to mercury................................................................................ 179 10.5.3 Resistance to nickel and cobalt ................................................................. 180 10.5.4 Resistance to copper .................................................................................. 180 10.5.5 Resistance to cadmium .............................................................................. 181 10.5.6 Resistance to zinc....................................................................................... 181 10.6 Factors affecting microbial remediation................................................................ 182 10.6.1 pH ............................................................................................................... 182 10.6.2 Ambient temperature ................................................................................. 182 10.6.3 Substrate species ........................................................................................ 182 10.6.4 Substrate concentration .............................................................................. 183 10.6.5 Condition of soil milieu............................................................................. 183 10.6.6 Bioavailability of pollutants and biosurfactants........................................ 183 10.7 Conclusion and future prospects............................................................................ 184 References............................................................................................................... 184

CHAPTER 11 Omics approaches to pesticide biodegradation for sustainable environment .................................................................. 191 11.1 11.2 11.3

11.4 11.5

Saurabh Gangola, Samiksha Joshi, Geeta Bhandari, Pankaj Bhatt, Saurabh Kumar and Satish Chandra Pandey Introduction ............................................................................................................ 191 Biodegradation ....................................................................................................... 192 Parameters affecting biodegradation of pesticides ................................................ 193 11.3.1 Pesticide structure ...................................................................................... 193 11.3.2 Pesticide concentration .............................................................................. 194 11.3.3 Pesticide solubility ..................................................................................... 194 11.3.4 Soil types.................................................................................................... 195 11.3.5 Soil moisture .............................................................................................. 195 11.3.6 Temperature ............................................................................................... 195 11.3.7 Soil pH ....................................................................................................... 195 11.3.8 Soil organic matter..................................................................................... 195 11.3.9 Soil microbial biomass............................................................................... 196 Proteomics of pesticide biodegradation................................................................. 196 Molecular basis of pesticide degradation .............................................................. 196

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11.6 Metagenomic analysis ............................................................................................ 198 11.6.1 Cultivation-independent methods .............................................................. 198 11.7 Conclusion .............................................................................................................. 199 References............................................................................................................... 200

CHAPTER 12 Microbial consortia and their application for environmental sustainability..................................................................................... 205 12.1 12.2

12.3

12.4

Prasenjit Debbarma, Rashmi Sharma, Nidhi Luthra, Satish Chandra Pandey and Shiv Vendra Singh Introduction ............................................................................................................ 205 Microbial bioremediation of pollutants ................................................................. 206 12.2.1 Potential microbial candidates................................................................... 206 12.2.2 Bioremediation: potential and sustainable process for environmental cleanup ............................................................................... 208 12.2.3 Mechanisms involved in bioremediation................................................... 210 12.2.4 Enzymes for bioremediation...................................................................... 211 12.2.5 Major bioremediation strategies/techniques and their types..................... 213 Rhizospheric soil-plant-microbe interactions ........................................................ 214 12.3.1 Plant growth-promoting rhizobacteria ....................................................... 214 12.3.2 Nitrogen-fixing microbes........................................................................... 215 12.3.3 Nutrient-solubilizing microbes .................................................................. 215 12.3.4 Nutrient-mobilizing microbes.................................................................... 215 12.3.5 Arbuscular mycorrhizal fungi.................................................................... 216 Conclusion .............................................................................................................. 216 References............................................................................................................... 217

CHAPTER 13 Recent advances in in silico approaches for removal of environmental pollutants .................................................................. 223 13.1 13.2 13.3 13.4 13.5 13.6 13.7 13.8 13.9 13.10 13.11

Tushar Joshi, Shalini Mathpal, Priyanka Sharma, Satish Chandra Pandey, Priyanka Maiti, Mahesha Nand and Subhash Chandra Introduction ............................................................................................................ 223 In silico approaches................................................................................................ 224 In silico approach for toxicity analysis of pollutants ............................................ 225 Molecular docking approach for bioremediation .................................................. 226 Molecular dynamics simulation approach for bioremediation.............................. 228 Biodegradation pathway prediction ....................................................................... 229 Metabolic pathway simulation of biodegradation ................................................. 229 Bioremediation using proteomics .......................................................................... 229 Bioremediation using genomics............................................................................. 230 Systems biology methods....................................................................................... 231 Removal of environmental pollutants through artificial intelligence ................... 232

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13.12 Conclusion .............................................................................................................. 233 References............................................................................................................... 234

CHAPTER 14 Significance of nanoscale in macro-scale in various sectors such as agriculture, environment, and human health .................... 239 14.1 14.2

14.3

14.4 14.5

Priyanka Basera, Shuchishloka Chakraborty, Meeta Lavania and Banwari Lal Introduction ............................................................................................................ 239 Nanomaterials in agriculture sector ....................................................................... 240 14.2.1 Crop enhancement: use of nanofertilizers ................................................. 241 14.2.2 Crop protection .......................................................................................... 243 14.2.3 Crop improvement ..................................................................................... 243 14.2.4 Fate of nanomaterial in soil ....................................................................... 244 Nanomaterial in environmental sector................................................................... 244 14.3.1 Wastewater and water remediation ........................................................... 245 14.3.2 Remediation ............................................................................................... 248 14.3.3 Sources of energy....................................................................................... 249 14.3.4 Environmental sensing............................................................................... 250 Negative aspects of nanotechnology...................................................................... 252 Conclusion .............................................................................................................. 253 References............................................................................................................... 253

CHAPTER 15 Recent advances in biofilm formation and their role in environmental protection.................................................................. 263 15.1 15.2 15.3

15.4

Shobha Upreti, Vinita Gouri, Veni Pande, Diksha Sati, Garima Tamta, Satish Chandra Pandey and Mukesh Samant Introduction ............................................................................................................ 263 Biofilm formation................................................................................................... 264 15.2.1 Events of signaling in biofilm formation .................................................. 266 Role of biofilms in environmental protection ....................................................... 267 15.3.1 Bioremediation ........................................................................................... 267 15.3.2 Heavy metal remediation........................................................................... 268 15.3.3 Remediation of hydrocarbons.................................................................... 269 15.3.4 Wastewater treatment................................................................................. 269 15.3.5 Biofilms in agriculture ............................................................................... 270 15.3.6 Polyethylene degradation........................................................................... 271 15.3.7 Biofilm formation for health ..................................................................... 271 Conclusion .............................................................................................................. 273 Acknowledgments .................................................................................................. 273 Conflict of interest.................................................................................................. 273 References............................................................................................................... 273

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CHAPTER 16 Antibiotics: action mechanism and modern challenges ................. 281 Utkarsha Sahu and Prashant Khare 16.1 Introduction ............................................................................................................ 281 16.2 History, classification, and mechanism of action of different antibiotics ............ 282 16.2.1 History of antibiotics ................................................................................. 282 16.2.2 Classification of antibiotics ....................................................................... 283 16.2.3 Antibiotics in the environment: modern challenges and future perspectives ................................................................................................ 286 16.2.4 Discussion .................................................................................................. 288 References............................................................................................................... 289

CHAPTER 17 Drug resistance in pathogenic species of Candida ........................ 293 Neha Jaiswal and Awanish Kumar 17.1 Introduction ............................................................................................................ 293 17.2 Epidemiology ......................................................................................................... 294 17.3 Overview of molecular mechanisms of drug resistance ....................................... 296 17.3.1 ERG genes.................................................................................................. 296 17.3.2 ATP-binding cassette ................................................................................. 297 17.3.3 FKS genes .................................................................................................. 297 17.4 Factors facilitating antifungal drug resistance....................................................... 298 17.5 Conclusion and future prospects............................................................................ 298 Acknowledgments .................................................................................................. 299 References............................................................................................................... 299 Index .................................................................................................................................................. 305

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List of contributors Sofiya Anjum Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India S.T.M. Aravindharajan Department of Microbiology, G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, India Priyanka Basera Environmental and Industrial Biotechnology Division, The Energy and Resources Institute, New Delhi, Delhi, India Geeta Bhandari Department of Biosciences, Himalayan School of Biosciences, Swami Rama Himalayan University, Dehradun, Uttarakhand, India Pankaj Bhatt Department of Agriculture and Biological Engineering, Purdue University, West Lafayette, IN, United States Sandhya Bind Department of Biological Sciences, College of Basic Sciences & Humanities, Govind Ballabh Pant University of Agriculture & Technology, U.S. Nagar, Uttarakhand, India Sudha Bind Department of Biological Sciences, College of Basic Sciences & Humanities, Govind Ballabh Pant University of Agriculture & Technology, U.S. Nagar, Uttarakhand, India Shuchishloka Chakraborty Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India Dinesh Chandra Department of Biological Sciences, College of Basic Sciences & Humanities, Govind Ballabh Pant University of Agriculture & Technology, U.S. Nagar, Uttarakhand, India; GIC Chamtola, Almora, Uttarakhand, India Subhash Chandra Computational Biology & Biotechnology Laboratory, Department of Botany, SSJ University, Almora, Uttarakhand, India Hemant Dasila Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Himachal Pradesh, India Prasenjit Debbarma School of Agriculture, Graphic Era Hill University, Dehradun, Uttarakhand, India Saurabh Gangola School of Agriculture, Graphic Era Hill University, Bhimtal, Uttarakhand, India

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Vinita Gouri Cell and Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University, Almora, Uttarakhand, India; Department of Zoology, Kumaun University, Nainital, Uttarakhand, India Neha Jaiswal Department of Biotechnology, National Institute of Technology, Raipur, Chhattisgarh, India Divya Joshi Uttarakhand Pollution Control Board, Regional Office, Kashipur, Uttarakhand, India Samiksha Joshi School of Agriculture, Graphic Era Hill University, Bhimtal, Uttarakhand, India Tushar Joshi Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India Amir Khan Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar (U.S. Nagar), Uttarakhand, India Prashant Khare Department of Microbiology, All India Institute of Medical Sciences, Bhopal (Madhya Pradesh), India; Center for Advanced Biotechnology Research, Absolute, Gurugram, Haryana, India Bharti Kukreti Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar (U.S. Nagar), Uttarakhand, India Amit Kumar Forest Ecology and Climate Change Division, Forest Research Institute, Dehradun, Uttarakhand, India Awanish Kumar Department of Biotechnology, National Institute of Technology, Raipur, Chhattisgarh, India Chandra Mohan Kumar ICAR-Research Complex for Eastern Region, Patna, Bihar, India Narendra Kumar Doon (PG) College of Agriculture Science and Technology, Dehradun, Uttarakhand, India Saurabh Kumar ICAR-Research Complex for Eastern Region, Patna, Bihar, India Amrita Kumari Sir J. C. Bose Technical Campus, Bhimtal, Kumaun University, Nainital, Uttarakhand, India Manshi Kumari Patna Women’s College, Patna, Bihar, India Banwari Lal Environmental and Industrial Biotechnology Division, The Energy and Resources Institute, New Delhi, Delhi, India

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Meeta Lavania Environmental and Industrial Biotechnology Division, The Energy and Resources Institute, New Delhi, Delhi, India Nidhi Luthra Department of Soil Science, Indian Agricultural Research Institute, New Delhi, Delhi, India Damini Maithani School of Biotechnology, IFTM University, Moradabad, Uttar Pradesh, India Priyanka Maiti Centre for Environmental Assessment and Climate Change, G.B. Pant National Institute of Himalayan Environment (GBP-NIHE), Kosi-Katarmal, Almora, Uttarakhand, India Govind Makarana ICAR-Research Complex for Eastern Region, Patna, Bihar, India Shalini Mathpal Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India Mahesha Nand ENVIS Centre on Himalayan Ecology, G.B. Pant National Institute of Himalayan Environment (GBP-NIHE), Kosi-Katarmal, Almora, Uttarakhand, India Veni Pande Cell & Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University Campus, Almora, Uttarakhand, India; Department of Biotechnology, Sir J.C. Bose Technical Campus, Bhimtal, Kumaun University, Nainital, Uttarakhand, India Anupam Pandey Sir J. C. Bose Technical Campus, Bhimtal, Kumaun University, Nainital, Uttarakhand, India Satish Chandra Pandey Cell & Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University Campus, Almora, Uttarakhand, India; Center for Advanced Biotechnology Research, Absolute, Gurugram, Haryana, India Divyansh Panthari Department of Botany, School of Basic and Applied Science, Sri Guru Ram Rai University, Dehradun, Uttarakhand, India Poornima Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India Arjita Punetha Research Scholar, CSIR-Central Institute of Medicinal & Aromatic Plants (CIMAP), Research Centre, Pantnagar (U. S. Nagar), Uttarakhand, India Smita Rana Department of Chemistry, Kumaun University, Nainital, Uttarakhand, India Sawan Kumar Rawat Department of Mathematics, Statistics and Computer Science, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India

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Utkarsha Sahu Department of Microbiology, All India Institute of Medical Sciences, Bhopal (Madhya Pradesh), India; Center for Advanced Biotechnology Research, Absolute, Gurugram, Haryana, India Mukesh Samant Cell & Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University Campus, Almora, Uttarakhand, India Diksha Sati Department of Zoology, Kumaun University, Nainital, Uttarakhand, India; Cell & Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University Campus, Almora, Uttarakhand, India Anita Sharma Department of Microbiology, G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, India Madhvi Sharma PG Department of Biotechnology, Khalsa College, Amritsar, Punjab, India Priyanka Sharma Department of Botany, Kumaun University, Nainital, Uttarakhand, India Raj Shekhar Sharma Department of Microbiology, School of Basic and Applied Science, Sri Guru Ram Rai University, Dehradun, Uttarakhand, India Rashmi Sharma School of Agriculture, Graphic Era Hill University, Dehradun, Uttarakhand, India Amanpreet K. Sidhu PG Department of Biotechnology, Khalsa College, Amritsar, Punjab, India Ajay Veer Singh Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar (U.S. Nagar), Uttarakhand, India Shiv Vendra Singh School of Agriculture, Graphic Era Hill University, Dehradun, Uttarakhand, India Deep Chandra Suyal Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Himachal Pradesh, India Neha Suyal Government Nursing College, Haldwani, Uttarakhand, India Gohar Taj Department of Molecular Biology & Genetic Engineering, College of Basic Sciences and Humanities, GBPUAT, Pantnagar, Uttarakhand, India Garima Tamta Department of Chemistry, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India

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Ankita H. Tripathi Sir J. C. Bose Technical Campus, Bhimtal, Kumaun University, Nainital, Uttarakhand, India Priyanka H. Tripathi Sir J. C. Bose Technical Campus, Bhimtal, Kumaun University, Nainital, Uttarakhand, India Viabhav Kumar Upadhayay Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar (U.S. Nagar), Uttarakhand, India; Department of Microbiology, College of Basic Sciences & Humanities, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India Shobha Upreti Cell and Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University, Almora, Uttarakhand, India; Department of Zoology, Kumaun University, Nainital, Uttarakhand, India Shulbhi Verma Department of Biotechnology, SDAU, Dantiwada, Gujarat, India

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CHAPTER

Beneficial microbes for sustainable agroecosystem

1

Sandhya Bind1, Sudha Bind1 and Dinesh Chandra1,2 1

Department of Biological Sciences, College of Basic Sciences & Humanities, Govind Ballabh Pant University of Agriculture & Technology, U.S. Nagar, Uttarakhand, India 2GIC Chamtola, Almora, Uttarakhand, India

1.1 Introduction According to the United Nations the world population will reach up to 9.8 billion by 2050 (Bongaarts, 2009). To nourish this ever-growing population, agricultural productivity has to be increased by 70%. Various strategies have been used to increase agricultural productivity. Conventional breeding negatively affects the physical, chemical, and biological properties of soil and carbon stocks, which makes them unsustainable for future food and fiber. The excessive manufacture and utilization of chemical fertilizers and pesticides are not sustainable. Production of synthetic nitrogen fertilizer is energy intensive. Potassium and phosphorus fertilizers are produced from mined resources, which are likely to deplete in 100 years. Excessive utilization of these chemical fertilizers and pesticides leads to environmental pollution and many health problems. Therefore an eco-friendly approach is needed for achieving global food security with sustainable agriculture. According to FAOSTAT (2021), the agroecosystem comprises 40% of the land area that provides food, fiber, and biofuels to the growing world population. Enhanced productivity in these systems depends on intense agricultural management and practices that have an impact on the important functions and services of the ecosystem, including soil fertility, renewal, and purification of groundwater, and also suppression of pathogens and pests (Dornbush & von Haden, 2017). Past and current agricultural practices will not be sustainable for a long time. Thus there is a need for agricultural practices that lead to high agricultural production and sustainable establishment of agroecosystem services (Pe’er et al., 2019). In agriculture a multifaceted network of connections exists between plants and microbes. Ecologically compatible and eco-friendly techniques helpful in providing adequate nutrients to the ever-growing population through improved quality and quantity of agricultural products is necessary. The application of beneficial microbes in agriculture served as an eco-friendly approach under the current scenario of climate change. Agriculturally important microbes play a key role in nutrient management, disease, and pest management and act as a substitute for chemical fertilizers and improve the quality of crops. Anthropogenic activities and intensive agricultural practices enhance greenhouse gas production (Hunter, 2008). The soil microbial community plays a vital role in the consumption of greenhouse gases (Bardgett, Freeman, & Ostle, 2008). Recent research aims to exploit the traits of microbes in improving the nutrient content and crop protection against abiotic and biotic stresses with changing climate to achieve sustainable agriculture. This chapter is Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00008-9 © 2023 Elsevier Inc. All rights reserved.

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Chapter 1 Beneficial microbes for sustainable agroecosystem

envisioned to emphasize the advent of the agriculturally important microorganism for the development of a model agricultural system through proficient use of nutrients and recycling of energy, preserving the resources of the natural ecosystem under changing climate.

1.2 Beneficial microbes in agriculture The world of microbes is a huge unexplored reservoir on the earth. According to Bhattacharyya and Jha (2012), only a minute portion of approximately 10% of microbial diversity is identified up to the last century. Though microbes are the smallest entity among living organisms, they play a vibrant role in all ranges of activities inside the living organism on the planet. Therefore microbial ecologybased research has become an imperative frontline in biological sciences. The plant rhizosphere is a chief niche where abundant microorganisms are found. The microbes present in the rhizosphere are mostly beneficial. The utilization of these beneficial microbes in bioformulation serves as an efficient way of enhancing crop productivity. Among microbial diversity, bacteria, fungi, algae, actinomycetes, protozoa, and viruses have enormous activities (Andreote & Silva, 2017). Plant body, considered as a multifaceted interplay of ecological niches that harbor a wide diversity of microorganisms in their rhizosphere, rhizoplane, phyllosphere, and endosphere, form a broad range of beneficial, harmful, and neutral interactions (Turner, James, & Poole, 2013). Plant root exudates are carbon-rich, having sugars, organic acids, vitamins, etc. Plants also release numerous compounds due to various biotic and abiotic stressors. Soil microbes (especially bacteria) can sense these chemical signals and secrete various compounds, activating the defense mechanism of plants (Glick, 2012). A native plant microbial community is known as a microbiome, which represents a group of various organisms that colonize a given environment (Boon et al., 2014). Microbiomes energetically interact with the plant host to establish a synergistic relationship, influencing the physiology of the host (Foo, Ling, Lee, & Chang, 2017; Sati et al., 2022). Plentiful studies have been conducted to explore the mechanism of microbiome development and its dynamics in shaping plant performance in the ecosystem. Microbes play an important and diverse role in agriculture, horticulture, and forestry. Agriculturally important microbes are huge groups of microbes that interact with plants and have beneficial effects (Higa & Parr, 1994). Various microbes play a significant role in plant growth and health promotion by increasing the disease resistance of plants against various plant pathogens, thereby helping in crop protection. According to Higa and Wididana (1991), effective microorganisms signify a group of beneficial microorganisms used efficiently as microbial inoculants for intensification of native microbial diversity in the rhizosphere and the bulk soil of growing plants. Microorganisms play a key role in the management of pests (invertebrates and vertebrates), weeds, and plant diseases that damage agricultural crops and forest plants. Fungi and bacteria play a key role in providing resistance toward various abiotic (drought, salinity, heat) and biotic (insect, pest, disease) stress (Chandra, Srivastava, Gupta, Franco, & Sharma, 2019b; Chandra et al., 2019a; Singh, Gill, & Tuteja, 2011). Viruses are seen to play a significant role even at extreme temperatures (up to 115 F), for instance, in Yellowstone National Park, where it forms a symbiotic association by colonizing plant roots (Roossinck, 2011). Due to their exceptionality—their impulsive nature and biosynthetic abilities—, microbes are relatively adaptable to specific environmental and cultural conditions that help in solving numerous problems related to disease suppression and crop improvement.

1.3 Beneficial microbes: a key element for sustainable agricultural system

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FIGURE 1.1 Schematic diagram depicting the role of beneficial microbes in sustainable agriculture.

Microbes are an alternative to synthetic fertilizers and pesticides, and as such, they are extensively used as biofertilizers in natural farming and agricultural practices (Chandra, Srivastava, Glick, & Sharma, 2020). Belowground soil biota exhibits a vital role in the functioning of agroecosystems. Among these biotas the microbial community is the key element of both natural and managed agroecosystems (Fierer, 2017). Microbes associated with plants and soil help in nutrient cycling and carbon storage, maintaining the physical, chemical, and biological characteristics of the soil (Garnica, Rosenstein, & Schon, 2020). The microbial community of the soil enhances plant growth and improves plant health through direct and indirect mechanisms. Modern agricultural practices focus on high yield with a low number of plants, which negatively affects the plant-associated soil microbial community, which ultimately reduces soil quality (Banerjee et al., 2019; Mariotte et al., 2018). The use of these belowground microbial communities as a management strategy for the agricultural system is gradually being recognized and also plays a key element in meeting the challenges of sustainable agroecosystems (Barka et al., 2016; Ray, Lakshmanan, Labb´e, & Craven, 2020). In the present day, more emphasis is given to the functional characteristic or diversity of crops as well as on the associated above- and belowground microbial community (Barot et al., 2017). A conceptual diagram demonstrating the role of beneficial microbes in sustainable agriculture is summarized in Fig. 1.l.

1.3 Beneficial microbes: a key element for sustainable agricultural system In the mid-20th century, agricultural technology that was used to ensure the green revolution earned high ecological costs, leading to various environmental problems, climate change, and destruction of biodiversity (Scherr & McNeely, 2008). Soil microbes produce different kinds of metabolites

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Chapter 1 Beneficial microbes for sustainable agroecosystem

and maintain the physical, chemical, and biological characteristics of the soil, enhancing soil health and fertility. An ideal agricultural system should be regenerative, self-sustaining, protective of the environment, and economically valuable for both producers and consumers. Soil microbes produce various plant growth regulators. Among the beneficial microbes, bacteria are present in enormous amounts. Plant growth promoting rhizobacteria (PGPR) are beneficial bacteria that enhance plant growth by producing indole acetic acid (IAA), cytokinin, gibberellin, hydrocyanic acid (HCN), lytic enzyme, siderophore, antibiotic, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, solubilization of phosphate, and by nitrogen fixation (Chandra, Pallavi, & Sharma, 2017).

1.4 Rhizosphere: a hot spot of beneficial microbes The rhizosphere represents the narrow zone of soil directly influenced by plant roots having a high turnover of nutrients and microbial density. It is the region where abiotic and biotic factors remain in strict control of each other (Hu et al., 2018). Beneficial microbes present in the rhizosphere in a high number include mycorrhizal fungi and PGPR (Sati et al., 2020). The variety and extent of organic nutrients in root exudates, root architecture, and root branching pattern determine the microbial diversity in the rhizosphere. The process of root exudation helps in the transfer of carbon into the soil. Up to 20% of fixed carbon is released into the soil through root exudates by photosynthesis.

1.4.1 Beneficial microbes 1.4.1.1 Plant growth promoting bacteria PGPR represents a diverse group of bacteria, residing in the rhizosphere and enhancing the growth of plants through various direct and indirect mechanisms, thus showing a positive effect on the environment. In most cases, such plant growth promoting bacteria belong to the following species: Pseudomonas, Arthrobacter, Achrombactor, Enterobacter, Variovorax, Alcaligenes, Bacillus, Klebsiella, Burkholderia, Azospirillum, Azotobacter, and Serratia. The interaction between plants and PGPR is synergistic, with both partners benefitting from it. Plants provide carbohydrates, organic acids, vitamins, and minerals through root exudates. In turn, PGPR help in plant growth by enhancing nutrient availability through nitrogen fixation, solubilization of phosphate, zinc, potassium, chelation of iron, and some other micronutrients (such as zinc, boron, and copper). PGPR also produce various phytohormones (IAA, gibberellin, cytokinin, ethylene, and abscisic acid), ACC deaminase (reduces ethylene concentration during stress condition), HCN, lytic enzymes, and antibiotics, which act against various plant pathogens and also play a key role in induced systemic resistance of plants (Backer et al., 2018). PGPR also produces hydrolytic enzymes such as glucanases and pectinases, which hydrolyze the fungal cell wall and inhibit the growth of fungal pathogens. PGPR also provides resistance to different kinds of abiotic stresses (water stress, salinity, and cold stress due to enzymatic antioxidant properties e.g., Pseudomonas frederiksbergensis, Bacillus spp., and Planomicrobium spp.) (Abbas et al., 2019). PGPR have the ability to release various osmolytes that synergistically act with the osmolytes produced by plants and increase plant growth (Paul & Nair, 2008). According to the study by Ansary et al. (2012), inoculation of maize with

1.4 Rhizosphere: a hot spot of beneficial microbes

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Pseudomonas fluorescens increased the proline content under water stress conditions. Higher proline content in inoculated plants indicates a higher plant tolerance toward water stress (Gusain, Singh, & Sharma, 2015). PGPR produce various volatile compounds that provide protection against soil-borne pathogens. Application of Bacillus and Pseudomonas sp. protect Vitis vinifera and Mentha piperita against soil-borne pathogens (Cappellari, Chiappero, Santoro, Giordano, & Banchio, 2017). The volatile organic compounds of microbes play an essential role in plant growth, impart resistance against both biotic and abiotic stresses, and act as a potential biocontrol agent (Chandra et al., 2017). PGPR also provide relevant benefits to agroforestry management. Various PGPR such as Pseudomonas, Bacillus, Azotobacter, Variovorax, Paenibacillus, and Azospirillum have been used for various crops (rice, wheat, maize). Pseudomonas and Bacillus sp. have proven to be excellent biofertilizers (Turatto, Dourado, Zilli, & Botelho, 2017). PGPR enhance the germination of seeds, stimulate the rooting of cuttings, act as a biocontrol agent against various diseases, and increase the survival percentage after transplantation due to better root development. Some of the beneficial functions of PGPR are summarized in Table 1.1.

Table 1.1 Beneficial role of PGPR in various crops. PGPR sp.

Crops

Beneficial effects

References

Achromobacter piechaudii

Solanum lycopersicum

Mayak, Tirosh, and Glick (2004)

Azospirillum brasilense sp245

Triticum aestivum Finger millet [Eleusine coracana (L.) Gaertn.] Helianthus annuus

Enhanced biomass reduced ethylene concentration under abiotic stress Increased yield and nutrient contents Improved plant growth and antioxidant enzymes

Enhanced yield

Akbari, Ghalavand, Sanavy, AghaAlikhani, and Kalkhoran (2011) Chandra, Srivastava, Gupta, Franco, and Sharma (2019)

Pseudomonas spp. (DPB13, DPB15, and DPB16)

Azotobacter and Azospirillum

Variovorax paradoxus RAA3; Pseudomonas spp. DPC12, DPB13, DPB15, DPB16; Achromobacter spp. PSA7, PSB8; and Ochrobactrum anthropi DPC9 Azospirillum lipoferum, Rhizobium radiobacter, and Bacillus megaterium Rhizobium leguminosarum Pseudomonas fluorescens DPB15 and P. palleroniana DPB16

Cerus, Sueldo, and Barassi (2004) Chandra, Pallavi, Barh, and Sharma (2018)

Wheat (Triticum aestivum L.)

Increased plant growth, nutrient concentrations, and antioxidant enzymes

Finger Millet [Eleusine coracana (L.) Gaertn.] Lens culinaris

Improved plant growth, yield, and nutrients

Tyagi, Durgapal, Arshi, and Chandra (2020)

Increased nodulation, growth, and yield Inoculants application increased plant growth, nutrient contents, and enzymatic and nonenzymatic antioxidants

Iqbal et al. (2012)

Wheat (Triticum aestivum L.)

Chandra, Srivastava, and Sharma (2018)

(Continued)

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Chapter 1 Beneficial microbes for sustainable agroecosystem

Table 1.1 Beneficial role of PGPR in various crops. Continued PGPR sp.

Crops

Beneficial effects

References

Bacillus megaterium

Brassica oleracea Triticum aestivum

Increased growth, nutrients, and hormone levels Increased root length, plant biomass, and relative water content Increased yield

Turan et al. (2014)

Increased yield under water and salinity stress Increased yield, resistance against insect pests Increased yield

Chatterjee et al. (2017)

Fragaria ananassa Glycine max

Increased productivity and fruit quality Increased nodule number, yield, and inhibitory effect against pathogens

Seema, Mehta, and Singh (2018) Zhao, Xu, and Lai (2018)

Mentha piperita

Increased plant biomass, Peroxidase activity under water stress

Chiappero, Cappellari, Sosa Alderete, Palermo, and Banchio (2019)

Klebsiella, Flavobacterium sp., and Enterobacter ludwigii Paenibacillus illinoisensis, Bacillus spp. Pseudomonas frederiksbergensis Bacillus spp., Pseudomonas spp. Azospirillum spp., Pseudomonas spp. Bacillus subtilis, Bacillus licheniformis Pseudomonas spp., Bacillus spp., Pantoea spp., Serratia spp., Acinetobacter spp., Agrobacterium spp., Burkholderia spp. Bacillus amyloliquefaciens

Arachis hypogea Capsicum annuum Triticum aestivum Oryza sativa

Gontia-Mishra, Sapre, Sharma, and Tiwari (2016) Liu et al. (2017)

Naeem et al. (2018) Braga et al. (2018)

1.4.1.2 Mycorrhizal fungi Mycorrhizal fungi describe the symbiotic relationship between plant roots and fungi. Mycorrhizae colonize plant roots extracellularly and intracellularly. Ectomycorrhizal fungi form a net in the outer cell wall layers of plant roots without invading plant cells (species of Ascomycotina and Basidiomycotina). Arbuscular mycorrhizal fungi (AMF) are the most important endophytic fungi that colonize plants intracellularly and make the arbuscules and vesicles in plant roots. The association between plant roots and fungi is mutual in that plants provide carbohydrate to mycorrhizal fungi and, in turn, get nutrients and water from the soil with their help. AMF form a symbiotic association with approximately 93% of the terrestrial plant family. AMF belong to glomeromycotina having orders Glomerals, Archaeosporales, Diversisporales, and Paraglomerales (Spatafora et al., 2016). AMF form the massive network of hyphae in the soil, thus increasing nutrient and water absorption by plants. Plants provide carbohydrate and lipid to AMF; in turn AMF enhance the uptake of nutrients and promote the uptake of phosphorus, iron, zinc, and nitrogen, thus enhancing crop growth and productivity by reducing the application of chemical fertilizers. Due to intensive practices of conventional agriculture, the diversity of mycorrhizal fungi have decreased, leading to the reduction in the ecosystem functionality of mycorrhizal fungi (Gianinazzi et al., 2010; Oehl et al., 2004). AMF can be used as a

1.4 Rhizosphere: a hot spot of beneficial microbes

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biofertilizer for sustainable agriculture as an alternative to chemical fertilizers and increasing the nutritional quality of crop products with higher productivity. Inorganic phosphate transporter (Pi) was reported in the Glomus versiforme that increased the absorption of phosphate from the soil (Parihar et al., 2020). The mycorrhizal association also has a role in the detoxification of both inorganic and organic pollutants in the soil. The application of mycorrhizal fungi inoculum in highly degraded soil leads to overcoming the situation of biotic and abiotic stress in the soil, helping to restore soil health (Verbruggen, Van Der Heijden, Rillig, & Kiers, 2013). Application of consortia of mycorrhizal fungi is more effective in the agricultural system than the application of single mycorrhizal sp. (Crossay et al., 2019). Some of the beneficial functions of AFM are summarized in Table 1.2.

Table 1.2 Beneficial role of arbuscular mycorrhizal fungi (AMF) in various crops. AMF sp.

Crop

Effect

Reference

Glomus intraradices and Scutellospora calospora

Triticum aestivum and Pisum sativum Solanum lycopersicum Fragaria ananassa

Enhanced uptake of zinc

Ryan and Angus (2003)

Enhanced yield

Makus (2004)

Enhanced productivity and quality Significantly enhanced yield Suppression of rootknot nematode Enhanced yield

Stewart, Hamel, Hogue, and Moutoglis (2005)

Zea mays

Increased yield and grain quality

Berta et al. (2013)

Helianthus annuus

Increased biomass

Manihot esculenta Cicer arietinum

Enhanced yield

Gholamhoseini, Ghalavand, Dolatabadian, Jamshidi, and Khodaei-Joghan (2013) Ceballos et al. (2013)

G. intraradices Glomus mosseae, G. intraradices, Glomus etunicatum G. intraradices G. inraradices Consortia of Glomus fasciculatum, Glomus clarum, G. etunicatum, Glomus versiforme Glomus aggregatum, Glomus viscosum, G. etunicatum, and Glomus claroideum G. mosseae and Glomus holi

Rhizophagus irregularis Funneliformis mosseae, Rhizophagus irregularis Rhizophagus irregularis Rhizophagus irregularis Rhizophagus irregularis and Funneliformis mossea

Solanum tuberosum S. lycopersicum Piper longum

S. tuberosum Gossypium hirsutum Crocus sativus

Increased production and quality of grain Enhanced yield Enhanced quality and yield of cotton Enhanced quality, antioxidant content, and yield of saffron

Douds, Nagahashi, Reider, and Hepperly (2007) Lax, Becerra, Soteras, Cabello, and Doucet (2011) Singh and Gogoi (2012)

Pellegrino and Bedini (2014) Hijri (2016) Gao et al. (2020) Caser et al. (2019)

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Chapter 1 Beneficial microbes for sustainable agroecosystem

1.4.1.3 Actinomycetes Actinomycetes are a vast group of prokaryotes comprising six classes and six orders having both cultivable and noncultivable sp. Actinobacteria are gram-positive bacteria that may be aerobic or anaerobic and exhibit variation morphologically, physiologically, and biochemically. They also have various pigmentation known as melanoid polymers, which exhibit similarity with humic acid present in the soil (Barka et al., 2016). Production of geosmin, an organic compound, by actinomycetes is accountable for the characteristic earthy odor. Actinomycetes adhere to the epidermal layer of plant roots and subcortical root cells, and they colonize plant roots endophytically. Arthrobacter, Corynebacterium, Micrococcus, Rhodococcus, Nocardia, Streptomyces, Microbacterium, Microbispora, Micromonospora, Streptosporangium, Streptoverticillium, and Frankia are some important genera belonging to actinomycetes. Actinomycetes have the ability to produce diverse bioactive compounds essential for human health and agriculture. More than 10,000 secondary metabolites known to be produced by these microbes have antimicrobial, antitumor, and antiinflammatory properties (Manivasagan, Venkatesan, Sivakumar, & Kim, 2014). Actinomycetes produce phytohormone and different organic acids that enhance plant growth under various abiotic and biotic stress (Bhatti, Haq, & Bhat, 2017). Actinomycetes play a key role in nitrogen fixation, phosphate solubilization, and siderophore production, thus increasing the availability of these nutrients for plants (Bouizgarne & Aouamar, 2014). Actinomycetes also produces various volatile organic compounds having a role in the suppression of various plant pathogens, acting as a chemical signal for communication, biofilm formation, mycelium formation, and modulating the pH of the soil (Lewin et al., 2016). Actinomycetes are a reservoir of various lytic enzymes (protease, amylase, pectinase, lipase, xylanase, exo- and endoglucanase). These lytic enzymes are responsible for plant cell wall degradation and help microbes to gain entry inside the plants (Bhatti et al., 2017). Lytic enzymes, chitinases, peroxidases, dextranases, cutinases, and laccases produced by actinomycetes degrade the cell wall of fungal pathogens inhibiting their growth (Martı´nez-Hidalgo, GalindoVillardo´n, Trujillo, Igual, & Martı´nez-Molina, 2014). Actinomycetes remain in the soil with high cell density and viability thus enhancing plant growth and health by various means. These microbes can be used as a biopesticide, insecticide, biocontrol agent, and biofertilizer. Some of the beneficial functions of actinomycetes in agriculture are summarized in Table 1.3.

1.4.2 Nutrient management by beneficial microbes According to Miao, Stewart, and Zhang (2011) nutrient management is a science of optimum use of soil, hydraulic factors, and critical NPK (nitrogen, phosphorus, potassium) inputs. It also optimizes nutrient use efficiency and improves soil health, plant growth, and environment (Miao et al., 2011). Plants take in various nutrients from the rhizosphere in the soil and from the phyllosphere in the atmosphere (Turner et al., 2013). A special environment is created in the rhizosphere with the help of diverse compounds released by the plant root system. Nowadays, people are more concerned about the quality of food. Due to the ever-growing population and climate change the pressure of producing food with good quality has become challenging. The pressure is increased due to the reduction of farmlands, rising labor costs, etc. Synthetic fertilizers are being used in agricultural fields to fulfill the requirement of macro and micronutrients,

1.4 Rhizosphere: a hot spot of beneficial microbes

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Table 1.3 Beneficial role of actinomycetes in agriculture. Actinomycetes

Crop

Beneficial effect

References

Streptomyces avermitilis

Vegetable crops

Streptomyces pactum Act12 and Streptomyces rochei D74

Aconitum carmichaelii

Sousa and Olivares (2016) Li et al. (2020)

Streptomyces sp.

Legume (Cicer arietinum, Pisum sativum, Glycine max) Zea mays

Biocontrol agent against insects and nematodes Growth promotion and biocontrol against southern blight (Slerotium rolfsii) and root rot (Fusarium oxysporum) Increased yield

Increased growth and drought tolerance

ChukwunemeBabaloa, Kutu, and Ojuederie (2020) Sreevidya, Gopalkrishnan, Kudapa, and Varchney (2016) Wang et al. (2018)

Streptomyces pseudovenezuelae

AbdElgawad et al. (2020)

Streptomyces sp.

Cicer arietinum

Increased nodule number and yield

Streptomyces griseoplanus (PSA1) Streptomyces sp. KLBMP5084 Micromonospora lupini Lupac 08 Amycolatopsis sp.

Zea mays

Increased yield

Solanum lycopersicum Lupinus angustifolius Cicer arietinum and Sorghum Vegetables and fruits

Enhanced plant growth and salt tolerance Enhanced growth and yield

Gong et al. (2020)

Increased plant growth and yield

Alekhya and Gopalakrishnan (2016) Salwan and Sharma (2020)

Solanum lycopersicum

Biocontrol agent against Rhizoctonia solani and improved plant health Inhibited growth of Pythium aphanidermatum thus reduced damping-off, crown, and root rot of cucumber

Corynebacterium spp., Pseudonocardia dioxanivorans, Streptomyces sp. Strain MBCN152-1 Streptomyces sp. NBM1, NBM2, NBM3, and NBM12 Actinoplanes campanulatus, Streptomyces spiralis

Cucumis sativus

Enhanced growth and yield and act as biocontrol agent

Trujillo et al. (2014)

Singh, Gupta, Gaur, and Shrivastava (2017) El-Tarabily, Nassar, Hardy, and Shivashithamparam (2009)

leading to environmental pollution. Nutrient mobilization through microbes is a chief driver of plant growth and occasionally turns into a rate-limiting step in ecosystem productivity (Schimel & Bennett, 2004). For sustainable agriculture, beneficial microbes in the soil are being used, which play a vital role in nutrient management (Adhya et al., 2015). Among the beneficial microbes, bacteria and fungi play a key role in the breakdown of soil organic matter and the recycling of nutrients (Neill & Gignoux, 2006).

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Chapter 1 Beneficial microbes for sustainable agroecosystem

1.4.2.1 Role of beneficial microbes in phosphorus solubilization Plants obtain phosphorus as phosphate ions from the soil. Phosphorus solubilizing microorganisms (PSMs) play a crucial role in phosphorus nutrition. PSMs enhance the phosphorus availability in plants through solubilization and mineralization (Chandra, Srivastava, & Sharma, 2016; Sharma, Sayyed, Trivedi, & Gobi, 2013). Beneficial microbes produce organic acids and acid phosphatase that reduces soil pH during phosphorus solubilization. In comparison to fungi, bacteria are more efficient in phosphorus solubilization (Sharma et al., 2013). When phosphorus solubilizing bacteria (PSB) are coinoculated with mycorrhizal fungi or some other beneficial bacteria, their efficiency of phosphorus solubilization increases (Mohammadi, 2012). Rhizospheric strains of Pseudomonas, Bacillus, Rhizobium, Enterobacter, and many endophytic bacteria are reported as efficient phosphate solubilizers (Khan, Zaidi, & Wani, 2007). Among fungal genera, Aspergillus and Penicillium are efficient phosphorus solubilizers (Saxena, Basu, Jaligam, & Chandra, 2013).

1.4.2.2 Role of beneficial microbes in potassium solubilization and mobilization Potassium is a vital component of plant nutrition and performs various biological and physiological functions. Potassium is usually abundant in soil. According to Bertsch and Thomas (1985), the total potassium content present in the topsoil ranges from 3000 to 1,00,000 kg/ha. Potassium is present in four forms: (1) water soluble, (2) exchangeable, (3) nonexchangeable, and (4) structural or mineral (Sparks & Huang, 1985). Changes in soil pH, texture, temperature, moisture level, and oxygen level determine the extent of release of potassium from soil (Basak & Biswas, 2009). Several beneficial microbes have the capability of potassium mobilization. Microbes produce organic acids that mobilize potassium present in feldspar, muriate of potash, or waste mica, making it available for plants (Sessitsch et al., 2013). Beneficial bacterial sp. such as Arthrobacter, Azotobacter sp., Acidithiobacillus ferrooxidans, Bacillus mucilaginosus, Bacillus edaphicus, Klebsiella sp., Pseudomonas sp., Paenibacillus sp., and Rhizobium sp. are reported to mobilize insoluble potassium into soluble form in the soil for better plant nutrition (Liu, Lian, & Dong, 2012).

1.4.3 Role of beneficial microbes in production of plant growth regulators Microbes produce various plant growth regulators, which combine with plant-produced phytohormones and exert various physiological functions in plants. Microorganisms residing in plant rhizospheres synthesize and release auxins (Kapoor, Kumar, Patil, & Kaur, 2012). Soil microorganisms are responsible for producing various bioactive compounds, which affect plant growth and development (Ahemad & Kibret, 2014). PGPR produce various phytohormones such as IAA, gibberellic acid, and cytokinin, which enhances plant growth (Kloepper, Gutierrez-Estrada, & Mclnroy, 2007). Most of the PGPR, either symbiotic or free-living species, produce IAA and gibberellic acid in the rhizosphere, which have enormous potential in the enhancement of root surface area and a number of root tips of plants (Han et al., 2005). According to many studies, fungi also play a vital role in plant growth promotion (Murali, Amruthesh, Sudisha, Niranjana, & Shetty, 2012). Beneficial fungal species produces various antibiotic and lytic enzymes such as chitinases, proteases, and glucanases, which act as biocontrol agents. Various Trichoderma strains are also reported to colonize plant roots and enhance plant growth and development (Saba et al., 2012).

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1.4.4 Beneficial microorganisms as biofertilizers and biopesticides The use of beneficial microbes as biofertilizers and biopesticides represent a sustainable approach in the modern agriculture system (Bhardwaj, Ansari, Sahoo, & Tuteja, 2014). Microbial biofertilizers comprises living microorganisms. These biofertilizers, when applied to the soil, seed, or plant surface, enhance plant growth by increasing the uptake of nutrients through plant roots (Bhattacharyya & Jha, 2012). Microbial biopesticides comprise living microorganisms that produce various compounds such as antibiotics, HCN, hydrolytic enzymes, and siderophore, promoting plant growth by inhibiting or killing phytopathogens (Chandler, Davidson, Grant, Greaves, & Tatchell, 2018). Various beneficial microbes such as Pseudomonas, Bacillus, Rhizobium, Azotobacter, Enterobacter, Variovorax, Azospirillum, Allorhizobium, Acetobacter, Azorhizobium, Aspergillus, Bradyrhizobium, Mesorhizobium, and penicillium have the vital capacity to be an efficient biofertilizer or biopesticide (Vessey, 2003).

1.4.5 Role of beneficial microbes in abiotic stress Abiotic stress, such as drought, extreme temperature, flood, excess light, salinity, and heavy metal toxicity, is a chief factor that negatively affects plant growth and development. According to Wang, Vinocur, and Altman (2003), abiotic stress can reduce the productivity and yield of major crops by more than 50% of arable land throughout the world by the year 2050. Ever growing world population creates new challenges for agriculture. To feed this huge population, there is a need to increase food productivity at the same pace to ensure food security. Abiotic stress alters nutrient acquisition and biosynthetic activities, inhibiting plant growth. Cell differentiation and growth require nutrients, energy, and biosynthetic activities. Restriction in any one of the factors leads to growth retardation and ultimately death of plants. Among the abiotic factors, drought is a major abiotic stress that reduces plant growth and, as such, plant yield. Drought is a threat to agricultural productivity worldwide (Gornall et al., 2010). Due to their sessile nature, plants modulate themselves morphologically, physiologically, and biochemically under stress conditions. Plants show various physiological changes such as the closure of stomata, expression of aquaporins, and vacuolar H-pyrophosphatases, maintenance of cell turgidity, and accumulation of osmolytes for osmotic adjustments (Sati, Veni, Pandey, & Samant, 2021). Under drought stress, ethylene concentration also increases, impairing plant growth (Burg, 1973). Reactive oxygen species (ROS) accumulate and lead to osmotic stress deteriorating the integrity and functionality of cells and ultimately plant survival (Gill & Tuteja, 2010). The rhizosphere and the endosphere are the main hotspots for beneficial microbes (Berg, Grube, Schloter, & Smalla, 2014). Among the beneficial microbes, mycorrhizal fungi and PGPB have the capability of modulating plants’ physiological responses under stress conditions, thereby increasing plant tolerance toward abiotic stress conditions. According to Perez-Montano et al. (2014), plants inoculated with beneficial microbes increased their growth by 40% under stress conditions suggesting the potential of beneficial microbes in agriculture under various stress conditions.

1.4.6 Role of beneficial microbes as a biocontrol agent Beneficial microorganisms have the ability to suppress various phytopathogens through a number of ways, such as by producing antibiotics, lytic enzymes, HCN, and siderophore and by competing with

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Chapter 1 Beneficial microbes for sustainable agroecosystem

pathogens for nutrients and space, thus limiting the availability of nutrients (Marasco et al., 2012). Beneficial microbes such as Actinomycetes and fungi such as Aspergillus, Penicillium, and Trichoderma are producers of various kinds of antibiotics with diverse actions (Zivkovic et al., 2010). Biocontrol represents the use of beneficial microbes that are natural enemies of various phytopathogens and thus reduce the population of pathogenic organisms. Beneficial microbes that act as biocontrol agents have antagonistic activities and are competitor microorganisms, inhibiting or killing various pathogenic microbes. Biocontrol agents are eco-friendly and more cost-effective than chemical pesticides (Bale, Van Lenteren, & Bigler, 2008). A bacterial formulation as a biocontrol agent is applied in the roots and seeds of plants to control various plant diseases. According to the study by Neeno-Eckwall and Schottel (1999), the application of nonpathogenic strains of Streptomyces sp. is able to control the scab of potatoes caused by Streptomyces scabies through the production of antibiotics and extracellular hydrolytic enzymes. Cronin et al. (1997) studied that P. fluorescens was effective against Erwinia carotovora subsp. atroseptica responsible for soft rot potatoes. Antagonistic activities are also found in 2,4-diacetylphloroglucinol and siderophore. Fungi such as Trichoderma and Gliocladium have antagonistic activity against various phytopathogens such as Alternaria, Rhizoctonia, Fusarium, Botrytis, Sclerotinia, Verticillium, Phytophthora, and Pythium (Hajieghrari, Torabi-Giglou, Mohammadi, & Davari, 2008). Various Pseudomonas species are reported to control crown gall disease in dicot plants (Tolba & Soliman, 2013). Bacillus sp. produces different kinds of antifungal compounds and showed antagonistic activity against Colletotrichum musae (Alvindia & Natsuaki, 2009), Fusarium moniliforme (Agarry, Akinyosoye, & Adetuyi, 2005), and Colletotrichum gloeosporioides (Demoz & Korsten, 2006).

1.5 Conclusion Global food demand will increase by 70% by 2050. Abiotic stress will also increase with the same frequency, and climate will change drastically. Also, excessive use of chemical fertilizers and pesticides will lead to various environmental problems, decreasing the naturally occurring nutrient contents in the soil and destroying the native microflora of the soil. In this scenario, the utilization of beneficial microbes presents as an eco-friendly and sustainable approach. Beneficial microbial communities in the rhizosphere and the endosphere represent the key contributor to sustainable agroecosystem. Beneficial microbes (PGPR, AMF, and Actinomycetes) have great potential to be used as biofertilizers and biopesticides. Soil rich in beneficial microorganisms enhances the natural immune system of plants, decreases the phytopathogen population, resists parasitic insects, increases the resistance toward various abiotic stress, thus creating an ideal situation for sustainable agriculture. The use of beneficial microbes for the management of the rhizosphere is an eco-friendly and costeffective approach for global food security and sustainable agriculture.

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108. Ryan, M. H., & Angus, J. F. (2003). Arbuscular mycorrhizae in wheat and field pea crops on a low P soil: Increased Zn uptake but no increase in P uptake or yield. Plant and Soil, 250, 225
239. Saba, H., Vibhash, D., Manisha, M., Prashant, K. S., Farhan, H., & Tauseef, A. (2012). Trichoderma—A promising plant growth stimulator and biocontrol agent. Mycosphere, 3, 524
531. Salwan, R., & Sharma, V. (2020). Molecular and biotechnological aspects of secondary metabolites in actinobacteria. Microbiological Research, 231, 126374. Sati, D., Joshi, T., Pandey, S. C., Pande, V., Mathpal, S., Chandra, S., & Samant, M. (2022). Identification of putative elicitors from plant root exudates responsible for PsoR activation in plant-beneficial Pseudomonas spp. by docking and molecular dynamics simulation approaches to decipher plant-microbe interaction. Frontiers in Plant Science, 13, 875494. Available from https://doi.org/10.3389/fpls.2022.875494. Sati, D., Pandey, S. C., Pande, V., Upreti, S., Gouri, V., Tushar, J., . . . Samant, M. (2020). Toward an enhanced understanding of plant growth promoting microbes for sustainable agriculture. In Recent advancements in microbial diversity, (pp. 87
112). Academic Press. Sati, D., Veni, P., Pandey, S. C., & Samant, M. (2021). Recent advances in PGPR and molecular mechanisms involved in drought stress resistance. Journal of Soil Science and Plant Nutrition. Available from https:// doi.org/10.1007/s42729-021-00724-5. Saxena, J., Basu, P., Jaligam, V., & Chandra, S. (2013). Phosphate solubilization by a few fungal strains belonging to the genera Aspergillus and Penicillium. African Journal of Microbiology Research, 7, 4862
4869. Scherr, S. J., & McNeely, J. A. (2008). Biodiversity conservation and agricultural sustainability: Towards a new paradigm of ‘ecoagriculture’ landscapes. Philosophical Transactions of the Royal Society B Biological Sciences, 363, 477
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602. Seema, K., Mehta, K., & Singh, N. (2018). Studies on the effect of plant growth promoting rhizobacteria (PGPR) on growth, physiological parameters, yield and fruit quality of strawberry cv. chandler. Journal of Pharmacognosy and Phytochemistry, 7, 383
387. Sessitsch, A., Kuffner, M., Kidd, P., Vangronsveld, J., Wenzel, W. W., & Fallmann, K. (2013). The role of plant-associated bacteria in the mobilization and phytoextraction of trace elements in contaminated soils. Soil Biology and Biochemistry, 60, 182
194. Sharma, S. B., Sayyed, R. Z., Trivedi, M. H., & Gobi, T. A. (2013). Phosphate solubilizing microbes: Sustainable approach for managing phosphorus deficiency in agricultural soils. Springer Plus, 2, 587. Singh, L. P., Gill, S. S., & Tuteja, N. (2011). Unravelling the role of fungal symbionts in plant abiotic stress tolerance. Plant Signaling & Behavior, 6, 175
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798. Sousa, J. A. J., & Olivares, F. L. (2016). Plant growth promotion by streptomycetes: Ecophysiology, mechanisms and applications. Chemical and Biological Technologies in Agriculture, 3, 24.

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Sparks, D. L., & Huang, P. M. (1985). Physical chemistry of soil potassium. In R. D. Munson (Ed.), Potassium in Agriculture (pp. 201
276). Madison, WI: American Society of Agronomy. Spatafora, J. W., Chang, Y., Benny, G. L., Lazarus, K., Smith, M. E., Berbee, M. L., . . . Gryganskyi, A. (2016). A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia, 108, 1028
1046. Sreevidya, M., Gopalkrishnan, S., Kudapa, H., & Varshney, R. K. (2016). Exploring plant growth-promotion actinomycetes from vermicompost and rhizosphere soil for yield enhancement in chickpea. Brazilian Journal of Microbiology, 47, 85
95. Stewart, L. I., Hamel, C., Hogue, R., & Moutoglis, P. (2005). Response of strawberry to inoculation with arbuscular mycorrhizal fungi under very high soil phosphorus conditions. Mycorrhiza, 15, 612
619. Tolba, I. H., & Soliman, M. A. (2013). Efficacy of native antagonistic bacterial isolates in biological control of crown gall disease in Egypt. Annals of Agricultural Sciences, 58, 43
49. Trujillo, M. E., Bacigalupe, R., Pujic, P., Igarashi, Y., Benito, P., Riesco, R., . . . Normand, P. (2014). Genome features of the endophytic actinobacterium Micromonospora lupini Strain Lupac 08: On the process of adaptation to an endophytic life style? PLoS One, 9, e108522. Turan, M., Ekinci, M., Yildirim, E., Gunes, A., Karagoz, K., Kotan, R., & Dursun, A. (2014). Plant growthpromoting rhizobacteria improved growth, nutrient, and hormone content of cabbage (Brassica oleracea) seedlings. Turkish Journal of Agricultural Science, 38, 327
333. Turatto, M. F., Dourado, F. D. S., Zilli, J. E., & Botelho, G. R. (2017). Control potential of Meloidogyne javanica and Ditylenchus spp. using fluorescent Pseudomonas and Bacillus spp. Brazilian Journal of Microbiology, 49, 54
58. Turner, T. R., James, E. K., & Poole, P. S. (2013). The plant microbiome. Genome Biology, 14, 209. Tyagi, V., Durgapal, A., Arshi, A., & Chandra, D. (2020). Effect of PGPR on overall performance of finger millet (Eleusine coracana (L.) Gaertn.). Research Journal of Agricultural Sciences, 11(4), 760
767. Verbruggen, E., Van Der Heijden, M. G. A., Rillig, M. C., & Kiers, E. T. (2013). Mycorrhizal fungal establishment in agricultural soils: Factors determining inoculation success. New Phytologist, 197, 1104
1109. Vessey, J. K. (2003). Plant growth promoting rhizobacteria as biofertilizers. Plant and Soil, 255, 571
586. Wang, C., Cui, J., Yang, L., Zhao, C., Wang, T., Yan, L., & Liu, S. (2018). Phosphorus release dynamics by phosphorus solubilizing actinomycetes and its enhancement of growth and yields in maize. International Journal of Agriculture and Biology, 20, 37
444. Wang, W., Vinocur, B., & Altman, A. (2003). Plant responses to drought, salinity and extreme temperatures: Towards genetic engineering for stress tolerance. Planta, 218, 1
14. Zhao, L., Xu, Y., & Lai, X. (2018). Antagonistic endophytic bacteria associated with nodules of soybean (Glycine max L.) and plant growth-promoting properties. Brazilian Journal of Microbiology, 49, 269
278. Zivkovic, S., Stojanovic, S., Ivanovic, Z., Gavrilovic, V., Popovic, T., & Balaz, J. (2010). Screening of antagonistic activity of microorganisms against Colletotrichum acutatum and Colletotrichum gloeosporioides. Archives of Biological Sciences, 62, 611
623.

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CHAPTER

Strategies and implications of plant growth promoting rhizobacteria in sustainable agriculture

2

Damini Maithani1, Anita Sharma2 and S.T.M. Aravindharajan2 1

School of Biotechnology, IFTM University, Moradabad, Uttar Pradesh, India 2Department of Microbiology, G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, India

2.1 Introduction Food security is one of the major factors required for the stability of social, economic, and political issues. Under changing environmental conditions, the need to produce an appropriate amount of food to feed a burgeoning population is a serious challenge. To obviate this problem, farmers are using modern agricultural practices where excessive use of fertilizers has led to pollution of soil, air, and water, subsequently affecting the environment. As a result of prevailing stress conditions and intensive agricultural practices, the functionality of an agricultural system and natural ecosystems is affected. Some major stress factors challenging food production are pathogenic microorganisms, water stress, nutrient deficiency, plant invasions, pests, salinity, and soil erosion (Kumar, Singh, Tripathi, Singh, & Singh, 2018). Pollutants from various agricultural practices, like sediments, nutrients, pathogens, pesticides, metals, and salts, have a huge effect on the quality of soil and water (Pande, Pandey, Sati, Pande, & Samant, 2020). Some agrochemicals become pollutants because of their use, misuse, or ignorance and contaminate agricultural produce, soil, streams, and groundwater. Malathion, Rogor, Kelthane, and other pesticides of synthetic nature can seep into water bodies and soil causing contamination of food and water, which may result in the death of nontargeted organisms including humans. Erosion of the topsoil containing herbicides and pesticides can contaminate water bodies and surrounding environment too. Agricultural practices using animals can also pollute the environment. For instance, atrazine, an herbicide used to control weeds growing within the crops can disrupt endocrine and reproductive systems in exposed mammals, amphibians, and fishes. Improper grazing practices, manure storage, and improper manure applications in fields can lead to the entry of pathogens in water and food systems. Pollutants can also affect the capacity of soil to receive, store, and transfer sufficient energy to support plant health (Gupta, Parihar, Ahirwar, Snehi, & Singh, 2015). A dramatic increase in the global population in recent decades has led to an increase in the practice of agricultural land conversion to meet food demands, which has negatively affected the environment. Considering the aforementioned issues, agricultural practices for environmental and economic developments need to be based on sustainable approaches that help in maintaining yield while preserving the integrity of the ecosystem. Sustainable agriculture is an idea that describes the way of agriculture where one continues to Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00013-2 © 2023 Elsevier Inc. All rights reserved.

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Chapter 2 Plant growth promoting rhizobacteria

produce what is necessary but does not impede the rights of upcoming generations. The rhizosphere is a metabolically and functionally important zone around the plant roots that houses an astounding number of microorganisms (Singh, 2018; Sivasakthi, Usharani, & Saranraj, 2014). Rhizosphereassociated microbes, or rhizobacteria, are diverse in regard to their habitat and also in their structure and functions. This zone is directly influenced by root secretions and remains associated with the most versatile and metabolic active soil microbes that feed on sloughed-off plant cells and rhizodeposition (amino acids, proteins, sugars, hormones, organic acids, cations, enzymes, etc.). Microbes present in this region survive by using root exudates and plant lysates as nutrients. There are tens of thousands more bacteria in the rhizosphere than in the bulk soil. However, bacteria have to be rhizosphere competent to exert their beneficial effects in the root environment by outcompeting other rhizospheric microorganisms to obtain available nutrients secreted by the roots and for occupying the sites required for their establishment. Bacteria constitute a dominant group in the microbial community of the soil, where approximately one gram of soil contains 108 to 109 bacteria (Ole´nska et al., 2020). An estimated number of 30,000 plant growth promoting prokaryotes have been reported in various literature and research works (Mendes, Garbeva, & Raaijmakers, 2013). Microorganisms constitute an important component of the soil, and they influence soil health through their beneficial metabolic activities. The microbiome constituting a collective genome enclosing plant roots is larger than that of the plant itself. Interactions within these microbial communities in the rhizosphere provide essential services to the crop plants that help to regulate their health. Rhizospheric microorganisms help in structuring the soil texture, decomposition of organic matter, nutrient cycling and acquisition, solubilization of mineral nutrients, phytohormone production, bioremediation of toxic compounds, improvement of soil fertility, biocontrol of soil and seed-borne plant pathogens, etc. (Bhardwaj, Ansari, Sahoo, & Tuteja, 2014; Pande, Pandey, Sati, Bhatt, & Samant, 2022; Sivasakthi, Usharani, & Saranraj, 2014). The ability of plant growth promoting rhizobacteria (PGPR) to aid plant growth under challenging conditions is recommendable where bacteria can help plants to stay fit and enhance their stress tolerance. Several plant-beneficial microbes and their products have been identified and marketed. Some beneficial bacteria promote plant growth directly, while others do this indirectly by protecting the plants against soil-borne fungal diseases. The beneficial group of microorganisms dwelling in the plant rhizosphere has been an interesting area of research in the past few years as they provide a sustainable and eco-friendly alternative to chemical fertilizers. Inoculation of plants with beneficial bacteria can be traced back to centuries and is still a widely recognized topic of research. In times of highly variable climatological and environmental conditions, providing additional evidence on bacterial traits associated with plant growth promotion could spur the development of innovative solutions to exploit these microorganisms.

2.2 Plant growth promoting rhizobacteria and plant interaction Interactions between plants and rhizospheric microorganisms, ranging from mutualistic to pathogenic, influence plant health and soil fertility to a large extent. Plant immune systems exert a major role in the maintenance of these interactions by keeping pathogens at bay while maintaining a number of beneficial microorganisms (Yu, Pieterse, Bakker, & Berendsen, 2019). Plant growth

2.2 Plant growth promoting rhizobacteria and plant interaction

23

promoting bacteria (PGPB) interact with plants either by residing inside (intracellular) or outside the plant tissues, either on the rhizoplane, phyllosphere, or rhizosphere (Weyens, van der Lelie, Taghavi, Newman, & Vangronsveld, 2009). Soil bacteria are primarily responsible for providing plants with essential nutrients to stimulate their growth and prevent pathogen attack. These microbes improve soil structure and assist bioaccumulation and bioleaching of inorganic compounds. The interaction between plants and microorganisms is critical for sustainable food production. Microbes help to mobilize and solubilize nutrients from a restricted pool. PGPR constitute about 2%
5% of overall rhizospheric bacterial diversity (Kumar, Dubey, & Maheshwari, 2012) and are reported to promote plant health, which occurs as a result of bacterial activities that include fixing of atmospheric nitrogen; producing phytohormones, siderophores, and volatile compounds; solubilizing phosphate, potassium, and zinc; and control plant diseases by suppressing or killing the phytopathogens. The rhizomicrobiome represents the total communities of microorganisms in the rhizosphere and this concept was introduced for the first time by Hiltner (1904). Plants secrete a variety of exudates as chemical signals to which bacteria are recruited around the root. The exudates include 20% of the photosynthetically fixed carbon and are reported to promote extensive growth of bacteria and fungi that make microcolonies on root surfaces and show beneficial effects on plant growth (Ole´nska et al., 2020). The zone all around the plant roots can contain up to 1011 microbial cells per gram of dry matter, which is higher than the bulk soil where it ranges from 106 to 109 microbial cells per gram bulk soil (Tian, Reverdy, She, Sun, & Chai, 2020). Microorganisms residing in the plant rhizosphere, including fungi, nematodes, bacteria, algae, protozoa, etc., have been proposed as predictors of aboveground plant diversity and productivity (Sekar, Raj, & Prabavathy, 2016). Pseudomonas plays an important role in bacterial colonization in the rhizospheric region in tomato plants by utilizing root exudates, rhizodeposition, sugars, and amino acids (Lugtenberg & Dekkers, 1999). For an appropriate plant
microbe interaction, it is necessary for a plant to have an activated immune response to ward off the pathogens, but at the same time the defense system must be suppressed for interaction with beneficial microorganisms (Tonelli, Figueredo, Rodrı´guez, Fabra, & Iban˜ez, 2020). Plant exudation patterns substantially impact the rhizosphere microbial community by signaling results in the selection of microorganisms, contributing to plant well-being, and creating a highly specific environment. Plant root exudates are chemically diverse and include sugars (mono- and disaccharides), organic acids, ions, free oxygen, enzymes, amino acids, plant growth regulators, sterols, fatty acids, nucleotides, tannins, terpenoids, alkaloids, and vitamins (Hayat, Faraz, & Faizan, 2017). Rhizodeposit is rich in carbon and nitrogen compounds and thus helps in the selection and growth of rhizomicrobiomes. Root exudates attract microorganisms toward the rhizosphere in a chemotactic manner. Chemotaxis, or motility toward root exudates, is a key determinant of root colonization. The chemistry between PGPR and root exudates lays the first line of communication and exerts a positive influence on plants by secreting enzymes and producing exopolysaccharides (EPS) and rhizobitoxine to withstand stressed conditions (Hayat et al., 2017). Root exudates act as adherents to which bacteria attach and move toward the plant. Microorganisms producing EPS form biofilms, which help in the attachment and colonization of root tissues by PGPR. Some of them produce biosurfactants that participate in signaling, motility, and biofilm formation, influencing plant
bacteria interaction (Danhorn & Fuqua, 2007; Primo, Ruiz, Masciarelli, & Giordano, 2015). Besides, quorum sensing (QS) in the rhizosphere inhibits the growth of various pathogenic microorganisms. Plant exudates attract various bacterial strains that are able to produce acyl

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Chapter 2 Plant growth promoting rhizobacteria

homoserine lactones (AHLs). These are signaling molecules responsible for phenomena like QS, biofilm formation, and rhizospheric colonization by PGPR. QS controls the production and secretion of virulence factors by pathogenic microorganisms (Hayat et al., 2017). In the context of the present scenario, the important objectives to be undertaken are (1) an increase in plant biomass and (2) a reduction in the dependence on chemical fertilizers and pesticides for an overall reduction in xenobiotic-mediated pollution worldwide. The major applications of plant growth promoting bacteria are related to agriculture, horticulture, forestry for plant growth promotion, and environmental restoration. PGPR, when applied on the right host and under the right environmental conditions, have been reported to cause real and positive effects on plant health (Lucy, Reed, & Glick, 2004). Abiotic stress, including water, salinity, extreme temperatures, unusual pH of the soil, heavy metal toxicity, and biotic stress conditions, severely affect agricultural crops. Beneficial PGPR could be used as efficient tools to improve plant growth under stressed environments by directly interacting with plants and enhancing the production and regulation of compounds involved in plant growth. PGPR also improve status of stress hormones in plants to combat various stress conditions. Indirectly these beneficial microorganisms affect plants by protecting them against diseases via competition with pathogens for highly limited nutrients, biocontrol of pathogens by producing antifungal compounds, synthesis of fungal cell wall lysing enzymes, and induction of systemic responses in host plants. Interaction between plants and PGPR is a complex network of signaling cascades that includes the participation of multiple genes influencing plant metabolism directly or indirectly (Bharti, Pandey, Barnawal, Patel, & Kalra, 2016; Meena et al., 2017). Bacteria as well as plants have evolved a plethora of ways to deal with abiotic and biotic stress conditions. In comparison to other agriculturally important crops, less emphasis is given to the use of PGPR under a forest system (Lucy et al., 2004). For instance, Pseudomonas koreensis AS15 was reported to improve agronomic parameters in different cultivars of Dalbergia sissoo (Dasila, Anjul, Damini, Manvika, & Salil, 2018). In addition, higher soil enzymatic activities, like alkaline phosphatase and fluorescein diacetate hydrolysis indicating higher availability of phosphate and carbon for plant uptake, were also observed under bacterial treatment. The ability of microorganisms to sustain and improve plant growth under adverse conditions is currently underappreciated. As a result, additional research is needed to better understand the process of plant
microbe interactions. It is also necessary to decode the bilateral molecular dialogs under biotic and abiotic stress conditions. Some commercially available formulations containing free-living PGPR are applied to crops. However, the inconsistency of results between laboratory, greenhouse, and field investigations has resulted in a decreased utility of PGPR in boosting agricultural productivity. More comparative studies are required between different cultivars and different strains of rhizobacteria (Lucy et al., 2004).

2.3 Plant growth promoting rhizobacteria: mechanisms of action To increase the yield and growth of plants, a number of mechanisms are employed by PGPR, which consist of both direct and indirect mechanisms (Sati et al., 2020). Direct mechanisms include nutrient acquisition; increasing bioavailability of phosphorus, nitrogen, zinc, and potassium;

2.3 Plant growth promoting rhizobacteria: mechanisms of action

25

sequestration of iron by producing microbial siderophores; production of plant hormones (auxins, cytokinins, and gibberellins); and lowering of plant ethylene levels. Whereas indirect mechanisms include the production of antibiotics, protection against pathogenic microbes, reduction of iron availability to phytopathogens in the rhizosphere, synthesis of cell wall lysing enzymes, and competition with detrimental microorganisms for colonization on plant roots (Kumar et al., 2018). Some of the mechanisms have been explained in brief in the following section.

2.3.1 Biological nitrogen fixation Nitrogen is a major element on the earth, which is used for the synthesis of protein, nucleic acids, phytohormones, chlorophyll, secondary metabolites, and a number of coenzymes in a growing cell (Hawkesford et al., 2011). It is one of the most important nutrients for plants and constitutes around 78% of the atmosphere. Nitrogen is a relatively inert and volatile gas and cannot be taken by plants easily (Allito, Nana, & Alemneh, 2015). For more than a century, biological nitrogen fixation (BNF), which is a unique characteristic of certain prokaryotes, has commanded the attention of scientists regarding its exploitation in agricultural practices. Generally, plants take up dinitrogen in the form of either ammonia (most reduced) or nitrate (most oxidized). Using the process of BNF, atmospheric nitrogen is converted to ammonia and offers an attractive and efficient means of reducing external nitrogenous fertilizer inputs and improving the internal resources of plants. BNF accounts for 65% of the total fixed nitrogen in agriculture, which makes it an important factor in sustainable crop production (Matiru & Dakora, 2004). BNF is an ecologically benign process that can help in the reduction of our dependency on fossil fuels and can also help in the restoration of abandoned lands to productive landforms. However, with the increasing amount of N-fertilizers used for the production of food and cash crops, the importance of BNF as a primary source of fixed nitrogen for crops has diminished in recent decades. The ability of prokaryotic microorganisms to fix atmospheric nitrogen is widely distributed. About 2 genera of archaea with 87 species, 38 genera of bacteria (Rhizobia, Azospirillum, Azotobacter, etc.), and 20 genera of cyanobacteria have been identified as diazotrophs (Arora, Verma, & Mishra, 2017). The most exploited and studied PGPR for the process of BNF are Rhizobia, which have significant ability to fix N2 under symbiotic conditions. A symbiotic system of legumes and rhizobia is the major source of fixed nitrogen in most of the leguminous crops. Fixed N2 supports plant growth in nitrogen deficient soils while nodules present a physically protected and well-nourished environment for nitrogen fixation. Beijerinck (1888) isolated and characterized bacteria in nodules and denoted them as Bacillus radicicola. He also provided conclusive proof of the same by isolating bacteria from nodules of Vicia faba and inoculated them into an uninfected V. faba. Rhizobium is a genus belonging to the family of Rhizobiaceae, which comes under the class of proteobacteria and comprises a number of species. With the advancement of molecular techniques, genus Rhizobium was distributed into several groups based on phylogenetic studies. According to Bloemberg and Lugtenberg (2001), group rhizobia include genera like Rhizobium, Mesorhizobium, Bradyrhizobium, Azorhizobium, Allorhizobium, and Sinorhizobium. One of the studies revealed that closely related rhizobia are Rhizobium, Agrobacterium, and Allorhizobium, while Sinorhizobium, Bradyrhizobium, Azorhizobium and Mesorhizobium form separate groups (Willems, 2006). Till now, rhizobia comprise 98 species and 13 genera.

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Chapter 2 Plant growth promoting rhizobacteria

During a microbial competition at high carbon and low nitrogen in a rhizosphere, N2 fixers specify the host and promote plant growth through symbiosis. Legumes produce flavonoids that induce the nodD gene in the rhizobia (Broughton, Jabbouri, & Perret, 2000). This activation paves the path for rhizobia to produce molecules such as lipochito-oligosaccharide (nod factors) containing 4
5 N-acetyl glucosamine with a free reducing end and lipid moiety at the nonreducing end (Gage, 2004). Lectins from the host plants also play a role of a successful receptor for symbiosis. After a successful infection, processes like root hair deformation, establishment of an intra- and intercellular infection, mitotic cell division and formation of bacteroides, and nodulation take place. Subsequently, these bacteroides are capable of producing an oxygen-sensitive nitrogenase enzyme that helps in the fixation of atmospheric nitrogen under anoxic conditions. At the genome level, nitrogenase is encoded by three major marker genes (nif H, D, and K). These genes are present on nif operon in most of the nitrogen fixing bacteria. Some important genera carrying out symbiotic N2 fixation include Rhizobium, Bradyrhizobium, Sinorhizobium, Mesorhizobium, and Azorhizobium; and some loosely or intimately localized (endophytic) bacteria such as Azospirillum, Azotobacter, Gluconacetobacter diazototrophicus, Cyanobacteria, etc. having association with legumes as well as nonlegumes (Reyes & Schmidt, 1979). Cyanobacteria are the first photoautotrophs having a wide range of symbiotic associations starting with fungi to higher plants. They can fix atmospheric N2 by utilizing CO2 as a carbon source in the presence of O2 under free-living and symbiotic associations (Stewart, Rowell, & Rai, 1980). A wide range of PGPR have been reported to interact with economically important C3 and C4 plants, including rice, wheat, maize, sugarcane, cotton, etc., and significantly increase their growth and yield (Kennedy, Choudhury, & Kecsk´es, 2004). For instance, Azospirillum lipoferum, an associative symbiotic, microaerophilic, gram-negative N2 fixer may lead to an increased yield of grasses (Reinhold-Hurek et al., 1993). Further, G. diazotrophicus, an endophytic bacterium of sugarcane fixed nitrogen (Chauhan, Bagyaraj, & Sharma, 2013), produced phytohormone and provided protection against red rot of sugarcane (Colletotrichum falcatum) (Muthukumarasamy et al., 2005). Some important N2 fixers are described in Table 2.1. Free-living heterotrophic diazotrophs, such as Azotobacter vinelandii and Azotobacter chroococcum, need a considerable supply of reduced carbon compounds for their growth and energy requirements. Application of straw along with Azotobacter in rice has been reported to increase microbial activity as a result of breakdown of cellulose into cellobiose and glucose molecules. Azotobacter has also been reported to enhance the yield of economically significant crops including rice, cotton, and wheat (Anjum et al., 2007, Barassi, Creus, Casanovas, & Sueldo, 2000). In contrast to Azotobacter, clostridia are obligate anaerobic heterotrophs and fix N2 under anaerobic conditions. They can be isolated from rice soils and their activity can also be enhanced after returning straw to the fields. In response to temporal gradients of various chemoeffectors, A. brasilense displays chemotaxis and chemokinesis, increasing the possibility of bacterial interaction with plant roots. Different species of Azospirillum are often associated with improved root respiration rate, metabolism, and proliferation. Azospirillum is reported to produce various antifungal and antibacterial compounds, growth regulators, and siderophores (Pandey & Kumar, 1989). Plants inoculated with Azospirillum sp. show better mineral and water uptake in comparison to uninoculated plants by producing phytohormones like indole acetic acid (IAA). According to a study conducted by Mirza et al. (2000), rice yield was

2.3 Plant growth promoting rhizobacteria: mechanisms of action

27

Table 2.1 Plant growth promoting rhizobacteria with nitrogen fixing ability. N2 fixers

Hosts

References

Pisum, Lathyrus, Vicia, Lens, Phaseolus, Trifolium Sesbania herbacea Astragalus

Frank (1889)

Symbiotic N2 fixation R. leguminosarum R. huautlense 1998 R. loessense

Indigofera Phaseolus vulgaris, Leucaena Medicago

Wang et al. (1998) Wei, Wang, Tan, Zhu, and Chen (2002) Wei et al. (2003) Martı´nez-Romero et al. (1991) Quan et al. (2005)

Melilotus, Medicago, Trigonella Glycine, Vigna, Cajanus

Dangeard (1926) Scholla and Elkan (1984)

Lotus, Lupinus, Anthyllis, Leucaena Rhizosphere of Clitoriaternatea

Jarvis, Pankhurst, and Patel (1982) Ghosh and Roy (2006)

Glycine max Beta vulgaris Neptunianatans Crotalaria Lupinus sp. Trifolium, Lupinus Sesbania rostrata

Jordan (1982) Rivas et al. (2004) de Lajudie et al. (1998) Jourand et al. (2004) Trujillo et al. (2005) Valverde et al. (2005) Dreyfus, Garcia, and Gillis (1988)

Azospirillum Azotobacter

Maize, rice, wheat Maize, wheat

Cyanobacteria Glucanoacetcbacter diazototrophicus Herbaspirillum

Rice Sorghum

de Salamone et al. (2012) Hurek, Wagner, and ReinholdHurek (1997) Hashem (2001) Isopi, Fabbri, Del-Gallo, and Puppi (1995) James et al. (2002)

R. indigoferae R. tropici 1991 R. daejeonense 2005 Sinorhizobium S. meliloti 1926 S. fredii Mesorhizobium M. loti M. thiogangeticum Bradyrhizobium B. japonicum B. betae Allorhizobium undicola Methylobacterium Ochrobactrum Phyllobacterium lupini Azorhizobium caulinodans Non-symbiotic N2 fixator

Sorghum

increased up to 6.7 g/plant under greenhouse condition inoculation with A. lipoferum (Mirza et al., 2000). An estimated increase of 1.8 t/ha in rice yield and 30% increase in wheat yield due to inoculation with A. lipoferum was observed under field conditions. Saubid et al. (2000) found that inoculation with A. brasilense promoted uptake of fixed nitrogen (in the form of nitrate), potassium, K1, and H2PO4 in some important crops like corn, sorghum, and wheat. Similarly increased cane yield was observed when Azospirillum sp. was inoculated in the form

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Chapter 2 Plant growth promoting rhizobacteria

of soil applications under field conditions (Shankariah and Hunsigi, 2001). In another report, inoculation with A. brasilense significantly increased nitrogen content in cotton and increased yield up to 0.91 mg/plant. Gluconacetobacter diazotrophicus is an acid-tolerant N2 fixing endophyte and grows best on sucrose-rich medium (Chauhan et al., 2013). Studies confirmed that nitrogen fixation by A. diazotrophicus contributed up to 60%
80% of nitrogen in sugarcane plants, which is almost equivalent to 200 kg N/ha/year. Graciolli, de Breitas, and Ruschel (1983) isolated a wide range of N2 fixers from roots, stem, and leaves of sugarcane. Dominant bacterial groups with potential of N2 fixation in nonlegumes are Acetobacter, Azotobacter, Derxia, Herbaspirillum, Azospirillum, and Enterobacter. Reinhold-Hurek et al. (1993) conducted an investigation on an endophytic N2-fixing bacterium Azoarcus sp. BH72, which was originally isolated from Kallar grass growing in the saline-sodic soils of Pakistan. Azoarcus sp. also colonizes rice under laboratory and field conditions. Genus Burkholderia comprises 67 species and several of these including B. vietnamiensis, B. kururiensis, B. tuberum, and B. phynatum are capable of fixing N2. Under field conditions, B. vietnamiensis was reported to boost rice yield significantly up to 8 t/ha while saving 25
30 kg N/ha of fertilizer (Van, Berge, Ke, Balandreau, & Heulin, 2000). Bacillus brasiliensis and B. tropicalis are two important endophytes of sugarcane. The former is present in roots, stems, and leaves of the sugarcane plant while the latter is confined to its roots and stems. Both the species are also reported to produce compounds with nematicidal activity. Herbaspirillum is another endophytic microorganism that colonizes crops like sugarcane, rice, maize, sorghum, and other cereals. It can fix 31%
45% of total plant nitrogen in rice seedlings (Bal & Adhya, 2021). The estimated nitrogen fixation by Herbaspirillum was 33
58 mg/tube under aseptic conditions (Reis, Baldani, Baldani, & Dobereiner, 2000). In a greenhouse study, inoculation with Herbaspirillum increased rice yield significantly up to 7.5 g/plant (Mirza et al., 2000). Two endophytic diazotrophic species of Herbaspirillum include Herbaspirillum seropedicae and Herbaspirillum rubrisubalbicans. The former colonizes roots and stems of wheat plant internally while the latter is an obligate endophyte colonizing roots, stems, and leaves (Kennedy & Islam, 2001; Reis et al., 2000).

2.3.2 Phosphorous solubilization Phosphorus is one of the most important macronutrients next to nitrogen for plant growth. It is found in the soil in amounts ranging from 400 to 1,200 mg/kg soil. Plants use organic and inorganic phosphates in the soil for biosynthesis, photosynthesis, respiration, and energy transfer mechanisms. Phosphorus is an important element of many macromolecules in the cell, such as nucleic acids, adenosine triphosphates, or phospholipids. It positively influences the flowering, formation, and ripening of seeds; improves disease resistance; and increases shoot stiffness and root development (Razaq, Zhang, & Shen, 2017). Phosphate limits plant growth as most phosphorus in the soil is unavailable to plants. The concentration of available phosphorus in the soil solution for plant uptake is very limited, as 95%
99% of the phosphorus present in the soil is in unavailable form (Ahemad & Kibret, 2014). Low levels of soluble phosphate can limit plant growth, and thus phosphorous deficiency is a major problem for economically important crops, which is usually compensated using phosphorous fertilizers. Production of chemical phosphate fertilizers, however, is an energy-intensive process. Besides, 75%
90% of phosphatic fertilizers are precipitated in the soil

2.3 Plant growth promoting rhizobacteria: mechanisms of action

29

(Khan, Zaidi, & Wani, 2007). Due to their extremely reactive nature, phosphate anions may be attained by plants with cation precipitations. Various bacterial as well as fungal genera present in the plant rhizosphere carry out phosphate solubilization (Gupta et al., 2015). Some bacteria facilitate plant growth by solubilizing phosphate from either organic or inorganic sources. Phosphate solubilizing bacteria (PSB) are a predominant group constituting 1%
50%, while fungi constitute only 0.1%
0.5% of the whole microbial rhizosphere (Satyaprakash, Nikitha, Reddi, Sadhana, & Vani, 2017). Several bacteria, particularly species of Pseudomonas and Bacillus and fungi belonging to Penicillium and Aspergillus genera, solubilize insoluble inorganic phosphorus in the soil and make phosphorus available to the plants. Among the various phosphate solubilizers, Aspergillus awamori improves the status of available phosphorus in the soil significantly, followed by Pseudomonas striata (Qureshi, Narayanasamy, Chhonkar, & Balasundaram, 2005). Pantoea sp. S32 has the dexterity to solubilize phosphate at higher frequencies, that is, 3.07, 18.38, 0.51, 0.16, or 2.62% of lecithin, CaHPO4 FePO4, phosphate rock (PR), or AlPO4 under in vitro conditions (Chen and Liu, 2019). Being a good PO42 solubilizer, PSB also allay metal toxicity in environments, mainly mercury (Hg), cadmium (Cd), arsenic (As), and lead (Pb) (Zhang, Xiao, & Wang, 2021). A significant increase in grains and biological yields of Triticum aestivum L. was observed when inoculated with PSMs under rainfed conditions (Afzal, Ashraf, Asad, & Farooq, 2005). The use of PSM can increase crop yield by up to 70% (Verma, 1993). PSB has also been reported to promote seedling development in Cicer arietinum (Sharma, Dak, Agrawal, Bhatnagar, & Sharma, 2007). Combined application of PSB and PGPR reduced exogenous phosphorous application by 50% without affecting corn yield (Yazdani, Bahmanyar, Pirdashti, & Esmaili, 2009). Similarly, sugarcane yield was also increased by 12.6% on inoculation with PSB (Sundara, Natarajan, & Hari, 2002). When inoculated with Bradyrhizobium, Glomus fasciculatum, and Bacillus subtilis, a 24% increase in the yield of green gram was reported (Zaidi & Khan, 2006). The process of phosphate solubilization by bacteria is either acid dependent or acid independent. The majority of phosphates are released as a result of acidification events in the soil. Bacteria release a variety of organic acids in the environment, including lactic, acetic, oxalic, malonic, etc., out of which the most commonly secreted acid by phosphate solubilizing microorganisms (PSMs) is gluconic acid (Naraian & Kumari, 2017; Vaid, Gangwar, Sharma, Srivastava, & Singh, 2013). Gluconic acid is an oxidation product of a chemical reaction catalyzed by glucose dehydrogenase (GDH). GDH requires a cofactor, pyrroloquinoline quinone (PQQ), a product of the PQQ operon (Ole´nska et al., 2020). Out of six core genes within the PQQ operon, four genes (A, C, D, and E) are essentially required, as it has been proved experimentally that mutation in any of these genes leads to decreased phosphate solubilization by PSB (Li, Jiao, Hale, Wu, & Guo, 2014; Suleman et al., 2018). Organophosphates constitute about 30%
65% of the total soil phosphorus, which is released in the rhizosphere as a result of the mineralization process carried out by PSB. Bacterial strains, such as Bacillus sp., Rhizobium sp., Delftia sp., and Serratia sp., have been reported to carry out the mineralization of organic phosphates. Enzymes involved in this process are divided into three groups, viz. nonspecific acid phosphatases (NSAPs), phytases, and phosphatases (Ole´nska et al., 2020). PSB are scattered in different genera, viz. Serratia, Enterobacter, Flavobacterium, Alcaligenes, Rhizobium, Acinetobacter, Burkholderia, Pseudomonas, Arthrobacter, Azospirillum, Erwinia, and Bacillus (Mehmood et al., 2018). The performance of some PSB is presented in Table 2.2.

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Chapter 2 Plant growth promoting rhizobacteria

Table 2.2 Phosphate solubilizing bacteria and their application in different crops. Phosphate solubilizing bacteria

Crops

References

B. megaterium Azotobacter chroococcum B. sphaericus Xanthomonas maltophilia Bacillus circulans

Brassica napus L. Wheat Brassica napus L. Brassica napus L. Tomato

Pseudomonas spp. Bacillus sp. Streptomyces laurentii Serratia sp., Enterobacter sp. Bacillus aryabhattai B8W22

Maize Phaseolus vulgaris L. Sorghum bicolor Mimosa pudica Maize

De Freitas, Banerjee, and Germida (1997) Maheshkumar, Krishnaraj, and Alagawadi (1999) De Freitas et al. (1997) De Freitas et al. (1997) Mehta, Walia, Kulshrestha, Chauhan, & Shirkot (2015) Vyas & Gulati. (2009) Kumar et al. (2012) Kour et al. (2020) Sanchez-Cruz et al. (2019) Wang et al. (2020)

2.3.3 Zinc solubilizing bacteria Agricultural practices making use of chemical fertilizers have impacted agriculture land drastically and resulted in increased soil pH, which has impeded plant uptake of essential micronutrients. Zinc is an essential micronutrient that becomes unavailable at high pH. Zinc deficiency in soils is a widespread problem throughout the world specially in rice crop land of Asia and in soil belonging to orders of aridisols, alfisols, mollisols, and vertisols (Srivastava, Gupta, & Jain, 1996). Owing to the prevalence of a large-scale deficiency of zinc, production of cereals suffers besides being a cause of zinc malnutrition in the population that consume cereals as their staple diet. Zinc deficiency in soils is usually attributed to its low solubility rather than low total zinc concentration in most of the agricultural soils. More than 90% of zinc is unavailable to plants. Many factors regulate zinc availability, which include soil type, moisture, minerals, organic matter, and soil life. Crops like barley and wheat are less sensitive to zinc deficiency in comparison to rice, sorghum, and maize (Takkar & Mann, 1975). The synthesis of tryptophan, which is a precursor in IAA synthesis, requires zinc. Besides, zinc is also a major component of several enzymes. Pseudomonas and Bacillus are reported to solubilize zinc compounds. Shahab and Ahmed (2008) have reported the zinc solubilizing ability of Acinetobacter along with Pseudomonas and B. thuringiensis where glucose acted as the best cosubstrate. The solubilizing level of the species of Pseudomonas and Bacillus for ZnO, ZnCO3, and sphalerite was in the range of 13.6
16.4 mg/kg (Saravanan, Subramoniam, & Raj, 2004). In a study by Vaid et al. (2013), Acinetobacter baumannii and Burkholderia cepacia were found to enhance available zinc in two wheat varieties (WH1021 and VL804). In wheat, apart from the enhanced level of zinc in its grains and straw, a significant increase in total protein, copper, manganese, iron, and methionine was also reported. Plants/bacteria release organic acids, cations, and H1 ions to solubilize the insoluble zinc compounds (Joshi, Negi, Vaid, & Sharma, 2013). Inoculation of wheat with three zinc solubilizing bacteria (Burkholderia and two strains of Acinetobacter) increased the residual effect of zinc applied to 2.5 kg/ha to 1-year preceding rice crop on grain yield, zinc concentration, and uptake in grains and straw and zinc uptake of succeeding wheat crops (Vaid et al., 2019). This crop

2.3 Plant growth promoting rhizobacteria: mechanisms of action

31

effective practice also improved the bioavailability of zinc by lowering down the level of phytic acid and enhanced methionine in wheat grains. The meticulous use of B. cepacia (H1) could enhance maize plant height and root length in the presence of 2% ZnO in each pot under glass house experiment (Upadhyay et al., 2021).

2.3.4 ACC deaminase production Plants experience biotic as well as abiotic stress conditions. Plant growth and development can be positively influenced by the application of some microbial inoculants, which can help plants to cope up with stress conditions and minimize potential yield losses. Numerous physiological and metabolic responses are activated in plants with the exposure of abiotic stress conditions such as synthesis of 1-aminocyclopropane-1-carboxylic acid (ACC). ACC deaminase activity has been widely reported in numerous species of bacteria (endophytic and rhizospheric) and fungi. It has been extensively studied in Agrobacterium, Azospirillum lipoferum, Alcaligenes, Bacillus, Burkholderia, Enterobacter, Methylobacterium fujisawaense, Pseudomonas, Ralstonia solanacearum, Rhizobium, Rhodococcus, Sinorhizobium meliloti, Variovorax paradoxus, etc. Glick, Karaturovic, and Newell (1995) discovered that in addition to the well characterized and documented PGPR attributes, Pseudomonas putida contained the enzyme that metabolizes ACC into α-ketobutyrate and ammonia. The breakdown of ACC helps to downregulate the production of ethylene, which is a stress hormone and inhibits plant growth during stress through several mechanisms. A model was proposed to explain the role of ACC deaminase producing microorganisms in lowering plant ethylene levels and spurring plant growth under stressed conditions (Glick, Penrose, & Li, 1998). PGPR synthesize IAA utilizing the tryptophan present in root exudates. Some of these microorganism-synthesized IAA is taken up by the plants, which stimulates cell proliferation and elongation. Some of the IAA, however, can stimulate ACC synthase activity resulting in increased ACC production. ACC deaminase enzyme breaks ACC to form ammonia and ketobutyrate, which are readily metabolized by PGPR. The presence of bacteria induces plants to produce more ACC than they would otherwise need. Plants treated with bacteria containing ACC-deaminase activity may have relatively extensive root growth due to less ethylene production and can better resist various stresses. The use of microorganisms with ACC deaminase activity in positively influencing plant health under stressed as well as normal conditions has recently piqued interests of various researchers. The treatment of plant seeds with ACC deaminase containing bacteria typically reduces ACC and ethylene levels about 2
4 times. These bacteria can reduce plant growth inhibition and protect plants against cold damage, drought, flooding, high salt, phytopathogens, poly aromatic hydrocarbons, and metals (Reed & Glick, 2005). ACC deaminase containing rhizobia are more efficient nodulators of their hosts. Mutants of R. leguminosarum bv. viciae (which cannot synthesize ACC deaminase) showed decreased nodulation efficiency (30%) compared with the parent strain. The application of Azospirillum sp. and Rhizobium sp. increased plant tolerance to salinity (Casanova, N´egrel, Kloppmann, & Aranyossy, 2001). Inoculated microbial strains increased water content, foliar area, total plant biomass and led to the reduction in decreased water potential and increased accumulation of proline. In addition, grains harvested from Azospirillum inoculated plants under drought showed increased content of K, Ca, and Mg compared with control wheat plants (Creus, Sueldo, & Barassi, 2004). Microbial inoculants also modulate root development that

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Chapter 2 Plant growth promoting rhizobacteria

FIGURE 2.1 Ethylene biosynthesis pathway depicting ACC synthesis.

allows better water and nutrient uptake due to greater root exploration in the soil. According to Nascimento, Rossi, Soares, McConkey, and Glick (2014) the number of PGPR possessing ACC deaminase enzyme catalyzes cyclopropane ring fragmentation and deamination of ACC into ketobutyrate and ammonia. These ACC products are utilized by bacteria as the source of C and N, which lower down the level of plant ethylene and consequently enhance plant tolerance to abiotic stresses. The bacteria may activate stress-induced mitogen-activated protein kinases (MPK6 and MPK3), which phosphorylate ACC synthase enzyme (Liu & Zhang, 2004). Due to the increased activity of ACC synthase, more ACC is made in the plant cells. Some ACC is eliminated from the roots, seeds, or leaves, which are used by bacteria. Here bacteria act as a sink for ACC and reduce the overall concentration for conversion into ethylene. Fig. 2.1 shows ethylene biosynthesis and ACC synthesis pathway.

2.3.5 Phytohormone production The production of phytohormones by PGPR is one of the most significant mechanisms in plant growth promotion and plays a vital role in sustainability by enhancing root and shoot growth. In addition to other hormones and certain volatiles, cofactor pyrroloquinoline quinones (PQQ) are produced by some PGPR. Auxin/IAA is the most common phytohormone synthesized in the shoot apical meristem and is distributed throughout the body of the plant. The root growth promoting auxins is usually synthesized from tryptophan (present in root exudates). Tryptophan concentration differs in root exudates of different plants (Kamilova et al., 2006). The pathway of biosynthesis of IAA in

2.3 Plant growth promoting rhizobacteria: mechanisms of action

33

FIGURE 2.2 Auxin biosynthesis.

plants and microorganisms is similar (Maheshwari, Dheeman, & Agarwal, 2015). Fig. 2.2 represents the auxin biosynthesis pathway. Auxins, which act as signaling molecules, are produced by approximately 80% of rhizospheric bacteria. The amount of auxin produced varies in different bacterial strains. Beneficial rhizospheric bacteria synthesize auxin via indole-3-pyruvate pathway using tryptophan as a precursor (Ole´nska et al., 2020). Bal, Das, Dangar, and Adhya (2013) reported root elongation in tropical rice plants after using five IAA producing strains, viz. Bacillus, Microbacterium, Methylophaga, Agromyces, and Paenibacillus. Similarly, IAA producing Bacillus sp. was reported to confer a phytostimulatory effect on Vigna radiata (Ali, Sabri, Ljung, & Hasnain, 2009). The inoculation of Pseudomonas fluorescens WCS365 did not increase the root and shoot weight of cucumber, sweet pepper, or tomato but led to a significant increase in the root weight of radish, which may be due to the fact that radish produces at least nine times more tryptophan in its exudates (Kamilova et al., 2006). A N2-fixing bacteria Azotobacter paspali, isolated from a subtropical grass species was reported to improve growth in a variety of dicot and monocot plants. However, the reason for plant growth promotion was attributed to the production of IAA, gibberellins (GA), and cytokinins rather than N2 fixation as experiments were conducted with added nitrogenous fertilizers. Some rhizobacteria such as B. subtilis, B. amyloliquefaciens, and Enterobacter cloacae promote plant growth by releasing volatile compounds (Ryu et al., 2003). The production of 2,3 butanediol and acetoin by some bacteria was related to higher plant growth as mutants of B. amyloliquefaciens IN937 (defective in production of volatiles) and B. subtilis (GBO3) were inactive in plant growth promotion.

34

Chapter 2 Plant growth promoting rhizobacteria

Zhang et al. (2008) found that the application of B. subtilis (GBO3) increased the photosynthetic efficiency and chlorophyll content of A. thaliana through the modulation of endogenous signaling of glucose and abscisic acid sensing. Another plant growth regulator, cytokinin, plays a crucial role in many physiological processes such as embryogenesis, maintenance of meristematic activity, development of vascular tissues, root elongation, lateral root, nodule formation, and apical dominance (Osugi & Sakakibara, 2015). Cytokinin-like plant growth regulators in the culture medium are produced by 90% of PGPR (Cohen, Bottini, & Piccoli, 2015). Zeatin and kinetin (different forms of cytokinin) are synthesized by rhizobacteria and found abundantly in nature (O’Brien & Benkov´a, 2013). Zeatin can be synthesized directly and indirectly. Direct synthesis takes place from dimethylallyl diphosphate while indirect synthesis takes place through cis-zeatin, which contains tRNA to release cytokinins (Tabassum et al., 2017). Naz, Bano, and Ul-Hassan (2009) revealed that under salt stress conditions, cytokinin producing bacteria, such as Arthrobacter sp., Bacillus sp., Azospirillum sp., or Pseudomonas sp., increased root and shoot biomass as well as the proline content in Glycine max. Similarly, Bacillus licheniformis, B. subtilis, and Pseudomonas aeruginosa strains were reported to promote cell division and fresh weight of etiolated cucumber seedlings (Hussain & Hasnain, 2009). In another study by Patel and Saraf (2017), rhizobacteria isolated from Coleus forskohlii, viz. Pseudomonas stutzeri MTP40, Stenotrophomonas maltophilia MTP42, and Pseudomonas putida MTP50, were reported to synthesize plant growth enhancing cytokinins. Another class of plant growth regulatory hormone, generally called gibberellins, is an entkaurene-derived diterpenoid phytohormone. They form a large family of plant growth substances with distinct functions and are involved in a number of physiological processes, including regulation of seed dormancy, quiescence, flowering, ripening of fruits, root growth, promoting seed germination, stem and leaf growth, floral induction, and flower or/and fruit growth. They also help to alleviate abiotic stress, regulate vegetative and reproductive (bud) dormancy, and delay senescence (Maheshwari et al., 2015). Initially, gibberellin was characterized in gnotobiotic cultures of Rhizobium meliloti where the presence of GA1, GA4, GA9, and GA20 was demonstrated (Atzorn, Crozier, Wheeler, & Sandberg, 1988). Since then, the presence of GA synthesis was confirmed in numerous rhizospheric bacteria, including Acetobacter diazotrophicus, Herbaspirillum seropedicae, Bacillus sp. or Azospirillum sp. Out of 136 different GAs reported to date, the most commonly occurring gibberellic acid in bacteria is GA3. GA3 producing PGPR show a positive effect on plant growth and development. The inoculation of maize roots with different Azospirillum strains increased the level of GA3 in the roots and promoted their growth (Revolti, Caprio, Mingotte, & Moˆro, 2018). In another report, GA4 synthesizing Sphingomonas sp. LK11 improved the growth of Solanum lycopersicum and increased its tolerance under salinity stress (Halo et al., 2015). Abscisic acid (ABA), a sesquiterpene plant growth regulator, mainly works as an inhibitor of growth and metabolic activities in plants but it fulfills many important roles in plants such as seed development and maturation, induction of seed and bud dormancy, senescence processes, synthesis of proteins and compatible osmolytes, and regulation of the ability of plants to survive in harsh and changing environments due to abiotic and biotic factors. Abiotic stress response booster ABA alters the expression of the complex network of genes that have a specific function related to stress. The inoculation of maize with the ABA producing Azospirillum lipoferum strain USA59b increased plant biomass in water-deficient conditions (Cohen et al., 2015). ABA has been characterized in A. brasilense sp. 245, Arthrobacter koreensis, and B. licheniformis using mass spectrometry

2.3 Plant growth promoting rhizobacteria: mechanisms of action

35

(Cohen, Bottini, & Piccoli, 2008; Piccoli et al., 2011; Sgroy et al., 2009). ABA-synthesizing Pseudomonas putida strain MTCC5279 associated with Cicer arietinum (chickpea) provided salt and drought tolerance to their host plants by altering morpho-physiological and biochemical properties and modulating the expression of stress-responsive genes (Tiwari, Lata, Chauhan, & Nautiyal, 2016). Some other ABA producing rhizobacteria are B. licheniformis, Brevibacterium halotolerans, A. brasilense (Cohen et al., 2009), Pseudomonas putida (Sgroy et al., 2009), B. subtilis, and Achromobacter xylosoxidans (Forchetti et al., 2007; Sgroy et al., 2009).

2.3.6 Siderophore production for iron acquisition Plants, microorganisms, and animals require iron to grow, survive, and perform metabolic activities. Iron is involved in a number of metabolic processes including the tricarboxylic acid cycle; oxidative phosphorylation; nitrogen fixation; and biosynthesis of aromatic compounds, porphyrins, toxins, vitamins, antibiotics, cytochromes, and pigments (Sayyed, Chincholkar, Reddy, Gangurde, & Patel, 2013). It is required as a cofactor by different enzymes and proteins. Iron is rarely found in free form as most of the free iron is converted into insoluble ferric oxides and oxyhydroxides at neutral pH in the presence of oxygen. Siderophores, the iron chelating agents’ low molecular weight organic compounds produced by numerous microbes in the stationary phase (secondary metabolites) are reported to increase and regulate the availability of iron in plant rhizosphere, which is otherwise unavailable at neutral pH (Leong, 1986). Siderophores are chelating compounds that predominantly form complexes with iron (Fe21) to increase iron mobility and availability and translocate it across plant cell membranes (Govindasamy et al., 2011; Kumar et al., 2018). Siderophore production has been recorded as one of the important mechanisms by certain PGPR for rhizospheric colonization (Bhattacharyya & Jha, 2012). Both bacteria and fungi produce siderophores under iron-limiting conditions (Table 2.3). Numerous evidences are available regarding iron uptake by plants through microbial siderophores, which enhance the availability of iron by converting the insoluble form of iron into a soluble form (Sayyed et al., 2013). Iron-regulated outer membrane proteins (IROMPs) on the cell surface of siderophore producing PGPR transfer ferric iron complex to the cognate membrane, and makes iron accessible for metabolic activities (Johri, Sharma, & Virdi, 2003). Siderophores have been classified broadly into three categories based on their main chelating groups or functional groups, viz. catecholates (e.g., enterobactins, vibriobactins, pyochelins), hydroxamates (alcaligin, Table 2.3 Microbial siderophores. Organisms

Siderophores

E. coli Streptomyces pilosus Aeromonas hydrophila Mycobacterium tuberculosis Pseudomonas aeruginosa Klebsiella pneumoniae Acinetobacter calcoaceticus

Enterobactin Desferrioxamines Amonabactin Mycobactin Pyoverdin, Pyochelin Aerobactin Acinetobactin

36

Chapter 2 Plant growth promoting rhizobacteria

staphyloferrin), and mixed types (mycobactins, petrobactins). The export of siderophores is mediated by three major types of the family of transporter proteins, the major facilitator superfamily (MFS); the resistance, nodulation, and cell division (RND) superfamily; and the ATP-binding cassette (ABC) transporter superfamily (Saha, Saha, Donofrio, & Bestervelt,2013). Siderophores producing PGPR have been implicated in increased rhizospheric competence and biocontrol of several plant diseases. By limiting the iron availability to the pathogens, siderophores are reported to slow down the growth of pathogens, especially fungi. For instance; a siderophore producing strain, B. subtilis CAS15, was reported to promote the growth of pepper and induced systemic resistance against Fusarium wilt (Yu, Ai, Xin, & Zhou, 2011). In another study, indigenous P. fluorescens strains were reported to suppress Fusarium wilt caused by Fusarium oxysporum f.sp. lycopersici in tomato (Arya, Rana, Rajwar, Sahgal, & Sharma, 2018). Pseudomonas aeruginosa PSA01 and P. fluorescens PSF02 significantly increased the iron and oil content, root and shoot length, and fresh and dry weight of Arachis hypogaea L. (Subramanium & Sundaram, 2020). Siderophore production is also reported to play a role in the suppression of plant pathogens in peanuts and maize. Several siderophore producing bacterial genera, including Azotobacter, Azospirillum, Bacillus, Streptomyces, Klebsiella, Pseudomonas, Serratia, Paenibacillus, and Pantoea, are reported to act as good biocontrol agents. Siderophore production is maximum in the rhizosphere compared with bulk soil (Ferreira, Soares, & Soares, 2019; Ferreira, Vilas-Boas, Sousa, Soares, & Soares, 2019). A siderophore producing P. aeruginosa FP6 was reported to suppress the growth of Rhizoctonia solani and Colletotrichum gloeosporioides (Sasirekha & Srividya, 2016). Bacillus and Paenibacillus species have been reported to enhance iron uptake in plants by producing siderophores. The growth of corn plants was reported to increase on inoculation of Pseudomonas polymyxa P2b-2R, which produced siderophores along with some other plant growth promoting traits possessing several PGP traits in addition to siderophore production (Padda, Puri, & Chanway, 2017). Similarly, reports reveal the presence of hydroxamate and catecholate type siderophores produced by Bacillus megaterium (ATCC 19213), B. anthracis (USAMRIID, 7702, and 34F2), and B. cereus (ATCC 14579) (Govindasamy et al., 2011; Wilson, Abergel, Raymond, Arceneaux, & Byers, 2006). Lysinibacillus sphaericus ZA9 produced siderophore and thus exhibited antagonistic activity against phytopathogens, which include Aspergillus sp., Trichophyton sp., Sclerotinia sp., Alternaria alternata, Bipolaris spicifera, and Curvularia lunata (Naureen et al., 2017). Apart from providing soluble iron to the plants for their growth and development, siderophores are also reported to form complexes with other metal atoms including zinc, copper, aluminum, lead, etc. (Hesse et al., 2018; Neubauer, Nowack, Furrer, & Schulin, 2000). In a study conducted by Yu et al. (2017) Bacillus sp. PZ-1 was reported to extract lead from the soil by means of siderophore production. Similarly, siderophore-producing Bacillus sp., Bacillus thuringiensis GDB-1, and Bacillus sp. SC2b has been reported to remove heavy metals including Cd and Zn and promote the growth of Alnus firma and Sedum plumbizincicola (Babu, Kim, & Oh, 2013; Ma et al., 2015). It can be concluded that siderophores play an important role in plant growth both directly through nutrient uptake (iron) and indirectly through heavy metal remediation and biocontrol.

2.3.7 Antibiotic production Antibiotic production by a number of soil bacteria is considered a major event in soil-borne disease suppression. Certain strains of root colonizing fluorescent pseudomonads are known to suppress a

2.3 Plant growth promoting rhizobacteria: mechanisms of action

37

variety of soil-borne plant diseases. Production of antimicrobials and iron chelating metabolites are considered to be the primary mechanisms of disease suppression in PGPR. The role of phenazine1-carboxylic acid (PCA); hydrogen cyanide (HCN); 2,4-diacetyl phloroglucinol; oomycin A; pyoluteorin; and pyrrolnitrin has been demonstrated by Thomashow and Weller (1996). Yellow-green siderophores (pyoverdines or pseudobactins) produced by fluorescent pseudomonads under iron limiting conditions are found inhibitory for Pythium, Fusarium, and Erwinia carotovora. Buysens, Heungens, Poppe, and Hofte (1996) reported that pyochelin contributed toward the protection of tomato plants from Pythium by a strain of P. aeruginosa. A strain of P. fluorescens (CHAO), isolated from a suppressive soil to tobacco black rot inhibited a variety of plant pathogens. Antibiotic pyrrolnitrin producing P. fluorescens was strongly inhibitory to Rhizoctonia solani. Pyoluteorin antibiotic was effective against Pythium ultimum, a causative agent of cotton seedlings. Bacillus subtilis strains produce an array of secondary metabolites, which mostly belong to antimicrobial peptides (AMPs) having antibiosis properties. These molecules often contain unusual moieties such as D-amino acids or intramolecular thioether bonds and are cyclic and hydrophobic. Some antimicrobial compounds produced by Bacillus strains have been enlisted in Fig. 2.3. Apart from antimicrobial peptides (AMPs), volatile antimicrobial compounds exhibit multiple roles. It is now reported that at least 4%
5% of the genome of any given strain of B. subtilis group is devoted to antimicrobial compounds (AMCs) production. Ribosomally synthesized peptides

FIGURE 2.3 Antimicrobial compounds produced by Bacillus species.

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Chapter 2 Plant growth promoting rhizobacteria

(RPs), usually derived from short precursors (100 AA) are processed to mature compounds through posttranslational modifications. It has been speculated that a wide variety of enzymes catalyze these modifications and therefore generate a wide range of chemical compounds. These compounds were originally known as bacteriocins, which are low molecular weight molecules that exhibit inhibiting growth activities against bacteria closely related to the producing strain (Chopra, Singh, Jena, & Sahoo, 2015). Aside from bacteriocins, several other ribosomally synthesized enzymes with antagonistic activities exist. These enzymes are involved in metabolic and physiological functions including QS, lysis of cells, and inducing genetic competence (Shafi, Tian, & Ji, 2017).

2.3.8 Biosurfactant production Biosurfactants are a structurally varied collection of surface-active compounds of microbial origin. These are amphipathic molecules that have both hydrophilic and hydrophobic moieties, which show partitioning based on H-bonding and polarity at the interface of fluid phases such as oil/water and air/water interfaces. Surface and interfacial tensions are reduced in aqueous solutions and hydrocarbon mixtures (Desai & Banat, 1997). Biosurfactants chemically fall into one of the following classes: glycolipids, lipopeptides, lipoproteins, phospholipids, fatty acids, and polymeric surfactants. The biological effectiveness of biosurfactants for plant protection was initially reported by Tomlinson, Wilson, Harris, and Jeffrey (1980) on lettuce big vein disease carried by a virus and vectored by Olpidium brassicae and on melon necrotic spots of cucumber. Cort´es-Camargo et al. (2021) reported that Bacillus tequilensis ZSB10 produced mixtures of biosurfactants such as surfactin, iturin A, and fengycin, which meanwhile worked as biopesticides against Helminthosporium sp. The lytic action of surfactants was not restricted to zoospores of Olpidium but also against Pythium aphanidermatum and P. dissotocum. The best-studied biosurfactant glycolipids, the rhamnolipids, are produced by Pseudomonas sp. Stanghellini and Miller (1997) demonstrated the lysis of suspension of zoospores of Pythium aphanidermatum, Phytophthora capsici, and Plasmopara lactucae within 1 min of treatment with the biosurfactant of Pseudomonas sp.

2.4 Plant growth promoting rhizobacteria in abiotic stress remediation Increasing pressure due to abiotic stress conditions is hampering the current situation of food production, which in turn negates plant growth and development, leading to food insecurity. A plethora of abiotic factors, including drought, salinity, acidic conditions, flooding, irradiations, heavy metals, nutrient starvation, anaerobiosis, and temperature fluctuations, pose threatening effects on plant survival, ultimately causing a reduction in yields (Kumar et al., 2018). All the abiotic stresses to which plants are exposed negatively affect their normal physiology and metabolism (Sati, Pande, Satish Chandra, & Samant, 2021). For instance, low temperatures could lead to freezing and dehydration in plant cells. On the contrary, if the temperature goes high, it may lead to protein denaturation and disruption of cell membranes due to the generation of reactive oxygen species (ROS). Heavy metal pollutants in the soil are noxious to soil microbiota as well as cause genotoxicity and reduction of polymorphism at the genetic level (Ole´nska et al., 2020). Water stress, either its inadequacy or waterlogging, also affects plant growth and metabolism. The moisture content of the soil,

2.5 Plant growth promoting rhizobacteria in biotic stress remediation

39

along with other factors, influences microbial communities found in the soil (Ojuederie, Olanrewaju, & Babalola, 2019). Under all kinds of stresses, overproduction of ROS occurs in different organelles, such as mitochondria, chloroplasts, and peroxisomes, which lead to a reduction in CO2 uptake in plants necessary for efficient photosynthesis. Plants acclimatization to unfavorable conditions requires appropriate signaling to overcome the physiological abnormalities, which makes identifying the key genes involved in stress tolerance a top objective for plant scientists (Ojuederie et al., 2019). It has been proven that PGPR improve abiotic stress tolerance by utilizing a multitude of mechanisms (as discussed above) to mitigate the damage imposed by stress stimuli on plant health. Researchers need to dig deeper into molecular and physiological alterations imposed after using PGPR for stress management. Reactions displayed by plants challenged with abiotic stress are extremely intricate systems involving sensor systems and tightly regulated gene expressions (Abd El-Daim, Bejai, & Meijer, 2019). Several reports regarding the role of PGPR in the alleviation of abiotic stress are available. Jian, Bai, Zhang, Song, and Li (2019) reported alleviation of heavy metal stress and increased biomass of the host plant after coinoculation with Ensifer meliloti and Rhizobium radiobacter. In another study, conducted by Raklami et al. (2019), a consortium composed of Proteus sp., Pseudomonas sp., and two strains of Ensifer meliloti RhOL6 and RhOL8 was reported to promote growth of Medicago sativa under heavy metal and heat stress. Rhizobium strain RD64 with high IAA producing attribute was reported to protect Medicago sativa against drought significantly by the production of low molecular weight osmolytes, like proline, and pinitol (Defez, Andreozzi, & Bianco, 2017). Bacillus velezensis 5113 was reported to improve abiotic stress tolerance in wheat by inducing metabolic and molecular reprogramming on exposure to cold, drought, and heat stress (Abd El-Daim et al., 2019). Bacillus amyloliquefaciens SQR9, a PGPR strain, was reported to confer salt tolerance to maize plants via ionic homeostasis (Chen et al., 2016). Remarkable EPS production has been observed in PGPR under stressed environments. In a study, Pseudomonas putida GAP-P45 was observed to show increased EPS production under drought and thermal stress. It also improved soil aggregation and the stability of aggregates (Sandhya & Ali, 2015). Achromobacter piechaudii ARV8 reported to confer tolerance in Capsicum annuum L. and Solanum lycopersicum L. plants toward drought stress predominantly by producing ACC deaminase (Mayak, Tirosh, & Glick, 2004). In another study, plant growth enhancement was observed in Lactuca sativa L. cv. post coinoculation of Pseudomonas mendocina and G. intraradices by possible mechanisms, including production of antioxidant enzymes like superoxide dismutase (SOD), catalase (CAT), peroxidase, phosphatase, and nitrate reductase, in plant leaves (Kohler, Hern´andez, Caravaca, & Rold´an, 2008).

2.5 Plant growth promoting rhizobacteria in biotic stress remediation The agriculture sector faces heavy losses in terms of yield and quality of produce due to pathogenic microorganisms, including bacteria, fungi, and viruses. Plants have developed various defense strategies against biotic stress stimuli such as phytopathogens. Pesticides are one of the common solutions opted for disease prevention these days. However, long-lasting use of these agrochemicals as soil supplements or foliar spray leads to adverse effects on the soil ecosystem and its residues on

40

Chapter 2 Plant growth promoting rhizobacteria

food products are harmful for the consumers as well. PGPR with biological control activity act as an important alternative for disease suppression and thus can substantially reduce the use of agrochemicals in agriculture (Sarhan, Abd-Elsyed, & Ebrahiem, 2020). Numerous microorganisms that inhabit the rhizospheric soil are capable of benefiting plants by enhancing plant growth and biomass. PGPR are employed as biofertilizers, biostimulants, and biopesticides to promote plant health in a sustainable manner. They have the capacity to mitigate the majority of the issues and downsides associated with contemporary farming techniques and promise sustainable solutions for the same (Bajracharya, 2019). These are safe and eco-friendly and have targeted activity. A better understanding of the overall interaction and mechanism of disease suppression by microbial antagonists is of great interest as these open new doors toward improving the efficacy and performance of these bioinoculants (Compant, Duffy, Nowak, Cl´ement, & Barka, 2005). The process of promoting plant growth involves a multitude of mechanisms affecting both plant development and nutrition (Bharti et al., 2016). PGPB exert positive effects on plants by significantly decreasing pathogenic infections under biotic stress (Ole´nska et al., 2020). Under biotic stress conditions, PGPB compete with pathogens for space as well as limited nutrient resources such as iron, produce antimicrobial compounds, synthesize hydrolytic enzymes, viz. chitinases, glucanases, lipases, etc., and induce systemic response in host plants (Glick, 2014; Ma, Oliveira, Freitas, & Zhang, 2016). Table 2.4 represents the positive effect of some biocontrol agents on host plants. Beneficial microorganisms improve plant resistance against pathogens by competing for nutrients with the pathogenic ones. For instance, siderophore production is often associated with the

Table 2.4 List of bacterial antagonists and their host crops. Bacterial antagonists Pseudomonas aeruginosa Streptomyces and Azospirillum Pseudomonas fluorescens (CHA0) Pseudomonas putida (WCS358) Serratia marcescens Serratia plymuthica Bacillus subtilis Pseudomonas oryzihabitans Serratia plymuthica Bacillus amyloliquefaciens Trichoderma asperellum

Pathogens

Crops

References

Pyricularia grisea

Rice

Fusarium graminearum

Wheat

Peronospora parasitica

Arabidopsis sp.

Pseudomonas syringae

Arabidopsis sp.

Colletotrichum orbiculare Botrytis cinerea

cucumber Cucumber

Podosphaera xanthii Acidovorax citrulli

Cucumber Cucurbits

De Vleesschauwer, Cornelis, and Ho¨fte (2006) Alsaady, Salim, Al-ani, Aboud, and Al Roubaie (2021) Iavicoli, Boutet, Buchala, and M´etraux (2003) Meziane, Van Der Sluis, Van Loon, Ho¨fte, and Bakker (2005) Gu et al. (2020) Kamensky, Ovadis, Chet, and Chernin (2003) Sarhan et al. (2020) Horuz (2021)

Sclerotinia sclerotiorum Xanthomonas perforans

Cucumber Tomato

Kamensky et al. (2003) Chien and Huang (2020)

Xanthomonas perforans

Tomato

Chien and Huang (2020)

2.6 Induced systemic resistance

41

biocontrol activity of these microorganisms. PGPB produce siderophores of hydroxamates, catecholates, and carboxylates for the sequestration of iron, as in the rhizosphere, the availability of iron is limited for microbial assimilation. By producing these low molecular weight compounds, they reduce the accessibility of iron pools to their competitors (Ole´nska et al., 2020). Furthermore, the production of antimicrobial compounds is yet another attribute of PGPB for disease suppression. Antimicrobial compounds identified in biocontrol agents include classical compounds like HCN (Haas & Keel, 2003) and phenazines (Mavrodi, Blankenfeldt, & Thomashow, 2006) of which the major are PCA; phenazine1-carboxamide; 2,4-diacetyl phloroglucinol (Thomashow & Weller, 1996); pyoluteorin (Nowak-Thompson, Chaney, Wing, Gould, & Loper, 1999); and pyrrolnitrin (Kirner et al., 1998). Zwittermicin and kanosamine are produced by Bacillus cereus. Further, a wide variety of antimicrobial compounds, viz. subtilin, sublancin, bacilysin, surfactin, iturin, etc., are produced by Bacillus sp. Similarly, Pseudomonas sp. are reported to produce 2,4-diacetyl phloroglucinol, rhamnolipids, PCA, butyrolactones, pyrrolnitrin, viscosinamide, azomycin, etc. (Compant et al., 2005; Goswami, Thakker, & Dhandhukia, 2016). Many PGPB are reported to synthesize and secrete hydrolytic enzymes like chitinase, cellulase, protease, etc. that hydrolyze cell wall components of targeted pathogens. Chitin is a major constituent of the fungal cell wall. Biological control of some phytopathogenic fungi has been reported by chitinases producing bacteria that lyse the fungal cell wall. For instance, the suppression of Sclerotium rolfsii has been reported by Serratia marcescens using chitinase enzyme production being the major mechanism (Ordentlich, Elad, & Chet, 1988). Similarly, Burkholderia cepacia has been reported to synthesize β-1,3-glucanase that destroys cell walls of several phytopathogenic fungi (Compant et al., 2005). Certain biocontrol agents help plants by nullifying the virulence of pathogens. Bacillus cepacia and Ralstonia solanacearum are able to hydrolyze fusaric acid, a phytotoxin produced by Fusarium species. However, to counteract such effects of biocontrol agents and other microbial competitors, pathogens secrete toxins with a broad-spectrum activity as a mechanism of self-defense (Compant et al., 2005). Besides using single microbial strain for biocontrol of plant diseases, nowadays consortia of microbial antagonists are also being widely used (Chien & Huang, 2020). These combinations may include bacterial isolates along with either other bacterial antagonists or fungal biocontrol agents for efficient and broad-spectrum control of diseases. Furthermore, strain improvement strategies by combining biotechnological aspects have also perpetuated the overall development of efficient bio-control agents (Compant et al., 2005).

2.6 Induced systemic resistance Microbial interactions with plant roots help to attain resistance against pathogens, including bacteria, fungi, and viruses. The increasing endurance of plants mediated by rhizobacteria is of significant importance. Rhizobacteria-induced resistance (R-ISR) in hosts is driven by the involvement of two significant molecules, namely, ethylene and jasmonic acid (JA) (Ole´nska et al., 2020). These molecules are synthesized by a set of genes that encode some precursors of antioxidant enzymes namely polyphenol oxidase (PPO), peroxidase (PO), tyrosine ammonia lysine (TAL), oxidative phenolics, and phenylalanine ammonia lyase (PAL) (Maithani et al., 2021). Induced systemic resistance (ISR) is comparable to innate immunity in humans (Lugtenberg & Kamilova, 2009).

42

Chapter 2 Plant growth promoting rhizobacteria

Plant immunity toward pathogens starts with the recognition of certain conserved patterns known as microbe-associated molecular patterns (MAMPs) that include bacterial lipopolysaccharides, fungal cell wall components, flagellin proteins, etc., with the help of a large family of receptors known as plant pattern recognition receptors (PRRs) (Saijo, Loo, & Yasuda, 2018). The interaction between MAMP and PRRs results in the activation of a first line of defense response in plants, which triggers immunity. Out of all the MAMPs, flagellin (a component of bacterial flagella) and chitin (a component of fungal cell wall) are most common and are recognized by flagellin-sensitive 2 receptor (FLS2) and chitin elicitor receptor kinase 1 (CERK1), respectively (Ole´nska et al., 2020). In some cases, however, to bypass the first line of defense, pathogens using their virulence effector molecules suppress the first line of defense. In such cases, the second line of defense comes into action and is known as effector triggered immunity (ETI). ETI results in a hypersensitive response (HR) and leads to cell death at the infection site (Tonelli et al., 2020). The ISR pathway is triggered by nonpathogenic rhizobacteria. Induced resistance shows a broad-spectrum efficiency on the basis of quicker and stronger initiation of the basal defense system of plants enabling them to react more efficiently under stress conditions. This enhanced immunity of plants is similar to the immunization of animals and humans. Such induction of systemic resistance by expressing basal defense mechanisms is known as priming (Panpatte, Jhala, & Vyas, 2020). Due to priming, plants get an increased ability for more quick and more efficient activation of cellular defense responses upon pathogen infection. The priming state is generally expressed at the transcriptional level, and ISR-related transcriptional factors remain inactive under pathogen-free conditions and accelerate defense response upon infection by pathogens. Apart from preformed physical and chemical barriers, plants, after detection of a pathogen attack, activate complex signaling networks, which lead to induced defenses that confer more tolerance to the host plant. These induced processes involve events such as phosphorylation reactions, ROS accumulation, cell wall rigidification, callose deposition, defense hormone signaling, and increased expression of pathogenesis-related proteins (Kumar et al., 2018). ISR mediated by rhizobacteria is a process in which they prime the entire plant for increased defense against a variety of pathogens. Rhizobacteria trigger the immune response by producing elicitors such as antibiotics, N-acyl homoserine lactones, siderophores, volatile compounds, etc., which elicit MTI in plants (Pieterse et al., 2014; Stringlis et al., 2018). Initially, the response toward the elicitor is local, which is further transformed into a systemic response. There is no accumulation of pathogenesis related (PR) proteins, such as in systemic acquired resistance (SAR) and ethylene, and JA signaling also starts a postpathogen attack (Pieterse et al., 2014). ISR has been demonstrated in Pseudomonas sp. widely against phytopathogens like viruses, fungi, and bacteria (Bhattacharyya & Jha, 2012). Similarly, Bacillus strains, such as B. subtilis, B. amyloliquefaciens, B. subtilis, B. pasteurii, B. cereus, B. pumilus, B. mycoides, and B. sphaericus, have been reported to elicit a significant reduction in disease incidence on a wide variety of plants (Kumar et al., 2018). Plenty of reports are there across the literature where inoculation of one or more rhizobacteria primed the plants against a variety of pathogens. For instance, Cicer arietinum, when inoculated with Rhizobium sp., a series of events occurred, including increased expression of polyphenol oxidase, peroxidase, phenyl ammonia lyase, and isoflavone reductase activity, which ultimately primed the crop against Fusarium oxysporum f.sp. Ciceris (Tonelli et al., 2020). Similarly, P. fluorescens strain WCS417 induced early root response ISR by priming Arabidopsis thaliana (Moreau, Bardgett, Finlay, Jones, & Philippot, 2019). It has been proven that ISR does not involve the

2.7 Commercialization of plant growth promoting

43

accumulation of PR proteins and salicylic acid, unlike SAR. Where the SAR pathway triggers the growth of necrotrophic pathogens, the ISR pathway helps to protect plants from necrotrophic pathogens (Panpatte et al., 2020).

2.7 Commercialization of plant growth promoting rhizobacteria-based bioproducts Over the past few decades, the interaction between plants and their rhizospheric bacterial communities has been well explored and the benefit is being taken with the application of microbial products as inoculants for improved plant health. Biofertilizer is a term that refers to the different formulations of agriculturally important beneficial microorganisms with certain desirable plant growth promoting characteristics, which are utilized for crop nutrition management programs. These are cost-effective, eco-friendly, and natural in origin (Pandey & Chandra, 2016). These have been used in integrated nutrient management (INM) systems for a long time. Besides offering nutritional benefits to plants, they also promote soil health (Pandey et al., 2001). With the expansion of organic farming practices, the use of biofertilizers is also being geared up. At present more than 200 active ingredients in biopesticides are registered worldwide and availability of over 700 products is reported in the market (Sekar et al., 2016). However, for the acceptance of any bioproducts, quality control is important. Biofertilizers are graded on the basis of eight parameters, which determine the overall quality of a biofertilizer. These parameters include the number of viable cells, pH, contamination, size, carbon and moisture content, appearance, and date of expiry (Suh, Jiarong, & Toan, 2006). The product must be well labeled with all the specifications, including the name of the product, target crop, manufacturer, carrier used, quantity, storage, and usage instructions (Pandey & Chandra, 2016). Biofertilizers may be composed of either a single bacterial strain or a combined application of multiple PGPR strains collectively termed a microbial consortium (MC), which promote plant growth and development under normal as well as stressed conditions in the agricultural system leading to global food safety and security (Sekar et al., 2016). The potentiality of many bacteria within the consortium also triggers defense pathways to produce secondary metabolites in plants (Santoyo et al., 2021). Some commercially available bioproducts for plant growth promotion are presented in Table 2.5. Table 2.5 Commercially available PGPR products. Strains (single or consortia)

Commercial names

References

Rhizobia 1 Penicillium bilaii Rhizobium sp. Streptomyces griseoviridis K61 Azotobacter Pseudomonas 1 Cellulomonas 1 Bacillus 1 Rhodococcus B. amyloliquefaciens GB99 Pseudomonas syringae

TagTeam (USA) Nodulaid (UK) Mycostop Azoteeka (India) Bio Super (India)

Sekar et al. (2016) Bhattacharjee and Dey (2014) Bhattacharyya and Jha (2012) Bhattacharjee and Dey (2014) Sekar et al. (2016)

Quantum 4000 Bio-save10

Bhattacharyya and Jha (2012) Bhattacharyya and Jha (2012)

44

Chapter 2 Plant growth promoting rhizobacteria

Despite being a cost-effective and environment-friendly technology, the market for bioproducts is still not as flourishing as synthetic fertilizers in many aspects. PGPR production before appearing on the farmer’s shelf from the laboratory requires a careful and extensive study and market survey. Thus, to become a global reality, it has to go a long way, which requires more effort as there are still a few biosafety concerns for environmentalists regarding the use of certain strains of PGPR. Besides this, another problem lies in the unparalleled regulatory measures (Pandey & Chandra, 2016). Even guidelines for commercialization as well as mass production of biofertilizers vary in developing, developed, and underdeveloped countries. Thus, there is a need for strong and strict authorized regulatory measures for the same.

2.8 Conclusion and future prospects In a nutshell, all kinds of pressure from biotic and abiotic factors cause agricultural productivity losses. Under such conditions, microbial resources offer a safer alternative to reduce existing agricultural constraints to increase global food production in a sustainable manner. Currently, mechanisms involved in plant growth promotion along with complete knowledge of stress responses are being primarily explored. Considering the positive role of PGPR in stress mitigation and crop production, they are the most active candidates for application in agriculture. The use of PGPR can prove to be instrumental in ensuring a sustainable agriculture system. Overall, fine-tuning the interaction between plants and PGPR may widen the knowledge of signaling pathways accommodating unknown functions under stress conditions. In future a clear definition of plant
microbe interaction and their necessary traits are required for optimal performance of the strain for a particular crop. Additionally, it would be helpful to understand how different bacterial strains work together to promote plant growth. It is necessary to conduct research for efficient delivery systems for the inoculants to facilitate the persistence of the PGPR strains in the environment.

Acknowledgment Authors are thankful to the Department of Microbiology, GBPUA&T Pantnagar, for providing all the facilities.

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273. Zhang, J., Xiao, Q., & Wang, P. (2021). Phosphate-solubilizing bacterium Burkholderia sp. strain N3 facilitates the regulation of gene expression and improves tomato seedling growth under cadmium stress. Ecotoxicology and Environmental Safety, 217, 112268.

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CHAPTER

Role of quorum sensing in plant
microbe interactions

3

Prasenjit Debbarma1, Chandra Mohan Kumar2, Manshi Kumari3, Poornima4, Govind Makarana2, Saurabh Gangola5 and Saurabh Kumar2 1

School of Agriculture, Graphic Era Hill University, Dehradun, Uttarakhand, India 2ICAR-Research Complex for Eastern Region, Patna, Bihar, India 3Patna Women’s College, Patna, Bihar, India 4Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India 5School of Agriculture, Graphic Era Hill University, Bhimtal, Uttarakhand, India

3.1 Introduction Population density-dependent intercellular communication in bacteria is termed as quorum sensing (QS). QS is considered a fundamental and universal strategy for communication where unicellular prokaryotic organisms coordinate their behavior and carry out several important functions in their ecosystem (Papenfort & Bassler, 2016). Several cooperative and competitive interactions in the bacterial community are mediated by the QS-based communication. QS plays a substantial role in the social behavior of bacteria, such as bioluminescence, pathogenicity, plant growth promotion, and biofilm formation (Wu & Luo, 2021). QS relies on the interactions between low molecular weight signal molecules [autoinducers (AIs)] and their receptors. Bacteria synthesize AIs intracellularly and release them into the surrounding environment actively or passively. AIs accumulation is achieved by the increase in bacterial population. After achieving a threshold concentration the AI interacts with cognate receptors, which in turn regulates gene expression and leads to cell-density-dependent behavior (Li & Nair, 2012). A wide variety of AIs produced by bacteria are mentioned in Table 3.1. QS has been reported in both gram-positive and gram-negative bacteria. In gram-negative bacteria, N-acyl homoserine lactones (AHLs) are a major class of AIs that have a lactone ring and an acyl side chain. (Papenfort & Bassler, 2016). The presence of different numbers of carbon atoms (C4 2 C16) in side chains attached to homoserine lactone (HSL) ring and oxo or hydroxyl groups in the C3 position of the acyl chains provides specificity to the AHL molecules (Savka et al., 2015). Contrary to this, in gram-positive bacteria, oligopeptides are used as AIs, which are subsequently detected by a bacterial two-component system or reinternalized with the help of an oligopeptide transport system (Monnet & Gardan, 2015). Bacterial QS compounds have been reported to be one of the critical modulators of plant
microbe interactions (Hartmann, Rothballer, Hense, & Schro¨der, 2014). Plants could sense microorganisms in their surroundings by the diffusible small molecules released by microorganisms and also influence rhizosphere microorganisms by their secretion (Ma, Oliveira, Freitas, & Zhang, 2016). Signaling molecules activate the transcription factors inducing specific genes present in the Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00017-X © 2023 Elsevier Inc. All rights reserved.

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Chapter 3 Role of quorum sensing in plant
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Table 3.1 Quorum-sensing molecules produced by bacteria. Bacteria

QS signaling molecules

Functions

References

Burkholderia glumae

C6 and C8 HSL

Produces toxoflavin

Bradyrhizobium japonicum USDA110

Bradyoxetin

Controls nod gene

Dickeya zeae

3-Oxo-C6-HSL and C6-HSL 3-Oxo-C14-HSL

Regulates cell motility

Gao, Ma, Zhuang, and Zhuang (2015) Sanchez-Contreras, Bauer, Gao, Robinson, and Allan Downie (2007) Hussain et al. (2008)

Ensifer meliloti (Sinorhizobium meliloti) Ensifer meliloti (Sinorhizobium meliloti strain Rm1021) Erwinia amylovora

Pantoea stewartia ssp. stewartii

Pectobacterium carotovorum Pseudomonas syringae pv. Syringae Pseudomonas syringae pv. tabaci Ralstonia solanacearum Rhizobium leguminosarum bv. viciae Rhizobium sp. strain NGR234 R. radiobacter F4 Rhizobium etli strain CNPAF512

Aphid protection in barley

Wehner, Schikora, Ordon, and Will (2021)

3-Oxo-C14-HSL, C16:1-HSL, and C18-HSL

Regulates galactoglucan (EPS II) production

Sanchez-Contreras et al. (2007)

N-(3-Oxo-octanoyl)HSL and N(hexanoyl)-HSL 3-Oxo-C6-HS

Provides tolerance to hydrogen peroxide

Baltenneck, Reverchon, and Hommais (2021)

Regulates exopolysaccharide (EPS) production, biofilm development, and host colonization Extracellular cell wall degrading enzymes Regulates exopolysaccharide production and oxidative stress tolerance Regulates swarming, flagellum synthesis, and chemotaxis

Koutsoudis, Tsaltas, Minogue, and von Bodman (2006)

Regulates exopolysaccharide production and endoglucanase Regulates nodulation process

Ansari and Ahmad (2018)

3-Oxo-C8-HSL

Regulate plasmid transfer

He et al. (2003)

C8-, C10-, and C12HSL 3-OH-(slc)-HSL

Induces systemic resistance in wheat Regulates nitrogen fixation and symbiosome development

Hartmann, Klink, and Rothballer (2021) Daniels et al. (2002)

3-Oxo-C6-HSL and C6-HSL 3-Oxo-C6-HSL

N-(3-Oxo-hexanoyl)HSL and N-(3-oxooctanoyl)-HSL 3-Hydroxypalmitic acid methyl ester C6 to C8-HSL

Cr´epin et al. (2012) Ansari and Ahmad (2018)

Baltenneck et al. (2021)

Sanchez-Contreras et al. (2007)

3.2 Quorum sensing in rhizobacterial community colonization

59

rhizobacteria. Therefore, the whole rhizobacterial community can modify their behavior toward cell density fluctuations. In this process, rhizobacteria can establish molecular communication among their population and with their plant partner and improve plant growth by controlling phytopathogens, heavy metal remediation, nutrient transformation, secretion of phytohormones, etc. Plant response to AHLs produced by bacteria was first demonstrated in Phaseolus vulgaris and Medicago truncatula (Joseph & Phillips, 2003; Mathesius et al., 2003). Bacterial QS molecules have also been reported to modulate plant responses toward contact with bacteria (Hartmann et al., 2014). Plant and microbial partners function in a bidirectional way in QS operating in a plant
microbe system. Therefore, highlighting the importance of QS in plant
microbe interactions is important for sustainable agriculture.

3.2 Quorum sensing in rhizobacterial community colonization The soil zone of plant roots that confers the phenomenal microbial activities influenced by root exudates is called the rhizosphere (Hinsinger, Bengough, Vetterlein, & Young, 2009). Beneficial plant growth promoting bacteria in the rhizosphere promote plant growth and crop productivity through nutrient acquisition, protection from plant pathogens, augmentation or colonization of microbial community, and rhizoremediation (Dessaux, Grandcl´ement, & Faure, 2016; Kumar, Choudhary, Suyal, Makarana, & Goel, 2022). These microbes play a vital role in the nitrogen cycle, soil mineral transformation, soil organic matter decomposition, and secretion of phytohormones, such as GA3, cytokinin, and IAA (Bhattacharyya & Jha, 2012; Joshi, Kumar, Suyal, & Goel, 2017; Suyal et al., 2021). The fundamental mechanism of these activities in the rhizosphere begins with the root secretions as well as extracellular diffusates attracting the plant growth promoting rhizobacteria (PGPR), and eventually their multiplication leading to high densities as compared with bulk soil. Organic compounds in plant secretions manipulate the rhizosphere to control the population of PGPR. Sensing AIs help bacterial cells to regulate gene expression coordinately through QS. In rhizobia, flavonoids released by leguminous plants have been reported to enhance the expression of AHL synthesis genes (P´erez-Montan˜o et al., 2011). Transgenic tomato plants expressing different AHLs have been shown to alter the activity of PGPR and increase abiotic stress tolerance in the plant (Barriuso et al., 2008). Phytohormones of Gypsophila have also been reported to influence QS by Pantoea plantarum (Chalupowicz, Barash, Panijel, Sessa, & Manulis-Sasson, 2009). AHLs producing Burkholderia graminis provide salt stress tolerance to Arabidopsis thaliana and enhance overall plant development (Hartmann et al., 2021). PGPR use QS for important communication and physiological processes such as Rhizobiumlegume symbiosis, competition, protection, motility, genetic material exchange, etc. It was reported that Burkholderia species and their colonization in host plants is facilitated by the QS mechanism (Zu´n˜iga, Donoso, Ruiz, Ruz, & Gonz´alez, 2017). Atmospheric dinitrogen-fixing Rhizobium bacteria communicate with themselves using AHL signaling molecules by attaining the quorum level and helping the bacteria to colonize the legume root. A similar regulatory system is followed by Pseudomonas for rhizospheric colonization (Wei & Zhang, 2006). Typically, gram-negative bacteria use LuxI and LuxR-type AHL synthase and receptors, respectively for QS (Churchill & Chen, 2011). The LuxI type AHL synthase facilitates the production of AHLs through the catalytic

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Chapter 3 Role of quorum sensing in plant
microbe interactions

reaction between ACP (acyl carrier protein) and SAM (S-adenosylmethionine). Later the AHLs interact with the LuxR-type AHL receptors to modulate the target gene and, therefore, the whole QS signaling cascade. Through evolution, the plant
microbe relationship emerged as an efficient functional aspect of plant growth and development. For instance, Azospirillum species acquired some functional genes from other bacteria that confer in plant root colonization. The QS system has been altered in such a way that LuxR genes could be incorporated in Azospirillum and PGPR through different evolutionary activities.

3.3 Quorum sensing and plant disease protection The importance of QS has been reported in suppressing plant disease-producing agents (Mu¨ller et al., 2009). Production of different types of AHLs in the plant rhizosphere modulated the plant defense mechanism, immune system, and overall plant growth (Ortı´z-Castro, Contreras-Cornejo, Macı´as-Rodrı´guez, & Lo´pez-Bucio, 2009). The inoculation of Serratia liquefaciens MG1 producing AHLs (C-4 and C-6 side chain AHLs) in tomato (Solanum lycopersicum) plants can induce systemic resistance proteins providing a necessary defense mechanism to plants against phytopathogens (Schuhegger et al., 2006). However, AHL-deficient S. liquefaciens MG44 inoculated plants were found susceptible. In different studies on Arabidopsis thaliana, it was observed that C-4 and C-6 side chains containing AHL molecules modifies the expression of regulatory genes for phytohormones production, which leads to hormone imbalance in the plant, specifically resulting in a higher ratio of auxin and cytokinin (Von Rad et al., 2008). When Arabidopsis thaliana was exposed to oxo-C14-HSL and subsequently challenged with flg22; phenolics and lignin content was found to increase along with the enhanced callose depositions in cell walls (Schenk, Stein, Kogel, & Schikora, 2012; Shrestha et al., 2019). Similarly, Serratia plymuthica HRO-C48 found in rapeseed (Brassica napus) rhizosphere secretes AHLs signaling molecules (C4-, C6-, and 3-oxo-C6-HSLs), which induce chitinase and antifungal volatiles production that acts as a biocontrol of Verticillium dahlia-mediated wilt (Mu¨ller et al., 2009). Comparative studies between AHL-negative splI mutant of Serratia plymuthica strain HRO-C48 and AHL producing wildtype revealed that the wildtype strain provides protection in Cucumis sativus against Pythium aphanidermatum as well as to tomato and Phaseolus vulgaris plants from infection with Botrytis cinerea (Pang et al., 2009). The inoculation of oxoC14-HSL producing strain of Ensifer meliloti in A. thaliana provides resistance to P. syringae (Zarkani et al., 2013). C14- or C12-HSL control P. syringae pv. tomato (Pst) infection in A. thaliana (Shrestha, Grimm, Ojiro, Krumwiede, & Schikora, 2020). AHLs (C10- to C14-HSL) have been reported to provide resistance in barley and A. thaliana against biotrophic and hemibiotrophic pathogens (Alabid et al., 2020). C8-, C10-, and C12-HSL producing Rhizobium radiobacter induce resistance against bacterial pathogens in wheat and A. thaliana (Alabid et al., 2020). The 3-oxo-C14-HSL producing Ensifer meliloti has been reported to reduce aphid feeding in priming sensitive barley genotypes (Wehner et al., 2021). Pretreatment of AHL in AHL-primable barley shows high resistance against powdery mildew (Shrestha et al., 2019).

3.4 Quorum sensing in nitrogen-fixing rhizobia

61

The application of AHLs to modulate plant defense is a sustainable strategy to protect the plant against phytopathogens but requires more detailed and systematic research for translational use. However, genes expressing the virulence factor of the pathogenic bacterium are regulated by the QS system. In terms of biocontrol, quorum quenching (QQ) has been reported to be a better means of maintaining plant health (Gao et al., 2015). Understanding the rhizosphere interactions and their effects on plant health should be the priority before the translational use of QS- and QQ-based plant disease control strategies.

3.4 Quorum sensing in nitrogen-fixing rhizobia Symbiotic nitrogen-fixing bacteria (rhizobia) establish a nitrogen-fixing symbiosis with legumes. QS is used as an important communication system in this symbiosis (Gonz´alez & Marketon, 2003). Several bioactive molecules (flavonoids, EPSs, nod factors, and AHLs) are responsible for controlling the regulatory network and coordinating effective legume-rhizobia symbioses. QS exerts its vital role in the nitrogen fixation of rhizobia by regulating their growth, nitrogen fixation activity, nodulation process, and formation of complete symbiosis with their legume hosts. Four different AHL-based QS systems (tra, rai, rhi, and cin) have been reported in Rhizobium leguminosarum bv. Viciae (Gao et al., 2015). The cinI-cinR-dependent regulation of QS is the most important regulation, which induces other regulatory systems. Disruption of cinR and cinI have been reported to terminate the synthesis of N-(3-hydroxy-7-cis-tetradecenoyl)-l-homoserine lactone. Mutation in cinR and cinI also negatively influence the production of AHLs produced by raiI, traIlike, or rhiI. CinI is responsible for the production of 3-OH-C14:1-HSL, which induces a growthinhibitory response in R. leguminosarum (Lithgow et al., 2000). In the S. meliloti 8530 QS system, SinI, which is induced by SinR, activates the production of diverse long-chain AHLs. Moreover, ExpR either induces the expression of SinI or downregulates SinR based on molecular signals (Charoenpanich, Meyer, Becker, & McIntosh, 2013). AI profiling of S. meliloti has shown the presence of long- and short-chain AHLs, including 3-oxo-C12homoserine lactone (3-O-C12-HSL), and 3-OH-C16-HSL (Gosai, Anandhan, Bhattacharjee, & Archana, 2020). The Sin QS system of the S. meliloti strain Rm1021 depends on SinR and ExpR, which are regulated by AHLs produced by SinI. The AHL signals are involved in the regulation of motility, swarming, nodule formation, and effective symbiosis formation with the host plant (Gao et al., 2015). Interestingly, water-soluble humic materials (WSHM) have been reported to downregulate the expression of the QS related genes (SinI, SinR, and ExpR) in S. meliloti, which leads to an increase in cell density (Xu et al., 2018). Therefore, WSHM increases nitrogen fixation in Medicago sativa and S. meliloti symbiosis. In bradyrhizobia the expression of nod genes are modulated by bradyoxetin, which are produced in a population-density-dependent manner. More bradyoxetin production was reported in highpopulation-density and iron-depleted conditions (Jitacksorn & Sadowsky, 2008). Bradyoxetin was first identified in the high cell density culture supernatant of B. japonicum USDA110. Bradyoxetin induces NolA, which then represses the expression of nod genes. Bradyrhizobium
Azospirillum interaction with the help of AHLs leads to the promotion of soybean symbiosis (dos Santos Lima Fagotti et al., 2019).

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Chapter 3 Role of quorum sensing in plant
microbe interactions

AHLs are critical symbiotic association-dependent signals in legume-rhizobia symbiosis. QS signaling plays a crucial role in the motility and colonization of rhizobia, EPS production, determining efficiency nodulation, and nitrogen fixation in these plant symbionts. Therefore, bacterial density-dependent behaviors benefit soil nitrogen cycling events in the soil and could be manipulated for sustainable agriculture production.

3.5 Quorum sensing in rhizosphere engineering Plant
microbe interactions at the plant rhizosphere are important in sustainable agriculture. Rhizodeposition establishes a unique microbial community in the rhizosphere, which promotes plant growth positively. The cross-talk between plants and their microbial partner is achieved by specialized signaling molecules. Alteration in these signaling molecules in the rhizosphere can be performed to enhance the plant beneficial pathways. A strong correlation was reported between QS signaling system and plant-beneficial properties of rhizobacteria (Ghosh & Mandal, 2022). Therefore, the bacterial QS-based communication in the rhizosphere can be modified for improving plant health by modifications in QS signaling. Rhizobia uses QS for biological nitrogen fixation. Thus perturbation in rhizobial QS could be used for enhanced nitrogen fixation. QS also regulates the pathogenicity of Agrobacterium tumefaciens, Erwinia amylovora, Pectobacterium carotovorum, P. syringae, and Ralstonia solanacearum (Imran et al., 2014). Therefore, the interruption of the QS signaling in pathogenic bacteria is another important strategy to control plant pathogens (Hakim et al., 2021). On the other hand, QQ is defined as an interruption of a sensing system that results in the inactivation of QS signaling molecules. The first report of enzymatic degradation of an AHL was reported in Variovorax and Bacillus genera isolated from the soil (Grandcl´ement, Tannie`res, Mor´era, Dessaux, & Faure, 2016). QQ is achieved by the degradation of signaling molecules by various factors (enzymes and chemical compounds), QS-signal cleavage, and competitive inhibition. Physical parameters like temperature and pH have also been reported to influence the mechanism of QQ (Grandcl´ement et al., 2016). QQ has been reported in the pathogenicity of various phytopathogens thus decreasing virulence and infection. This approach does not disrupt the essential genes in microorganisms and has low incidences of resistance development (Defoirdt, 2018). Therefore, this approach could be more beneficial than antibiotics application because this will limit the excessive use of antibiotics and there will be lesser chances for development of antibiotic resistance.

3.6 Conclusion QS exerts its crucial role in several important events like rhizosphere colonization, biological nitrogen fixation, and biocontrol of plant diseases where it modulates the cross-talk between plants and microorganisms. Perception of AHLs by plants leads to several responses like changes in gene regulation, hormonal imbalance, induced defenses, and cytoskeleton modification, which could impact plant health. QS signaling molecules tend to operate in a bidirectional way and influence both plant

References

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and microbial partners. Therefore, the role of QS in plant
microbe interactions needs to be studied in detail for a better understanding of communication between plants and microbes.

References Alabid, I., Hardt, M., Imani, J., Hartmann, A., Rothballer, M., Li, D., . . . Kogel, K. H. (2020). The N-acyl homoserine-lactone depleted Rhizobium radiobacter mutant RrF4NM13 shows reduced growth-promoting and resistance-inducing activities in mono-and dicotyledonous plants. Journal of Plant Diseases and Protection, 127(6), 769
781. Ansari, F. A., & Ahmad, I. (2018). Quorum sensing in phytopathogenic bacteria and its relevance in plant health. Biotechnological applications of quorum sensing inhibitors (pp. 351
370). Singapore: Springer. Baltenneck, J., Reverchon, S., & Hommais, F. (2021). Quorum sensing regulation in phytopathogenic bacteria. Microorganisms, 9(2), 239. Barriuso, J., Ramos Solano, B., Fray, R. G., C´amara, M., Hartmann, A., & Guti´errez Man˜ero, F. J. (2008). Transgenic tomato plants alter quorum sensing in plant growth-promoting rhizobacteria. Plant Biotechnology Journal, 6(5), 442
452. Bhattacharyya, P. N., & Jha, D. K. (2012). Plant growth-promoting rhizobacteria (PGPR): Emergence in agriculture. World Journal of Microbiology and Biotechnology, 28(4), 1327
1350. Chalupowicz, L., Barash, I., Panijel, M., Sessa, G., & Manulis-Sasson, S. (2009). Regulatory interactions between quorum-sensing, auxin, cytokinin, and the Hrp regulon in relation to gall formation and epiphytic fitness of Pantoea agglomerans pv. gypsophilae. Molecular Plant
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3236. Churchill, M. E., & Chen, L. (2011). Structural basis of acyl-homoserine lactone-dependent signaling. Chemical Reviews, 111(1), 68
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565.

CHAPTER

Microbial services for mitigation of biotic and abiotic stresses in plants

4

Viabhav Kumar Upadhayay1, Damini Maithani2, Hemant Dasila3, Gohar Taj4 and Ajay Veer Singh5 1

Department of Microbiology, College of Basic Sciences & Humanities, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India 2School of Biotechnology, IFTM University, Moradabad, Uttar Pradesh, India 3 Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Himachal Pradesh, India 4Department of Molecular Biology & Genetic Engineering, College of Basic Sciences and Humanities, GBPUAT, Pantnagar, Uttarakhand, India 5Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar (U.S. Nagar), Uttarakhand, India

4.1 Introduction Plants are subjected to a wide range of environmental stresses, which reduces and limits the productivity of food crops. Two types of environmental stresses are encountered in plants, which can be categorized as (1) abiotic stress and (2) biotic stress (Pandey et al., 2017). The abiotic stress, which includes radiation, salinity, floods, drought, extreme temperature, heavy metals, etc., causes the loss of major crop plants worldwide (He et al., 2018); while, attacks by various pathogens such as fungi, bacteria, oomycetes, nematodes, and herbivores are included in biotic stresses (Moustafa-Farag et al., 2019). Rampant agrochemicals used to conquer the effect of abiotic and biotic stresses and dearth of nutrients have resulted in the contamination of the environment, posing a threat to human health. Therefore there is an urgent need to explore other environmental friendly options for sustainable agriculture production. Exploration and use of plant growth-promoting bacteria as potential microbial resources provide alternative solutions for agricultural production in a sustainable manner (Backer et al., 2018). Bacteria that reside in the rhizosphere are known as plant growth-promoting rhizobacteria, which provide beneficial traits to the host plant through the establishment of a distinctive interaction (Saeed et al., 2021). Plant growth-promoting rhizobacteria (PGPR) adapt different forms of strategies to enhance plant growth (Basu et al., 2021). However, besides exhibiting plant growth-stimulating responses, plant growthpromoting microorganisms also protect plants from abiotic and biotic stresses by displaying various indirect mechanisms (Bhattacharyya et al., 2020). Microorganisms alleviate abiotic stresses in plants through a broad array of mechanisms such as through the production of phytohormones (Khan et al., 2020), osmolytes (Ilangumaran & Smith, 2017), and exopolysaccharides (EPS) (Morcillo & Manzanera, 2021); 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity (Danish et al., 2020); and induction of stress-responsive genes (Bharti et al., 2016). PGPR, as potential biocontrol agents, shows benefits for the environment, over chemical-based methods, due to their nontoxic nature (dos Santos et al., 2020). Microbes alleviate biotic stress through various mechanisms, such as the production of antibiotics, siderophore, cell wall degrading enzymes and induction of systemic resistance in plants (Jiao et al., 2021). Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00003-X © 2023 Elsevier Inc. All rights reserved.

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Thus several microorganisms, particularly PGPR, protect plants from the severity of diseases caused by plant pathogens (Joshi et al., 2020). Several pieces of literature illustrated the role of microorganisms in the alleviation of abiotic and biotic stresses. The present chapter is an endeavor to highlight the potential role of microorganisms in alleviating abiotic and biotic stresses.

4.2 Different types of stresses 4.2.1 Abiotic stress As a phenomenon of environmental factors, abiotic stresses pose several threats to the agriculture system that illustrate the loss of crop yield. Drought, high salinity, high or low temperature, and heavy metals are instances of abiotic stress that create hostile conditions for crop production. Salt stress is magnified by escalating salinization of cultivable lands worldwide. The survivability of plants cannot be fruitful as the concentration of sodium chloride goes beyond 200 mM. Extreme soil salinity impairs the growth of plants because of osmotic pressure, ion toxicity, short nutritional supply, and oxidative damage. Drought poses a threat to worldwide agricultural production as it reduces plant growth and affects overall crop yield (He et al., 2018). The scenario of the last 40 years has been a 10% reduction in yields of cereals (Lesk et al., 2016). It has been predicted that drought will affect crop production for about 50% of arable land by 2050 (Vinocur & Altman, 2005). Plant growth is mainly reduced due to low water and nutrients supply from the soil and low rate of photosynthesis (Kour et al., 2020). Cold stress conditions, which include chilling temperature, that is, 0 C
10 C, and freezing temperature, that is, ,0 C, slow the overall growth and development of plants and eventually a decline in crop yield (Su et al., 2015).

4.2.2 Biotic stress Different pathogens, weeds, and insects collectively contribute to biotic stress. Biotic stress causes adverse impacts on plants, including hormonal and nutritional imbalance, physiological disorders, susceptibility to diseases, etc., and results in reduced economic yield (Sindhu & Sharma, 2019).

4.3 Microbial resources for alleviation of stress in plant A variety of abiotic and biotic stresses considerably affect crop production, and the pattern of global climate change at a worldwide level accelerates these stresses showing adverse effects on agriculture, bioremediation efficiency, and ecosystem. However, plant growth-promoting microorganisms have received greater attention for developing an efficient and eco-friendly bioinoculant, as an alternative to chemical-based fertilizers (Ma et al., 2019). Nevertheless, the current demand is to develop bioinoculants having both traits: plant growth-promoting activities and tolerance toward abiotic and biotic stresses. Such a multifunctional behavior makes microbial inoculants a potential candidate to fulfill demands concerning agricultural and environmental systems. Moreover, a large volume of literature on plant
microbe interactions, focused on biochemical, physiological, and molecular aspects, illustrate microbial-directed plant responses to various kinds of stresses (Farrar et al., 2014).

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4.3.1 Bacterial-assisted drought mitigation in plants Plant growth-promoting microorganisms colonizing plants promote plant growth directly (through providing growth-related factors) or indirectly (protecting against environmental stress). Such microorganisms may also exhibit the potential to mitigate drought stress in plants through the production of phytohormones, ACC deaminase, EPS, volatile compounds; accumulation of osmolytes; increases in antioxidant compounds; regulation of stress-responsive genes; stimulation of systemic tolerance; alteration in root morphology; etc. (Mohammadipanah & Zamanzadeh, 2019; Waghmode et al., 2019). The symbiotic relationship between plants and microbes can potentially diminish the harmful effects of drought stress on plant growth and development. Several pieces of research illustrated the potential effect of microbial inoculants on reducing the adverse effect of abiotic stresses on the plant system. Bacterial secreted osmolytes under drought act synergistically with osmolyte compounds secreted by plants, such as proline, trehalose, and polyamines, making plants acquire strength in stressful environments (Paul et al., 2008; Sati, Pande, Pandey, & Samant, 2022). Bacillus spp. increased osmolytes, such as proline, sugars, and amino acids, and reduced electrolyte leakage in maize plants, alleviating negative influences of drought stresses (Vardharajula et al., 2011). Under drought stress, proline exhibits immense potential to regulate cytosol acidity and reduce lipid peroxidation by scavenging reactive oxygen species (ROS) and stabilizing proteins and membranes of plant cells (Gill & Tuteja, 2010). The overexpressing biosynthetic genes of trehalose accumulated in Azospirillum brasilense increased trehalose and bestowed drought tolerance in the maize plant (Zea mays) (Rodrı´guez-Salazar et al., 2009). Zhang et al. (2020) evaluated mycorrhizal-mediated drought tolerance improvement in orange plant (Poncirus trifoliate) by polyamine metabolism modulation. The inoculation of wheat by EPS producing bacterial strains (Bacillus subtilis and A. brasilense) augmented the level of osmolytes (proline, amino acid, sugar, and protein) and also enhanced the production level of antioxidant enzymes (superoxide dismutase, catalase, and peroxidase by 35.1%, 77.4%, and 40.7%, respectively) (Ilyas et al., 2020). The lower oxidative damage measured was due to improved antioxidant pathways (enzymatic and nonenzymatic) in Neotropical trees by PGPR (A. brasilense and Bacillus sp.) association, and enhanced ability of drought tolerance was depicted in these trees (Tiepo et al., 2020). The inoculation of rice plants with Pseudomonas and Trichoderma reduced ROS burden as a result of overexpression of genes related to superoxide dismutation (SODs), H2O2 peroxidation (APX, PO), phenylpropanoid (PAL), and oxidative defense response (CAT), and eventually mitigated drought stress (Singh et al., 2020). Moreover, rhizobacterial strains possessing the coexistence of EPS production and ACC deaminase property improved the physiological traits of maize plants, such as the rate of photosynthesis, vapor pressure, stomatal conductance, and water use efficiency under drought stress (Nadeem et al., 2021). ACC deaminase, Bacillus licheniformis K11, having the quality of ACC deaminase production, declined the effect of drought stress in pepper (Lim & Kim, 2013).

4.3.2 Bacterial-assisted salinity mitigation in plant In agricultural soil, salinity appears as a major issue showing terrible effects on the growth and productivity of a broad range of food-based crops (Orozco-Mosqueda et al., 2020). To counter the effect of salinity, microorganisms exert plenty of mechanisms and protect plants from the saline effect. Plant growth-enhancing bacteria control water potential and opening of stomata by

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influencing hydraulic conductivity and the rate of transpiration. One plant growth-promoting bacteria, namely Bacillus megaterium, exhibited enhanced root hydraulic conductivity of maize plants compared with uninoculated control (Marulanda et al., 2010). Accumulation of osmolytes induced by PGPR facilitates plants to counter primary osmotic shock after salinization. The well-illustrated activity, namely the production of ACC deaminase by bacteria, is somewhat general in stressful environments, provoking interaction between microorganisms and plants (Orozco-Mosqueda et al., 2020). Kang et al. (2019) reported that ACC deaminase and IAA producing Leclercia adecarboxylata (MO1) appreciably improved the capability of tomato plants to bear salt stress. Moreover, ACC deaminase-producing bacteria may facilitate the colonization of other native microflora (Orozco-Mosqueda et al., 2020). Moreover, as a bioinoculant, the ACC deaminase producing microbe Pseudomonas fluorescens YsS6 enhanced rhizobial nodulation in leguminous plants (Nascimento et al., 2019). Microbes having the trait of EPS production have been attributed to play an imperative role in mitigating salinity stress as EPS interacts with cations (such as Na 1 ) and reduces the bioavailability of ions for plant uptake (Kumar et al., 2020). Soil microorganisms, producing EPS in the soil as a slime substance, form a protective capsule around soil aggregates, and show resistance against salt stress (Kumar et al., 2020; Naseem, Bano, 2014). In Ansari et al. (2021), illustrating the role of biofilm-producing Pseudomonas azotoformans FAP5 mediated drought stress tolerance in wheat, the production of biofilms by PGPR was also considered as a mechanism of drought tolerance. The study carried out by Brotman et al. (2013) showed that Trichoderma ameliorated salinity stress by producing stress-responsive enzyme ACC deaminase. Two bacterial species Acinetobacter sp. and Pseudomonas sp. triggered the production of indole-3acetic acid (IAA) and ACC-deaminase at an enhanced level in barley and oats (Chang et al., 2014). Streptomyces sp. strain PGPA39 was found to alleviate salt stress and promote tomato plant growth (Palaniyandi et al., 2014).

4.3.3 Bacterial-assisted heavy metal stress mitigation Some anthropogenic activities contaminate soils through the addition of various heavy metals namely arsenic, cadmium, cobalt, lead, and zinc. The exceeded concentration of such kinds of metals poses threats to human health and the environment. Applications of microorganisms having plant growth-promoting traits show a striking tactic in alleviating heavy metal stress. Heavy metal tolerance mechanisms entailed by microorganisms involve transformation of heavy metals into bioavailable/soluble form, biosorption, bioaccumulation, production of EPS, and siderophores, etc. (Pande, Pandey, Sati, Bhatt, & Samant, 2022; Singh et al., 2019). In the rhizosphere, microbial communities promote plant growth through exhibiting numerous plant growth-promoting traits such as secretion of extracellular enzymes, metal chelating compound (siderophores), phytohormones, solubilization of inorganic minerals (phosphate, zinc, and potassium), and fixation of atmospheric nitrogen, reducing the negative effect of heavy metals on plant health simultaneously (Mishra et al., 2017). Two bacterial strains, Pseudomonas aeruginosa and Burkholderia gladioli, enhanced plant growth in terms of root and shoot length and fresh weight in the seedlings of Lycopersicon esculentum seedlings under cadmium stress (Khanna et al., 2019). In a study by Islam et al. (2014), P. aeruginosa presented as the best candidate for bioremediation and assisted in wheat plant growth promotion against zinc-induced oxidative stress through displaying antioxidant activity and hampering zinc uptake. Serratia sp. tolerated the toxic level of zinc by biosorption and maintained the

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growth of crop plants, especially maize, under zinc stress (Kour et al., 2019). Rhizobacteria, namely Halomonas sp. Exo1, as an efficient EPS producer, sequestered arsenic and assisted rice plant growth under salinity and heavy metal (arsenic) stresses (Mukherjee et al., 2019). Two plant growth-promoting bacterial strains such as Enterobacter ludwigii (HG 2) and Klebsiella pneumoniae (HG 3) exhibited enhanced growth of wheat seedlings under mercury stress (Gontia-Mishra et al., 2016).

4.3.4 Bacterial-assisted cold stress mitigation The psychrophilic Bacillus strains also assisted in the induction of cold stress adaptation in wheat through regulating abscisic acid, lipid peroxidation, proline accumulation pathways, and phytohormones expression in a positive manner (Zubair et al., 2019). The cold adaptive Pseudomonas isolates inoculation enhanced the cellular metabolites, such as free proline, total phenolics, chlorophyll content, starch content, available iron content, and amino acids, and also reduced the membrane injury (electrolyte leakage) as an indication of cold stress mitigation in wheat plants (Mishra et al., 2011). The study by Wang et al. (2016) found that a consortium of three bacteria (Bacillus cereus, B. subtilis, and Serratia sp.) induced chilling tolerance in tomato by the higher accumulation of soluble sugar, proline, and osmolytes, and also enhanced the antioxidant activity. Burkholderia phytofirmans strain PsJN induced cold stress tolerance in Arabidopsis thaliana and promoted plant growth (Su et al., 2015).

4.3.5 Bacterial-assisted biotic stress mitigation Besides inducing abiotic stress tolerance in plants, rhizobacteria also show the induction of biotic stress tolerance in plants. Plants have physical and chemical barriers that prevent the entry of pathogens. Besides this, the complex induced defense systems in plants also confer more biotic stress tolerance ability. Different cellular events, such as phosphorylation, result in increased ROS, rigidification of the cell wall, deposition of callose, expression of genes that encode pathogenesis associated proteins, and defense hormone signaling (Kaur, Pareek, & Singla-Pareek, 2019). Usually, competition for the acquisition of nutrients, ISR, niche exclusion, and production of allelochemicals are the primary way of biocontrol action in plant growth-promoting microorganisms (Lugtenberg and Kamilova, 2009). Plenty of studies compiled the effect of beneficial bacteria on disease suppression via induced systemic resistance (ISR) against many plant diseases (Kumari & Srivastava, 1999). PGPR-mediated ISR has been characterized at a broad level. Nonpathogenic bacterial genera, mainly Pseudomonas, has been determined for inducing ISR against different plant pathogenic microorganisms, such as bacteria, fungi and viruses. (Bhattacharyya and Jha, 2012). Though the mechanism of induction of ISR varies with the strains or species of microorganisms. For example, Pseudomonas fluorescens (strain WCS417r) elicited patterns of systemic disease resistance in the host via a number of signal translocation pathways such as SA-independent JAethylene-dependent signaling, ISR-related gene expression, and NPR 1-dependent signaling (Choudhary and Johri, 2009). The production of defense-related enzymes at an enhanced level during ISR is considered a key player in host resistance (Chen et al., 2000). Bacteria from the genera Bacillus and Pseudomonas are well-known to induce resistance against microbial pathogens (bacterial and fungal) (Singh & Jha, 2017). Bacillus subtilis (UFLA285) inoculated plant showed

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expression of disease resistance protein against damping-off causing fungus Rhizoctonia solani and observed increased proline accumulation in a plant (Medeiros et al., 2011). Two bacterial isolates B. megaterium and P. aeruginosa induced defense-related enzymes such as phenylalanine ammonia-lyase and β-1, 1,3-glucanase in the host plant (maize) infected with the fungal pathogen Aspergillus niger (Jha, 2018). Many PGPR have the ability to produce iron chelating compounds (siderophore), antibiotics, volatile compounds (HCN), and a variety of enzymes that play an imperative role in the inhibition of phytopathogens (Chandran et al., 2021). The ability of PGPR to produce siderophores and other compounds helpful in antibiosis encourages the authors to explore the further rhizobacterial isolates bearing multiple plant growth-promoting traits. Siderophores produced by pseudomonads have been studied at a wide level for their higher affinity to iron (ferric ion) (Luj´an et al., 2015). Rhizospheric isolates, P. aeruginosa FP6 having the profound ability of siderophore production, showed antagonistic properties against Colletotrichum gloeosporioides and Rhizoctonia solani (Sasirekha & Srividya, 2016). Many PGPR secret a variety of antibiotics for inhibiting pathogens. Antibiotics (mainly oligopeptides) produced by PGPR showed the nature of pathogen inhibition through some mechanisms such as (1) interruption of cell wall synthesis of pathogens (2) demolition of membrane architecture of cells, and (3) inhibition of synthesis of macromolecules such as proteins (Maksimov et al., 2011). Antibiotics produced by PGPR act against different groups of microbes. The antibiotic DAPG produced by Pseudomonas sp. is one of the potential metabolites determined to show its deleterious effect against fungi, bacteria, nematodes, and viruses (Meyer et al., 2016). Another example of broad spectrum antibiotic, Pyrrolnitrin, produced by Pseudomonas, showed antifungal activity against Fusarium sambucinum (Burkhead et al., 1994). In a study, Pyrrolnitrin from Burkholderia cepacia NB-1 exhibited antimicrobial activity against fungi and streptomycetes (el-Banna & Winkelmann, 1998). Bacillus atrophaeus CAB-1 also displayed biocontrol efficacy against various fungal pathogens and inhibited the progression of tomato gray mold and cucumber powdery mildew through the production of a bioactive lipopeptide (fengycin A) (Zhang et al., 2013). The production of other antibiotics, namely oomycin A, amphisin, phenazine, oligomycin A, pyoluteorin, cyclic lipopeptides, zwittermicin A, kanosamine, and xanthobaccin by competent PGPR also contribute in biocontrol for progression of phytopathogens (Jadhav et al., 2017). The secretion of cell wall degrading enzymes by microbes is also an important mechanism of biocontrol in demolishing pathogen growth (Legein et al., 2020). Cell wall degrading enzymes, namely chitinase, β-1,3-glucanase, cellulase, and protease produced by PGPR having antipathogenic properties exhibit a direct inhibitory potential against fungal pathogens (El-Sayed et al., 2014). The study carried out by Khan et al. (2018) illustrated the production of chitinase by B. subtilis 30VD-1 and studied the antagonistic activity against Fusarium spp. The antagonistic traits of Trichoderma virens against Rhizoctonia solani were determined where a mutant culture of T. virens showed the highest inhibitory property against pathogens due to the production of cell wall degrading enzymes, such as chitinase and cellulases (Ghasemi et al., 2020).

4.4 Microbial effects on crop productivity under stress conditions Seed germination is affected by drought stress, but the intensity of the stress varies from species to species in plants (Li et al., 2013). Azotobacter strains (Az63 and Az70) showed plant growth-promoting

4.5 Agricultural application of stress-tolerant microorganisms

73

traits (siderophore production, phosphate solubilization, and IAA production) under artificial drought conditions (in PEG 6000) by efficiently increasing plant height, dry weight, chlorophyll content, macronutrients (such as nitrogen and phosphorous), and micronutrients (iron) concentration in maize (Shirinbayan et al., 2019). Two plant growth-promoting bacterial isolates, namely Bacillus sp. (12D6) and Enterobacter sp. (16i), significantly maintained the seedlings of both maize and wheat more vigorously under water deficit state through the exhibition of an alteration in the root architecture (Jochum et al., 2019). The combination of PGPR (Micrococcus yunnanensis) and Arbuscular mycorrhiza (Claroideoglomus etunicatum) assisted Dracocephalum moldavica plants to survive under drought by augmentation in the nutrients, photosynthetic pigments, and secondary metabolites (Ghanbarzadeh et al., 2020). Bacillus subtilis HAS31 maintained the growth and yield of potato under drought conditions. Moreover, the enhanced pattern of various parameters, such as enzymatic activities (catalase, peroxidase, and superoxide dismutase), amount of total soluble sugars, proline and soluble proteins, was observed in the potato plant inoculated with B. subtilis HAS31 compared with the uninoculated control (Batool et al., 2020). Danish and Zafar-ul-Hye (2019) concluded that simultaneous application of PGPR and biochar as an effective technique mitigated the effect of drought in wheat. PGPR might have alleviated drought stress due to the production of ACC deaminase while biochar application provided nutrients to plants. Bacillus subtilis 30VD-1 showed the most efficient antagonistic effect against Fusarium spp. with considerable reduction in wilt severity in pea plants. The bacterium also increased the dry biomass of plants cultivated in fungal-infested soil (Khan et al., 2018). The influence of microorganisms on growth characteristics of plants under stress conditions has been illustrated in Table 4.1.

4.5 Agricultural application of stress-tolerant microorganisms Microorganisms, having beneficial traits of inducing stress tolerance capability in plants, can be used as potential bioinoculants for various food crops. There is a positive demand for stress tolerating microorganisms bearing massive plant growth enhancing traits to use them as biofertilizers. Biofertilizers are formulated products that contain living microorganisms, and they are applied for enhancing crop production. Biofertilizers have several plant growth-promoting properties attributed as production of phytohormones, siderophores, ammonia, EPS, solubilization of phosphate, potassium and zinc, and fixation of atmospheric nitrogen. Plant growth-promoting bacteria having stress-tolerant traits have been decoded for nutrient mobilization and atmospheric nitrogen fixation (Kantachote et al., 2016). Most common bacteria such as Acetobacter, Azospirillum, Azotobacter, Bacillus, Glucanacetobacter, Stenotrophomonas, Paenibacillus, and Pseudomonas bearing stress tolerance capacity were used as bioinoculants (Bhardwaj et al., 2014). Moreover, Bacillus spp and Pseudomonas have been illustrated as effective biocontrol and plant growthpromoting agents under stress conditions (Praveen Kumar et al., 2014). The advantageous effects of biofertilizers comprises enhanced level of crop growth and development, improved crop yield, enhancement in nutrient accessibility, maintenance of soil health, and reduced vulnerability to diseases. However, microorganisms also provide the biofortification benefit to plants through improving the concentration of imperative micronutrients, such as zinc, iron, copper, selenium, etc. (Upadhayay et al., 2018; 2022a,b,c). Thus bioinoculation of crops with stress-tolerant microorganisms in the farming field is a prospective alternative of inorganic fertilizers (Kumar & Verma, 2018).

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Table 4.1 Effect of various microorganisms on plant growth and development under various stress conditions.

Microorganisms 1 2

Bacillus subtilis strain DHK Pseudomonas pseudoalcaligenes

Types of stress Drought Salinity

Plants Zea mays L. Glycine max (L.)

3

Bacillus methylotrophicus PM19

Salinity

Wheat

4

Pseudomonas azotoformans FAP5

Drought

Wheat

5

Trichoderma asperellum

Drought

Sugarcane

6

Bacillus halotolerans, Enterobacter hormaechei, and Pseudomonas frederiksbergensis Achromobacter xylosoxidans

Heavy metal

Wheat

Drought

8

Bacillus fortis strain SSB21

Salinity

Maize (Zea mays) Capsicum annum L.

9

Serratia marcescens strain SRM Bacillus pumilus strain JPVS11

Cold

Wheat

Salinity

Rice (Oryza sativa L.)

7

10

Plant growth and development under stress

References

Significant increment in root and shoot biomass Considerable augmentation in shoot length, fresh and dry weight of shoot and root, and leaf area Elongated roots and enhanced vegetative shoot growth as well as fresh and dry weights of seedlings Improvement in growth attributes and photosynthetic pigment efficiency Enhancement in root and stalk development Improvement in wheat seed germination and plant growth

Sood et al. (2020) Yasmin et al. (2020)

Improved growth and productivity of maize

Danish et al. (2020)

Significant increase in shoot length, root length, and fresh and dry biomass Enhancement in plant biomass and nutrient uptake of wheat seedlings Significant enhancement in plant height, root length, chlorophyll content, carotenoids content, and plant fresh and dry weight

Yasin et al. (2018)

Amna et al. (2019) Ansari et al. (2021) Scudeletti et al. (2021) Fahsi et al. (2021)

Selvakumar et al. (2008) Kumar et al. (2021)

4.6 Conclusion As natural resources, microorganisms, having massive plant growth-promoting traits, modulate plant growth and physiology under abiotic and biotic stresses. The positive consequences illustrated the enhanced growth and development pattern of plants under environmental stresses. The different growth-stimulating mechanisms and stress tolerance ability make microorganisms as frontier candidates in sustainable agriculture. The appraisal of the vital role of microorganisms in stress alleviation, all of which show a significant impact on crop productivity, necessitate their huge application in agriculture. Biotechnological interventions can further develop strain effectiveness and give

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information of corresponding genes or enzymes in mitigating stress responses. Further research requires plant
microbial interactions, which may open other helpful unexplored signaling pathways and unidentified roles under stressful environments.

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513. Available from https:// doi.org/10.1007/s00203-011-0693-x. Mohammadipanah, F., & Zamanzadeh, M. (2019). Bacterial mechanisms promoting the tolerance to drought stress in plants. In H. Singh, C. Keswani, M. Reddy, E. Sansinenea, & C. Garcı´a-Estrada (Eds.), Secondary metabolites of plant growth promoting rhizomicroorganisms. Singapore: Springer. Available from https:// doi.org/10.1007/978-981-13-5862-3_10. Morcillo, R., & Manzanera, M. (2021). The effects of plant-associated bacterial exopolysaccharides on plant abiotic stress tolerance. Metabolites, 11(6), 337. Available from https://doi.org/10.3390/metabo11060337. Moustafa-Farag, M., Almoneafy, A., Mahmoud, A., Elkelish, A., Arnao, M. B., Li, L., & Ai, S. (2019). Melatonin and its protective role against biotic stress impacts on plants. Biomolecules, 10(1), 54. Available from https://doi.org/10.3390/biom10010054. Mukherjee, P., Mitra, A., & Roy, M. (2019). Halomonas rhizobacteria of avicennia marina of Indian sundarbans promote rice growth under saline and heavy metal stresses through exopolysaccharide production. Frontiers in Microbiology, 10(MAY). Available from https://doi.org/10.3389/fmicb.2019.01207. Nadeem, S. M., Ahmad, M., Tufail, M. A., Asghar, H. N., Nazli, F., & Zahir, Z. A. (2021). Appraising the potential of EPS-producing rhizobacteria with ACC-deaminase activity to improve growth and physiology of maize under drought stress. Physiologia Plantarum, 172(2), 463
476. Available from https://doi.org/ 10.1111/ppl.13212. Nascimento, F. X., Tavares, M. J., Franck, J., Ali, S., Glick, B. R., & Rossi, M. J. (2019). ACC deaminase plays a major role in Pseudomonas fluorescens YsS6 ability to promote the nodulation of alpha- and betaproteobacteria rhizobial strains. Archives of Microbiology, 201(6), 817
822. Available from https://doi. org/10.1007/s00203-019-01649-5. Naseem, H., & Bano, A. (2014). Role of plant growth-promoting rhizobacteria and their exopolysaccharide in drought tolerance of maize. Journal of Plant Interactions, 9(1), 689
701. Available from https://doi.org/ 10.1080/17429145.2014.902125. Orozco-Mosqueda, M., del, C., Glick, B. R., & Santoyo, G. (2020). ACC deaminase in plant growthpromoting bacteria (PGPB): An efficient mechanism to counter salt stress in crops. Microbiological Research. Available from https://doi.org/10.1016/j.micres.2020.126439. Palaniyandi, S. A., Damodharan, K., Yang, S. H., & Suh, J. W. (2014). Streptomyces sp. strain PGPA39 alleviates salt stress and promotes growth of ‘Micro Tom’ tomato plants. Journal of Applied Microbiology, 117 (3), 766
773. Available from https://doi.org/10.1111/jam.12563. Pande, V., Pandey, S. C., Sati, D., Bhatt, P., & Samant, M. (2022). Microbial interventions in bioremediation of heavy metal contaminants in agroecosystem. Frontiers in Microbiology, 13, 824084. Pandey, P., Irulappan, V., Bagavathiannan, M. V., & Senthil-Kumar, M. (2017). Impact of combined abiotic and biotic stresses on plant growth and avenues for crop improvement by exploiting physio-morphological traits. Frontiers in Plant Science. Available from https://doi.org/10.3389/fpls.2017.00537. Paul, M. J., Primavesi, L. F., Jhurreea, D., & Zhang, Y. (2008). Trehalose metabolism and signaling. Annual Review of Plant Biology, 59, 417
441. Available from https://doi.org/10.1146/annurev.arplant.59.032607.092945. Praveen Kumar, G., Mir Hassan Ahmed, S. K., Desai, S., Leo Daniel Amalraj, E., & Rasul, A. (2014). In vitro screening for abiotic stress tolerance in potent biocontrol and plant growth promoting strains of Pseudomonas and Bacillus spp. International Journal of Bacteriology, 2014, 1
6. Available from https:// doi.org/10.1155/2014/195946.

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Rodrı´guez-Salazar, J., Su´arez, R., Caballero-Mellado, J., & Iturriaga, G. (2009). Trehalose accumulation in Azospirillum brasilense improves drought tolerance and biomass in maize plants. FEMS Microbiology Letters, 296(1), 52
59. Available from https://doi.org/10.1111/j.1574-6968.2009.01614.x. Saeed, Q., Xiukang, W., Haider, F. U., Kuˇcerik, J., Mumtaz, M. Z., Holatko, J., . . . Mustafa, A. (2021). Rhizosphere bacteria in plant growth promotion, biocontrol, and bioremediation of contaminated sites: A comprehensive review of effects and mechanisms. International Journal of Molecular Sciences, 22(19), 10529. Available from https://doi.org/10.3390/ijms221910529. Sasirekha, B., & Srividya, S. (2016). Siderophore production by Pseudomonas aeruginosa FP6, a biocontrol strain for Rhizoctonia solani and Colletotrichum gloeosporioides causing diseases in chilli. Agriculture and Natural Resources, 50(4), 250
256. Available from https://doi.org/10.1016/j.anres.2016.02.003. Sati, D., Pande, V., Pandey, S. C., & Samant, M. (2022). Recent advances in PGPR and molecular mechanisms involved in drought stress resistance. Journal of Soil Science and Plant Nutrition, 1
19. Scudeletti, D., Crusciol, C. A. C., Bossolani, J. W., Moretti, L. G., Momesso, L., Servaz Tuban˜a, B., . . . Hungria, M. (2021). Trichoderma asperellum inoculation as a tool for attenuating drought stress in sugarcane. Frontiers in Plant Science, 12. Available from https://doi.org/10.3389/fpls.2021.645542. Selvakumar, G., Mohan, M., Kundu, S., Gupta, A. D., Joshi, P., Nazim, S., & Gupta, H. S. (2008). Cold tolerance and plant growth promotion potential of Serratia marcescens strain SRM (MTCC 8708) isolated from flowers of summer squash (Cucurbita pepo). Letters in Applied Microbiology, 46(2), 171
175. Available from https://doi.org/10.1111/j.1472-765X.2007.02282.x. Shirinbayan, S., Khosravi, H., & Malakouti, M. J. (2019). Alleviation of drought stress in maize (Zea mays) by inoculation with Azotobacter strains isolated from semi-arid regions. Applied Soil Ecology, 133, 138
145. Available from https://doi.org/10.1016/j.apsoil.2018.09.015. Sindhu, S. S., & Sharma, R. (2019). Amelioration of biotic stress by application of rhizobacteria for agriculture sustainability. In R. Sayyed (Ed.), Plant growth promoting rhizobacteria for sustainable stress management. Microorganisms for sustainability (13). Singapore: Springer. Available from https://doi.org/10.1007/ 978-981-13-6986-5_5. Singh, D. P., Singh, V., Gupta, V. K., Shukla, R., Prabha, R., Sarma, B. K., & Patel, J. S. (2020). Microbial inoculation in rice regulates antioxidative reactions and defense related genes to mitigate drought stress. Scientific Reports, 10(1). Available from https://doi.org/10.1038/s41598-020-61140-w. Singh, R. P., & Jha, P. N. (2017). The PGPR stenotrophomonas maltophilia SBP-9 augments resistance against biotic and abiotic stress in wheat plants. Frontiers in Microbiology, 8(OCT). Available from https://doi. org/10.3389/fmicb.2017.01945. Singh, S. K., Singh, P. P., Gupta, A., Singh, A. K., & Keshri, J. (2019). Tolerance of heavy metal toxicity using PGPR strains of Pseudomonas species. PGPR amelioration in sustainable agriculture, 239
252. Available from https://doi.org/10.1016/b978-0-12-815879-1.00012-4. Sood, G., Kaushal, R., & Sharma, M. (2020). Alleviation of drought stress in maize (Zea mays L.) by using endogenous endophyte Bacillus subtilis in North West Himalayas. Acta Agriculturae Scandinavica Section B: Soil and Plant Science, 70(5), 361
370. Available from https://doi.org/10.1080/09064710.2020.1743749. Su, F., Jacquard, C., Villaume, S., Michel, J., Rabenoelina, F., Cl´ement, C., . . . Vaillant-Gaveau, N. (2015). Burkholderia phytofirmans PsJN reduces impact of freezing temperatures on photosynthesis in arabidopsis thaliana. Frontiers in Plant Science, 6(OCTOBER). Available from https://doi.org/10.3389/fpls.2015.00810. Tiepo, A. N., Constantino, L. V., Madeira, T. B., Gonc¸alves, L. S. A., Pimenta, J. A., Bianchini, E., . . . StolfMoreira, R. (2020). Plant growth-promoting bacteria improve leaf antioxidant metabolism of droughtstressed Neotropical trees. Planta, 251(4). Available from https://doi.org/10.1007/s00425-020-03373-7. Upadhayay, V. K., Singh, A. V., & Khan, A. (2022a). Cross talk between zinc-solubilizing bacteria and plants: A short tale of bacterial-assisted zinc biofortification. Frontiers in Soil Science, 1, 788170. Available from https://doi.org/10.3389/fsoil.2021.788170.

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2418. Available from https://doi.org/10.20546/ijcmas.2018.706.286. Vardharajula, S., Ali, S. Z., Grover, M., Reddy, G., & Bandi, V. (2011). Drought-tolerant plant growth promoting Bacillus spp.: Effect on growth,osmol ytes,and antioxidant status of maize under drought stress. Journal of Plant Interactions, 6(1), 1
14. Available from https://doi.org/10.1080/17429145.2010.535178. Vinocur, B., & Altman, A. (2005). Recent advances in engineering plant tolerance to abiotic stress: Achievements and limitations. Current Opinion in Biotechnology. Available from https://doi.org/10.1016/j.copbio.2005.02.001. Waghmode, M., Gunjal, A., Patil, N., & Nawani, N. (2019). Role of rhizobacteria in drought tolerance. In R. Sayyed, N. Arora, & M. Reddy (Eds.), Plant growth promoting rhizobacteria for sustainable stress management. Microorganisms for sustainability (12). Singapore: Springer. Available from https://doi.org/10. 1007/978-981-13-6536-2_17. Wang, C., Wang, C., Gao, Y. L., Wang, Y. P., & Guo, J. H. (2016). A consortium of three plant growthpromoting rhizobacterium strains acclimates Lycopersicon esculentum and confers a better tolerance to chilling stress. Journal of Plant Growth Regulation, 35(1), 54
64. Available from https://doi.org/10.1007/ s00344-015-9506-9. Yasin, N. A., Akram, W., Khan, W. U., Ahmad, S. R., Ahmad, A., & Ali, A. (2018). Halotolerant plantgrowth promoting rhizobacteria modulate gene expression and osmolyte production to improve salinity tolerance and growth in Capsicum annum L. Environmental Science and Pollution Research, 25(23), 23236
23250. Available from https://doi.org/10.1007/s11356-018-2381-8. Yasmin, H., Naeem, S., Bakhtawar, M., Jabeen, Z., Nosheen, A., Naz, R., . . . Hassan, M. N. (2020). Halotolerant rhizobacteria Pseudomonas pseudoalcaligenes and Bacillus subtilis mediate systemic tolerance in hydroponically grown soybean (Glycine max L.) against salinity stress. PLoS One, 15(4). Available from https://doi.org/10.1371/journal.pone.0231348. Zhang, F., Zou, Y. N., Wu, Q. S., & Kuˇca, K. (2020). Arbuscular mycorrhizas modulate root polyamine metabolism to enhance drought tolerance of trifoliate orange. Environmental and Experimental Botany, 171. Available from https://doi.org/10.1016/j.envexpbot.2019.103926. Zhang, X., Li, B., Wang, Y., Guo, Q., Lu, X., Li, S., & Ma, P. (2013). Lipopeptides, a novel protein, and volatile compounds contribute to the antifungal activity of the biocontrol agent Bacillus atrophaeus CAB-1. Applied Microbiology and Biotechnology, 97(21), 9525
9534. Available from https://doi.org/10.1007/ s00253-013-5198-x. Zubair, M., Hanif, A., Farzand, A., Sheikh, T. M. M., Khan, A. R., Suleman, M., . . . Gao, X. (2019). Genetic screening and expression analysis of psychrophilic Bacillus spp. reveal their potential to alleviate cold stress and modulate phytohormones in wheat. Microorganisms, 7(9). Available from https://doi.org/10. 3390/microorganisms7090337.

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CHAPTER

Prospects of biotechnology for productive and sustainable agroenvironmental growth

5

Madhvi Sharma1, Amanpreet K. Sidhu1 and Diksha Sati2,3 1

PG Department of Biotechnology, Khalsa College, Amritsar, Punjab, India 2Cell & Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University Campus, Almora, Uttarakhand, India 3Department of Zoology, Kumaun University, Nainital, Uttarakhand, India

5.1 Introduction Biotechnology, a wonder to behold, has the potential to improve our ecological systems and agricultural production. Stress conditions like drought, floods, and high heat, among other factors, have a great impact on agricultural production than pests and illnesses. Genetic engineering, by means of the deployment of genes, provides tolerance and resistance to biotic and abiotic stresses, enzymes, and nutrients. Thereby it contributes to sustainable agriculture by reducing dependence on agrochemicals, particularly pesticides; boosting productivity and quality; improving nitrogen fixation, nutrient uptake, and use efficiency; and enhancing technologies for developing biomass-derived energy. Microorganisms present in the soil would be used to boost agriculture production. Naturally, existing organisms are employed to develop biofertilizers and biopesticides, stimulating plant productivity while somehow eradicating weeds, pests, and infections. Soil microorganisms significantly assist plants in absorbing more nutrients. Plants and these beneficial microorganisms are both involved in nutrient recycling. The microorganisms enable the plants to absorb vital energy. Plants, in turn, contribute their waste byproducts for the microorganisms to consume. Scientists employ these beneficial microbes to produce biofertilizers. Biological communities live under a variety of stress environments, which include extreme environments of high temperatures, salinity, water scarcity, and pH level. To survive in such conditions, microorganisms have developed adaptive properties that allow them to live, multiply, and produce bioactive compounds and secondary metabolites under extreme/ harsh conditions (Yadav et al., 2015). In recent years, microbial communities (archaea, bacteria, and fungi) in extremely harsh habitats have been attracting interest from different areas, such as white and green biotechnology, medicine, and food production and processing.

5.2 Genetic engineering and sustainable agriculture A transgenic approach allows for both the introduction of foreign genes and/or the disruption of existing functions so that desired traits can be passed from generation to generation, thus reducing Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00015-6 © 2023 Elsevier Inc. All rights reserved.

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the frequency of mass releases. Various methods can be used to introduce DNA into insect germ cells, such as microinjection, biolistics, electroporation, and several transposable elements, such as Sindbis viruses and retroviruses, as gene vectors (Atkinson, Pinkerton, & Brochta, 2001). Therefore the term biotechnology can include traditional and local knowledge, organic and agroecological practices, conventional breeding, techniques such as tissue culture and genomics, marker-assisted breeding, and gene splicing. As a result, modern biotechnology has evolved to become “the manipulation of genetic material and fusion of cells beyond normal breeding barriers,” with gene engineering being the most common example in which genes are inserted or deleted through transgenic technologies to create genetically modified organisms (GMOs). Genetic engineering methods include (1) techniques that use vector systems for recombinant DNA, (2) methods of introducing hereditary material directly into an organism after being recombined outside that organism. A combination of genetically modified (GM) treatment and biofertilizers can provide substantial nutrition to plants and greatly improve soil quality (Bhattacharya, Iftikar, Sahariah, & Chattopadhyay, 2012; Hussain et al., 2016). Leguminous plants, which are renewable sources of nitrogen, are the most commonly encountered GMOs (Kouyat et al., 2000). It has also been shown that crop remnants recycled as GMOs can be used to recover the soil atmosphere for sustainable crop production (Lee et al., 2009). Abbasi and Yousra (2012) have shown that biofertilizer inoculants significantly enhanced the efficacy of organic fertilizers when added to the soil. Crop improvement has relied on the introduction of beneficial genes into crop plants or by inhibiting the expression of endogenous genes in crop plants. These are only some of the qualities that genetically modified crops possess, which include herbicide resistance, insect resistance, susceptibility to abiotic stresses, disease resistance, and enhanced nutritional value. Currently, the United States has licensed 525 different transgenic events across 32 crops. Transgenic technology has been found to increase crop yields while reducing pesticide use in many parts of the world, leading to reduced CO2 emissions and agricultural production costs (Klumper & Qaim, 2014; Kumar et al., 2020). The use of transgenic crops with genetic modification is explained in Table 5.1. Traditional approaches for removing hazardous compounds from the environment have failed miserably. Thus improvement in the novel remediation techniques could be one strategy to improve bioremediation quality. The rising pollution in the environment prompted researchers to look into microorganisms and the creation of genetically modified microorganisms (GMMs) for pollution abatement via bioremediation. Physical and chemical tactics have been used to remediate home and industrial pollutants in the past, but these techniques are costly and harmful to the environment. In comparison, using engineered microorganisms can be a considerably safer and more cost-effective technique. Bacteria, fungi, and algae have all been employed as GMMs. For example, camphor, hexane, naphthalene, toluene, octane, xylene, halobenzoates, and decomposed oil spills trichloroethylene (Pant et al., 2020).

5.3 Role of microorganisms in agriculture Millions of microorganisms live in plants and soil, forming a microbial community known as the microbiome. An effective microbiome provides a lot of benefits to its hosts, such as plant growth

5.3 Role of microorganisms in agriculture

85

Table 5.1 Transgenic crops: the modified traits and their use. Genetic modifications

Crops Tomatoes, potatoes, corn, rice, lettuce, coffee, cabbage family, apples Peppers, tomatoes, cucumbers Potatoes, tomatoes, cantaloupe, squash, cucumbers, corn, oilseed rape (canola), soybeans, grapes Soybeans, tomatoes, corn, cotton, oilseed rape (canola), wheat Corn, sunflower, soybeans, rice Oilseed rape (canola), peanuts

Purpose

Insect resistance Fungal resistance Viral resistance

Reduces insecticide use and crop loss

Herbicide tolerance Improved nutrition Heat stability

Improves weed control

Reduces fungicide use and crop loss Reduces diseases caused by plant viruses, reduces use of insecticides and crop loss

Increases amount of essential amino acids, vitamins, or other nutrients in host plants Improves processing quality; permits new food uses for healthier oils

Table 5.2 Carrier materials compatible with beneficial microorganisms. Inoculants

Carriers

References

Agrobacterium radiobacter (K-84) Rhizobium sp. Bradyrhizobium japonicum Sinorhizobium meliloti Rhizobium sp. Rhizobium sp.

Vermiculite

Pesenti-Barili et al. (1991)

Mineral soil Mineral granules

Chao and Alexander (1984) Fouilleux, Revellin, Hartmann, and Catroux (1996) Rebah, Tyagi, and Pr´evost (2002) Paczkowski and Berryhill (1979) Kremer and Peterson (1982)

Sludge from wastewater treatment plant Coal Lyophilized cells mixed in oils (soybean, peanut, etc.)

promotion, nutrient use efficiency, and pest and phytopathogen control. As a result, there is an urgent need to incorporate the functional potential of plant-associated microbiomes and their innovation into crop production (Ray, Lakshmanan, Labb´e, & Craven, 2020).

5.3.1 Biofertilizers in agroecosystem Biofertilizer materials significantly contribute to the success of organic farming by improving soil fertility and organic farming, thereby increasing crop yield (Kachroo & Razdan, 2006; Son, Thu, Chin, & Hiraoka, 2007; Subashini, Malarvannan, & Kumaran, 2007). The various beneficial microorganisms with different inoculants and their carriers are explained in Table 5.2. They contribute significantly to soil fertility enhancement by symbiotically and asymbiotically fixing atmospheric nitrogen, solubilizing insoluble bonded inorganic phosphates, and occasionally

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Table 5.3 Symbiotically associated biofertilizers in agroecosystems. Biofertilizers

Roles

Symbiotic association with plants

References

Rhizobium

It belongs to the family of Rhizobiaceae. They are capable of fixing atmospheric nitrogen in bioavailable form while residing mostly in the roots of legumes and some special groups of plants (via a symbiotic mechanism) Nitrogen fixing bacteria that produce some of the growth regulating substances Have large specialized cells called heterocyst that function as nitrogen fixing machinery of the organism

Symbiotic associations with Parasponia sp.

Reddy and Reddi (2010)

Symbiotic associations with some C4 plants (maize, sorghum, and sugarcane) Symbiotic association with fungi, some lower vascular plants, as well as angiosperms, such as pteridophyte, Azolla, and cyanobacteria, Anabaena azollae

Arun (2007)

Azospirillum

Cyanobacteria

Barman et al. (2019)

releasing plant growth hormones in the soil (Sheraz Mahdi et al., 2010). Furthermore, using such biofertilizers in the soil improves soil health by reducing the negative effects of synthetic fertilizers (Subashini et al., 2007). Despite the use of chemical fertilizers, long-term use of biofertilizers is less expensive, more environmentally friendly, more productive, and more easily accessible to marginal farmers (Venkataraman & Shanmugasundaram, 1992; Venkatashwarlu, 2008). Because the legume has a large population of beneficial bacteria on its roots, it may be able to use naturally available nitrogen instead of the more expensive conventional nitrogen fertilizer. Biofertilizers encourage plants to use all of the food available in the soil and air, allowing farmers to use fewer synthetic fertilizers. This contributes to the preservation of the ecosystem for future generations (Yang et al., 2009). The various symbiotically associated biofertilizers in the agroecosystem are explained in Table 5.3.

5.3.2 Biopesticides, biofungicides, and bioinsecticides in agroecosystem The widespread use of synthetic fertilizers and pesticides has a detrimental impact on soil microbial biodiversity and environment. In response to this rising concern, the use of microorganisms as biofertilizers has been recommended as an alternative agricultural approach. Plant growth-promoting microorganisms (PGPMs) benefit plants through both direct and indirect methods. In comparison to the utilization of bacteria and mycorrhizal fungi, the use of yeasts as PGPMs has received relatively little attention. The majority of yeast colonies are located in the rhizosphere rather than in the soil (Botha, 2011). In fact, a growing number of studies suggest that yeasts may promote plant root growth in the rhizosphere (El-Maraghy, Tohamy, & Hussein, 2020; Fu et al., 2016; Rosa-Magri, Avansini, Lopes-Assad, Tauk-Tornisielo, & Ceccato-Antonini, 2012), though a wide variety of soil yeasts have also been studied for their potential as biofertilizers (Amprayn et al., 2012; Nakayan et al., 2013). The various applications of algae as plant growth promoters, biofungicides, bioinsecticides, or biodegraders are explained in Table 5.4.

5.3 Role of microorganisms in agriculture

87

Table 5.4 Applications of algae as plant growth promoters, biofungicides, bioinsecticides, or biodegraders. S. No

Mechanism

Parameters

Yeasts

References

1

NH3 production

Plant growth promotion

M. guilliermondii, P. rugulosa, C. flavus, P. antarctica, Meyerozyma sp., M. caribbica

2

P solubilization

Plant growth promotion

C. tropicalis, L. thermotolerans, Rhodotorula sp., H. uvarum, Y. lipolytica, S. cerevisiae

3

K solubilization N2 fixation

Plant growth promotion Plant growth promotion Plant growth promotion

T. globosa, R. glutinis, P. anomala

Fernandez-San Millan et al. (2020); Fu et al. (2016); Nutaratat, Srisuk, Arunrattiyakorn, and Limtong (2014) Amprayn et al. (2012); El-Latif, Mohamed (2011); Fernandez-San Millan et al. (2020); Mukherjee and Sen (2015); Mundra, Arora, and Stobdan (2011) Rosa-Magri et al. (2012); RojasTapias et al. (2012) Mukherjee and Sen (2015)

C. tropicalis, Cryptococcus sp.

Amprayn et al. (2012); Deng, Wang, Tan, and Cao (2012)

Plant growth promotion

C. tropicalis, M. guilliermondii, S. cerevisiae, A. pullulans, H. uvarum, M. caribbica, W. californica, C. laurentii, R. fluvialis, C. maltosa, P. kudriavzevii, R. paludigenum A. pullulans against P. expansum and M. laxa; Issatchenkia terricola, P. anomala, M. pulcherrima, S. cerevisiae, Schizosaccharomyces pombe, H. uvarum and P. kluyveri against B. cinerea R. glutinis and R. rubra degrades chlorpyrifos; R. mucilaginosa degrades neonicotinoid insecticide; S. terricola degrades glyphosate Insecticide C. lusitaniae degrades dinitroaniline herbicide; P. kudriavzevii degrades s-triazine group herbicides

Bunsangiam et al. (2019); Fernandez-San Millan et al. (2020); Fu et al. (2016); Mukherjee and Sen (2015); Nutaratat, Srisuk, Arunrattiyakorn, and Limtong (2016); Rao, Hunter, Kashpur, and Normanly (2010) Cordero-Bueso et al. (2017); De Simone et al. (2020); Di Francesco, Ugolini, D’Aquino, Pagnotta, and Mari (2017)

4 5

6

ACC deaminase activity IAA production

7

Competition for nutrients and space

Biofungicide

8

Insecticide biodegradation

Biodegrader

9

Herbicide biodegradation

Biodegrader

C. tropicalis

Stosiek et al. (2019); Zhang, Khan, Heckel, and Bock (2017)

Abigail, Abdul Salam, and Das (2013); Han et al. (2019)

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Chapter 5 Prospects of biotechnology for productive and sustainable

5.3.3 Plant
microbial interaction: mycorrhiza and plant growth-promoting rhizobacteria Over a century ago, the rhizosphere was defined as the zone around the root that contains microorganisms and processes important for plant growth and health. According to recent research, the diversity of microorganisms associated with the root system is enormous. The rhizosphere microbiome expands plants’ functional repertoire beyond imagination (Bakker, Berendsen, Doornbos, Wintermans, & Pieterse, 2013). Bacteria, fungi, protozoans, nematodes, algae, and microarthropods are the most common rhizosphere residents. Microbial activities such as solubilization of inorganic compounds, degradation and mineralization of organic compounds, and secretion of bioactive components such as plant hormones, antibiotics, and ion chelators all help to improve plant growth and thus make the soil ecosystem more productive (Sati, 2020). Although many microbial communities are present in rhizospheric habitats, bacterial communities are the most numerous among them (Bhattacharyya and Jha, 2011; Hayat, Ali, Amara, Khalid, & Ahmed, 2010; Kaymak, 2011; Saharan & Nehra, 2011). Microscopic organisms such as Pseudomonas, Bacillus, Klebsiella, Serratia, Enterobacter, Azospirillum, Burkholderia, and Azotobacter have a significant impact on plant growth. PGPR play a vital role across both direct and indirect pathways (Glick, Cheng, Czarny, & Duan, 2007; Zahir, Arshad, & Frankenberger, 2003). The direct mechanisms stimulating plant development are nitrogen fixation, phosphorus solubilization, siderophores generation, and growth hormones. The indirect mechanisms include many enzymes such as chitinase, beta-glucanase, and ACC-deaminase defending against pathogens (Berg, 2009; Hayat et al., 2010). They can also substantially improve resistance to multiple diseases by modulating host
plant interaction via induced systemic resistance (ISR) (Saravanakumar et al., 2007) (Fig. 5.1). Plant growth promoting fungi (PGPF) are noninfectious organisms that feed on dead and decaying organic matter and are thought to act as fungal and bacterial disease suppressors in a variety of crop plants. Colonization of the root by PGPF can result in broad-spectrum resistance in the plant’s distal parts. The PGPF amalgamation with the roots of various plant species and infection has proven to transform the host plant’s growth, morphology, nitrogen incorporation, mineral assimilation, and resource distribution, as well as raising the host’s reproductive fitness by improving plant growth, increasing biomass, and grain yield of crop plants (Deshmukh et al., 2006). Microalgae, along with bacteria and fungi, are important plant growth promoting microbes. They play an important role in soil renovation, increasing productivity, managing agricultural wastewater and agricultural contagion, and developing microbiological crusts. Furthermore, microalgae contribute to agriculture by performing a variety of functions such as carbon content, aeration, texture, nitrogen fixation, biofertilizers, and soil conditioning. Green algae such as Chlorella sp., Acutodesmus sp., Scenedesmus sp., Dunaliella sp., Nannochloris sp., and others are making agriculture more sustainable (Sati, 2020; Sati, Pande, & Pandey, 2022). PGPR play a significant role in improving soil fertility and, thereby, enhancing plant growth and development. Cyanide emission, for example, is a defining characteristic of certain Pseudomonas species, and it is regarded as both a growth promotion and a growth retardation property depending on the host. Pseudomonas sp. can also be used as a biocontrol agent against plant pathogenic bacteria (Martı´nez-Viveros, Jorquera, Crowley, Gajardo, & Mora, 2010). However, they can occasionally have a detrimental impact on plant development (Bakker & Schippers, 1987).

5.4 Nanotechnology in agriculture

89

FIGURE 5.1 Mechanisms used by plant growth-promoting rhizobacteria and mycorrhizae to enhance plant growth. AM, arbuscular mycorrhizae.

5.4 Nanotechnology in agriculture Nanotechnology has received a lot of attention in recent years due to its numerous applications in fields such as medicine, pharmaceuticals, catalysis, energy, and materials. Nanoparticles (NPs) with a small size but a large surface area (1
100 nm) may find applications in the medical industry and agriculture (Ghidan & Antary, 2020). In agriculture, nanotechnology holds enormous promise for the development of nanofertilizers and nanopesticides, which will improve nutrient use efficiency, have a positive effect on the environment, and increase plant productivity and protection Fig. 5.2. Nanoscale science and nanotechnology are expected to transform agricultural production and agrofood systems. The use of nanofertilizers and nanopesticides boosts nutrient use efficiency, improves soil health/ fertility, reduces the frequency of their applications before the technology reaches the farm gate, and avoids harmful consequences associated with overdosing. The indiscriminate use of chemical pesticides has resulted in a slew of environmental issues, including resistance and pollution (Yadav et al., 2019).

5.4.1 Nanofertilizers Nanofertilizers may include nano zinc, silica, iron, and titanium dioxide, as well as ZnCdSe/ZnS core-shell QDs, InP/ZnS core-shell QDs, Mn/ZnSe QDs, gold nanorods, core-shell QDs, and coreshell QDs, among others. In the last decade, extensive research on the absorption, biological destiny, and toxicity of many metal oxide NPs, including Al2O3, TiO2, CeO2, FeO, and ZnONPs, has been conducted for agricultural production (Dimkpa, 2014). Carbon nanotubes and Au, SiO2, ZnO, and TiO2 NPs can help plants develop better (Fig. 5.1) by improving elemental uptake and nutrient utilization. The true influence of nanomaterials on plants, however, is determined by their composition, concentration, size, surface charge, and physical and chemical properties, as well as the species’ vulnerability (Fraceto et al., 2016).

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FIGURE 5.2 Applications of nanotechnology in various fields of agricultural sustainability.

5.4.2 Nanopesticides NPs may play an important role in the management of insect pests and host infections. A new nanoencapsulated pesticide formulation with improved solubility, specificity, permeability, and stability has recently been developed (Bhattacharyya, Duraisamy, Govindarajan, Buhroo, & Prasad, 2016). The development of nanoencapsulated pesticides resulted in a reduction in pesticide dosage and human exposure, making crop protection more environmentally benign (Nuruzzaman, Rahman, Liu, & Naidu, 2016). Few chemical companies have recently openly advertised nanoscale pesticides for sale as microencapsulated insecticides. Some Syngenta (Switzerland) products, such as Karate ZEON, Subdue MAXX, Ospray’s Chyella, Penncap-M, and BASF microencapsulated insecticides, may be suitable for nanoscale use (Gouin, 2004).

5.5 Conclusion and future prospects

91

5.4.3 Nanotechnology for improved soil quality Hydrogels, nanoclays, and nanozeolites have been shown to increase soil water-holding capacity by acting as a slow-release water source and reducing hydric scarcity during the crop season. Such systems are advantageous for agricultural purposes as well as the reforestation of degraded areas. Organic nanomaterials such as polymers and carbon nanotubes, as well as inorganic nanomaterials such as nano metals and metal oxides, have been used to absorb environmental contaminants, improving soil remediation capacity and decreasing treatment times and costs (Khin, Nair, Babu, Murugan, & Ramakrishna, 2012; Sekhon, 2014).

5.4.4 Nanotechnology in food industry Nanotechnology has recently become popular in the food processing industry, including nanocarrier systems for vitamin and supplement delivery as well as organic nanosized additives for food, supplements, and animal feed. Various nutrients, mostly vitamins, have been encapsulated and transported into the bloodstream with high efficiency through the digestive system. NPs were added to some foods and beverages without altering their taste or appearance. In ice creams, NP emulsions are used, which can improve the texture and consistency of ice creams (Berekaa, 2015). Some packaging materials incorporating nanosensors to detect the oxidation process in food have been developed and tested in the food business. The working principle is straightforward: when oxidation happens in a food package, NP-based sensors signal a color change, and information about the nature of the packaged meals is visible. This method has been used in packaged milk and meat with great success (Bumbudsanpharoke & Ko, 2015).

5.5 Conclusion and future prospects The accelerated process of land degradation, loss of nutrient-rich top soils due to erosion threats, contamination of toxic substances, and denudation of organic matter in arable soils all pose significant challenges to food security and environmental protection. Under these conditions, we are required to implement organic-based nutrient management to halt the process of soil degradation. The primary goal of this research is to highlight all of the scientific and technological details of agroecosystems and their applications. One of the newer approaches to overcoming agricultural challenges is to maximize the use of microbial inoculants. Biofertilizers, bioinsecticides, biopesticides, bioherbicides, or any other active microbial stimulants can be a primary determinant in accelerating land quality recovery and ensuring food security for future generations, thereby boosting the organic economy. As a result, scientists in developing countries may need to develop target-specific formulations to encourage the production of high-quality foods. Future research should focus on the mechanisms of action of plant
microbe interactions in extreme environments to improve plant well-being. Biotechnological techniques may become more receptive to plant
microbe interactions to provide a foundation for agroenvironmental sustainability.

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CHAPTER

Biofertilizers: a microbial-assisted strategy to improve plant growth and soil health

6

Amir Khan1, Divyansh Panthari2, Raj Shekhar Sharma3, Arjita Punetha4, Ajay Veer Singh1 and Viabhav Kumar Upadhayay1 1

Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar (U.S. Nagar), Uttarakhand, India 2Department of Botany, School of Basic and Applied Science, Sri Guru Ram Rai University, Dehradun, Uttarakhand, India 3Department of Microbiology, School of Basic and Applied Science, Sri Guru Ram Rai University, Dehradun, Uttarakhand, India 4Research Scholar, CSIR-Central Institute of Medicinal & Aromatic Plants (CIMAP), Research Centre, Pantnagar (U.S. Nagar), Uttarakhand, India

6.1 Introduction A continuously growing population and deteriorating agricultural system demand a sustainable, eco-friendly, and effective approach to support soil and crop productivity and wellness. Current research is focused mostly on augmentation in plant growth and productivity and maintaining soil health by plant beneficial microorganisms. Such microorganisms possess various plant growthenhancing properties, namely phosphate solubilization; nitrogen fixation; and production of siderophores, phytohormones, exopolysaccharides, ammonia, and hydrogen cyanide (Khan, Upadhayay, Panwar, & Singh, 2020). Maintaining soil health is another benevolent trait of microorganisms, as they increase organic matter in soil and maintain a nutrient pool in the soil through a balancing of nutrient cycling. These bacteria are plant probiotics that make effective colonization in the rhizospheric region and prop up plant growth as auxiliary partners (Parveen, Singh, Khan, Prasad, & Pareek, 2018). In organic farming, the use of plant-beneficial bacteria as potential bioinoculants is widely accepted to circumvent rampant chemical fertilization applications. Microorganisms with desirable plant growth-promoting activities can be used as biofertilizers for sustainable plant growth (Singh, Singh, Upadhayay, & Khan, 2020). The development of an effective biofertilizer is a competent and laborious task that requires stepwise procedures such as: (1) isolation of microorganisms from soil/plant, (2) screening of isolated microorganisms for various plant growth-promoting traits, (3) determining the effect of microorganisms on plant growth under greenhouse and farm conditions using carrier material, (4) selecting potential microbial strains for biofertilizer preparation, and (5) commercialization of potential biofertilizer with industry collaboration. Biofertilizers are mainly considered reliable, cost-effective, easy to use, eco-friendly, and effective under farm field operation for acquiring an increased yield. Biofertilizers can be prepared by using either a single bacterial strain or more than one microbial strain (microbial consortium) to Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00007-7 © 2023 Elsevier Inc. All rights reserved.

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provide direct and indirect benefits to plants (Sati, Pande, Pandey, & Samant, 2021). Biofertilizers are an economically feasible way of increasing the nutritional status of plants by providing essential macro- and micronutrients. Biofertilizers increase the availability of macronutrients, such as nitrogen, phosphorus, and potassium, in plants. Moreover, it is also an easy way of achieving micronutrient-related malnutrition in plants through the augmentation of the concentrations of zinc, iron, copper, and selenium in different plant parts, thereby providing the benefit of biofortification (Khan, Singh, Upadhayay, Singh, & Shah, 2019). Microbial enzymes and other metabolites maintain soil fertility and provide a continuous nutrient supply to host plants. Biofertilizers are also reported to support native beneficial soil microbial populations and protect plants from the attack of disease-causing microorganisms. Commercialization of primary bioformulation-based biofertilizers was started in 1895 in the United Kingdom and the United States. Over time, the eco-friendly impact of biofertilizers and their success has gained the attention of researchers and farmers worldwide. Researchers are mostly interested in screening the number of microbes for different plantbeneficial traits and testing different carrier materials and adjuvants to augment the effective delivery and viability of biofertilizers. The present manuscript focuses on types of microbial biofertilizers, their development procedure, and their role in plant growth promotion and soil health management.

6.2 What is a biofertilizer? Biofertilizers are primarily ready-to-use products containing agriculturally important microorganisms in a viable state. In other words, a biofertilizer is a modernized form of organic fertilizer that contain beneficial microorganisms (Swathi, 2010). However, the method for determining the implication of biofertilizers may differ for different types of crops. Either seed or soil can be treated with specific biofertilizers, but on the other hand, seedling treatment with biofertilizers is the desirable method for paddy. Microorganisms initiate colonization on or around the root after providing treatment of soil, seed, or root with biofertilizer and stimulate plant growth of the target crop. The secreted component, namely root exudates from plant roots, encourages the proficient colonization of microorganisms in the rhizosphere (Sati et al., 2022). Biofertilizers are also determined as bioinoculants or microbial inoculants to increase nutrient availability in soil and rectify a number of challenges engendered by intensive chemical fertilizer use. Microbes such as bacteria, fungi, and mycorrhizae, belonging to the Bacillus, Lactobacillus, Azotobacter, Pseudomonas, photosynthetic bacteria, Trichoderma sp., Glomus sp., Gigaspora sp., Pezizella sp., and yeasts, which are capable of fixing nitrogen; solubilizing phosphate, zinc, iron, potassium; and producing phytohormones and cellulolytic enzymes, are primarily utilized as biofertilizers (Roshani, Singh, Upadhayay, & Prasad, 2020). Biofertilizers, by means of nitrogen fixation, solubilization of phosphate, potassium, and zinc; secretion of plant growth regulating substances (hormones and vitamins), and biodegradation of organic matter, keep the soil environment rich with macro- and micronutrients (Bhattacharjee & Dey, 2014). Besides increasing the uptake of nutrients to plants, biofertilizers also perform other plant physiological tasks, such as augmenting water uptake and the photosynthetic rate of plants. A number of biofertilizers have been reported to improve the abiotic and biotic tolerance of plants. Moreover, they also help in the bioremediation of pesticides (Kour et al., 2020). The

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biofertilizers also act as bio-controller of diseases as they exhibit antagonistic properties against soil-borne multiple plant pathogens such as Rhizoctonia root rot, chill wilt, pythium root rot, mung bean root rot, and parasitic nematodes (Jiao, Takishita, Zhou, & Smith, 2021). These functions of the biofertilizers can play a constructive role in the productivity of the crop along with soil sustainability. The mode of action can differ for every biofertilizer as the formulation and function (biological activity) of the incorporated microbial strain change. The effect of biofertilizers is long lasting compared with chemical fertilizers due to the slow release of nutrients through microbial activities. Biofertilizers are safe and economically feasible for farmers, and they provide a wide scope for research in organic farming. Biofertilizers are a renewable source of nutrients to sustain soil health, making them an important component of an integrated nutrient management system for sustainable agricultural productivity and an eco-friendly environment (El-Ghamry, Mosa, Alshaal, & El-Ramady, 2018).

6.3 Need for biofertilizers at higher altitudes Agriculture in mountainous areas across the globe faces numerous issues. Two of these are of significant relevance: (1) a spectacular expansion in population placing unparalleled pressure on natural resources and (2) an exaggerated requirement for commercial items (crops and animals), which escalates the immediate resource consumption to assure high production efficiency. Agriculture in hilly areas is chiefly influenced by low atmospheric and soil temperatures, particularly during the winter season. Soils of hilly areas are generally acidic and have very poor nutrient availability. There is a significant demand for environmentally friendly, sustainable farming practices and techniques that can provide quality food in a sufficient quantity to an ever-increasing human population in hilly places without compromising the soil fertility of the area. However, no new technologies are available for increasing the yield of many mountain crops, and even if they are available, they are either not affordable to farmers, or there is a lack of awareness regarding their use among the farmers of remote areas. As a result, farmers are using chemical fertilizers on their fields indiscriminately to meet the needs of an expanding population. Excessive use of chemical fertilizers has a deleterious impact on soil quality and renders the soil infertile. Therefore introducing biofertilizers to farmers in hilly areas can prove to be an effective solution for improving the fertility of mountainous soils and increasing the agricultural productivity. The use of biofertilizers significantly eliminates the use of synthetic agrochemicals. Biofertilizers are cost-effective, preserve hilly environments and people from the harmful effects of chemicals, and aid in the conservation of native species and plant varieties that play critical roles in human diets and traditional civilizations, which are otherwise threatened with extinction. Bioinoculants have been shown to improve plant growth and output through a variety of direct and indirect processes. They improve nutrient cycling through direct mechanisms, such as biological nitrogen fixation, phosphate solubilization, formation of siderophores, and phytohormone synthesis, and through indirect mechanisms, such as the formation of specific biocontrol substances (Ahemad & Kibret, 2014). However, the use of commercially available biofertilizers in mountainous ecosystems has not proven to be much effective. Low temperatures in the mountain areas inflict a grave threat to the metabolic activities of microorganisms. For example, reducing the temperature by 10 C is thought to cause a two- to fourfold drop in

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enzyme activity (Yarz´abal, Monserrate, Buela, & Chica, 2018). As a result, particular microbial inoculants are required for mountain agroecosystems, which must be able to withstand freezing temperatures while simultaneously maintaining their ability to support plant growth (Trivedi, Pandey, & Palni, 2012). Psychrotrophic bacteria that help to alleviate cold stress are beneficial for plants growing at high altitudes and low-temperature conditions (Yadav, Sachan, Verma, & Saxena, 2016). As per a metagenomic analysis, the dominating phyla of high-altitude soils are Proteobacteria, Acidobacteria, and Actinobacteria (Singh, Takahashi, Kim, Chun, & Adams, 2012), while Bacteroidetes and Firmicutes dominate the lower altitude regions (Kumar, Soni, Kanwar, & Pabbi, 2019; Shtarkman, 2015).

6.4 Preparation of biofertilizer: steps and standards At the time of the application of potent microbes in the field, some differences arise between the results obtained under laboratory conditions and the field results. Because laboratory or glasshouse conditions cannot be maintained in the field, microbial efficiency gets reduced. The situation intensifies when dealing with gram-negative or nonspore-forming bacteria. Because of their tendency to not to form spores, gram-negative bacteria become more susceptible to deleterious factors that occur during processing and field applications (Berninger, Gonz´alez Lo´pez, Bejarano, Preininger, & Sessitsch, 2018). Therefore, there is a need to fix biofertilizer in a suitable carrier-based bioformulation to increase its efficacy at the target site and to facilitate farmers. Advancement in bioformulation development technologies is necessary for the industrial commercialization of the competent microbial strain having potential biocontrol and plant growth-promoting traits. The characteristics of a good biofertilizer are: (1) must be eco-friendly, (2) microbial strains used for biofertilizer preparation must be nonpathogenic, (3) should be able to provide good quality of nutrients to the crops, and (d) must have a long shelf life. For the production of a biofertilizer, the selection of microorganisms with desirable traits is the most crucial aspect. Understanding the characteristics of the microorganism and their interaction with the crop and the environment is imperative for improving crop growth (Owen, Williams, Griffith, & Withers, 2015). Microbes used for bioformulation preparation are tested multiple times under in situ and in vivo conditions to observe desired property retention and results. Moreover, microbes selected for biofertilizer preparation should be genetically stable, target the crop, keep pace with the native population of microbes, and be able to survive even in the absence of the host. Biofertilizer is usually developed by using only one strain. However, the study of the complex relationship between microbes in the soil resulted in the development of inoculums consisting of more than one strain of beneficial microbes. Research demonstrated that the consortia are found to be more efficient and farmer-friendly, as the different mechanisms of action of different microbes take place simultaneously, which helps the crops in various ways (Vassilev et al., 2015). One of the most successful results was observed in legumes treated with biofertilizer consisting of arbuscular mycorrhizal fungi (AMF) and rhizobia (Wang, Pan, Chen, Yan, & Liao, 2011). While the use of phosphate solubilizing bacteria and plant growth promoting rhizobacteria (PGPR) showed auspicious results in the case of nonleguminous plants. In horticultural crops, the consortia of different PGPR and AMF were found beneficial and lessened chemical fertilizer application (Wu, Cao, Li, Cheung, & Wong, 2005).

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In the case of industrial production, the pure culture of bacteria is prepared by using large bioreactors (Malus´a, Sas-Paszt, & Ciesielska, 2012). While in the case of AMF-based biofertilizers, the inoculants consist of either spores, hyphae, or their mixture, and are mixed with specific carrier materials. As AMF is in obligate symbiosis with plants, their industrial proliferation and production of AMF-based biofertilizers need highly developed skills and proper infrastructure (Herrmann & Lesueur, 2013). At present, most of the AMF-based biofertilizers are prepared using the pot-culture propagation method (Herrmann & Lesueur, 2013). However, recently a new method has been developed to produce a high concentration of spores based on transformed root organ cultures. This method is suitable for industrial production as it requires limited space and AMF are simply inoculated on petri plates supplemented with nutritive media and transformed roots. The only drawback of this method is that it is expensive, and its cost is estimated to be the same as that of chemical phosphatic fertilizer, which it might replace. While developing the consortium of microbes for biofertilizer development, it should be kept in mind that many groups of bacteria get firmly associated with AMF, resulting in higher colonization of roots. While some of the strains of bacteria show antagonistic behavior toward AMF, resulting in decreased colonization of roots (Vesterga˚rd et al., 2008). The difference in adaptation to different environmental conditions should also be considered when selecting the different strains of microbes for the production of biofertilizers (Malus´a et al., 2012). Biofertilizer development is a complex process that undergoes several assessments to qualify for biofertilizer standards (Fig. 6.1). One of the major concerns is the viability of microorganisms. Biofertilizers have to be formulated in such a way that microbes remain viable and should be able to improve the soil fertility even after a long period of time after the packaging has been done. Formulation of biofertilizers can be made in dried powder form, granular form, or in liquid form by using different kinds of carrier materials that support the growth of associated microbes and their efficient delivery. Among all, liquid biofertilizers can have a special cell protectant that encourages the formation of the resting spores, which helps in the increased shelf life of the biofertilizer. Also, liquid biofertilizers are recommended in lower dosages compared with other types of biofertilizers (Itelima, Bang, Onyimba, Sila, & Egbere, 2018). Choosing a good carrier material for the inoculums is also an important aspect, as each carrier has its own advantages and disadvantages that affect the overall quality of the developed product. A carrier is nothing but a delivery vehicle that transports the microbes from the factory to the field. A major proportion in the biofertilizer is represented by the carrier (by weight or volume), which has immense importance in the delivery of viable cells as it provides an interim protective (physically and nutritionally) niche for the microbes while in the package as well as in the soil (Arora, Khare, & Maheshwari, 2010). An ideal carrier should be: (1) nontoxic, (2) have high moisture absorption properties, (3) have high water holding capacity, (4) have a longer shelf life, and (5) should be lump-free and easy to process. The encapsulation of the inoculants with the carrier ensures easy handling, effectiveness of the biofertilizer, and long-term storage. Before incorporating inoculants with the carrier, it should be ensured that the carrier is properly sterilized either by gamma radiation or by autoclaving (Itelima et al., 2018). In addition to carriers, some adjuvant is also added in the development of biofertilizers, which act as a sticking and shielding agent for the microbial cells (Table 6.1).

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Identification Microorganisms in soil

Isolation of microorganisms

Packaging and storage

Field trial and validation

Screening for PGP potential

Selecting suitable carrier Preparation of bioformulation

Product registration

Product commercialization

FIGURE 6.1 Flowchart representing steps involved in bioformulation preparation.

6.5 Types of bioformulations Based on carrier materials, bioformulation preparation has been categorized into solid, liquid, and encapsulated bioformulation (Table 6.1).

6.5.1 Solid bioformulation Solid formulations are present in dried form in the market. They are easy to store and transport and have a longer shelf life than other types of formulations. The solid formulation includes granules, dried powders, wettable powders, wettable/water-dispersible granules, and dust. They are produced by mixing binders, wetting agents, and dispersants.

6.5.1.1 Dried powder (dust) Soil, organic, inorganic, or inert materials are used to prepare dry powdered bioformulation. These types of formulations have been used for ages and contain a very fine grounded mixture of active compounds. Only 10% of the particle’s size ranges from 50 to 100 μm. In most cases, the dried bioformulation is prepared using peat, the top organic layer of the soil. Peat is formed by the biodegradation of organic matter that falls on the ground over a period of time. Peat provides nutrition to plants as well as to microorganisms. The reason for using peat as a carrier in most formulations is

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Table 6.1 Types of bioformulation and carrier used. Physical forms

Types of formulations

Solid

Granular formulation

Wettable powders and wettable/ water dispersible granules Dusts Liquid

Liquid formulation

Encapsulation

Encapsulation

Carriers used

References

Wheat meal granules, cornmeal baits, gluten cottonseed flour, gelatin, acacia gum, sodium alginate, semolina Inert charcoal, fly ash, wheat bransand mixture, organic cakes, bagasse-molasses and sand mixture, cow dung and sand mixture, diatoms Peat, soil, organic, and inert materials Water, mineral oil, organic oil, mixture of water and oil

Mishra and Arora (2016); Navon (2000); Guijarro et al. (2007); Batta (2007)

Gelatin, cellulose starch, copolymer of acrylic and methacrylic acid esters, ethylcellulose

Brar et al. (2006); Khan, Zaidi, and Wani (2007); Cheng, Linling, Juan, Honghui, and Cheng (2015); Mishra and Arora (2016) Bashan et al. (2014); Mahanty et al. (2017) Malus´a et al. (2012); Herrmann and Lesueur (2013); Mahanty et al. (2017) Amiet-Charpentier, Gadille, Digat, and Benoit (1998); Che`ze-Lange et al. (2002)

that it has a high content of organic matter and good water retention capacity. It is highly absorptive, easily sterilizable, and low in cost. The toxic materials present in the peat must be removed during sterilization as it may hinder the growth of microbes and the quality of the bioformulation (Bashan, de-Bashan, Prabhu, & Hernandez, 2014).

6.5.1.2 Granules The granular bioformulation overcomes the limitations of the dried form. The demand in the market is steadily increasing due to its effectiveness. The granules are made from wheat meal granules, cornmeal baits, sodium alginate, small marbles, peat prill, silica grains, gluten, etc. They are added with an adhesive and then mixed with powdered inoculums (Herrmann & Lesueur, 2013). These types of formulations are less dusty and easier to handle. On the basis of granule size, they can be divided into two major types: (1) coarse particles (size 100
1000 μm), and (2) microgranules (size 100
600 μm). These formulations are noncaking, free-flowing, nondusty, and disintegrate immediately into the soil to release their active components. The limitation of these granules is that they are bulky and hard to transport, making them costlier than the dried form of bioformulation. Several studies have been conducted to test the superiority of granular bioformulation over dried and liquid forms.

6.5.1.3 Wettable powders It is one of the oldest types of bio-formulation. As described by the international units, a wettable powder should consist of 50% powder, 15%
45% filler, 3%
5% surfactant, and 1%
10% dispersant by weight (Brar, Verma, Tyagi, & Val´ero, 2006). The raw materials by which these

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types of formulations are being prepared include wheat bran and sand mixture, a mixture of sawdust and molasses, corn cob and sand molasses mixture, organic cakes, cow dung mixed with sand, compost, charcoal, fly ash, etc. (Mishra & Arora, 2016). These formulations are highly miscible with water or added to the liquid carrier just prior to their application. As the moisture content is almost negligible, the shelf life of this bioformulation is relatively high compared with other types.

6.5.1.4 Wettable/water-dispersible granules Also known as dry flowables, water-dispersible granules are manufactured in such a way that wet powders become eco-friendly, user-friendly, nondusty, and rapidly dissolvable in water. Like the wettable powder, they also consist of wetting agents and dispersing agents, but in higher concentrations. They are generally used to control nematodes and are the most common bioformulations found, capturing up to 90% of the total market. Ampelomyces quisqualis, an antagonistic fungus, is formulated as wettable/water-dispersible granules as it helps in controlling the powdery mildew in crops like grapes, apples, cucurbits, etc. Bacillus megaterium was used by Chumthong, Kanjanamaneesathian, Pengnoo, and Wiwattanapatapee (2008) for the development of this type of formulation for the biocontrol of rice sheath blight.

6.5.2 Liquid bioformulation The liquid formulations are prepared using broth cultures, mineral oil, organic oil, oil in water, or polymer-based suspensions. Liquid biofertilizers are easy to use on seeds as well as on the soil. The concentration of cells is higher than the two other types of bioformulations. This type of bioformulation helps the farmers use it in lesser quantities, making it less expensive with the same efficiency. The liquid bioformulation has a longer shelf life, less contamination, and excellent protection against environmental stress. Liquid formulations are compatible with farming machinery such as air seeders (Bashan et al., 2014). The only limitation of such formulations is that microbes lose their viability on seeds too quickly. However, this problem has been solved by applying sucrose, glycerol, and gum arabic (Mahanty et al., 2017). Liquid formulations can be developed as suspension concentrates. These formulations are produced by mixing solid active compounds that are generally poorly soluble in water. These formulations need to be diluted in water or other carriers before application. Adding different types of surfactants and additives improves their storage and solubility. They have gained a good amount of importance among farmers over the past few decades. A new soybean oil-based Trichoderma asperellum bioformulation has been developed by Mbarga et al. (2014), and upon application, they found that such bioformulations have more potential to biocontrol cacao black pod disease. While handling the oil dispersion-based bioformulation containing fungi, a few protective measures are to be taken in case of prolonged storage. Some of the active compounds (conidia) may settle on the suspension’s bottom. Oil-based formulations are known to be better in foliar spray and are effective in entomopathogenic activities. Trichojet, Trichorich-L, and Enpro-Derma are some of the oil-based bioformulations that contain Trichoderma and are used for biocontrol. As the evaporation rate of oil is much lesser than water, it remains attached for a longer time and can be applied as an emulsion or as an invert emulsion (Mishra & Arora, 2016).

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6.5.3 Encapsulated bioformulations In this formulation, the microbial cells are coated or trapped with or within a polymeric material to produce beads that are permeable to nutrients, gases, and metabolites for maintaining the viability of cells within the beads. Two types of encapsulates are produced based on the size of the beads, macro-encapsulation (ranging from a few millimeters to centimeters) and micro-encapsulation (ranging from 1 to 1000 μm). Gelatin, cellulose, starch, and many other polymers are generally used for encapsulating bioactive materials (e.g., PGPR). Before encapsulation, the nature of the active materials is being identified and stabilization is done through a chemical process (polymerization), physio-chemical process (gelation or coacervation), or physical process (evaporation or solidification). For additional protection, the active materials can be coated with special kinds of dyes. It has been documented that bioformulation prepared through encapsulation generally persists a longer shelf life as the coating material protects the inner bioactive agent from environmental stresses (Schoebitz & Lo´pez Belchı´, 2016).

6.6 Types of biofertilizers Extensive research on plant-beneficial microorganisms resulted in the development of different kinds of biofertilizers, satisfying the various needs of plants and soil in the environment (Owen et al., 2015). Biofertilizers have been divided into different categories. It solely depends upon the type of microorganism it contains. Some other kinds of biofertilizers are described in the following section.

6.6.1 Nitrogen-fixing biofertilizers Nitrogen constitutes about 78% of the atmosphere but the molecular form of nitrogen cannot be acquired and used by plants. Plants cannot use this nitrogen for their metabolic processes (Mahanty et al., 2017). Plants can absorb nitrogen only when atmospheric nitrogen is converted into ammonia or ammonium ions or nitrate, the only usable form for plants, by nitrogen-fixing biofertilizers. During biological nitrogen fixation, gaseous nitrogen is converted into ammonia with the help of an enzyme called dinitrogenase (Smith, Richards, & Newton, 2004). These nitrogen-fixing biofertilizers improve the nitrogen status to support plant growth upon application. Nitrogen-fixing biofertilizers are classified into symbiotic nitrogen-fixing biofertilizers, free-living nitrogen-fixing biofertilizers, and associative symbiotic nitrogen-fixing biofertilizers.

6.6.1.1 Symbiotic nitrogen-fixing biofertilizers Biofertilizers developed with nitrogen-fixing microorganisms can fix the nitrogen symbiotically with plants. These biofertilizers exploit the microorganisms that belong to the Rhizobiaceae family (α-proteobacteria) and infect and form a relationship with the roots of leguminous plants. It majorly consists of Azorhizobium, Allorhizobium, Rhizobium, Bradyrhizobium, Mesorhizobium, and Sinorhizobium (Kour et al., 2020). Rhizobium is a symbiotic bacterium that lives in the root nodules of legumes and forms a mutual relationship with its host plant. Rhizobium reduces atmospheric nitrogen to ammonia by nitrogenase consisting of dinitrogenase reductase and dinitrogenase

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with iron and molybdenum as its cofactor (Mahanty et al., 2017). Moreover, Frankia is also a symbiotic nitrogen fixer that generally forms a relationship with the Alder tree. Anabaena azollae is one of the most potential biofertilizers of nitrogen in rice fields. Some researchers considered Azolla as a substitute for commercial nitrogen fertilizer. It has been concluded from a study reported from Vietnam that Azolla enables rice yield increment by 10%
25% compared with Azolla-free rice fields (Kour et al., 2020). Acetobacter, an obligatory aerobic nitrogen fixer, mainly colonizes the roots of several varieties of sugarcane, as well as also shows a symbiotic association with coffee.

6.6.1.2 Free-living nitrogen-fixing biofertilizers Nonsymbiotic or free-living biofertilizers contain microorganisms (both free-living and endophytic) like Azotobacter, cyanobacteria, Azospirillum, etc. (Bhattacharyya & Jha, 2012). Azotobacter, belonging to the family of Azotobacteriaceae, is the main free-living nitrogen-fixing bacteria present in alkaline as well as neutral soils. It fixes atmospheric nitrogen in nonlegume crops like rice, cotton, vegetables, etc. (Kour et al., 2020). Ei-Lattief (2016) reported that the bioinocultaion of Azotobacter enhances the grain yield, growth, biomass, and protein content in wheat crops. Several different species of Azotobacter have been reported to produce vitamin B complex, phytohormones, and other bioactive compounds, which act as biocontrol agents against root pathogens (Mahanty et al., 2017). Cyanobacteria, a primitive form of microbes on earth, were first reported in rice fields as biofertilizers and from then, many diverse forms of cyanobacteria have been reported in various other habitats. Paddy fields provide the most suitable ecosystem for the growth of cyanobacteria due to the proper availability of temperature, light, nutrients, and water (Kour et al., 2020). Cyanobacteria are photosynthetic, free-living nitrogen fixers that majorly include Nostoc, Calothrix, Anabaena, and Aulosira (Sahu, Priyadarshani, & Rath, 2012). Cyanobacteria increase soil fertility by secreting various plant growth-promoting substances like vitamins, amino acids, phytohormones, etc.

6.6.1.3 Associative symbiotic nitrogen-fixing biofertilizers Azospirillum is mainly studied under associative symbiotic nitrogen fixers because of its association with different grasses. Currently, 17 species of Azospirillum have been reported and among them, Azospirillum lipoferum and Azospirillum brasilense are mainly studied, and described (Kour et al., 2020). These species have been isolated from the soil as well as from the aerial parts of plants having nitrogen-fixing abilities. Apart from nitrogen fixation, these microorganisms also produce indole acetic acid (IAA), cytokinins, and gibberellins. It has been reported that Azospirillum also helps plants to survive during stress conditions by promoting changes in cell wall elasticity and osmotic adjustments (Groppa, Benavides, & Zawoznik, 2012).

6.6.2 Phosphate solubilizing biofertilizers Just like nitrogen, phosphorus is also a limiting factor and an essential macronutrient for plants. It is present at the levels of 400
1200 mg/kg of soil. Despite its presence, the soluble concentration of phosphorus is very low and hence remains unavailable to plants as plants can only absorb its two forms, monobasic and dibasic. Insoluble forms of phosphorus are mainly present in inorganic materials, that is, inositol phosphate (soil phytate), apatite, phosphorus, and tri esters (Mahanty

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et al., 2017). Phosphate solubilizing microbes possess the ability to convert the insoluble forms of phosphate into soluble forms. These phosphatic biofertilizers help the soil to reach its finest phosphorus level and correct the level of phosphorus inside the soil (Asoegwu et al., 2020). Several mechanisms that convert the insoluble form of phosphorus to soluble form include acidification (chelation and change reaction) produced by phosphorus-solubilizing bacteria or fungi, which play an important role in soil phosphorus solubilization. Different species of Pseudomonas and Bacillus isolated from the rhizospheric soil of different crops possess phosphate solubilizing attributes (Mishra, Joshi, Suyal, Bisht, & Bhatt, 2014). Other microorganisms, such as Burkholderia, Brevibacterium, Corynebacterium, Escherichia, Mycobacterium, Xanthomonas, Serratia, Sarcina, etc., have also been reported to possess phosphorus solubilization potential (Kour et al., 2020). Phosphate solubilizing biofertilizers enhance the essential phosphate availability for plants.

6.6.3 Phosphate-mobilizing biofertilizers These kinds of biofertilizers scavenge the phosphates from the organic phosphorous complexes with the help of enzymes like acid phosphatases and phytases and then mobilize them for plants. Mycorrhizae, forming asymbiotic association between fungi and roots of higher plants, play a central role in the mobilization of phosphorus (Itelima et al., 2018). Indigenous AMF present in the soil colonize to help in phosphorus uptake. All plants do not depend upon mycorrhizal association. However, some studies indicate that plants growing in low phosphorus-containing soil when inoculated with mycorrhiza results in increased productivity. Hence, the use of AMF will lead to the achievement of effective levels of yield as well as reduced cost and environmental risks (Dalpe & Monreal, 2004).

6.6.4 Potassium-solubilizing biofertilizers Potassium is an essential element that plays an important essential role in the growth and development and the metabolic activities of plants. It is also involved in almost 60 different plant enzyme systems, acting as an essential regulator. Besides these, it also has a crucial role to play in disease and drought resistance (Billore, Ramesh, Vyas, & Joshi, 2009). Several other roles of potassium include involvement in controlling root growth, starch production, regulation of stomata movement, etc. The insufficient supply of potassium results in poor development of roots, slow growth rates, small production of seeds, susceptibility to diseases, and lower yields (McAfee, 2008). In the soil continuum, potassium occurs mainly as silicate minerals that are inaccessible to plants, and it is only made available when it is slowly weathered or solubilized (Itelima et al., 2018). Various rhizospheric microorganism releases potassium from different insoluble compounds present in the soil. Multiple studies reported that inoculating seeds or treating seedlings of plants with potassiumsolubilizing microbes enhances the percentage of germination, growth, yield, seedling vigor, and potassium uptake (Zhang et al., 2013). Potassium-solubilizing microbes reported in several studies include Bacillus, Burkholderia, Acidothiobacillus, Panibacillus, Pseudomonas, Glucanolyticus, Enterobacter, Sphingomonas, etc. (Kour et al., 2020). Microorganisms having potassiumsolubilizing potential solubilize silicates through organic acid production. This causes the decomposition of silicates and help in the removal of metal ions, thereby making them available to plants for their growth and development.

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6.6.5 Iron-solubilizing biofertilizers Iron is an essential micronutrient for all life forms. In aerobic and alkaline environments, iron mainly exists in the Fe31 oxidation state, which forms insoluble hydroxides and oxyhydroxides. Hence a major part of iron remains unavailable for uptake (Mahanty et al., 2017; Sharma, 2017). To overcome this problem, bacteria acquire iron through secreting low molecular compounds (iron chelators) called siderophores, which possess a high affinity toward complex iron. Siderophores are water-soluble compounds and can be classified into extracellular and intracellular siderophores (Hider & Kong, 2010). Many genera, such as Pseudomonas, Bacillus, Serratia, have been reported to produce siderophores and are mainly used for iron-solubilizing biofertilizers. These biofertilizers make siderophores available for plants and prevent the growth of phytopathogenic fungi through competition. Rhizobacteria commonly vary in siderophore utilizing ability. A few rhizobacteria use homologous siderophores, while others use heterologous siderophores (Parray et al., 2016). In bacteria (gram-positive and gram-negative), the reduction of iron from Fe31 to Fe21 occurs in the bacterial membrane, which is released further into the cell from the siderophore through a gating mechanism that connects inner and outer membranes. Thus siderophores act as iron-solubilizing agents under iron stress conditions (Ahemad & Khan, 2011). It has been reported that certain algae and actinomycetes under iron limiting conditions also produce siderophores, which can be used to prepare bioformulations. Siderophores also forms stable complexes with other heavy metals and radioactive elements like neptunium and uranium (Rajkumar, Sandhya, Prasad, & Freitas, 2012). Siderophore binding increases the soluble metal concentration, helping plants to alleviate the stress imposed by high levels of heavy metals in soil (Sati et al., 2020). From bacterial siderophore, plants assimilate iron by several different mechanisms, like chelating and releasing iron, direct uptake of Fe-siderophore complex, and ligand exchange methods (Thomine & Lanquar, 2011), thereby improving soil health.

6.6.6 Zinc-solubilizing biofertilizer Zinc is an essential trace element vital for all crops. It is required by almost all biological enzymes to work perfectly. Nearly 2800 proteins need zinc for their structural intactness and activity. Zinc deficiency leads to physiological stress, which causes many enzymes to fail in performing their function (Alloway, 2009). Most of the time, reservoirs of zinc are not readily available to plants due to its presence in insoluble forms. The bioavailability of zinc is achieved by the application of zinc sulfate as a chemical fertilizer, but only 1%
5% of applied zinc is utilized by plants and the rest is converted into insoluble forms (Nitu, Rajinder, & Sukhminderjit, 2020). The selection and inoculation of zinc solubilizing bacteria either in pure form or in consortium or their bioformulations overcome zinc deficiency. Several workers reported that rhizospheric bacteria and fungi are found effective in solubilizing insoluble zinc compounds both under in vitro and in vivo conditions (Nitu et al., 2020). Microorganisms like Bacillus subtilis, Pseudomonas, Cyanobacteria, Acinetobacter, Burkholderia, Bacillus thuringiensis etc. have been found effective in solubilizing insoluble zinc complex and thus can be used as biofertilizers (Abaid-Ullah et al., 2015). Fungi like Aspergillus nomius, Aspergillus niger, and Aspergillus oryzae were also found to be effective in solubilizing insoluble zinc compounds (Nitu et al., 2020). During the growth phase,

6.7 Mode of biofertilizer application

109

soil microorganisms produce organic acids, which combine with the minerals present in the soil and bind with zinc ions, lowering nearby soil pH. Organic acids like gluconic acid and ketogluconate in various configurations chelate zinc via carboxyl and hydroxyl groups and increase zinc solubility (Nitu et al., 2020).

6.7 Mode of biofertilizer application A huge number of crops are cultivated in different agroclimatic conditions, and different crops are associated with their mode of planting and growth. As per the planting conditions and accessible parts (root, seed, shoot) for biofertilizer application, different biofertilizer implication methods have been devised. Some commonly used methods are discussed below.

6.7.1 Foliar application Generally, liquid formulations are needed to apply on the foliar part of the plant to control foliar pathogens or improve plant growth. Its efficacy mainly depends upon the microclimate of the crop canopy. The canopy of the different crops has different concentrations of nutrients like organic acids, amino acids, sugars, lenticels, wounds, and hydathodes. These factors play an important role in the efficacy and survival of antagonists phylloplane (Berninger et al., 2018). Advantages of foliar application of biofertilizers include: (1) biofertilizers (bacteria/ fungi) on phylloplane can act as antagonists to several plant pathogens (if suitable strains are used), (2) nitrogen-fixing bacteria fix nitrogen close to its place of assimilation (3) leaf leachates are the source of food in phylloplane, biofertilizers utilizes this food and eliminates cuticle degrading pathogen through competitive inhibition, (4) biofertilizers (bacteria/ fungi) face less competition by other microflora on the phylloplane concerning the soil (Sudhakar, Chattopadhyay, Gangwar, & Ghosh, 2000). For the first time, Sudhakar et al. (2000) used Azotobacter as a foliar biofertilizer and observed increased mulberry leaf production. According to Fernando, Nakkeeran, Zhang, and Savchuk (2007), Bacillus amyloliquefaciens (E16) and Pseudomonas sp. DF41 have proven effective against Sclerotinia sclerotiorum, a causative agent of stem rot of canola. Trichoderma sp. can also be used in foliar sprays to control the disease of above-ground parts. Before applying foliar treatment, the frequency and dosage of application need to be standardized according to the crop value, which could be considered a practical and reliable approach. Additives like spreaders, stickers, emulsifiers, and adjuvants are vital for applications in monocots. They facilitate the adhesion of microorganisms on plant tissue and as such could be the reason for their wide use in foliar sprays (Harvey, 1991). Nowadays liquid formulations with high potency, cost-effectiveness, good suspension properties, good stability, etc. are available globally, and they are successfully adopted by several farmers for foliar application in various crops (Berninger et al., 2018). Ultralow volume suspension is a technology that is used for the foliar application of liquid bioformulations. Ultralow volume suspension spray is used to deliver microbial biofertilizers precisely to the foliar parts of the plants. It is advantageous as it delivers minimal quantity in each spray.

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6.7.2 Seed treatment Seed treatment is generally used to deliver bioformulations applied to the seed on the spermosphere of plants. Seed treatment is also an applied method of delivery system for bacterial as well as fungal biocontrol agents. Biocontrol agents or PGPR need to be put onto the seed for the effective delivery of biofertilizers. Upon sowing of seeds, coated biofertilizers get colonized and multiply their races and ultimately protect plants against various types of seed-borne pathogens of crop or increase plant vigor and growth through numerous biological mechanisms (Jambhulkar & Sharma, 2013). Using biological agents as seed treatment provides equal adequate protection from seedborne pathogens compared with the traditional seed treatment. Recently the application of microbial inoculants to seeds has increased because of increasing public awareness of the environment, sustainable development, and health hazards caused by the excessive use of agrochemicals (Chandra, Greep, & Ramarathinam, 2006). During the planting of the seedlings, biofertilizers may be used directly, that is, in the form of powder or liquids. In seed priming, seeds are mixed with biofertilizers consisting of additives like xanthan gum or gum Arabic, which are used to extend the life of microbes and for adhesion to seeds (Jambhulkar, Sharma, & Yadav, 2016). There are many seed treatments that include seed protection during storage and after planting, and environmental side effects are minimized to a great extent. It also helps to break seed dormancy and improve emergence and plant stand (Sharma, Singh, Sharma, Kumar, & Sharma, 2015).

6.7.3 Soil treatment Soil treatment is mainly used when the microbial constituent of the bioformulation is very sensitive to desiccation. In soil treatment, a dose of bioformulation is mixed with a certain amount of soil, generally depending upon the microbial load in the bioformulation and the physicochemical properties of the soil. Upon delivery in the soil, the microbial agent produces a large amount of population in the soil. As the number of introduced microorganisms increases, they provide essential nutrients to plants, making them unavailable for soil pathogens and other less important microflora (Lumsden, Lewis, & Fravel, 1995). The soil acts as a medium for both pathogenic as well as nonpathogenic microorganisms. Inoculation of the soil with microbes helps to increase the population dynamics of augmented bacterial antagonists and suppress the establishment of pathogenic microorganisms in the infection court. Fungi and bacteria could both be used as an agent of biocontrol in soil treatment. However, the major limitation in the case of fungi is that the seed coatings remain. Hence they do not colonize in the rhizosphere as commonly as the bacterial agents (Warrior, Konduru, & Vasudevan, 2002). According to Bankole and Adebanjo (1998), the soil drench having a suspension of Trichoderma viride was found effective in reducing infection from cowpea infected with Colletotrichum truncatum. An enrichment technique of farmyard manure with Trichoderma sp. for soil is widely accepted by farmers for soil treatment against soil-borne pathogens (Jambhulkar et al., 2016).

6.8 Challenges of biofertilizer commercialization Several biofertilizers have been assessed in different countries and are commercially available for farmers (Table 6.2). The commercialization of biofertilizers is hampered by a number of factors:

Table 6.2 Commercially available biofertilizers-based product. Products

Microorganisms

Carriers

Role

Company

Sources

TagTeam BioniQ

Penicillium bilaiae, Rhizobium leguminosarum, Bacillus amyloliquefaciensTrichoderma virens

Peat

Novozymes

https://biosolutions. novozymes.com/en/products/ pulses/tagteam-bioniq-us

Optimize

Bradyrhizobium sp. Arachis

Aqueous carrier .99%

Improves nodule formation, increases nitrogen fixation, and enhances efficiency of phosphate use Increases the rate of early peanut nodulation

Novozymes

JumpStart

Penicillium bilaiae

Wettable powder

Novozymes

Serifel

Bacillus amyloliquefaciens strain MBI600

Wettable powder

Nodulator Duo

Rhizobium leguminosarum biovar viceae, Bacillus subtilis

Solid core granules

Improves efficiency of soil and fertilizer phophorous uptake Biocontrol of Botrytis cinereaSclerotinia sclerotorium Trichoderma aggressivum Root-strengthening biofilm bacteria help in water and nutrient uptake

Vault IP Plus

Bradyrhizobium japonicum

—

Nitrogen fixation

BASF, Global

Biomix

Microbial Consortia

powder

Biomax/ Biomaxnaturals

Biozink

Microbial consortia

Liquid

Fix atmospheric nitrogen, solubilize residual phosphates, iron, and magnesium Zinc-solubilizing ability

https://biosolutions. novozymes.com/en/products/ peanuts/optimize-peanuts https://biosolutions. novozymes.com/en/products/ forages/jumpstart-forages https://agriculture.basf.com/ global/en/business-areas/ crop-protection-and-seeds/ use-areas/BioSolutions.html https://agriculture.basf.com/ global/en/business-areas/ crop-protection-and-seeds/ use-areas/BioSolutions.html https://agriculture.basf.com/ global/en/business-areas/ crop-protection-and-seeds/ use-areas/BioSolutions.html http://www.biomaxnaturals. com/multi-purposemicrobial-fertilizer.html

Sanjivini N1

Rhizobium culture

Liquid

Forms root nodules

BASF, Global

BASF, Global

Biomax/ Biomaxnaturals Subico

http://www.biomaxnaturals. com/zinc-solubilizer.html http://www.subico.in/ products1.php#1

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(1) unavailability of suitable strain and appropriate material that can serve as a carrier, (2) dearth of skilled and experienced staff in biofertilizer producing units, (3) unavailability of required funds and equipment, (4) shortness in storage and transport facilities, (5) inadequate knowledge among farmers, (6) marketing constraints, and (7) lack of regulations and standards for production.

6.8.1 Biological constraints Choosing the right PGPR strain(s) for biofertilizer development is a difficult task in itself. The nature of strain(s) should not be very selective or highly targeted (to specific crops), while it should exhibit their activity on a broad range of hosts. Biofertilizers should have the potential to adequately colonize the roots of host plants, develop a proper rhizospheric region for plant growth, and boost the bioavailability of nitrogen, phosphorus, and potassium (Vejan, Abdullah, Khadiran, Ismail, & Nasrulhaq Boyce, 2016; Vessey, 2003). Biofertilizers must also be able to endure the conditions of soil, exhibit compatibility with the crop inoculated, and interact with other microflora in the soil.

6.8.2 Technical constraints The Shelf life of PGPR strains is one of the major obstacles faced in the process of their commercialization as effective biofertilizers (Arora et al., 2010; Zandi & Basu, 2016). Biofertilizers that have a short shelf life possess the risk of getting recycled from time to time in case they are not brought to use before their expiry, which results in a financial loss to the marketing agency. Biofertilizers have to be stored and transported with extreme caution since they contain living microbial cells. The possibility of product deterioration due to shorter shelf life or spontaneous mutations arising at the time of fermentation or during storage is also a major technological limitation in the commercialization of biofertilizers (Mahajan & Gupta, 2009).

6.8.3 Regulatory constraints Registration of the product and filing a patent before its commercial use are examples of regulatory limitations. The rules frequently fluctuate between areas and countries and are inconsistent. Furthermore, the regulatory processes are fairly complicated, and the cost, which, though varies, is often on the upper end of the scale. The documentation procedures for product registration are equally extensive and complicated (Meena et al., 2020; Timmusk et al., 2015).

6.8.4 Marketing constraints The lack of suitable transportation and storage facilities is one of the most significant barriers that limit the establishment of these products in the market. Besides, farmers are unaware of the advantages of biofertilizers over agrochemicals for sustainable agriculture, which reduces the demand for such eco-friendly products.

Acknowledgment

113

6.8.5 Field-level constraints Since agricultural crops are cultivated under a range of physicochemical and environmental conditions, such as temperature, rainfall, soil type, and crop variety, biofertilizer developers face a considerable challenge. These conditions tend to change even within a small area, such as a field. As a result, such variations lead to incongruity in the effectiveness of biofertilizers (Barea, 2015; Kamilova, Okon, de Weert, & Hora, 2015). Besides, crops respond to the application of biofertilizers quite slowly, and sometimes, the biofertilizers can be ineffective on the crops. Due to these reasons, the level of acceptance for biofertilizers among farmers is very low (Arora et al., 2010).

6.8.6 Biofertilizer carrier Because bioinoculant agents have a short shelf life, a suitable carrier is necessary for field administration of biofertilizers. Peat, charcoal, lignite, and other suitable carriers are utilized in the manufacturing of biofertilizers. Since most of these carriers are unavailable in developing nations like India, they pose another technological challenge. There is a scarcity of these carriers in sufficient quantities and of a satisfactory grade. As a result, one of the greatest restrictions to its widespread use in fields is the lack of adequate carriers (Basu et al., 2021).

6.9 Conclusion The prime focus of this research is improving agricultural productivity for the escalating global population. The use of biofertilizers containing beneficial microorganisms is appreciable for improving plant productivity and soil health status while reducing the huge dependency on chemical-based fertilizers. Biofertilizers, such as nutrient solubilizers and nitrogen fixers, showed their efficacy in agricultural productivity and provided a greener approach. Due to their reliability, efficiency, and economic feasibility, biofertilizers can improve farmers’ income. Biofertilizers perform multiple functions, but many challenges are still to be addressed in further and advanced biofertilizer technology. Future research is required to develop genetically engineered bioinoculants with higher efficacy and all the necessary traits depending on farm conditions. Continuous exploration of inexpensive sources of carrier materials is also essential. Current research will also direct the future for using biofertilizers at massive levels as potent tools for crop and soil management.

Acknowledgment Amir Khan (First author) is highly grateful for financial help from National Mission on Himalayan Studies (NMHS), Ministry of Environment Forest and Climate Change, Govt. of India as the author is getting Senior Research Fellowship (SRF) under such scheme.

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47.

CHAPTER

Biocontrol: an efficient solution for sustainable agriculture and food production

7

Amrita Kumari , Ankita H. Tripathi , Priyanka H. Tripathi and Anupam Pandey Sir J. C. Bose Technical Campus, Bhimtal, Kumaun University, Nainital, Uttarakhand, India

7.1 Introduction The global population situation has radically changed during the last 20 years. Crop production must be redefined in an inventive way, along with sustainable methods, to meet the growing requirement for food and nutrition among the world’s population, while also combating the threat of climate change due to global warming. According to the UN Food and Agriculture Organization (FAO), farmers would need to cultivate and produce more than 70% of food by 2050 to meet the growing food demand of the world’s 9 billion population (http://www.fao.org). The major challenge in front of farmers, agriculture-based industries, scientists, and researchers is crop improvement with high quality and higher yield using various environmentally friendly methods. Insect/pest management for agricultural crops is one of the major hurdles owing to the low crop yield. Globally, crop loss due to insects, plant pathogens, and weeds is estimated to be around 15%, 13%, and 13%, respectively (Zhang, 2018). The global use of pesticides by the year 2020 has been estimated to increase to around 3.5 million tons (Sharma et al., 2019). China, the United States, Argentina, Thailand, Brazil, Italy, Canada, Japan, and India are among the top 10 most pesticideconsuming countries (Sharma et al., 2019). The use of chemical pesticides for insect/pest/weed management has its own devastating impact on the environment. The residual remnants of the chemical pesticides remain in the environment for much longer, and even the chances of bioaccumulation through the food chain are higher. The use of biological control agents can mitigate the hazardous effect of these chemicals. Biocontrol, in general, can be defined as the use of natural enemies against invasive species or insects/pests to control the population of these organisms beyond their normal population size. The natural enemy can act as a pathogen, parasitoid, and predator to their enemy. The biocontrol agents span a wide range of life forms, including invertebrates, vertebrates, bacteria, viruses, and fungi. As the crop-feeding insect population exceeds its natural population threshold, it can manifest into havoc for the related agricultural crop. In nature the balance of the insect/pest populations is maintained by their natural predators. In order for the biocontrol agents to work sustainably, elaborate studies on ecological interactions with various agricultural crop systems are essential (Shanker et al., 2012). A safe and effective biocontrol agent 

These authors are equally contributed.

Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00009-0 © 2023 Elsevier Inc. All rights reserved.

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should have attributes such as narrow prey range, climatic adaptability in a new habitat, synchronized life cycle to the prey, high rates of fecundity, ability to search prey population efficiently, shorter handling time, and survival even at lower host population densities. Biological control strategies are classified into numerous categories based on these attributes, as mentioned in the next section. There are four approaches regarding biocontrol technology based on either the natural substance or microorganism type, namely; macroorganisms, including nematodes and insects, microorganisms, including bacteria, viruses, fungi, semiochemicals (pheromones); and natural substances (animal, mineral, or plant-based).

7.2 Biological control: types According to plant pathology and agroecology, biological control is defined as the use of natural substances and living organisms to provide protection and reduce damage induced by different harmful pathogens, such as weeds, animal pests, and pathogens (Bale et al., 2008).

7.2.1 Types of biocontrol strategies Classical, augmentative, and conservative biological control are the three basic types of biological control strategies (Dent, 2000; Van Lenteren et al., 2003).

7.2.1.1 Classical biological control Classical control, also known as inoculative biological control, is mostly employed to combat various pathogens that have established themselves in various regions all around the world. In inoculative biological control, small quantities of around 1000 species of natural enemies of pathogens damaging plants are gathered from the pest’s habitat, inoculated into the new habitat, and allowed to establish a degree of control that can be sustained for long time periods. The inoculated biological control is found to be very successful for forest trees and plants, fruit plantations, and perennial crops, where the ecosystem’s enduring landscape allows exchanges between the pest and the natural enemy to become completely entrenched over time. For instance; in 1900, the predatory ladybird Rodolia cardinalis was efficaciously introduced and released in Mediterranean Europe to conquer the inadvertently introduced Icerya purchase (citrus pest) and the release of the natural parasitoid Aphelinus mali in apple orchards of Europe for controlling Eriosoma lanigerum (woolly apple aphid) (Greathead, 1976).

7.2.1.2 Augmentation control Augmentation biological control involves the introduction of natural opponents of the diseasecausing plant pathogens, and it usually necessitates the commercial manufacture of the released agents (van Lenteren, 2000a). The control agent is bulk produced and released in vast numbers during an inundation. For example, Trichogramma egg parasitoids, including Diatraea saccharalis (sugarcane borer) and Ostrinia nubilalis (European corn borer) (Van Lenteren & Bueno, 2003).

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The interaction of the natural enemy of plant pests/pathogens is debilitated due to different cultivation systems, including short-term annual cultivation of crops, which hampers the formation of viable breeding populations of the species of natural enemy between the production cycles of crops. The goal of inundative releases, similar to the application of a pesticide, is to produce a large ratio in favor of the natural enemy, resulting in a quick decline or local extinction of the pest. Individuals who have been liberated, rather than their progeny, are in charge of maintaining control. However, the control is usually only temporary, requiring rereleases on a regular basis, once or more in a year.

7.2.1.3 Seasonal biological control: type of augmentation In seasonal inoculative control, natural enemies are mass bred in the laboratory and then put into short-term crops where many pest generations can occur in a single growing season (Van Lenteren & Woets, 1988). Similar to augmentative control, a high number of natural enemies are released to gain quick control, but the natural enemy population is also built up over multiple generations within the same growth season. When the cropping scheme stops inoculative biological control from extending over many years, this approach can be used. For example, the introduction of predators and parasitoids in greenhouses for controlling thrips, whiteflies, aphids, and leaf miners (Van Lenteren, 2000b).

7.2.1.4 Conservative biological control The use of natural parasitoids and predators, usually against native pests, is referred to as conservation biological control. Various strategies, such as crop microclimate manipulation and the construction of overwintering refuges, such as beetle banks, are used to increase the quantity or movement of natural enemies resulting in enhancing the accessibility of different preys and hosts providing critical food resources for aphidophagous hoverflies and adult parasitoids (Bale et al., 2008).

7.3 Biocontrol and biofertilization with microorganisms for sustainable agriculture 7.3.1 Plant growth-promoting rhizobacteria Plant growth-promoting rhizobacteria (PGPR) are the most widely used biocontrol agents and biofertilizers presently employed in agriculture (Paterson et al., 2017; Pii et al., 2015). PGPR usually colonize the rhizosphere around different species of plants. PGPR are very useful for the plant species as they promote growth of plants and decrease susceptibility toward different plant pathogens, including nematodes, viruses, bacteria, and fungi (Kloepper, Ryu, & Zhang, 2004; Sati et al., 2020). The most common genera of PGPR are Arthrobacter, Azotobacter, Alcaligenes, Azospirillum, Klebsiella, Burkholderia, Serratia, Bacillus, Pseudomonas, Enterobacter, and Rhizobium (Kloepper Ryu & Zhang, 2004). PGPR are beneficial as they increase the uptake of nutrients by plants improving the rate of seed germination; growth of root, protein, and chlorophyll content; increase in root and shoot weights; and delayed senescence (Adesemoye & Kloepper,

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2009; Sati et al., 2021). As a result, PGPR are frequently used as biofertilizers. Azotobacter vinelandii and Azotobacter chroococcum are widely used as nitrogen-based fertilizers all over the world. Bacillus amyloliquefaciens IT45, Pseudomonas fluorescens, Bacillus megaterium are a few of the PGPR used for the fertilization of phosphorus. Biofertilizers containing Frateuria aurantia are used for supplying potassium to the crops. In Asia, Bacillus sp., Thiobacillus thiooxidans, and Delfia acidovorans are used as PGPR-based biofertilizers for providing sulfur, zinc, and silicate to the plants. Pseudomonas sp. generates antibiotics such as 2,4-diacetylphloroglucinol, pyrrolnitrin (PRN), pyoluteorin (PLT), and hydrogen cyanide, while P. fluorescens ZX strain secretes lytic enzymes (Sati et al., 2022; Sharma et al., 2017). P. fluorescens A506 strain prevents fire blight disease caused by Erwinia amylovora on pome fruits (Cabrefiga et al., 2007) (Table 7.1). Table 7.1 Commercially available PGPR as biocontrol agents and biofertilizers. Microorganism

Commercial name

References

Bacillus amyloliquefaciens A. chroococcum Bacillus megaterium Azotobacter sp. Frateuria aurantia P. fluorescens Pseudomonas aureofaciens strain Tx-1 Pseudomonas syringae ESC-10, ESC-11 Bacillus subtilis GB03, Bacillus amyloliquefaciens IN937a Burkholderia vietnamiensis P. fluorescens A506 Bacillus velezensis Bacillus firmus P. fluorescens Pseudomonas chlororapsis Streptomyces griseoviridis K61 P Bacillus amyloliquefaciens ssp. plantarum Pseudomonas sp. DSMZ 13134 Azospirillum str. Az39 Bacillus amyloliquefaciens IT45 Bacillus amyloliquefaciens Bacillus subtilis P. fluorescens Bacillus pumilus QST 2028 Bacillus megaterium var. phosphaticum Bacillus subtilis Frateuria aurantia

Amylo-X Azotovit Bio-P Bio-N Bio-K Biomonas Bio-Ject Spot-Less Bio-save 10LP BioYield Botrycid Blight Ban A506 Botrybels Flocter WP5 Ecomonas, Florezen P Cedomon, Cedress Mycostop FZB24 Proradix Nitrofix Rhizocell Rhizovital 42 Serenade Rizofos Liq Maı´z Sonata Symbion-P Taegro Symbion-K

Pirttila¨ et al. (2021)

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7.3.2 Rhizobia Rhizobia are one of the oldest agricultural tools, with industrial manufacturing beginning at the end of the nineteenth century. The use of Rhizobia in agriculture is limited to mainly leguminous plants. They are responsible for fixing about 200
300 kg nitrogen/ha/crop. The major nitrogen-fixing bacteria of the α-proteobacteria group, which includes Agrobacterium, Bradyrhizobium, Devosia, Allorhizobium, Sinorhizobium, Phyllobacterium, Rhizobium, Ochrobactrum, Mesorhizobium, Methylobacterium, and nitrogen-fixing bacteria of the β-proteobacteria group, which include Cupriavidus and Burkholderia, are involved in nodule formation in host plants (Franche et al., 2009). While cyanobacteria, active in nitrogen fixation, as well as Azolla, are commonly employed as manure in rice cultivation (Franche et al., 2009).

7.3.3 Endophytic fungi Despite their numerous beneficial impacts on crops and their utility as biofertilizers and biocontrol agents, endophytic fungi have been underutilized as biotechnological tools in agronomy. Piriformospora indica is a well-studied endophytic fungus that colonizes the roots of cereal plants like maize and barley (Pirttila¨ et al., 2021). The fungus is involved in the acquisition of sulfur and phosphorus, promoting early flowering and seed formation and increasing biomass. Piriformospora indica protects crops/plants from biotic and abiotic stress and also provides resistance against pathogens, toxins, insects, and heavy metals. Clavicipitaceous endophytes are used as biocontrol agents in agronomy. Epichloe coenophiala are inoculated into tall fescue to improve insect tolerance. In New Zealand and Australia, ryegrass cultivars inoculated with fungal endophytes are utilized to minimize grassland harm by insect herbivores (Pirttila¨ et al., 2021) (Fig. 7.1).

7.3.4 Mycorrhizal fungi Mycorrhizal fungi are one of the most widely utilized biofertilizers worldwide (Vos´atka et al., 2012). They assist crop plants to acquire water and nutrients by enhancing the growth of the root system. They minimize abiotic stress and prevent the roots from disease-causing pathogens, such

FIGURE 7.1 Commercially available fungal biocontrol agents.

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Table 7.2 Microorganism-based biocontrol agents for plant/crop pathogens (Walia et al., 2021). Host crops/plants

Biological control agents

Target pathogens

Tobacco and tomato Arabidopsis and rice

Glomus mosseae, G. intraradices, G. fasciculatum Cryptosporiopsis quercina, Piriformospora indica, Penicillium sp. Trichoderma asperellum, T. koningii, T. viride, T. harzianum

Ralstonia solanacearum, Nacobbus aberrans, Alternaria alternata Pyricularia oryzae, R. solani, Pseudomonas syringae pv. Tomato

Tomato, groundnut, mustard, bean Stone pine, scots pine, rice, shortleaf pine Cotton Apple

Thelephora terrestris, Pisolithus tinctorius, Suillus luteus, Laccaria bicolor Verticillium nigrescens Pichia anomala, Cryptococcus laurentii and Sporobolomyces roseus

Botrytis cinerea, Fusarium oxysporum f. sp., Sclerotium rolfsii, Meloidogyne javanica, Alternaria brassicae, A. brassicicola, Lycopersici Phytophthora cinnamomic, F. oxysporum, F. moniliforme V. dahliae B. cinerea

From Walia, A., Putatunda, C., Sharma, R., Sharma, S., & Thakur, A. (2021). Biocontrol: A sustainable agricultural solution for management of plant diseases. In Microbial biotechnology in crop protection (pp. 1
54). Springer, Singapore.

as Pythium, Fusarium, nematodes, and Phytophthora (Smith & Read, 2010). Mycorrhizal fungi are usually involved in enhancing the vitamin and antioxidant content of crop plants, increasing the food quality of plants (Gianinazzi et al., 2010). Besides contributing to the food quality, they are also involved in improving the physiochemical properties of the soil. For instance, their hyphae are involved in the entanglement of soil-producing microaggregates (Miller & Jastrow, 2000). The most widely used mycorrhizal fungi for agricultural plants and crops are the arbuscular mycorrhizal fungi (AMF). AMF are involved in modifying the pH of the soil and improving crop yield and quality (Zhang et al., 2019). AMF are found to increase the yield of tomato crops by 26% and carrot yield by 300% by preventing the plants from pathogens, including nematodes (Affokpon et al., 2011). According to meta-analysis, AMF are more successful in nonlegumes, C4 grasses, and woody plants than for C3 grasses and legumes, where the soil structure is complicated, and phosphorus rather than nitrogen is limited (Table 7.2).

7.3.5 Rhizospheric fungi Different soil-based fungi, especially rhizospheric fungi, are employed in agriculture to improve the fitness and health of crops. Rhizospheric fungi are capable of controlling biotic and abiotic stresses on plants and are therefore used in different agriculture-based products for providing protection against nematodes and pathogens; for example, epiphytic Trichoderma sp. along with rhizospheric fungus are used as biocontrol agents (Vos´atka et al., 2012). Penicillium bilaiae is involved in the acquisition of phosphate. Rhizospheric fungi Trichoderma harzianum and Trichoderma viride act as antagonists toward different pathogens, such as Sclerotium, Pythium, Rhizoctonia, Botrytis,

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Sclerosis, Gaeumannomyces, and Fusarium, and are the most important part of mycorrhizal soil (Pirttila¨ et al., 2021).

7.3.6 Bacterial endosymbionts and endophytes Endosymbionts and bacterial endophytes that colonize cells of host plants and internal tissues of plants are found to provide long-term advantages to host crops/plants than apo-plastic endophytes or rhizobacteria. Being well suited to the specific niche, they would be more protected from environmental variables such as abiotic stress (Mercado-Blanco & Lugtenberg, 2014; Sati et al., 2021). Many biocontrol properties and growth-promoting activity shared by endophytic bacteria and PGPR include plant hormone production and nitrogen fixation, production of antibiotic compounds, and systemic resistance induction (Pirttila¨ et al., 2021). The presence of shoot endophytes in the edible sections of crops/plants could limit their use in agriculture (Mercado-Blanco & Lugtenberg, 2014). After bacterial cells are applied to germinating roots, the endosymbiont Methylorubrum extorquens DSM13060 colonizes the crop plant in a systematic manner. An endophytic fungus, Curvularia protuberata, is important in imparting heat tolerance to Dichanthelium lanuginosum grass. The fungus is utilized in the cultivation of wheat, tomato, and watermelon to enhance heat tolerance. Piriformospora indica, an endophytic fungus identified from a desert plant, is engaged in imparting tolerance to plants/crops to biotic stress and high salt conditions (Pirttila¨ et al., 2021) (Fig. 7.2).

7.3.7 Microbes of various environments Screening diverse environments with high diversity of microorganisms for new biofertilizers and biocontrol agents is a reasonable choice when searching for new biocontrol agents and biofertilizers. Land-use change is measured as the utmost serious threat to biodiversity because soils contain the highest pools of microorganisms (Pirttila¨ et al., 2021). According to a recent study, forest soil conversion to agricultural land alters the diversity of bacteria and viruses, while the diversity of Archaeans is less susceptible. The variety of foliar fungal endophytes falls over a gradient of pine trees growing in managed forests, old-growth forests, and nurseries in a forest setting. As a result, habitats with a

FIGURE 7.2 Commercially available bacterial biocontrol agents.

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Table 7.3 Microorganisms used as commercial biocontrol agents and biofertilizers. Microorganism

Commercial name

P. fluorescens, Trichoderma viride Azospirillum brasilense, Bacillus megaterium, A. vinelandii, B. circulans, P. fluorescens, B. subtilis A. brasilense, P. fluorescens, Bacillus megaterium, A. vinelandii, B. polymyxa P. fluorescens, Bacillus amyloliquefaciens, Candida tropicalis, Bacillus subtilis Bacillus spp., Glomus intraradices P. fluorescens, Azotobacter Agrobacterium radiobacter AR 39, Streptomyces spp. SB 14, Bacillus subtilis BA 41, Glomus spp. GB 67, G. viscosum GC 41, Funneliformis mosseae GP 11, Pochonia chlamydosporia PC 50, Pichia pastoris PP 59, Trichoderma harzianum TH 01 A. brasilense NAB 317, Bacillus sp, Azoarcus indigens NAB 04, Azorhizobium caulinodans NAB 38 Pseudomonas putida, Bacillus circulans, A. chroococcum, Bacillus megaterium Bacillus megaterium, Frateuria aurantia, Rhizophagus irregularis Azotobacter vinelandi, Rhizophagus irregularis 14 bacterial species (Rhizobium spp., Pseudomonas spp., Bacillus spp.) and 7 fungal species (Trichoderma spp.) Rhizobium leguminosarum, Penicillium bilaii Azospirillum, Acetobacter, Rhizobium A. caulinodans NAB 38, A. brasilense NAB 317, Azoarcus indigens NAB 0

ANOKA T BactoFil B10 BactoFil A10 Biogro CataPult SuperFine Gmax PGPR Micosat F Uno

Nitroguard Phylazonit-M Rhizosum PK Rhizosum N Suma Grow Tagteam Symbion-N Twin N

From Pirttila¨, A. M., Mohammad Parast Tabas, H., Baruah, N., & Koskima¨ki, J. J. (2021). Biofertilizers and biocontrol agents for agriculture: How to identify and develop new potent microbial strains and traits. Microorganisms, 9(4), 817.

diverse range of plant species are likely to have a large pool of microbes that are advantageous to crops/plants (Pande, Pandey, Sati, Bhatt, & Samant, 2022). In forests, rather than on agricultural land, finding new strains of microbes, which can be exploited as sole inoculants in biofertilization and biocontrol or members of healthy engineered plant microbiomes, is more productive (Pirttila¨ et al., 2021) (Table 7.3).

7.3.8 Viruses: biological control agents By altering naturally occurring pathogens, pathogenic viruses demonstrate their importance as biological controls for insects/pests. Viruses are collected, grown to obtain high mass, intensified, crammed, stored, and spurted when needed to manage insects/pathogens/pests rather than waiting for disease caused by viruses to occur in a population of insects/pathogens/pests (Falcon, 1982). Baculovirus has been commercially accessible as 60 products that synthesize distinctive occlusion bodies for improved insect invasion and environmental survival. Because of the high pH in the midgut, occlusion bodies fragment after absorption and release virions for infestation by epithelial cells before infecting the entire organism. The use of potato tuberworm granulovirus (PoGV) to manage potato tuberworm disease is an example of a virus as a biocontrol agent. PoGV is being

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developed by numerous government agencies in some countries, such as the Middle East, Asia, North Africa, and South America, to combat Phthorimaea operculella. Phthorimaea operculella, a prevalent pathogen of crops belonging to the Solanaceae family, is responsible for 100% financial losses of potato tubers.

7.4 Examples of biocontrol agents used in agriculture Throughout the world, many important crop systems are being managed from pest infestation using their natural enemies. Some of the popular examples are discussed below.

7.4.1 Biocontrol of sugarcane Pyrilla Pyrilla perpusilla, commonly known as sugarcane leafhopper/planthopper, feeds on the sap of this plant leading to damage and compromised quality of the crop. P. perpusilla is native to Southern Asia, and sporadic outbreaks of the pest have been recorded in India, Sri Lanka, Afghanistan, Bangladesh, and Pakistan (Kumarasinghe & Wratten, 1996). Besides sugarcane, P. perpusilla has been reported to use a range of alternative host plants, including maize, rice, sorghum, pearl millet, oat, bamboo, etc., for their breeding (Kumarasinghe & Wratten, 1996). The insect has a life span of 14
200 days; however, female insects tend to live a bit longer. On average, a female insect lays around 20
50 eggs at a time and in a lifetime, approximately 37
880 eggs. The incubation period of the eggs varies between 6 and 30 days, depending on the season. It has five nymphal growth stages of around 134 days. In the month of March, overwintered nymphs grow into adults. Furthermore, their oviposition starts in April. The rapid reproduction of the pest occurs in the months of April and May. Heavy infestation of the insect on crop occurs in the months of September to October (Kumarasinghe & Wratten, 1996). Parasitoid lepidopteran Epiricania melanoleuca is the most dangerous natural enemy of P. perpusilla and are used to biocontrol the population of P. perpusilla. The female parasitoid moth lays 400
800 eggs. It feeds on the P. perpusilla nymph and adult, leading to the death of the host, thereby keeping the pest population in check (Kumarasinghe & Wratten, 1996; Seneviratne & Kumarasinghe, 2002). P. perpusilla has been found to be attacked by 16 species of natural parasitoid enemies in India. Cheiloneurus pyrillae, Ooencyrtus pyrillae, Proleuroceroides pyrillae, Parachrysocharis javensis, and Tetrastichus gala are some of the reported egg parasitoids that feeds on P. perpusilla egg. Additionally, Agonatopoides pyrillae, Richardsidryinus pyrillae, Epiricania melanoleuca, and Pyrilloxenos compadus are insects that feed on the nymph of P. perpusilla. It is also prone to some predators and fungal pathogens (Kumarasinghe & Wratten, 1996).

7.4.2 Biocontrol of cotton bollworm Helicoverpa armigera, commonly known as American cotton bollworm, is a pest that causes serious damage to cotton crops. Extensive use of chemical insecticides, such as pyrethroid and organophosphates, has led to the development of resistance against these chemicals in H. armigera. Other hosts of this pest include maize, soybean, groundnuts, chickpea, pigeon pea, sorghum, and

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sunflower. Trichogramma sp. is an egg parasitoid that kills the H. armigera eggs before hatching. Trichogramma sp. is used worldwide for biocontrol of the H. armigera pest singly or combined in integrated pest management (Alavo, 2006). Ants and Chrysopids are found to be the important predators of H. armigera pest. Chrysopids can feed up to 463 H. armigera individuals per day. In addition to this .60 arthropod species are known as predators of H. armigera (Romeis & Shanower 1996). Fungal pathogen Beauveria bassiana, bacteria Bacillus thuringiensis, and virus H. armigera nucleopolyhedrovirus (HaNPV) has also been reported to reduce H. armigera population density (Alavo, 2006; Sandhu et al., 1993). HaNPV can infect other Helicoverpa sp. as well. HaNPV has been found significant in reducing the H. armigera population on chickpea in India (Alavo, 2006). The gram-negative bacterium Bacillus thuringiensis is used as a biopesticide against cotton bollworms. It has also been included in integrated pest management formulations for cotton crops. Bacillus thuringiensis is known to produce inactive crystalline (Cry proteins) delta-endotoxin. Upon ingestion by insects the inactive toxin is proteolytically cleaved inside the midgut of the insect and causes a leaky gut leading to the death of the insect (Alavo, 2006).

7.4.3 Biocontrol of water hyacinth The water hyacinth, Eichhornia crassipes, is originally an ornamental aquatic plant. Due to its fast growth on water bodies, the plant creates a mat on the surface of the water, hindering the exchange of oxygen supplies. The reduced oxygen levels cause problems for aquatic animals like fish. Arthropod weevils, Neochetina eichhorniae, Neochetina bruchi, Niphograpta albiguttalis, Eccritotarsus catarinensis, Xubida infusellus, and Orthogalumna terebrantis, have been reported to control the excessive growth of water hyacinths (De Groote, et al., 2003; Julien, 2000).

7.4.4 Biocontrol of woolly apple aphid Eriosoma lanigerum, a Hemiptera woody aphid, is known to cause hypertrophic gall on apple trees. The aphid is native to America, although it can be found throughout the world wherever apple crops are being cultivated. The aphid feeds the sap by infecting the root and shoot of the apple tree. The restriction of sap flow and rupture of the gall at the site of infection leads to more available feeding sites for the aphid creating chances of further infections. This also makes the plant more prone to fungal infections at the site of gall formation by aphid feeding. Intense infestation of this aphid can result in reduced growth, decreased fruit quality, and yield of the apple tree (Childs, 1929; Nicholas, et al., 2005; Weber & Brown, 1988). Hoverflies, earwigs, ladybirds, and lacewings are some of the important natural enemies of the Eriosoma lanigerum aphid. Parasitoid Aphelinus mali has been reported to have significant control of the aphid population. Forficula auricularia, a European earwig, can feed up to 106 aphid/day and provide significant control of this woody aphid population (Nicholas, et al., 2005).

7.4.5 Biocontrol of white woolly aphid Ceratovacuna lanigera is a pest of sugarcane commonly known as white woolly aphids. The aphid hinders the growth and sugar content of the sugarcane plant. Sporadic infestation of this aphid on

References

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sugarcane has been seen in many states of India (Mehetre, Mukherjee, & Kale., 2008). Metarhizium anisopliae and Penicillium oxalicum are entomopathogenic fungi known to control the aphid population (Mehetre, Mukherjee, & Kale., 2008). Seven species of parasitoids and thirty predator species are studied to control the Ceratovacuna lanigera aphid. Dipha aphidivora Meyrick, syrphids, chrysopids, coccinellids, and Micromus sp. are predatory to this aphid (Pandey, Singh, & Singh, 2004).

7.5 Conclusion Management of insects/pests in the agricultural field is a cumbersome task. Owing to climate change and the emergence of resistance to extensively used insecticides, the dynamics and strategies of insect manifestation to crops are also changing. In recent years, locust attacks on many crop systems have been witnessed in many countries, leading to excessive loss of crop productivity. Integrated pest management programs incorporating the use of natural enemies of the crop-damaging insects/pests have been seen as an effective management solution for a few crop systems. The majority of presently accessible microbiological instruments colonize the rhizosphere of different agricultural crops/plants, which are mostly made up of epiphytes, PGPR, and soil or mycorrhizal fungi. As a result, their use in agriculture frequently leads to inconsistencies in field performance. These differences can be linked to inoculant competency in the field, interactions with the existing plant-host microbiome, plant genotype, and variable environmental factors. The ecosystem of soil is changeable, with localized microenvironments influenced by humidity and temperature fluctuations. Microbial communities in the soil can play an important role in influencing the survival of entering microorganisms. Biocontrol agents and biofertilizers can have varied degrees of efficacy in raising crop output depending on environmental conditions, inoculants, soil quality, and microbiome
host plant interactions. The key to developing steady instruments for improved and sustainable production of crops will be an enduring quest for new stable, potent strains, and a profound acquaintance with the mechanisms of action of biofertilizers and biocontrol agents.

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217. Alavo, T. B. (2006). Biological control agents and environmentally-friendly compounds for the integrated management of Helicoverpa armigera Hu¨bner (Lepidoptera: Noctuidae) on cotton: Perspectives for pyrethroid resistance management in West Africa? Archives of Phytopathology and Plant Protection, 39(2), 105
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Impact of environmental pollutants on agriculture and food system

8

Sofiya Anjum1 and Smita Rana2 1

Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India 2Department of Chemistry, Kumaun University, Nainital, Uttarakhand, India

8.1 Introduction Agriculture and the environment are intricately linked, and environmental pollutants have a significant impact on agriculture. In recent decades, one of the most pressing concerns for science and the general public has been the ever-increasing contamination of the environment. Contamination of food by environmental pollutants is a primary global food safety concern that poses a serious health risk. Metals/metalloids, polycyclic aromatic hydrocarbons (PAHs), persistent organic pollutants, perfluorinated compounds, pharmaceutical, and personal care products (PPCPs), radioactive elements, electronic waste, plastics, nanoparticles, dyes, and other chemicals are among these chemicals. The use of pesticides in agriculture has the potential to contaminate food. They have the potential to pollute our agriculture and food supply, putting our health at risk (Thompson & Darwish, 2019). Pollutants that are either introduced by humans or occur naturally in water, air, or soil are referred to as environmental pollutants (Rather et al., 2017). These include compounds derived from natural sources and those derived from industry and agriculture. Microbiological pollutants, such as dangerous bacteria, bacterial toxins, and fungal toxins, make up a large portion of naturally occurring contaminants in food. (Aflatoxin, a contaminant of peanuts and grains, is an example of a fungal toxin or mycotoxin.) Organic compounds, metals, their complexes, and radionuclides fall under the second category of environmental pollutants. This chapter examines the effects of various new contaminants on agriculture and their implications for the food chain. Most food contamination occurs as a result of naturally occurring contaminants and pollutants or as a result of food processing, packing, preparation, storage, or transportation. Chemicals contaminate foods in various ways based on their chemical and physical qualities, their application, and the source or mechanism of contamination. Agricultural and industrial chemicals are the most common organic compounds that cause food contamination (Pandey et al., 2019). According to studies, pesticides are the major agricultural chemicals identified as potential environmental pollutants in food and agriculture. The absorption of hazardous pollutants by plants and subsequent buildup along the food chain poses a risk to animal and human health. Chemical hazards are one of the most common causes of food contamination connected to foodborne illness (Rather et al., 2017). Foodborne illness caused by chemical contamination can cause anything from mild gastroenteritis to lethal hepatic, renal, and neurological disorders. Food contamination makes the news Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00005-3 © 2023 Elsevier Inc. All rights reserved.

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from time to time due to its adverse repercussions. Between 2009 and 2010, there were 1527 outbreaks of foodborne diseases in the United States, resulting in 29,444 disease cases and 23 deaths (CDC, 2013). Furthermore, food poisoning has become more problematic in recent years due to industrial development and the resulting pollution of the environment (Song et al., 2016). Additionally, consuming pesticides and heavy metal-contaminated food can result in gastrointestinal illnesses (Song et al., 2016). In Nigeria, for example, an estimated 400
500 children died of severe lead poisoning after consuming food contaminated with lead-laced soil and dust (Rather et al., 2017; Tirima et al., 2017). Metals and metalloids, radioactive substances, nuclear reactors, plastics, nanoparticles, various dyes, sewage waste, pharmaceuticals, and personal care products, and e-waste are the primary sources of chemical contaminants affecting agriculture and the food system (Fig. 8.1).

8.1.1 Metals and metalloids Heavy metal poisoning of food crops is a global hazard that leads to toxicity and sickness in humans and animals because of consuming contaminated soils and foods (Onakpa et al., 2018). Heavy metal contamination impacts agricultural productivity and quality, affects the atmosphere and water bodies, and may eventually accumulate in the human body, posing major health risks (Hu et al., 2019; Pande, Pandey, Sati, Bhatt, & Samant, 2022). Metals and metalloids in the environment come from various natural and manmade sources, including industries, sewage, and mining; developments in agricultural chemicals like fertilizers and pesticides; and urbanization activities of man (Rai et al., 2019) (Fig. 8.2). Dust and gases are released into the atmosphere during the mining and refining processes. Metallic salts produced during the recovery and refining activities can leach into the surface and groundwater as waste products, posing a threat to the food system by entering the food chain. Artisanal gold mining is one source of lead and mercury. For example, the concentration level of these metals in locally produced vegetables and grains exceeded regulatory tolerance limits in Tongguan, Shaanxi, China, posing a potential health danger to consumers who ate them (Xiao et al., 2017). Lead and cadmium from a Moroccan iron mine resulted in cadmium concentrations in cattle organs that exceeded acceptable limits (Nouri & Haddioui, 2016). Similarly, sheep near a mine in Spain were found to be contaminated with lead, with levels in liver samples of 87.5% above European Union’s maximum residue levels (MRLs) (Pareja-Carrera et al., 2014). Metal contamination of the environment is common in industrial areas. In Romania, lead-, cadmium-, copper-, and zinc-polluted crops were reported, with some samples above the maximum permissible levels (Nedelescu et al., 2016). Cadmium from a zinc smelter particularly polluted leaf and root vegetables in China (Li et al., 2016), whereas cadmium was reported in locally produced foods grown near nonferrous metal industries in Belgium (Vromman et al., 2008). In Bangladesh, arsenic, cadmium, and lead were detected in raw rice and leafy vegetables, and chromium content was found in vegetables, milk samples, and poultry products (Hezbullah et al., 2016). In southern China, thallium from a steel plant was reported initially to contaminate soil and then crops, exceeding the permissible limit and causing hyperaccumulation in plants like chard, leaf lettuce, and pak choi (Liu et al., 2017). Metal contamination is common in vegetables and fruits, such as, in China, where cadmium was reported in navel oranges, and in Argentina, where lead and cadmium were found in soybeans (Cheng et al., 2015; Salazar et al., 2012). Inedible seeds were also found to contain various metals in China, with copper levels high enough to pose a health danger to those who

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FIGURE 8.1 Main sources of contaminants affecting agriculture and food system.

consume them (Chen et al., 2010). On the other hand, in rice samples from a city in eastern China, mercury contamination levels were below levels expected to harm human health (Wang et al., 2017). Lead, cadmium, and mercury have been reported in human milk samples, with increased levels of lead associated with higher consumption of potatoes in Spain (Garcı´a-esquinas et al., 2011; Thompson & Darwish, 2019). Several metals, most particularly toxic heavy metals, such as mercury, cadmium, polychlorinated biphenyl (PCB), and lead, contaminate food via the industrial environment. The industrial area of

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FIGURE 8.2 Sources of heavy metal contamination, both natural and artificial, and their effects on human health.

Huludao in Northeast China has been reported to be contaminated with heavy metals, such as copper, cadmium, zinc, lead, and mercury, as a result of heavy metals smelting in the area (Zheng et al., 2007). Another source of food contamination is the soil environment. Plants constitute the foundation of the food chain, and heavy metals and other harmful compounds from industrial regions may penetrate the soil and into the food chain, infecting not just raw food sources like fruits and vegetables but even seafood (Krishna & Govil, 2007; Peralta-Videa et al., 2009; Rather et al., 2017). Methyl mercury has been found in fish and other seafood from all around the world (Fr´ery et al., 2001; Peng et al., 2015). Zinc, iron, copper, and manganese contamination was discovered in Turkish fish tissues (Tekin-Ozan, 2008). Diverse metals have also been found in Sicilian fish, with quantities surpassing European regulatory limits (Copat et al., 2012). Surveys of human samples provide more evidence of metals’ possible health concerns for individuals. Mercury and monomethyl mercury were found in human hair samples from French Guiana, which were linked to a high fish diet, with mercury levels in 57% of those tested above the WHO safety limit (Fr´ery et al., 2001). Pesticides employed as plant protection agents also infiltrate the food chain, causing various health issues such as immune suppression, reproductive abnormalities, cancer, decreased IQ, and hormone disruption in humans (Abhilash & Singh, 2009). Pesticides are used in the amount of approximately 3 billion kg per year throughout the world (Pimentel, 2005), posing a severe concern since the chemicals contaminate raw food sources. The MRL of pesticides, on the other hand, is a key predictor of the threat they cause to human and animal health (Rather et al., 2017). The use of sewage sludge as a fertilizer on agricultural land also creates a risk of food contamination. Crops grown on treated soil can absorb trace metals included in the sludge. The trace metals in sludge causing the most

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Table 8.1 Health hazards caused by heavy metals. Heavy metals Lead Zinc

Cadmium

Copper Arsenic

Chromium Mercury

Health hazards

References

Diseases of the heart, kidneys, neurological system, blood, and bones Liver disease, noncarcinogenic hazardous impact, such as neurologic involvement, headache, and disturbed immune system Nervous system, with symptoms including headache and vertigo, olfactory dysfunction, parkinsonian-like symptoms, slowing of vasomotor functioning, peripheral neuropathy, decreased equilibrium, decreased ability to concentrate and learning disabilities, kidneys, neurological system, blood and bones, cardiovascular diseases, postmenopausal breast cancer, itai-itai disease Willson’s disease, noncarcinogenic hazardous such as neurologic involvement, headache, and liver damage Hyperkeratosis, restrictive lung disease, black foot disease, gangrene, ischemic heart disease, diabetes mellitus, melanosis, hypertension, liver cancer, hepatic, dermal, gastrointestinal, cardiovascular, hematological, immunological, developmental, respiratory, renal, genotoxic, reproductive, neurological, and mutagenetic effects Hemolysis and gastrointestinal bleeding, dermal corrosion, dermatitis, and skin allergies Allergies, lung injury, kidney damage, proteinuria, and amalgam disease, disrupting central nervous system synchronization

Hu et al. (2019), Ja¨rup (2003) Hu et al. (2019), Sun et al. (2013)

Hezbullah et al. (2016), Hu et al. (2019), Ja¨rup (2003), Sun et al. (2013)

Hu et al. (2019), Kooner et al. (2014), Sun et al. (2013) Hezbullah et al. (2016), Proshad et al. (2019)

Hezbullah et al. (2016) Rai et al. (2019)

concern include cadmium, iron, copper, chromium, lead, nickel, and manganese (Rai et al., 2019). Epidemiological studies demonstrate that heavy metal deposition causes a variety of health problems, and it has a significant impact on human health (Table 8.1).

8.1.2 Electronic waste Electronic waste (e-waste) has become a global concern as modern civilization is overloaded with electrical gadgets. Inadequate processing of such products, such as incomplete combustion, releases a variety of pollutants such as polybrominated diphenyl ethers, polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans, PAHs, PCBs, polyhalogenated aromatic hydrocarbons, and metals/metalloids (Sitaramaiah & Kusuma-Kumari, 2016; Wong et al., 2007). Furthermore, pollution from such devices has the potential to contaminate drinking water and food. (Liu et al., 2009; Thompson & Darwish, 2019). The majority of e-waste is dumped in landfills, causing a negative impact on soil. The e-waste dumped into the soil releases toxic heavy metals when degraded, which leach into the soil and affect the growth and development of plants. Despite the low

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bioaccumulation coefficients (0.01), plant absorption may enhance the entrance of these pollutants into food chains, allowing them to spread deeper into the food chain and cause harmful effects on human health (Robinson, 2009; Sitaramaiah & Kusuma-Kumari, 2016; Thompson & Darwish, 2019). Rice samples from Taizhou (Zhejiang province), another e-waste processing town in Eastern China, revealed lead and cadmium concentrations in polished rice that were 2
4 times higher than the maximum acceptable concentration range (Fu et al., 2008), whereas rice paddy soils adjacent to e-waste recycling areas in Zhejiang province were shown to reduce rice germination rates (Jun-hui & Hang, 2009; Robinson, 2009). E-waste is a probable source of genetic mutation and may cause cytogenetic damage to those who are exposed to e-waste pollution (Robinson, 2009).

8.1.3 Plastics The increasing use of plastic materials in agricultural land impacts soil health, especially the physical properties of soil (Maji & Mistri, 2021). In recent times, we increasingly rely on packaging materials, particularly plastic materials, to preserve food and proper delivery of food items. As numerous chemicals are released into foods and beverages from food contact materials, these materials are not inert and may contaminate food and beverages. Agricultural plastic is difficult to recycle due to contamination by agricultural chemicals (Thompson & Darwish, 2019). Furthermore, plastics decomposing into microplastics has a negative impact on soil health, bacteria, and helpful species such as earthworms. Microplastics, which are plastic particles with a maximum dimension of less than 5 mm, are an emerging pollutant of growing concern in agricultural soils (Isari et al., 2021). Plastic bags are usually nonbiodegradable and difficult to break down and can take up to 1000 years to dissolve in soil (Jalil et al., 2013). Microorganisms or mechanical forces cause macroplastics to degrade and disseminate throughout the soil. With the deposition of plastic additives such as phthalate in the soil, these stacks of synthetic materials are nothing but a threat to the soil environment and agricultural growth (Maji & Mistri, 2021; Zhang et al., 2020). Endocrinedisrupting, carcinogenic, and mutagenic effects of plastic additives are a major source of worry for human health (Zhang et al., 2020).

8.1.4 Nanoparticles Nanotechnology plays a crucial role in encouraging agriculture and agricultural products (Ali et al., 2018). Irrespective of the wide application of nanotechnology in several sectors (e.g., medicine, energy, environment, and agriculture), it may have adverse environmental repercussions through the unregulated release of nanoparticles (NPs) and associated toxic metals. The effects are harmful for the ecosystem as well as human well-being (Rai, 2018; Thompson & Darwish, 2019; Xiong et al., 2017). Although the mechanisms and impacts of NPs in the biota are yet a mystery, they have been observed to pass through the food chain (Kalman et al., 2015; Bhatt et al., 2021). Food crops should be subjected to an impact assessment for nanotoxicity, for example, copper oxide nanoparticles (CuONPs), because the presence of NPs can lead to adverse effects on both crop physiology (especially reduced photosynthesis) and human health (Rai et al., 2019; Xiong et al., 2017). Several nanoparticles, such as Ag-NPs, TiO2-NPs, ZnO-NPs, FeO-NPs, NiO-NPs, CuO-NPs, and Al2O3-NPs, have been reported from time to time to have adverse effects on plant species as well as on human well-being (Ali et al., 2018; Naseer et al., 2018). Nanosized components have

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been reported in foods such as wheat-based items (Gatti et al., 2008; Thompson & Darwish, 2019). Nanoparticles can lead to oxidative stress in human body cells. They can traverse from the lungs to blood, cell nuclei, and central nervous system, causing Parkinson’s syndrome, gastrointestinal inflammation, Alzheimer’s disease, and DNA damage. Long-term exposure to nanoparticles has been linked to adverse effects on the kidneys, liver, and other important organs (Naseer et al., 2018).

8.1.5 Radioactivity/nuclear reactors Nuclear or radioactive incidents can contaminate agricultural land and crops. Contaminants are substances not purposely added to agricultural land and crops but are present in or on them. They may comprise either stable or radioactive materials and can originate from natural or artificial sources. Accidental emissions can contaminate plants by particle deposition on leaves and soil, as well as on water. Volatile elements like iodine and tritium, and those with volatile precursors like strontium-90 and cesium-137, would most likely be involved in gaseous discharges. Iodine radioisotopes from nuclear reactors, particularly 131I, constitute a significant source of concern (Bell & Bell, 1981). Most radioactive elements do not occur naturally, and contamination of soil with such materials has only been a concern since the development of nuclear weapons and reactors (Thompson & Darwish, 2019). Radionuclides have also been found in Indian seafood, different cuisines in the Balkans, and Swiss food and drinking water (Brennwald & Dorp, 2009; Carvalho & Oliveira, 2010; Khan & Wesley, 2011). Risk assessments are carried out to validate that levels do not exceed permissible limits. Furthermore, experimental models are used to examine the safety of ingestion mechanisms, taking into account a variety of food intakes (Prohl et al., 2005; Thompson & Darwish, 2019).

8.1.6 Pharmaceuticals and personal care products Personal care products are items that are used to cleanse, change, or improve the look of the body, along with enhancing the quality of daily life. The products can be in the form of drugs (mouthwashes, acne, and pimple medicines; steroid creams, sunscreens, soaps, etc.) or cosmetics (lotions, make-up, hand sanitizers, perfumes, lip balms, etc.) (Boxall et al., 2012; Paulsen, 2015). Pharmaceutical products are generally used to treat human and animal diseases, including antibiotics, hormones, and drugs. These products are commonly used by humans and are considered emerging environmental contaminants (Table 8.2). They can seep easily into the agriculture and food system through water used for irrigation, sewage sludge applied to land, animal slurries used as fertilizers, and finally, into the food chain. It is reported that even after treatment of water containing PPCPs, it is not fully purified, and most of the contaminants are not eliminated and will remain in the treated water partially or fully (Kosma et al., 2014; Lin et al., 2010; Tabe et al., 2010). When a person or animal consumes a medicine, only a portion of it is absorbed and digested by the body, leaving the remainder to follow one of three paths: (1) pharmaceuticals are mineralized into CO2 and water; (2) drugs with lipophilic characteristics are not completely degradable, so some of them are suspended in the sludge; and (3) pharmaceuticals are metabolized into a more hydrophilic form, which wastewater treatment plants cannot entirely remove. It therefore remains intact in the effluents and is discharged from treatment plants (Carlsson et al., 2006). These pollutants

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Table 8.2 Most commonly used pharmaceutical and personal care products (Daughton & Ternes, 1999; Liu & Wong, 2013). Contaminant groups

Representative compounds

Analgesics, antiinflammatory drugs Antiepileptic drugs Antimicrobial agents/ disinfectants β-blockers Blood lipid regulators Contrast media Cytostatic drugs Fragrances Hormones

Paracetamol, diclofenac, codeine, acetaminophen, fenoprofen, ibuprofen, acetylsalicylic acid Primidone, carbamazepine Triclosan, triclocarban

Human antibiotics and veterinary Insect repellents Lipid regulators Preservatives Psychiatric drugs Sunscreen agents/ ultraviolet filters Synthetic musks/ fragrances X-ray contrasts

Sotalol, metoprolol, timolol, propranolol, atenolol, sotalol Clofibrate, gemfibrozil Diatrizoate, iopromide Ifosfamide, cyclophosphamide Phthalates, nitro, polycyclic and macrocyclic musks Estriol, estrone (E1), estradiol (E2), ethinylestradiol (EE2), 17β-estradiol, mestranol,17α-ethinylestradiol Roxithromycin, trimethoprim, ciprofloxacin, erythromycin, amoxicillin, norfloxacin, lincomycin, sulfamethoxazole, sulfadimethoxine, chloramphenicol, clarithromycin N,N-diethyltoluamide; N,N-diethyl-m-toluamide (DEET) Bezafibrate, clofibric acid, fenofibric acid, etofibrate, gemfibrozil Parabens (alkyl-p-hydroxybenzoate) Diazepam, carbamazepine, primidone, salbutamol 4-Methyl-benzilidine-camphor (4MBC), methylbenzylidene camphor, Benzophenone, 2-ethyl-hexyl-4- trimethoxycinnamate (EHMC) Galaxolide (HHCB), toxalide (AHTN) Iopromide, iopamidol, diatrizoate

From Daughton, C. G., & Ternes, T. A. (1999). Pharmaceuticals and personal care products in the environment: Agents of subtle change? Environmental Health Perspectives, 107(6), 907
938. Liu, J. L., & Wong, M. H. (2013). Pharmaceuticals and personal care products (PPCPs): A review on environmental contamination in China. Environment International, 59, 208
224. https://doi. org/10.1016/j.envint.2013.06.012.

are chemically, biologically, and physically destroyed before being trapped in the soil particles of agricultural lands and are taken up by plants (Clarke & Cummins, 2015; Unuofin, 2020).

8.1.7 Sewage wastewater and sludge Sewage wastewater and sludge can contaminate agricultural lands in many ways as this is a wide source of metalloids and heavy metals, organic contaminants, antibiotics, antibiotic resistance genes, human pathogens, etc. As metals and metalloids, such as nickel, chromium, zinc, mercury, lead, and arsenic, are soluble in nature, they are absorbed by various living organisms, causing harmful effects and food chain pollution. They may also accumulate in higher trophic level animals (Barakat, 2011; Singh et al., 2013; Younus et al., 2019). Plants, microorganisms, and other biological organisms are significantly impacted when the presence of heavy metals and metalloids exceeds

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the acceptable limit (Diaconu et al., 2020; Humberto et al., 2020; Zemanov´a et al., 2020). Increased use of pesticides and herbicides in agricultural activities is a vital source of agroecosystem contamination. Coal, wood, and natural gas are typical sources of polycyclic aromatic hydrocarbons in today’s homes, and they are all substantial sources of polycyclic aromatic hydrocarbons (Khillare et al., 2018). After degeneration, polybrominated diphenyl ethers found in polyurethane foam used in home furniture find their way into sewage (Wang et al., 2007). Organochlorine pesticides, such as PCB, have been reported in sewage water in several investigations (Clarke et al., 2010; Zhang et al., 2013). These herbicides and pesticides have a negative impact on soil-dwelling microorganisms, altering microbial activities and fauna diversity, which results in perturbations in soil productivity. Antibiotics and antibiotic resistance genes (ARGs) have been identified as emerging agricultural pollutants in the agroecosystems. Sewage water is a source of several antibiotic compounds as a large portion of antibiotics are excreted by humans in unmodified forms into the sewage, ultimately excreting in an aquatic ecosystem (Watkinson et al., 2009). As aquatic microorganisms are continuously exposed to antibiotics, this induces resistance development in microorganisms and results in the spread of ARGs via horizontal gene transfer and mutation (Ding & He, 2010; Liu et al., 2016; Summers, 2006). Various microorganisms, including gram-positive and gram-negative bacterial species viruses, and yeasts, can be found in sewage effluents and sludge, posing a threat to human health owing to their pathogenic activities. The most common bacteria found in sewage water are Escherichia coli, Salmonella, Campylobacter, and Enterococcus, while viral pathogens such as rotavirus, hepatitis virus, and adenovirus are the most common viral pathogens reported in sewage water (El-senousy & AbouElela, 2017; Guimara˜es et al., 2016; Jiang et al., 2018, 2020; Magri et al., 2015). It will be hazardous if these pathogens are present in higher numbers than WHO’s acceptable limits. If pathogenic microbes from sewage and polluted water find their way into freshwater, soil, crop products, and live animals, they will pose a serious hazard to human health (Bradford et al., 2013).

8.1.8 Particulate matter Rapid urbanization and unplanned industry have grown exponentially in India in the modern age. Air pollution has an adverse influence on agriculture, causing unwanted changes in the biochemical parameters of agricultural plants as well as a reduction in overall plant growth and development. Plants develop various adaptation techniques to alleviate stress and make the most of internal and external organizations when environmental circumstances change, including short-term physiological responses and long-term physiological, structural, and morphological changes (Agrawal & Agrawal, 1990; Rai & Singh, 2015; Rai & Panda, 2014). All plants are constantly exposed to air, so they are in regular contact with dust, atmospheric gases, and particle contaminants. Particulate matter with an aerodynamic diameter of less than 2.5 μm deposits on the foliar surface, reducing respiration and changing leaf temperature, ultimately affecting agricultural output. (Hirano et al., 1995). The availability of solar radiation in plants has reduced as a result of particulate matter with an aerodynamic diameter of less than 2.5 m, lowering photosynthesis, plant development, late-blooming, and hormonal disparity in plants (Chameides et al., 1999; Farmer, 1993; Liu et al., 2016). As the dust particles fix polycyclic hydrocarbons and other metals, they can limit critical enzymes required for chlorophyll synthesis, reducing chlorophyll production. Dust can attract light that is available for photosynthesis and obstruct the stomatal holes for air expansion, putting plants’ metabolism under stress (Anthony, 2001; Borka, 1980). Various scientists have previously reported that plant species

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cultivated in polluted locations had lower total chlorophyll content than those cultivated in control settings (Prajapati & Tripathi, 2006; Samal & Santra, 2002). It has previously been reported that air pollution can result in significant production losses in a variety of essential crops (Agrawal et al., 2003). Several workers have found that dust and other air pollutants have an adverse impact on photosynthetic pigments and yield in various crops (Joshi et al., 2009; Rajput & Agrawal, 2005).

8.1.9 Dyes from textile industries Each year, roughly 10,000 tons of different manufactured dyes and diverse shades are utilized in the textile industry, and more than 70,000 tons of designed dyes are supplied throughout the world (Aftab et al., 2011; Daneshvar et al., 2007; Parshetti et al., 2015). These dyes are utilized in various sectors, including paper and pulp manufacturing, fabric dyeing, leather treatment, plastics, and printing, resulting in dye-containing industrial effluents being discharged into aquatic and soil environments (Aksu, 2005). These dyes, which can take the form of azo, triphenylmethane, anthraquinone, phthalein, nitro, methane, and quinoline dyes, are poisonous (Pande et al., 2019). They pose a hazard to animal life when released in streams, lakes, ponds, and soil, resulting in ecological pollution (Mani & Bharagava, 2016; Saxena & Bharagava, 2015). The dye-containing wastewater reduces sunlight penetration into freshwater bodies, lowering dissolved oxygen levels, which has negative consequences for aquatic life, including zooplanktons, phytoplanktons, amphibians, and various other organisms (Garg & Tripathi, 2017). Chlorine, formaldehydes, solvents, organic and inorganic chemicals, aromatic amines, xenobiotics, pigments, alkali salts, and toxic heavy metals, including chromium, lead, and mercury, are among the harmful substances found in dye particles (Chowdhary et al., 2017; Mishra & Bharagava, 2015; Yadav et al., 2017). The dye particles in freshwater lakes combine with rain to join water bodies, which is utilized in irrigation and has proven to be extremely harmful to soil microbes, plant development, and germination (Choudhury, 2017; Rehman et al., 2018). Since these contaminants are absorbed by plants in agriculture, they become part of the food chain (Fig. 8.3).

8.2 Remediation for removal of chemical contaminants Once the causes of contamination have been identified, numerous techniques for improving food safety can be considered. The type of pollutants present and the environment in which they are found influence the remediation methods used. Remediation may focus on lowering pollutants in the environment or on lowering concentrations in particular foods. Soil remediation is a common method used to reduce environmental exposure to contaminants. One simple technique is to remove polluted topsoil from agricultural regions, which often contains greater quantities of toxins than subsoil. (Lai et al., 2010). Microbial bioremediation can also be utilized to minimize metal pollution in soils while being environmentally friendly (Thompson & Darwish, 2019). Plant contamination can be affected by crop management strategies. Slow-release nitrogen fertilizers can lower cadmium levels in plants like pak choi as the plants have a higher tolerance to the metal and lower effectiveness of translocation to edible plant parts than those cultivated with conventional fertilizers (Zhang et al., 2016). Environmental scanning electron microscopy may be used to look for inorganic micro- and nanosized contaminants in bread and biscuits, which can assist in reducing

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FIGURE 8.3 Transportation of dye contaminants to agriculture fields.

nanopollutants. In case of radioactive contamination, adding lime to calcium-deficient soils can reduce the uptake of radionuclides such as strontium-90 and strontium-89 by plants. However, radionuclide-affected fruits and vegetables should be thoroughly washed before being canned or frozen to degrade the short-lived radionuclides (Bell & Bell, 1981). In the mitigation of particulate matter, zero-tillage agriculture, crop residue interference, enhanced water management, and laser field leveling procedures should be used. (Singh et al., 2018; Vedachalam, 2019). In the case of dyes, it is reported that these can be degraded physically and chemically by various methods. However, these methods have their advantages and disadvantages (Robinson et al., 2001). Microbial degradation of these dyes is another possible way of reducing contamination. Further, there is a need to make proper strategies and policies to minimize agriculture pollution for food safety purposes and address human and animal health issues.

8.3 Conclusion Environmental contaminants, food safety and security, and human health are all interconnected. Food safety and contamination attitudes are typically based on history and habit. Bacteria, molds,

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parasites, pesticides, fertilizers, heavy metals, and other contaminants are typically tested in food. This chapter includes literature about the effects of various new contaminants on agriculture and their implications for the food chain. Metals and metalloids, radioactive substances, nuclear reactors, plastics, nanoparticles, various dyes, sewage waste, pharmaceuticals and personal care products, and e-waste, as well as the potential adverse effects of these chemicals on agriculture and the health of the exposed population, are given particular emphasis. Overall, the findings point out the necessity for a thorough examination of the contaminants to decrease health risks.

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CHAPTER

Hazardous waste: impact and disposal strategies

9

Hemant Dasila1, Divya Joshi2, Shulbhi Verma3, Damini Maithani4, Sawan Kumar Rawat5, Amit Kumar6, Neha Suyal7, Narendra Kumar8 and Deep Chandra Suyal1 1

Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Himachal Pradesh, India 2Uttarakhand Pollution Control Board, Regional Office, Kashipur, Uttarakhand, India 3Department of Biotechnology, SDAU, Dantiwada, Gujarat, India 4School of Biotechnology, IFTM University, Moradabad, Uttar Pradesh, India 5Department of Mathematics, Statistics and Computer Science, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India 6Forest Ecology and Climate Change Division, Forest Research Institute, Dehradun, Uttarakhand, India 7Government Nursing College, Haldwani, Uttarakhand, India 8Doon (PG) College of Agriculture Science and Technology, Dehradun, Uttarakhand, India

9.1 Introduction Hazardous wastes (HWs) are substances, whether in liquid, solid, or gaseous form, which do not have any future role due to changes in its physical and chemical properties. These substances may become a potential threat for health and environment, whether alone or in combination with other wastes. Further, they can occur in liquid, gaseous, or solids states. HWs have been classified under a special category of waste because of the problems that arise during its disposal. HWs cannot be disposed of like any other waste that is disposed in our day-to-day life. HWs may arise from different sources. HWs may be present in sludges, solids, liquids, or contaminated gas, as a potential risk to human health and nearby surroundings. The source of HWs may vary from byproducts of industrial manufacturing processes to substances that come under household hazard category. The adverse effect caused by the indiscriminate disposal of HWs falls under the category of environmental disaster. The Environmental Protection Agency (EPA) has developed certain regulatory definitions and processes that recognize and categorize substances into hazardous categories based on their impact on humans and the environment. For example, 2242 residents were evacuated from their houses when the soil was found to be contaminated with dioxin in Missouri, the United States, in 1982. In 1984 release of lethal gas, methyl isocyanate caused a severe disaster in India. To avoid such drastic disasters in future we need to gear up and start taking preventive measures (Akpan & Olukanni, 2020). The industrial sector is a major source of HWs. Although several guidelines have been set up for industries to manage HWs, in reality, only a few industries follow correct management practices for HW disposal. Proper attention is required to develop good HW management practices, which will involve transportation and storage in such a way that it reduces the exposure risks of HWs to the environment and humans (Kanagamani, Geethamani, & Narmatha, 2020). HW management Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00006-5 © 2023 Elsevier Inc. All rights reserved.

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requires a proper framework that includes: (1) identification protocol, (2) transportation, (3) storage, and (4) disposal and recycling (EPA, 2005). The whole world is facing the issue of managing HWs generated from various sources. To manage HWs, a practice that is being followed is transboundary dumping. Transboundary transfer of HWs involves the dumping of HWs generated in one country/state to another. This kind of practice involves huge risks and can put numerous lives under threat. For example, in India, at a port in Bombay, around 160 containers of HWs were illegally imported, which was full of toxic substances. Some important characteristics of HWs include: 1. Flammability: HWs include ignitable wastes and are measured by flush point tests. Generally, nonliquid HWs create a vigorous hazard by spontaneously catching fire. 2. Reactivity: HWs are substances that might spontaneously explode or undergo violent reactions, resulting in the release of toxic fumes or gases in the environment. 3. Corrosiveness: HWs may involve substances that are either acidic or alkaline and can easily dissolve in the environment. For example, leakage of sulfuric acid from automotive batteries. 4. Toxicity: Leaching of toxic compounds from industrial and other sources is the most common way for HWs to enter into groundwater and landfills, resulting in easy consumption by the general population according to EPA Rule 2014.

9.2 Classification of hazardous wastes Classification of HWs is generally based on the source from where the wastes are being generated, which have been listed as: (1) F-list, (2) K-list, (3) P-list, and (4) U-list. These lists are categorized on the basis of associated potential threats posed by HWs to the environment and public health (EPA, 2005). The F-list and K-list are further divided into subgroups. 1. F-list: HWs released from the common manufacturing process by industry comes under the Flist. F-list wastes are also commonly called nonspecific sources because the manufacturing products can be made in different industry sectors. F-list is further divided into seven subgroups; a) Solvent wastes (F001
F005)This subcategory includes solvents that are used for cleaning or degreasing in mechanical repair, electronic manufacturing, and dry cleaning. b) HWs originating from electroplating and other metal finished processes (F006
F012, F019): F006
F009 applies to electroplates; F010
F012 involve metal HWs, resulting from metal heating; and F019 involves HWs generated during aluminum processing. c) Dioxin-containing wastes (F020
F023 1 F026
F028): HWs generated during the production of chemical pesticides fall under this subcategory. d) Hydrocarbons (F024
F025): This subcategory includes aliphatic hydrocarbon HWs generated via a narrow industrial sector. e) Wood preserving HWs (F032, F034, and F035): This subcategory includes the operations used to run to avoid wood deterioration by using chemical treatments such as chromium and arsenic.

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f) Petroleum waste treatment HWs (F037
F038): Contaminated wastewater, which comes from oil refining processes and is further discarded into the river, comes under this subcategory. g) Multisource leaching (F039): This subcategory includes liquid material that remains in hazardous landfills due to leaching. 2. K-list: This major category includes HWs originating from specific sources, which are further classified into 13 subcategories. These subcategories range from K001 to K181 and include HWs generated during explosives manufacturing, iron and steel production, veterinary pharmaceuticals, lead processing, inorganic and organic chemical manufacturing, etc. 3. P-list and U-list: These two categories include HWs more or less from similar sources, for example, HWs generated during oil spills, commercial chemical production process, residues that remain in containers, etc. One major difference is that the chemicals on the U-list are considered toxic HWs and chemicals on the P-list are considered acute HWs.

9.3 Impact of hazardous waste 9.3.1 Environment If HW is not properly managed, it may cause severe environmental damage in the form of contamination, which consequently affects all creatures on the planet. In the long term, the consequences are much more severe and long-lasting than anticipated. These pollutants or contaminants may be roughly divided into three categories: biological, chemical, and radioactive contaminants. Some of the factors that influence the level of risk associated with HWs include reactivity (fire, explosion, leaching); biological effects (toxicity, both acute and chronic); persistence (fate of the environment; bioremediation potential); indirect health risks (pathogens, vectors); and local conditions, which include temperature, soil, water, humidity, light, receiving systems, etc. Even more alarming is the fact that the full extent of the damage may go unnoticed for an extended period. In most cases, HW has immediate and short-term consequences, resulting in urgent and shortterm public health concerns. Water contamination is a rising source of worry in this context at the moment. The chemicals that are heavily disposed of into the water bodies (streams, rivers, lakes, and aquifers) render the water unsuitable for drinking and agricultural uses (Ferronato & Torretta, 2019). HWs also have a long-term effect on our water table. As long-term effects of HWs, animals have shown indications of mutation, cancer, and other illnesses as a result of being in contact with such harmful contaminants for a long time. Additionally, a huge decline in natural resources is also evident. The depletion of biodiversity is a matter of concern as insect populations, for example, bees, which are critical to maintaining plant life and thus the ecological balance, are declining at a faster rate than they can repopulate (Kawahara, Reeves, Barber, & Black, 2021). Chemicals can penetrate the soil and reach aquifers; a tiny spill affecting a small region may rapidly spread and affect a very wide area. Soil, a natural foundation for plant development, anchors plants and feeds them with different nutrients necessary for growth. It is a critical ecosystem because it not only offers habitat for a variety of species but also participates in a variety of biogeochemical cycles whether directly or indirectly. However, in recent times, as a result of numerous human activities, the soil has undergone

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disastrous changes, resulting in sterility, and pollution with hazardous substances. This widespread contamination has rendered a large stretch of land unusable and dangerous for both animal and human populations (Rashtian, Chavkin, & Merhi, 2019). In contrast to many other organic pollutants that breakdown into soils, certain hazardous chemicals such as heavy metals, pesticides, polycyclic aromatic hydrocarbons, and phthalates are of particular concern since the majority of these are recalcitrant (Chamas et al., 2020). Crops may absorb chemicals from HWs through soil-bound particles, polluted surfaces, groundwater, or polluted water used for irrigation. Wastes scattered on agricultural land provide additional routes for the contamination of plants and crops. Humans and animals consuming polluted plants may result in the transmission of dangerous chemicals. When livestock grazes, they may consume huge amounts of dirt; this is often a major source of exposure in regions with polluted soils. Additionally, it presents a significant danger to groundwater and soil resources. Heavy metal pollution of soil has a detrimental impact on soil productivity (Srivastava et al., 2017). Heavy metals have caused havoc on soil health and fertility over the past few decades as a result of increasing environmental contamination from industrial, agricultural, and local sources. Metals create physiological disturbances in soils because they are absorbed via the root system, retarding plant development and depleting its vitality (Cheng, 2003). Depending on the pollutants, HWs either end up in soil-held water or are leached into subterranean water. Vegetation diversity is closely related to soil parameters. Numerous studies demonstrate the severity of the dangers posed by open trash dumping, which eventually affects plant life, resulting in an irreversible erosion pattern until the current land use pattern is altered. Solid waste pollutants operate as an external influence, modifying the physicochemical properties of soil and eventually leading to low vegetation production. Pollutants impair plants’ natural metabolism, unseen damages that result in apparent injury. It is destroying the natural equilibrium of our environment and resulting in irreversible damage. The chemical properties of soil are the primary factor influencing vegetation changes in a place (Akintola, Adeyemi, Olokeogun, & Bodede, 2021). Chemical element accumulation in plants is determined not only by their absolute concentration in the soil, but also by the degree of fertility acidic
alkaline, oxidative
reductive, and organic matter conditions (Ali, Pervaiz, Afzal, Hamid, & Yasmin, 2014). In terms of animals, the ingestion of contaminated vegetation may result in the transmission of dangerous chemicals. Some notable effects of pollution on wildlife include mortality, debilitating injury and disease, physiological stress, mutation, and bioaccumulation. When livestock grazes, they may consume huge amounts of dirt; this is often a major source of exposure in regions with polluted soils. The environmental consequences may be just as severe: harming organisms in a lake or river, damaging animals and plants in a polluted region, creating serious reproductive problems in animals, or generally impairing an ecosystem’s capacity to exist (Kumar, Sankhla, Kumar, & Sonone, 2021). Certain hazardous chemicals may potentially explode or start a fire, posing a danger to both animal and human populations.

9.3.2 Humans Recent years have seen the publication of many studies documenting a broad range of health hazards to local people living near HW disposal sites. Rapid industrialization and urbanization over the past several decades, along with population expansion, have wreaked havoc on natural resources. Climate

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change is caused by a variety of human actions such as pollution with harmful chemicals like pesticides or heavy metals on a regional or global scale. Large-scale mortality of the most vital wildlife of living organisms, such as sea mammals, and an increasing threat to human health, including chronic respiratory diseases, cancer, and damage to several major organs such as the brain, lungs, and kidneys, have been observed in recent years as a result of anthropogenic perturbations (Kumar et al., 2021). The population living near HW has shown to have reproductive problems (spontaneous abortion, fetal and newborn mortality, and low birth weight), as well as birth deformities. Disposal of biomedical wastes in public areas, water bodies, and municipal dustbins, among other places, contributes to disease transmission (Sangkham, 2020). The release of hazardous gases during open trash burning may result in respiratory illnesses and cancers. Humans have always been in contact with dangerous chemicals, dating back to ancient times when they breathed noxious volcanic gases or died from carbon monoxide poisoning caused by improperly vented cave fires. Inadequate waste management methods, on the other hand, may generate potentially dangerous conditions and pose serious dangers to society. Generally, any chemical may cause serious health problems or can be fatal if consumed in sufficient quantities by humans. Also, there are substances that, even in trace amounts, may have a detrimental effect on health. The potential for adverse health effects in populations exposed to these harmful wastes may involve damage to any part of the human body, based on the particular chemicals contacted, the extent of exposure, the exposed individual’s characteristics (e.g., age, sex, genetic makeup), the chemical’s metabolism, etc. (Misra & Pandey, 2005). Human response to toxic chemicals can be affected by a variety of factors as depicted in Fig. 9.1. These factors more or less affect the degree or extent to which humans are affected when exposed to certain hazardous substances.

FIGURE 9.1 Factors governing human response to hazardous waste.

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9.3.2.1 Health consequences of exposure to hazardous chemicals Exposure to harmful chemicals may occur at the source (location of the chemical’s origin) or when the chemical is transported to a location where it comes in contact with humans. The many ways in which an individual may come into contact with dangerous substances are referred to as exposure routes. Three primary routes of exposure exist: inhalation, ingestion, and skin contact. Chemicals may be transported through the air, soil, or water. They may also be found on animals or plants and can contaminate our air, food, and water (Briffa, Sinagra, & Blundell, 2020). Exposure to these substances may cause a variety of malignancies by interfering with the endocrine system, breaking DNA, causing tissue damage, and activating or deactivating genes. Direct damages can be conformational changes to biomolecules due to the metals; while indirect damages are a result of the production of reactive oxygen and nitrogen species, which comprise the hydroxyl and superoxide radicals, hydrogen peroxide, nitric oxide, and other endogenous oxidants (Briffa et al., 2020). However, the assessment of health risks due to cumulative exposure to toxic chemicals is currently constrained by the quantification of exposure dose (e.g., duration, frequency, model, and intensity), the effects of chemical mixtures (e.g., additive, synergistic, or antagonistic), and toxicological interactions between toxic chemicals. Additionally, hundreds of novel synthetic chemicals are introduced into the environment each year and bioaccumulate in people before their toxicity and potential for exposure are completely known. Moreover, individuals react differently to chemical exposure. Some individuals exposed to a certain chemical may not become ill, while others may be more susceptible to the chemicals and develop illnesses or severe reactions more quickly or severely than others. Factors, such as age, gender, heredity, pregnancy, or other healthrelated problems, contribute to an individual’s vulnerability to chemical exposure and the severity of health consequences (Khan et al., 2019). The unfavorable health consequences due to chemical exposure may be considerably higher in a fetus, child, or teenager than in an adult. The fetus is particularly vulnerable, since its growing organs may sustain irreversible harm. Similarly, children, particularly those between the ages of one and six, who are undergoing fast growth, may absorb more chemicals owing to their body chemistry, amount of activity, and relatively small body size. People exposed to hazardous substances may experience a variety of health consequences that are of major concern. Carcinogenesis (development of cancers); genetic defects, such as mutagenesis (causing hereditary gene alterations); reproductive abnormalities (damages to the developing fetus not necessarily related to the toxic effects on the mother); alteration of immunobiological homeostasis, central nervous system disorder; and congenital anomalies are some of the health consequences of exposure to pesticides (Briffa et al., 2020). Eye and skin irritation, chemical burns, difficulty breathing, headaches, nausea, etc. are some prominent effects, though less severe, of exposure to harmful chemicals.

9.4 Methods for identification and monitoring of hazardous waste HW identification and their monitoring are important for effective management. Only after the identification of HWs can their route be carefully monitored. The Hazardous Waste Identification Rules (HWIR) developed by EPA determines the global identification of HWs. The first HWIR came into the picture on November 30, 1998. The second rule came on May 16, 2001, which was

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later modified to increase its impact. The purpose of HWIR is to provide flexibility and accessibility to HW identification systems. HWIR (with amendments) finally addresses four important issues: (1) Streamlining the process of HWs remediation from sites for obtaining easy permits, (2) EPA has developed a new unit, for example, “staging pile,” to solve the issues that come up during storage of HWs, (3) Excludes dredged materials permitted under Marine protection or clean Water Act, and (4) Finalized the issue of authorization of all the operations run during HWIR regulation.

9.4.1 Identification of hazardous waste: Indian scenario In India, HWs are well characterized and documented in government literature into three major groups: Incinerable, Recyclable, and Disposable. After the identification of HWs certain tools need to be addressed: Collection of data: After identification of HWs the library of data is created by conducting surveys through well-defined questionnaires to each available identified source. The collected data from one source is further recertified from second source data that may include already published data or available data from other industries with similar kinds of HW products. Quantification of HWs: After data collection, HWs are quantified according to their features. The HWs that are recyclable are put into one category, which includes lead wastes, waste oil, and zinc wastes. Disposal site identification: After the identification and quantification of HWs the next step involves the identification of disposal sites for HWs for their treatment, disposal, and storage. To identify these disposable sites, remote sensing technology can be used, which is further physically verified in the field. The sites are allocated and ranked according to their receptorrelated, waste characteristics-related, and waste management practices-related potential (Babu & Ramakrishna, 2000). Environmental Impact Assessment (EIA) monitoring: After the selection of sites, there is a provision for conducting audits by the EIA to make sure that all the conducting sites must be given consent by the public so that they know of the future impacts.

9.5 Strategies for hazardous waste management HW management involves reducing the number of hazardous substances produced, treating them to reduce their toxicity, and applying sound engineering controls to reduce or eliminate exposures to these wastes. In the current scenario, developing countries often dispose of HWs directly into the environment posing health and environmental risks. HWs can be managed and disposed of by various processes; some of them are discussed below:

9.5.1 Physical strategies 9.5.1.1 Incineration Incineration is an excellent approach to destroy HWs waste by burning them at high temperatures. It is a controlled process that involves the oxidative conversion of combustible solid materials into

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nontoxic gases that can be released into the atmosphere. It reduces the volume, toxicity, and noxiousness of wastes by converting them to a less bulky, poisonous, or noxious material. Carbon dioxide, water, and ash are the primary end products of incineration, but chemicals containing sulfur, nitrogen, and halogens have hazardous consequences for the environment, releasing unwanted materials into the atmosphere. In such cases, a supplementary treatment, such as afterburning, scrubbing, or filtering, is required to reduce the concentrations to safe levels before being released into the atmosphere (Misra & Pandey, 2005). It reduces the volume of waste by up to 90% and its weight by 60%
70% (Orloff & Falk, 2003). HWs to be incinerated do not need to be pretreated, but they must have a moisture content of less than 30%, combustible matter content of more than 60%, noncombustible fines of less than 20%, noncombustible solids of less than 5%, and a low heating value of less than 2000 kcal/kg.

9.5.1.2 Landfilling It is the most popular means of HW disposal (Orloff & Falk, 2003). HWs must be disposed of in secure landfills with a minimum distance of 3 m (10 feet) between the landfill’s bottom and the underlying bedrock or groundwater table. It consists of the blending of wastes with soil, evaporation, infiltration, and/or shallow burial. Solid wastes are usually included in a landfill and buried. Liquids, slurries, and sludges can also be included in a landfill. Highly poisonous wastes along with soils infected with polychlorinated biphenyls or mercury compounds are buried in closed landfills in which the wastes are remoted from the outer surroundings by means of a concrete floor, wall, and roof (Misra & Pandey, 2005). Landfilling of some industrial solvents should be avoided, since they can increase the permeability of natural clay liners, and may affect some synthetic liners as well (Orloff & Falk, 2003).

9.5.1.3 Solidification/stabilization It is a process of converting HWs into an environmentally acceptable waste form for land disposal, which involves combining waste with a binder to reduce contaminant leachability through both physical and chemical means. Furthermore, it provides an acceptable mechanical performance for waste to withstand transport and handling. Cement and other inorganic binders are effective at immobilizing heavy metals via chemical and physical containment mechanisms.

9.5.1.4 Deep-well injection Liquid HW is pumped through a steel casing into a porous layer of limestone or sandstone, where it is then absorbed. As a result of high pressure, the liquid is forced deep into the rock, where it is to be stored for the rest of its life. A layer of impervious rock or clay must cover the injection zone, which may extend more than 0.8 km (0.5 miles) below the surface. It is generally affordable and requires little or no processing of the garbage, but it creates a risk of HW leakage and contamination of underground water supplies.

9.5.1.5 Encapsulation It is a pretreatment process for HW before it is disposed of. A high-density polyethylene box and a metallic drum are used to contain the chemical or pharmaceutical wastes and sharps residues, and then immobilizing materials such as cement, clay, bituminous sand, and plastic foam are added to the boxes to prevent them from being moved or tipped. They are sealed and disposed of in landfills

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once the medium has dried up. Sharps and chemical or pharmaceutical wastes are disposed of using this process, which is safe and relatively inexpensive.

9.5.1.6 Inertization Water, lime, and cement are used in this technique to ensure that toxic waste does not percolate into the surface or groundwater. The mixing creates a homogeneous mass that can be transported in liquid form to a landfill and disposed of as municipal waste after it has been thoroughly mixed. Burning ashes with a high metal content as well as pharmaceutical wastes can be inertized. Water makes up about 5% of the mixture; cement and lime make up 15% of the mixture. To make the process even cheaper, simple equipment are utilized.

9.5.1.7 Autoclaving It is an efficient low-heat thermal process based on the pressure cooker principle. Infectious substances, contaminated solids, and sharp wastes are exposed to 121 C at 15 psi for 60
90 min to steam, which penetrates waste components and kills most microorganisms. It is expected that 99.99% of microorganisms are inactivated. Before autoclaving solid and sharp wastes, it is recommended that it is shredded and crushed so that it can be disposed of as regular municipal wastes. However, wet thermal processes can be either in batches or continuous (Samant, Pandey, & Pandey, 2018).

9.5.1.8 Microwave irradiation Using microwave irradiation, HWs are cleaned and disinfected. Some of the microorganisms can be killed using microwaves with a frequency of 2450 MHz and a wavelength of 12.24 cm. A microwave quickly heats the wastewater, destroying any infectious agents through heat conduction, in this process.

9.5.2 Chemical strategies 9.5.2.1 Chemical disinfection It is a less-lethal process than sterilization (Pohanish, 2008). In general, it reduces the burden of microorganisms, but it does not eliminate them (e.g., endospores). Urine, sewage, blood, and other liquid wastes can be effectively treated with this method of treatment. Chemical disinfection can also be used for solid wastes as well as for microbial cultures and sharps. Before disinfection, solid wastes should be shredded. The waste volume is reduced by 60%
90% and disinfectant-to-waste interaction is increased as a result of this. While it is possible to discharge the waste into sewers after disinfection, it is also possible that the disinfectant will cause serious harm to the environment.

9.5.2.2 Chemical degradation When it comes to the chemo-degradation of HWs, several methods are used. It is not possible to degrade all hazardous materials with a single chemical procedure. Organophosphorus pesticides can be destroyed most effectively by hydrolysis; polychlorinated pesticides can be degraded using chemical dechlorination. Some pesticides and herbicides can be destroyed using strong oxidants,

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such as hydrogen peroxides. Biodegradation of pesticides by incorporating them into the soil may be a cost-effective method of disposing them of. This method of detoxification is also possible in countries like India where photochemical degradation can be used (Samant et al., 2018).

9.5.3 Biological strategies The biological treatment of HWs involves natural or engineered biological systems with living microorganisms for the treatment of HW. It includes HWM; biostimulation, bioaugmentation, and biotransformation, aerobic and anaerobic systems, enzymatic sytsems, landfilling, etc. (Fig. 9.2) (Zhang, Surampalli, Tyagi, & Benerji, 2017). Soil microbes are diverse and are generally aerobic in well-drained soil. Microbial growth present in waste-amended soil depends on soil characteristics such as moisture (usually between 30% and 90%), oxygen level, nutrition, soil temperature (activity decreases below 10 C), and soil pH (near 7). Predominantly soil possesses bacteria, actinomycetes, fungi, algae, protozoa, and other micro-and macro-fauna such as nematodes and insects.

9.5.3.1 Land treatment In land treatment waste is mixed with soil surface through properly transformed or immobilized microorganisms. Landfilling is done in seminatural terrestrial ecosystems and covers land that has shallow soil, nutrient deficiency, elevated temperature, unsuitable for vegetation, and gas problems.

9.5.3.2 Enzymatic system Enzymes are proteinous and complex and are capable of transforming HW chemicals to nontoxic products, which can be harvested from microorganisms that grow in mass culture. Such crude enzyme extracts derived from microorganisms have been shown to convert pesticides into less toxic

FIGURE 9.2 Bioremediation of different waste materials.

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and persistent products. Immobilized enzyme extracts are used in several liquid waste streams. Factors like moisture, temperature, aeration, soil structure, organic matter content, seasonal variation, and the availability of soil nutrients influence the presence and abundance of enzymes.

9.5.3.3 Bioremediation Microorganisms can simply break down the complex chemical compounds from the surrounding environment. Their interaction contributes to the reduction in wastes produced. This can be assessed and aided by the use of various omics and biodegradation studies (Jaiswal, Singh, & Shukla, 2019; Teng, Xu, Wang, & Christie, 2019). The major bioremediation processes include biostimulation, bioaugmentation, bioventing, bio piles, bio attenuation, and composting. The principles involved in composting organic HWs are the same as those in the composting of all organic materials, though with moderate modifications. Composting degrades biodegradable wastes and its products are used as biofertilizers. With this technology biodegradable wastes can be managed by releasing greenhouse gases (CO2, SO2, and NO2).

9.5.3.3.1 Aerobic methods Bioreactors with modifications like nanofiltration, moving bed membrane, marsh sediment membrane, and column sequencing are being increasingly used. It contains methanotrophic, ammonia oxidation bacteria, and occasional special bacteria like Trichoderma asperellum and Arthrobacter spp. for the management of wastes.

9.5.3.3.2 Anaerobic methods Bioreactors that maintain anaerobic conditions are used for these processes. They have been modified into fluidized bed reactors, flow-switched anaerobic baffled reactors, and added with ultrafiltration, ozonation, activated carbons, and other filters.

9.5.4 Modern hybrid technology Waste management needs advanced technologies for more efficient treatment on a large scale. The balanced scorecard model and the analytical hierarchy process are used as a hybrid tool for analyzing the performance of the waste disposal management system developed for municipal corporations in India (Prasad, Dwivedi, & Sharma, 2019). Waste incineration facilities have been provided in residential and commercial areas and gas, smoke, and dioxin generated from waste-related problems have also been resolved through different measures. This technology was developed in Japan and they have changed over to new generation incinerators technology by implementing improved combustion quality, improved quantification; control of garbage supply, colling of stoker, improved durability of fire-resistant furnace wall material, recycling incinerate ash, and sophisticated operation control system. Japan has also established safe and appropriate disposal of medical wastes in furnaces following strategies such as burning in incinerations, melting in melting facilities, sterilizing with high-pressure steam and dry heat sterilizers, disinfecting, etc. PET bottle recycling technology follows the 3R policy of reducing, reusing, and recycling. In this technology, PET bottles, food trays, etc. can be separated for reuse and also used as recycled resources in the manufacturing of new products such as carpets, cars, mats, hot covers, etc. Japan

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developed these technologies to efficiently recover electricity and fuel from biomass wastes. IoTbased approaches have also been introduced where the discarded waste from the smart bin is continuously monitored by sensors that inform the filling level of each compartment in real time. They monitor waste collection for resource management and provide services to the community (Pardini, Rodrigues, & Diallo, 2020). SOLbox provides clean, affordable, and reliable access to energy through its peer-to-peer solar microgrids, an energy exchange platform that empowers the efficient use of clean energy [SOLbox
empowering people. Network (siemens-stiftung.org)].

9.6 Impact of mismanagement: illegal trafficking and poor transportation facility Mismanagement of HWs presents a potential threat to people and the environment. After identification, recycling, and monitoring of HWs it is very essential to effectively manage HWs transportation. Too many risks are involved during HWs transportation, which sometimes leads to the illegal trafficking of HWs. -

9.6.1 Hazardous waste transportation Transportation of HWs can be either through intra-country or intercountry transport. But the major form of transport is intra-country. Transportation in intra-country involves transport within national borders that includes state-to-state transfer. HWs transfer directly comes under the general regulations of transport of dangerous goods. Apart from toxicity, which is a major problem, there are many other problems associated with the transportation of HWs. HWs do not add any value to the generator and on top of that, additional safeguard equipment are also required to ensure its proper arrival at disposal sites. In some cases, HWs are a complex mixture of substances and their physical and chemical properties are also unknown. In such cases, it becomes an incompatible waste that offers acute problems and results in inconvenience during transit. Certain rules are needed to be followed to ensure the safe transport of HWs: 1. All vehicles used for carrying HWs should be properly labeled and these vehicles should be subjected to regulations that govern the transport of dangerous goods. 2. Sources of all HWs should be registered, and all interim treatments, disposal facilities, and storage should be properly licensed. 3. Proper contractual agreements should be negotiated between the operators of the receiving facility and the waste producers. 4. Proper licensing of transportation contractors is needed to ensure the quality of equipment used in transportation and personnel training.

9.6.2 Illegal trafficking Illegal trafficking involves the deliberate transportation of HWs to countries that do not have proper equipment or facilities to treat waste. Nations involved in this kind of activity are taking advantage of the enforcement loopholes in the law, which somehow become different from human trafficking

References

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or smuggling. The trade involves the illegal or inadequate transfer of HWs from the global north (Japan and the United States) to the global south (Southeast Asia, Africa, and South America) (Puckett & Smith, 2002; Puckett, Westerven˜t, Gutierrez, & Takmiya, 2005). Although the exact figure is not available, enforcement actions coordinated by the European Union Network to develop IMPEL (Implementation and Enforcement of Environmental Law) have resulted in some evidencebased data monitoring the scale of violations. According to this report, there is an increase of about 33%
38% in illegal shipment from the EU (European Union), and about one in five containers of HWs is illegally transferred. EU inspection statistics revealed that about 10% of illegal wastes contains a high level of plastic, low-quality products with faulty documentation, and has a country disposal destination that is not allowed (Baird, Curry, & Cruz, 2014).

9.7 Conclusion HWs disposal and their management have become a major challenge for all nations. If it is not taken seriously it can lead to disastrous consequences for humans and the environment and can hamper a nations’ stability. Although there are many governmental and nongovernmental agencies to monitor HW disposal due to poor transportation and illegal trafficking the risks from HWs always remain high. It has become a matter of intellectual integrity to keep, manage, or dispose of HWs safely.

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340). Amsterdam, Netherlands: Elsevier Inc..

CHAPTER

Bioremediation of heavy metals by soil-dwelling microbes: an environment survival approach

10

Amir Khan1, Raj Shekhar Sharma2, Divyansh Panthari3, Bharti Kukreti1, Ajay Veer Singh1 and Viabhav Kumar Upadhayay1 1

Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar (U.S. Nagar), Uttarakhand, India 2Department of Microbiology, School of Basic and Applied Science, Sri Guru Ram Rai University, Dehradun, Uttarakhand, India 3Department of Botany, School of Basic and Applied Science, Sri Guru Ram Rai University, Dehradun, Uttarakhand, India

10.1 Introduction A heavy metal consists of ions with partially or completely filled d-orbitals and is generally classified as a metal having high atomic weight, number, and density. Generally, metals are required in tiny concentrations by animals and plants for their sustenance, development, and optimum performance. Metals serve as cofactors with enzymes and stabilize protein structures and bacterial cellwall, and help to maintain osmotic balance (Khan, Singh, Upadhayay, Singh, & Shah, 2019). Metals such as iron (Fe), cobalt (Co), manganese (Mn), copper (Cu), molybdenum (Mo), and zinc (Zn) are among them. Zn is obligatory for cell division and growth, protein synthesis, and metabolism of nucleic acids, carbohydrates, and lipids. Boron contributes in the translocation of carbohydrates (Khan & Singh, 2021). Cu is a constituent of plastocyanin, which is a compound of the electron transport chain. Mn and Mo serve as electron carriers or activators for plenty of enzymes that participate in nitrogen and respiration metabolism. Fe, Cu, and Ni are employed with redox processes, and Mg and Zn stabilize various enzymes and DNA through electrostatic forces. Also, Fe, Mg, Ni, and Co are part of molecular complexes with a wide array of functions (Singh & Singh, 2017). However, the presence of increased heavy metals in the atmosphere is due to various processes such as the expansion of human industrial activity. The development of mining and production of synthetic compounds and their unorganized disposal has exponentially boosted the amount of heavy metals in the environment, causing life-threatening conditions. Widespread heavy metal in the soil and water bodies is a major global health concern. Heavy metals dwell in the most basic elemental form, therefore their degradation is not possible and possesses a long shelf life. Metals for instance arsenic, cadmium, chromium, copper, lead, mercury, nickel, selenium, silver, zinc, etc., are poisonous even in minute concentrations. They are cytotoxic, carcinogenic, and mutagenic as well (Kumar, Singh, Barman, & Kumar, 2016). Currently, various techniques are being practiced to reduce or remove such heavy metal contamination. But their efficiency, impact, and success rate are not able to satisfy the complete requirement. Recently, bioremediation technology Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00002-8 © 2023 Elsevier Inc. All rights reserved.

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has gained attention from researchers. The word bioremediation consists of two words: bio, which means biological, and remediation, which means to remedy. Therefore bioremediation implies the removal of contaminants from polluted sites by the interference of biological entities such as microorganisms and plants. In the bioremediation process, mainly microorganisms like bacteria and fungi and their enzymes are used (Pande, Pandey, Sati, Pande, & Samant, 2020; Gangola, Joshi, Kumar, & Pandey, 2019). It is relatively low cost, eco-friendly, and with high public acceptance. Various microorganisms are known to possess the capability of reducing or removing heavy metal contamination from polluted sites. Therefore this chapter provides a glimpse of available heavy metal exclusion technologies and detailed literature about bioremediation through microorganisms and the factors affecting bioremediation technology.

10.2 Sources of heavy metals The whole world is suffering from heavy metal pollution, occurring either from anthropogenic or natural sources. There are several diverse sources for the entry of excessive metals into the environment, classified as (Fig. 10.1): (1) industrial sources, (2) natural sources, (3) domestic sources, (4) agricultural sources, and (5) other sources (Pande, Pandey, Sati, Bhatt, & Samant, 2022; Nagajyoti, Lee, & Sreekanth, 2010).

10.2.1 Industrial source of heavy metals Unorganized urbanization and speedy industrialization together in the long term cause the accretion of toxicants in water, soil, and air. This expeditious expansion of industries resulted in a noteworthy amplification of metal contamination (Zwolak, Sarzy´nska, Szpyrka, & Stawarczyk, 2019). Industrial sources consist of refinement, mining, and transportation of ores, spoil heaps, and tailing;

FIGURE 10.1 Sources of heavy metal and their route in the environment.

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smelting; metal finishing; and metal recycling). Smelting or casting of metals releases metal in vapor and particulate forms, these forms of heavy metal unite with water to form aerosols. Such aerosols either precipitate in rainfall (wet deposition) or are dispersed by air (dry deposition), causing soil and water body contamination (Nagajyoti et al., 2010). Moreover, the utilization and mobilization of mercury (Hg) from gold mines have become a major source of mercury pollution (Lacerda, 1997). Energy-supplying power stations like nuclear power stations, thermal power stations, and petroleum combustion release numerous heavy metals like Ni, Cd, Cu, Cs, Se. Several other industrial sources like textiles, plastic processing plants, electronics, and paper processing contribute to the discharge of metals (Wang et al., 2017). Several studies showed that the COVID19 lockdown, implemented in 2020, resulted in a decrease in heavy metal amplitude in soil due to the temporary stoppage of anthropogenic activities (industries, transport, manufacturing/production, etc.) (Sharma, Panthari, Semwal, & Uniyal, 2021).

10.2.2 Natural source of heavy metals One of the key natural sources of metals is volcanoes and rock outcroppings. Heavy metal concentration in rock depends upon the rock type and environmental conditions. For example, igneous rocks like augite, olivine, and hornblende contain a good amount of Ni, Cu, Mn, and Co. If we talk about sedimentary rocks, with respect to limestone and sandstone, shale has the highest concentration of Mn, Cr, Co, Sn, Ni, Hg, Cu, Cd, and Pb. According to Seaward and Richardson (1989), volcanoes emit high concentrations of Zn, Pb, Ni, Hg, Cu, and Mn along with several harmful gases. A natural process, known as bubble bursting, is a cause of airborne Cu, Cd, Ni, Pb, Cd, and Zn. Forest fires and marine aerosols also have a major role to play on heavy metal transport in environments. Volatile metals like Se and Hg (part of carbonaceous matter) form during the fire. Moreover, a fraction of heavy metal from natural vegetation seeps into the soil and atmosphere via leaching and leads to an imbalance in metal concentration in the soil (Nagajyoti et al., 2010).

10.2.3 Agricultural source of heavy metal Heavy metals are widely spread in the environment, which are taken up by plants, and eventually they seep into the food chain, posing a threat to human lives. Fertilizer is another major source of increasing heavy metal concentration in agricultural soil (Zwolak et al., 2019). According to Zwolak et al. (2019), organic, inorganic and phosphate fertilizers contain varying levels of Cr, Ni, Pb, and Cd. Overexploitation of fertilizers leads to the accumulation of heavy metals in vegetables, a severe problem faced in the current system of agricultural practices. The amplitude of heavy metal pollution in the agricultural soil depends on the soil characteristics and the pace of fertilizer application with its elemental concentration. Other than fertilizer, some other sources of heavy metal contaminations like pesticides, fungicides, irrigation water, etc., accumulate in the soil and in native crops. Among all heavy metals, cadmium toxicity is a major concern because it accumulates in the leaves of plants at very high levels, which are consumed by humans or animals, and leads to disease. Generally, a low amount of heavy metal has been reported in agricultural soil, but the repeated exercise of chemical fertilizer in high concentrations and their prolonged half-life have made them persistent for a long time in the agricultural soil (Yang-Guang, Qin, & Yan-Peng, 2016).

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10.2.4 Domestic sources Domestic effluents contain elevated levels of heavy metals. It may consist of untreated or partially treated wastewater, substances that pass from the filters of biologically treated plants, and waste substance passed over sewage outfalls (Nagajyoti et al., 2010). According to Ali et al. (2020), untreated domestic effluents contain oil, dyes, phenols, suspended solids, organic compounds, and heavy metals (Pande et al., 2019). Among them, heavy metals can easily accumulate in the surrounding environment and their removal becomes very difficult due to their existence in different chemical forms. Moreover, detergents used in our day-to-day life can also cause pollution hazards, since it can affect water quality as it includes elements like Mn, Zn, Fe, Co, Sr, Cr, and B in trace amounts (Angino, Magnuson, Waugh, Galle, & Bredfeldt, 1970).

10.2.5 Other sources of heavy metal effluence Other heavy metal sources include transportation appliances (aircraft, automobiles), refused incineration, and landfills. Major anthropogenic sources that mainly contaminate soil are the deterioration of commercial-waste products and fly ash produced during coal burning, which add Cu, Pb, Cr, and galvanized metals to the environment. Oil burning also adds Fe, Pb, and Ni in the surroundings, while coal burning adds Cd, Mn, Hg, Ni, Ti, and Fe in the soil. The incineration of municipal wastes produces a noticeable amount of Zn, Al, Pb, Fe, Cu, etc. in the atmosphere. While transportation vehicles add Ni and Zn from tires, Cd and Cu from diesel/petrol engines, and Ni and Zn from aerosol emissions. Lubricants of vehicles also emit Cd, Zn, Pb, Ni, etc., and the burning of leaded petrol/gasoline is a chief source of lead in the surrounding environment (Nagajyoti et al., 2010).

10.3 Consequences of heavy metal toxicity on human and plant health Based on biological roles, metals can be subcategorized into three categories: (1) Essential metals (Na, Ca, K, Mn, Mg, V, Fe, Cu, Co, Mo, Ni, Zn, and W): metals, which have a biological role but demonstrate toxicity upon over accumulation; (2) Toxic metals (Ag, Sn, Cd, Au, Ti, Hg, Pb, Al and metalloids Ge, Sb, As, and Se): metals that do not have any biological function but cause high toxicity; (3) Nonessential metals (Rb, Sr, Cs, and T): metals with no biological function and toxicity are categorized into this group. Among all metals, many of these are harmful either to plants or animals in some way (Gall, Boyd, & Rajakaruna, 2015). EPA and ATSDR have listed some of them among the topmost dangerous substances (ATSDR, 2007; Bhatt et al., 2021; Rai et al., 2018; Table 10.1). Similar to the essential metals, toxic metals preferentially bind with oxygen binding sites and thiol group leading to the conformational modification in biological molecules such as nucleic acid and protein. Ligand interaction can cause metal toxicity in the biological system by displacing vital metals from their indigenous binding sites. Heavy metal toxicity reduces microbial diversity and their activity in the soil milieu. The significant effects of toxic metal concentrations in plants are inhibition of seed germination and growth, carbohydrate and protein content alteration, and nutrient-uptake impairment (Siddiqui, 2012). Elevated heavy metal load obstructs plant physiology

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Table 10.1 Permissible content of heavy metal in soil, plant, and fodder.

Elements

Target value of soil (mg/kg)

Intervention value of soil (mg/kg)

Permissible value of plant (mg/kg)

Permissible value of fodder (mg/kg)

Cd Zn Cu Cr Pb Ni Fe Mn

0.8 50 36 100 85 35 — 10
20

12 — 190 360 530 210 — —

0.02 0.60 10 1.30 2 10 20 2.0

0.5 — — 10 5.0 — — —

References Denneman and Robberse (1990); Osmani, Bani, and Hoxha (2015); Bhatti et al. (2016)

and results in cytoplasmic enzyme inhibition, while oxidative stress can directly harm plant health. In addition, heavy metals cause oxidative stress, altering the balance of pro-oxidants and antioxidants in plant cells (Table 10.2). Reduced plant growth is the most common symptom of heavy metals lethality (Sharma & Dubey, 2007). Other symptoms of heavy metal accumulation include leaf necrosis, chlorosis, turgor loss, reduced seed germination, and damage to the photosynthetic apparatus (DalCorso, Farinati, & Furini, 2010; DalCorso, Farinati, Maistri, & Furini, 2008). Heavy metal toxicity also influences homeostatic processes like transportation, water uptake, transpiration, and nutrient metabolism as well as agitate Mg, K, and Ca uptake (Benavides, Gallego, & Tomaro, 2005). Pollution caused by heavy metals has spread across the globe, causing environmental damage and human health risks. Heavy metals can be relocated to further media via the food chain since most heavy metals accumulate in soil and crops. Consumption of heavy metals accumulated in vegetables can lead to nutrient depletion and immunological weakness in human bones and fatty tissues. Intrauterine growth retardation may also be caused by heavy metals, such as Al, Cd, Mn, and Pb (Rai & Lee et al., 2018). People, especially children, suffer from cardiovascular and neurological diseases due to lead contamination (Al-Saleh, Al-Rouqi, Elkhatib, Abduljabbar, & AlRajudi, 2017). Pb and Cd are particularly carcinogenic (Trichopoulos, 1997). Moreover, carcinoma and dermal and respiratory problems can be caused by high levels of arsenic (As) in the soil (ElKady & Abdel-Wahhab, 2018). A lot of literature has been written about Cd contamination in food crops and its effects on health (Yang-Guang, Qin, & Yan-Peng, 2016). Humans with high Zn levels have lower HDL levels and less efficient immune systems. Similarly, too much copper can cause liver and stomach issues in humans (Zhou et al., 2016). Human health risks from heavy metal accumulation in soil include neurologic problems, headaches, and liver infections (Liu et al., 2013). In terms of stability, Cr(VI) is superfluous and more hazardous than Cr(III) and other ionic forms. Thus, compared with the latter, the former is suspected of causing more lung cancers (Liu et al., 2013). Cd is commonly ingested via polluted food crops, particularly rice (Hiroaki et al., 2014). Because urease contains nickel, excessive amounts can be harmful to human health (Marschner, 2012). Contrarily, cadmium is a highly toxic metal that can damage DNA.

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Table 10.2 Adverse effects of heavy metal toxicity on plants and humans. Heavy metals Mercury

Lead

Cadmium

Cobalt

Chromium

Manganese

Copper

Zinc

Nickel

Adverse effects on plant

Adverse effects on human

References

Reduced root length, ion accumulation, nodulation, flowering, plant height, germination and distortion of chloroplast Leaf senescence, oxidative stress, distortion of chloroplast, low respiration rate, blocking of ion absorption Reduced photosynthesis and stomatal density, germination inhibition, reduced nutrient uptake, reduced root length, oxidative stress, halt in nitrate uptake and transportation Reduced nutrient uptake, decreased antioxidant enzyme activity, reduction in leaf area, declined amino acid, sugar and protein content Reduced germination level, declined root and stem morphology, reduction in pigment synthesis, decreased water potential Chlorosis, declined growth rate, low O2 evolution, slower plant growth Necrosis, chlorosis, stunting, discoloration of leaf, reduced root growth, oxidative stress, declined photosynthesis and respiration, reduced biomass Lower germination rate and height, alteration in chlorophyll structure, reduction in photosynthetic efficiency Lower Carotenoid and chlorophyll content, reduced stomatal conductance and enzymatic activity, diminished shoot yield

Alteration in protein structure, neurological disorder, renal dysfunction, bloody diarrhea, necrosis in the gut mucosa, asthma Nephrotoxicity, cardiac dysfunction, anemia, osteopenia, osteoporosis, cancer, mental inability Lung cancer, hypercalcemia, nephrotoxicity, lipid peroxidation, hepatocyte cytotoxicity, osteoporosis, sperm motility

Chibuike and Obiora (2014), Bernhoft (2012)

Cardiomyopathy, Neurotoxicity, Polycythemia, Dysfunction of the respiratory tract, Skin disease

Chibuike and Obiora (2014), Leyssens, Vinck, Van Der Straeten, Wuyts, and Maes (2017)

Renal necrosis, Tracheobronchial irritation, dermatosis, ulceration, lung cancer

Kumar, Suryakant, Kumar, and Kumar (2016), Baruthio (1992)

Neurological disorder, cardiovascular toxicity, infant mortality, liver dysfunction Kidney damage, developmental disorder, immune-toxicity, anemia, respiratory infection, Wilson’s disease

Chibuike and Obiora (2014), O’Neal and Zheng (2015) Yruela (2005), Lorincz (2018)

Metal fume fever, prostate cancer, lethargy, repressed copper and iron absorption

Chibuike and Obiora (2014), Plum, Rink, and Haase (2010)

Respiratory tract cancer, lung fibrosis, cardiovascular disease, reproductive disorder, allergy

Chibuike and Obiora (2014), Genchi, Carocci, Lauria, Sinicropi, and Catalano (2020)

Sharma and Dubey (2005), Debnath, Singh, and Manna (2019) Haider et al. (2021), Hocaoglu-Ozyigit and Bedriye-Nazlı (2020)

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173

10.4 Techniques for heavy metal removal Heavy metal pollution has significantly increased due to the growing demand and overexploitation of various metals and metal-associated products. In natural conditions, these metals are present in the environment, but pollution occurs when their concentration increases in the soil, air, and water by various anthropogenic or natural activities (Awa & Hadibarata, 2020). These heavy metals enter into the food chains and environment, eventually causing severe health impacts on animals, humans, and environmental sustainability. Hence, there is a bigger need for techniques for heavy metal removal, remediation, and recovery from contaminated sites. Earlier, heavy metal contamination was controlled by on-site management or through excavation or disposal in landfills because there were no advanced technologies to perform remediation processes. However, this method did not correctly solve the contamination problem, as it just involved the transfer of heavy metal from the metal-contaminated environment to landfills (Tangahu et al., 2011). With the advancement in bioremediation techniques, various physical, chemical, and biological methods have been used to rectify this problem.

10.4.1 Physical methods When metals are introduced into the environment, they may persist there for a long time, depending upon their type and half-life. Complete or partial substitution of polluted soil by noncontaminated soil was the standard physical method used before 1984. Soil replacement is carried out by spading and fresh soil importing techniques. The replaced contaminated soil is usually treated to eliminate heavy metal or dump in to other places. The soil replacement method decreases the amplitude of heavy metal in contaminated soil and increases its functionality (Khalid et al., 2017). The second important physical method includes soil isolation. In this method, contaminated soil is separated from uncontaminated soil, but for complete remediation, it also needs some extra auxiliary engineering measures to eradicate heavy metals (Zheng & Wang, 2002). These techniques are mainly used to avoid off-site expels of heavy metals by controlling them in a specific area to restrict further spread in groundwater supplies (Zhu et al., 2012). Vitrification is also a physical technique for the bioremediation of heavy metals. In this method, the mobilizing capacity of heavy metals inside the soil is reduced by applying high-temperature treatment, which leads to the creation of vitreous substances. During this process, metals, such as Hg, become volatilized and are then collected for additional treatment. As the vitrification process is complex, it is not considered the classical metal bioremediation technique (Mallampati, Mitoma, Okuda, Simion, & Lee, 2015). An innovative cost-effective physical method for the bioremediation of heavy metals is soil electrokinetic remediation, which works on the principle of electric field gradient of suitable intensities established on the two sides of an electrolytic tank containing contaminated soil. Metals mixed in the soil get separated through electrophoresis or electromigration or electric seepage and decrease the contamination. This method has also been utilized in combination with other methods like electrokinetic chemical joint remediation, electrokinetic microbe united remediation, electrokinetic
oxidation/reduction joint remediation, etc. (Khalid et al., 2017).

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10.4.2 Chemical remediation Chemical remediation mainly includes immobilization techniques, encapsulation, and soil washing. In immobilization techniques, metal mobility, bio-accessibility, and bioavailability of heavy metals get decreased in the soil by adding up immobilizing mediators to contaminated soil. Heavy metals polluted soil are also immobilized by complexation, adsorption, and precipitation reactions. These processes help in the redeployment of heavy metals from soil solution to solid particles, limiting their bioavailability and transport in soil (Ashraf et al., 2017). Immobilization is mainly carried out by using organic and inorganic amendments in the soil. The most common amendments include clay, zeolites, cement, minerals, phosphate, and organic amendments (Sun et al., 2016). During encapsulation, the contaminated soil is mixed with other components like lime, concrete, or asphalt, and then the contaminated soil becomes immobile, preventing contamination. Several binding supplies are used in solid block formation, but cement is mostly preferred due to its cost-effectiveness, easy availability, and versatility (Pandey, Kinrade, & Catalan, 2012). Soil washing is a technique in which metal is removed from the soil through various extractants and reagents that can filter the metals from contaminated soil. The use of such suitable extractants has proven to be an alternative to some conventional techniques for contaminated soil cleanups (Park & Son, 2017).

10.4.3 Phytoremediation Phytoremediation also called green remediation, botano-remediation, vegetative remediation, or agroremediation, can be defined as the exploitation of plants to remediate soil and water from elevated heavy metal concentration and render harmless by degrading or adsorbing the polluting contaminants. This type of remediation is called biological remediation because plants are biological components utilized to clean contaminated environments. Phytoremediation is considered effective, environmentally friendly, noninvasive, and provides an alternative solution for heavy metal exclusion (Ali et al., 2020). Multiple mechanisms like phytoextraction, phytovolatilization, phytostabilization, rhizofiltration, and rhizodegradation are being adopted for the phytoremediation of heavy metals.

10.4.3.1 Phytoextraction Phytoextraction or phytoaccumulation involves the uptake of various heavy metals through plant roots. This technique is based on the potential of plant roots to uptake, translocate, and deposit heavy metals from soil to aboveground harvestable plant parts. After the completion of phytoextraction, the plant is then harvested and burnt to obtain energy and recycle metal from the ash (Erakhrumen & Agbontalor, 2007). Phytoextraction provides a solution for the elimination of metals from contaminated sites. Phytoextraction is suitable for contaminated sites, which are being polluted by low or moderate levels of metals because most of the plants are not able to grow in heavily polluted sites (Khalid et al., 2017).

10.4.3.2 Phytovolatilization In this process of remediation, heavy metals are utilized or taken up by the plants from the contaminated soil, transported via the xylem, and converted into less-toxic vapors or volatile forms, and then liberated into the environment via transpiration (Awa & Hadibarata, 2020). This process is mainly used to remove metals like selenium and mercury owing to their lofty volatility. In

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phytovolatilization, metals are liberated into the air as biomolecules (Khalid et al., 2017). Plants like Arabidopsis thaliana convert Hg21 to Hg0, which in turn increases the volatility of mercury. Some other plants, such as Chara canescens and Brassica juncea can also take heavy metals from contaminated soil and transform them into gaseous/volatile species (Verbruggen, Hermans, & Schat, 2009). The drawback of phytovolatilization is that it only transforms contaminants into less toxic forms but does not completely remove the contaminants. Sometimes edible plant parts, such as fruits, may also contain contaminants (Awa & Hadibarata, 2020).

10.4.3.3 Phytostabilization Phytostabilization means the precipitation or adsorption of heavy metals inside the rhizosphere, which decreases the mobility and bioavailability of contaminants in the soil. Plants used in phytostabilization change the chemistry of the soil and carry out the precipitation and adsorption process (Basharat, Novo, & Yasmin, 2018). The plants secrete a particular redox enzyme during this process, which converts heavy metals in the soil to a less toxic state. The process of phytostabilization restores soil fertility, and hence contributes in restoring the ecosystem.

10.4.3.4 Rhizofiltration In this remediation process, organic or inorganic contaminants are absorbed and precipitated by plant roots to eliminate them from contaminated wastewater, surface water, and groundwater. Compared with aquatic plants, terrestrial plants are more eligible to perform ex situ or in situ rhizofiltration due to the presence of more fibrous systems and developed roots, which gives them more surface area for the amalgamation of heavy metals (Awa & Hadibarata, 2020).

10.4.3.5 Rhizodegradation Organic contaminants that persist in the soil are degraded by the microorganisms present in the rhizosphere. There are several microorganisms like bacteria, fungi, and yeast that play a very crucial task in rhizodegradation (Wang et al., 2017). More microorganisms are present in the rhizosphere than on the ground surface owing to the discharge of root exudates. These exudates are rich in carbohydrates, amino acids, and flavonoids. This nutrient-rich environment increases the efficacy of extraction and elimination of contaminants. Apart from this, plants also produce some enzymes that support soil microbe’ growth and help in the breakdown of contaminants. Studies confirm that the larger surface area of roots promotes microbial growth by providing them with more oxygen, which is the main reason behind the decrease in the efficiency of rhizodegradation in deep soil (more than 20 cm) (Awa & Hadibarata, 2020).

10.4.4 Microbial remediation of heavy metals The accretion of heavy metals is a threat not only to human beings but also to animals and plants. Microorganisms are ubiquitous in the environment and are known to be helpful to the environment and humans in many ways. They can participate in resolving the trouble of metal toxicity. Various physical and chemical restoration methods have been developed in the previous decades, but most of them are either expensive, inefficient, or generate secondary pollutants. Bioremediation can come to the rescue for this purpose as it is highly efficient due to its low cost and does not produce secondary pollutants. Compared with plants and animals, microbes are known to tolerate environmental stress more as they can swiftly mutate and evolve. The interaction of microbes with a small quantity of heavy metals does not

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express any visible effect on the presence of the heavy metal. However, a large amount of heavy metal is required for any visible changes in microbial metabolism and expression pattern. It implies that the response of microbes to heavy metals depends on the availability and amplitude of heavy metal ions (Emenike, Jayanthi, Agamuthu, & Fauziah, 2018). The ultimate aim of microbial remediation is to immobilize the heavy metal under in situ conditions to remove the bioavailability of heavy metal from the environment. The interaction of microbes with a heavy meal is an intricate process that depends on a variety of factors, such as the type of the metal, the concentration of the metal, the nature of the medium, and the species of the microbe. Microbes can alter the toxicity of heavy metals by transforming them from one oxidation state to another or from one organic complex to another. Heavy metals are transformed to a water-soluble, less toxic state, or to a low water-soluble state, leading to heavy metal precipitation and making it less bioavailable or removed by physical means. Microbes use heavy metals for their progression and development, thereby removing them from the site. To achieve these targets, microbes use different approaches such as oxidation, immobilization, transformation, binding, and volatilization of heavy metals (Fig. 10.2). Some microbes reduce metals to a low toxic state through enzymatically metabolic processes as these metals are not involved in assimilation. All the categories of microbes, that is, fungi, bacteria, yeast, and algae, are involved in the bioremediation of heavy metals up to an extent. However, the most potent among them are bacteria, which include Bacillus sp., Pseudomonas sp., and Streptomyces sp. (Uslu & Tanyol, 2006). The heavy metal ions get adsorbed by the functional groups (sulfate, amino, and carboxyl) present in the bacterial cell. Fungi also show great potential in this process owing to their lofty metal binding capacity and high amount of cell-wall material. The presence of chitin-chitosan complexes, phosphate, glucuronic acid, and polysaccharides present in the cells of fungi play a vital part in

FIGURE 10.2 Microbial mediated mechanisms for heavy metal bioremediation.

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the heavy metal adsorption process through ion exchange and coordination (Yin, Wang, Lv, & Chen, 2019). Some examples of fungi and yeast with high capability of biosorption potential are Aspergillus sp., Streptoverticullum sp., Trichoderma sp., and Saccharomyces sp. The different mechanisms adopted by microbes for the bioremediation of heavy metals comprise changes in the redox state of metals, adsorption, biosorption, biotransformation, biomineralization, and bioleaching (Dixit et al., 2015).

10.4.4.1 Remediation by adsorption Microbes have the ability to bind heavy metals to their cellular structure without any involvement of energy, which is achieved by an electro-static contact between negatively charged components of the cell wall and the positively charged heavy metals (Yin et al., 2019). The microbial cell wall comprises various active compounds and extracellular polymeric substances (EPS). The adsorption phenomenon of the heavy metal is majorly achieved with the help of functional groups present in the active compounds, including amines, carboxyl, phosphonate, hydroxyls, etc. For instance, Cu21, Pb21, etc., could be accumulated by a carboxyl group or an amino group via the displacement of protons (Yin et al., 2019). EPS are known to possess remarkable effects on metal adsorption and acid-base properties. EPS exhibits prominent metal-binding potentials with complex heavy metals via various processes, such as proton exchange and micro precipitation of heavy metals. Recent research have documented and quantified the adsorbed metals on bacteria cells and EPSfree cells to establish the relative impact of EPS molecules in metal removal. The practice of bioremediation is still being obstructed by the fact that there is still incomplete knowledge of genomics and genetic characteristics of the microbes used for heavy metal adsorption, the metabolic pathways involved, and their kinetics (Dixit et al., 2015).

10.4.4.2 Remediation by biosorption Biosorption is a biological process, where microbes bind with the heavy metals present in solutions. It is a passive process of uptaking heavy metals involving physical and chemical attachments by their functional groups present on the outer surface of the microbes. Forces like ion exchange, covalent bonding, van der Waals forces, and electrostatic interactions are crucial for this process. A range of immobile and nonliving microbes with an assorted series of biosorption properties have been explored for this process. Temperature, pH, ionic strength, the porosity of the biosorbent, and heavy metal concentration greatly influence the process of biosorption by microbes. For an enhanced biosorption process, chemical modifications have also been documented in microbes. Microbes can bind to a high range of heavy metals through a variety of mechanisms: Accumulate metals by either a metabolism-independent (passive) or a metabolism-dependent (active) process, and remove heavy metals through bioaccumulation or biosorption (Hrynkiewicz & Baum, 2014). In bioaccumulation, the heavy metals are transported from the outside environment to the cell cytoplasm by the cell membrane, where metal sequestration takes place. Microbes’ metal accumulating tendency could be utilized for removing, diluting, or recovering heavy metals from mine tailings or industrial effluents (Jin, Luan, Ning, & Wang, 2018; Verma & Kuila, 2019).

10.4.4.3 Remediation by bioleaching Bioleaching is a common term used for biomining, in which the microbes are used for metal extraction from low-grade ores. It engages the mobilization of positively charged heavy metal ions from the insoluble ores by biological dissolution processes and bio-oxidation. The metabolism of

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microbes produces secretions like organic acids having a low molecular weight that can disintegrate heavy metals in soil particles. Studies show that microorganisms can exploit energy and nutrients to secrete organic acids that promote cadmium’s bioleaching in nutritious conditions. For example, a study showed that Citrobacter could generate free inorganic phosphate, which leads to the development of an insoluble metal phosphate coat that entraps a large amount of toxic metals (Marchenko, Pshinko, Demchenko, & Goncharuk, 2015). Similarly, Corynebacterium and other microbes can reduce toxic water-soluble Cr61 to a low water-soluble Cr31. Bioleaching is an ecofriendly and low-cost method compared with other methods. Some studies even reveal that bioleaching of heavy metals is more proficient than chemical leaching (Deng et al., 2013).

10.4.4.4 Remediation by redox state change Altering the redox status of heavy metals to a less harmful state can be achieved via microorganisms, which play a splendid job in the bioremediation of heavy metals in the environment. Various microbes catalyze this reaction by utilizing metals (Fe(III) or metalloids as electron acceptors). The enzymatic transformation of toxic Cr(VI) to nontoxic Cr(III) is widely studied to better understand the remediation of metals via microbes where insoluble hydroxide is formed by reducing Cr(VI) to Cr(III). Sulfatereducing bacteria (SRB) based up-flow of anaerobic bed reactors have been invented, which are used to clean Ni(II), Cu(II), Zn(II), Mg(II), Al(III), and Fe(III) from polluted water bodies. For these metals, SRB can achieve up to 95% of efficiency in the first 7
8 weeks without any hindrance of SRB multiplication. With the help of SRB, the elimination of heavy metals can be achieved very efficiently by the production of sulfide, reduction of sulfate, and precipitation of heavy metals. Sulfate-reducing bacteria increase the concentration of sulfide by reducing sulfate, generating insoluble metal sulfide, and inactivating heavy metal ions from the contaminated water. Bacillus amyloliquefaciens utilizes glucose to reduce Cr(VI) in aerobic conditions. The bio-oxidation of vastly soluble and toxic AS (III) into a relatively low soluble and little toxic form can be achieved in anaerobic and aerobic environments by bioenzymes called arsenite oxidase.

10.5 Genes involved in determining resistance against different heavy metals in bacteria Bacteria are ubiquitous in nature. The discharge of lethal heavy metals in their habitat leads to the development of resistance to heavy metals in them. The genetic basis of heavy-metal resistance in bacteria can be either on the plasmid or in the chromosome (Hall, 2002). However, both mechanisms of resistance are fairly different from each other. Chromosomal-mediated resistance is more complex compared with plasmid-mediated resistance (Silver & Walderhaug, 1992). The bacterial plasmid contains numerous genes for the resistance of heavy metals like Sb31 and Zn21, which are transferable to other microorganisms. As there is no specific mechanism for heavy metal tolerance, various mechanisms have been reported, such as extracellular efflux pumps, complex formation with other components, redox reactions, intra- and extracellular sequestration, for this purpose. Some bacteria sometimes utilize metal ions during anaerobic respiration as a terminal electron acceptor. The complete degradation and detoxification of heavy metals is a near-to-impossible task.

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These organisms have adopted an efflux mechanism that actively pumps the toxic heavy metals out of their cells, reducing the concentration of toxic metal ions in their cells. The role of metallothioneins in heavy metals has also been documented. It is a small protein, rich in cysteine, which binds with metal ions. All eukaryotes and various bacteria produce metallothioneins. The first-ever bacteria metallothionein was cadmium-induced SmtA in Synechococcus sp. RRIMP N1. Homologous of SmtA has also been documented in cyanobacteria (Pseudomonas), gammaproteobacteria, alphaproteobacteria, and firmicutes (Blindauer, 2011; Gupta et al., 2016).

10.5.1 Resistance to antimony and arsenic Arsenic and antimony have similar chemical properties, exhibiting similar transport and tolerance genetics in bacterial cells. Bacteria reduce As(V) to As(III), which is then expelled from the cell via a metal efflux system. The resistance to these two metals is regulated by the ars operon of E. coli and S. aureus. As(V) usually enter the bacterial cell through transporters used to carry other compounds, such as phosphate transporters (Pit and Pst pump) in E. coli. In E. coli, the ars operon bears three structural genes: arsA (catalytic subunit), arsB (membrane subunit), and arsC (arsenate reductase), and two regulatory proteins ArsR, which is a repressor and ArsD, which is a coregulator and also govern the arsRDABC operon. ArsC catalyzes the conversion of As(V) to As (III). An arsenite efflux pump powered by ATP hydrolysis is created by the interaction of the ATPase ArsA protein with ArsB. ArsB is a membrane protein that can expel arsenite from the cell cytoplasm, reducing the deposition of arsenite (Lin, Yang, & Rosen, 2007). In E. coli, Glutathione acts as a resource for reducing the potential. In S. aureus the reducing potential is generated by thioredoxin assistance (Nanda, Kumar, & Sharma, 2019; Nies & Silver, 1995).

10.5.2 Resistance to mercury In bacterial plasmids (Pseudomonas, S. aureus, and E. coli), the mer operon imparts resistance to mercury in gram-positive and gram-negative bacteria. Mercuric reductase, an inducible, intracellular enzyme, is encoded by the merA gene that converts Hg21 into volatile mercury through an NADPH-dependent process (Wagner-Do¨bler, Von Canstein, Li, Timmis, & Deckwer, 2000). The mer resistance system is responsible for both inorganic mercury and organic methyl mercury, i.e., phenyl mercury. The mer operon also consists of two regulatory proteins: merR and merD; and two proteins for transport: merT and merP. The negative and positive regulation of other genes is regulated by merR, and it also controls negative self-expression. merD is a secondary controller gene that downregulates the mer operon. While the proteins determined by structural genes, that is, merT and merP, assist in mercuric ion transport. Many bacterial species carry the merB gene that encodes for organomercurial lyase, which provides resistance to diverse forms of mercury like methylmercury, organomercurials, and phenylmercury. This enzyme breaks the C-Hg bond and reduces Hg21 into volatile metallic mercury, which is secreted out from the cell. In the case of P. stutzeri, the merB gene is present between merR and merT. In gram-negative bacteria, merB is rarely present. Other genes found to be imparting resistance to mercury are merG and merE (Nanda et al., 2019).

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10.5.3 Resistance to nickel and cobalt Cobalt Co(II) is present in living organisms in trace amounts where it functions as a cofactor for some enzymes. However, the high deposition of cobalt and nickel in the bacterial cell can be toxic. Therefore detoxification of these two metals is achieved by cation efflux. The uptake of Co and Ni is aided by a secondary transport system or by an ATP binding cassette (ATCase) system (Rodionov, Hebbeln, Gelfand, & Eitinger, 2006). Plasmid-mediated nickel and cobalt-resistant determinants comprise cation antiporter CzcCBA (cobalt-zinc cadmium), cobalt-nickel resistance (CnrCBA), and nickel-cobalt cadmium resistance, which is an NccCBA efflux system. The RNDdriven efflux system imposes a tough resistance against cobalt in bacterial cells (Nies, 2003). In the case of E. coli, the resistance to nickel and cobalt is expressed by the yohM (rcnA) gene located in the chromosome. The RcnA/YohM protein is a member of the NiCoT transporters family (Eitinger, Suhr, Moore, & Smith, 2005). Other tolerance systems for nickel in bacteria has been documented, such as cnr/ncc and cnr/ ncc/nreB tolerance systems. The ncc and cnr gene consists of a protein called resistance nodulation division (RND). Nickel is exported through the CnrCBA protein complex (Nies, 2003). The cnrYHXCBAT gene system expresses the cnrCBA efflux system. It is made up of three structural genes (cnrC, cnrB, cnrA). The efflux system comprising the protein product complex of these three structural gene forms pumps out the nickel from bacterial cells. When the nickel reaches the periplasmic space, the regulatory genes (cnrY and cnrC) initiate the transcription process on a promoter region. The cnrYXH gene encodes a protein that governs the expression of further genes, and cnrH, in turn, activates cnrCBA expression.

10.5.4 Resistance to copper Cu is widely used in mining, agriculture, and industrial processes that are discharged into the atmosphere, making bacterial cells regularly exposed to the high deposits of Cu. A low concentration of Cu is required by bacterial cells to synthesize metabolic enzymes like cytochrome c oxidase, and it also acts as a cofactor for many enzymes. But the high concentrations of Cu can be toxic, but bacteria have evolved with certain mechanisms to shield themselves against the toxicity of Cu (Issazadeh, Jahanpour, Pourghorbanali, Raeisi, & Faekhondeh, 2013). In the case of bacteria, genetic determinants for Cu regulation are present in their plasmids. Research shows that a combined effect of chromosomal and plasmid genes is required to control Cu in bacterial cells. Cu resistance is majorly regulated by P-type ATPase, which pumps out Cu from the bacterial cells. In E. coli, a multiprotein complex (CusCBA) controls the efflux of Cu. CusA (an RND protein) is driven by a proton motive force that transports Cu out from the cell through CusB and CusC encoded proteins. Another component that controls the homeostasis of Cu in E. coli is multicopper oxidase (MCO), which converts Cu(I) into Cu(II) and defends the periplasmic proteins from damage (Singh, Grass, Rensing, & Montfort, 2004). In Pseudomonas sp., a Cu-inducible cop operon is present on the plasmid, which provides resistance to the bacteria from the high concentrations of copper. It has four proteins: CopA, CopC, and CopD. They accumulate Cu and simultaneously compartmentalize in the periplasm of the cell and in the outer layer membrane, which provides protection against Cu. As the extracellular

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Cu21 enters the bacterial cell via the porous outer membrane, CopA (periplasmic protein) binds with Cu21 and sends it to CopD (Cu21 transporter protein present on the inner membrane) through CopC protein. CopD exports Cu21 to the bacterial cell (inner-membrane protein) and senses the increased concentration of Cu21 in the periplasmic space. Afterward, CopS transmits the signal to CopR, which in turn induces the expression of CopABCD genes. According to Solioz & Stoyanov (2003), in E. hirae, copper homeostasis is maintained by copYZAM operon. Resistance against Cu is regulated by CopA protein, which mediates Cu intake under copper-limiting conditions. CopB, a P-type ATPase, pumps out the excess Cu ions from the bacterial cells. The expression of the cop operon is regulated by a transcriptional repressor (CopY) and by a Cu chaperon, i.e., CopZ.

10.5.5 Resistance to cadmium The resistance to cadmium depositions in gram-positive bacteria is governed by the CadA system present in the bacteria’s plasmid. When Cd-resistant gram-positive bacteria encounter with Cd-metal stress, it gets entry into the bacterial cells by metal ion transporters (MIT). CadA resistance system on the plasmid pumps the cadmium out of the bacterial cell (Bruins, Kapil, & Oehme, 2000). Cad C, a regulatory protein, controls the expressions of another gene present in the resistant system. The protein, a CadA gene product (P-type ATPase), pumps the cadmium outside of the cell. While in gram-negative bacteria, the cells manage resistance against Cd via the Czc system, an RND-driven zinc exporter, and a nickel exporter (Ncc). In cyanobacteria, MTs protein (smt) has been discovered, which is responsible for determining the tolerance of Cd in their cells. The smt operon comprises an SmtA gene (MT protein) and an SmtB gene. SmtB regulates smtA expression, by controlling the operator and the promoter region present among genes (Nanda et al., 2019). SmtA gene encodes for metallothioneins (class II), responsible for Cd resistance.

10.5.6 Resistance to zinc Zinc forms an essential part of many enzymes and complexes such as the zinc finger of DNA, etc. However, the high accumulation of Zn may inhibit or hinder multiple cellular enzymes and processes. The entry of Zn in the bacterial cells is unspecified but a rapid process. To date, two efflux systems have been discovered, which regulate the resistance to Zn in bacterial cells. The first system is chromosomally regulated P-type ATPase, which is encoded by the zntA gene. It directs the zinc efflux through an ATP-driven transport system. Another system is a proton gradient-driven RND transporter, commonly found in gram-negative bacteria (Nies, 1999). The Czc system is another zinc-resistance system present in the gram-negative bacteria Ralstonia. It is present on the plasmid, which not only provides resistance to zinc but also to Cd and Co. It functions as a cation/ proton antiporter, which effluxes cations from the bacterial cell. The czc operon comprising three structural genes, that is, czcC, czcB, and czcA, forms a cation efflux system. In the case of P. aeruginosa, a resistance system against Cd and Zn has been reported, called the Czr system. It comprises czrCBA genes, which are very similar to the Czc system of R. eutrophus. (Hassan et al., 1999; Nanda et al., 2019).

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10.6 Factors affecting microbial remediation 10.6.1 pH For microbial-driven biosorption, pH is crucial, and optimal pH is usually dissimilar for microorganisms. An inappropriate pH has negative impacts on microbial growth for several reasons. 1. It alters the enzymatic activities of microorganisms, influencing the rate of microbial metabolism of heavy metals. 2. The surface charge of the microbe is influenced by pH, altering the adsorption of metal ions. 3. Furthermore, pH affects the hydration and mobility of several ions in the soil. Studies by both Rodrı´guez-Tirado, Green-Ruiz, and Go´mez-Gil (2012) and Wierzba (2015) found that the removal rate of heavy metals by microbes increases with increasing pH across a narrow range, but the removal rate begins to decline when the pH reaches a specific value. Specifically, for Pb21 and Zn21 with pH values ranging from 2.0
5.5, the removal rate increased. The adsorption ability (70 mg/g, 20 mg/g) at a pH of 5.5 is almost seven times high versus two times higher at a pH of 2.0 (10 mg/g). However, at a pH value of more than 5.5, the removal rate decreases to the same level as the pH of 2.0. Leung, Chua, and Lo (2001) showed that the optimal pH range for most of the bacteria is 5.5
6.5, but there are exceptions. Rodrı´guez-Tirado et al. (2012) reported that the optimum pH is 7.0 for Bacillus jeotgali. This might be because certain metal ions generate hydroxide precipitate and become less susceptible to microbial sorption when the pH rises over a certain threshold (Hu, Luo, Song, Wu, & Zhang, 2010). Additionally, the optimal pH for aerobic microorganisms may differ from anaerobic microorganisms. At acidic pH, heavy metals begin to form unbound ionic species, with more protons available to saturate metalbinding sites. At an elevated hydrogen ion concentration, the surface becomes more positively charged, lowering the attraction of adsorbent to metal cations, thereby increasing its toxicity.

10.6.2 Ambient temperature Ambient temperature primarily influences the absorption amplitude of heavy metal by modulating the growth and proliferation of microorganisms (Fang et al., 2011). The optimal temperature for diverse microorganisms is generally different; Thiobacillus ferrooxidans, T. acidophilus, and T. tepidarius are medium-temperature bacteria. Sulfolobus solfa tataricus and Acidianus brierleyi are extremely thermophilic bacteria. Temperature has a considerable impact on heavy metal adsorption. An elevation in temperature accelerates the speed of adsorbate diffusion around the boundary layer. Heavy metal solubility increases with an increment in temperature, which improves heavy metal bioavailability. Moreover, microbial actions also increase with temperature until a suitable range, which facilitates the environment for microbial metabolism or enzyme activity and significantly improves bioremediation.

10.6.3 Substrate species Three appropriate factors are required to understand substrate species, that is, heavy metal ions, soil type, and soil additive. The adsorption phenomenon of heavy metal on diverse soil often

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diverges significantly. Obviously, the adsorption speed of soil and its bonding with heavy metal ions (i.e., its low desorption rate) results in low heavy metal ion mobility and renders the removal of these ions by microbial adsorption difficult (Jin et al., 2018). Heavy metal ion species influence heavy metal removal through affecting the generation time of microorganisms. Thiobacillus ferrooxidans utilize sulfur as a substrate and have 10
25 h of generation time, which is far superior to the substrate generation time, which is about 6.5
15 h on Fe. Different heavy metals have varying degrees of solubility; metals like Ni, Zn, and Cu are readily dissolved, but Pb21 and chromium are slightly soluble. Soil additives can significantly enhance heavy metal removal by microbes, and the magnitude of additives can have varied impacts on the leaching rate of heavy metal ions. Tyagi et al. (2014) showed that the addition of 20 g/L FeSO4  7H2O increased the leaching efficacy of Zn and Cu by factors of 2 and 1.9, respectively, but the leaching rate did not augment when the concentration was greater than 20 g/L. With the identical additive, Cu and Zn elimination rates were increased up to 85% and 93%, respectively, and 6 and 3.2 times better than the control. Research indicates that using more than one additive, such as a combination of FeSO4  7H2O, leads to a higher removal rate than using these additives separately (Race, 2017).

10.6.4 Substrate concentration The adsorption speed of microbes is also affected by the amount of heavy metals. Generally, a proper assessment should be employed to know the accumulative properties of a bio-sorbent (Jin et al., 2018). The concentrations of heavy metal ions with the highest adsorption rates differ depending on the microorganisms and the heavy metal ions investigations. However, the pattern, which is consistent across all examples, suggests that the adsorption rate rises to a certain point and then stays constant as the amount of heavy metal ions increases (i.e., the equilibrium concentration).

10.6.5 Condition of soil milieu The soil environment, including soil type, aeration status, temperature, the bioavailability of nutrients, presence of other inhibitory pollutants or cocontaminants, soil moisture, water activity, and microbial competition, significantly impacts the efficiency and effectiveness of a remedial system (Varjani & Upasani, 2017). Proper optimization of these factors is required to improve remedial efficiency and assure field scale success.

10.6.6 Bioavailability of pollutants and biosurfactants Bioavailability refers to the quantity of a substance that is physicochemically accessible to microorganisms (Souza, Vessoni-Penna, & de Souza Oliveira, 2014). Environmental persistence of persistent organic pollutants (POP) due to their low water solubility and ability to be absorbed into soil organics, limits their availability to degrading microorganisms (Chakraborty & Das, 2016). It is documented that the identical compounds present in dissimilar pollutants can be detoxified or degraded to varying extents by the same organism or consortium due to the bioavailability of the particular compound rather than its chemical structure (Varjani, 2017). Bioavailability is also influenced by soil physiochemical properties (including composition, texture, moisture, pH, sorption, occlusion, and aging) and strongly affects the feasibility of risk-based remediation, type of microbial transformations, and whether POPs

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will serve as a primary, secondary, or cometabolic substrate, or energy source (Kuppusamy et al., 2017). Soil microorganisms can produce different products (i.e., gases, biosurfactants, biopolymers, solvents, and acids) to enhance remediation (Varjani & Upasani, 2016). Among these products, biosurfactants are well-studied as they play a critical role in improving hydrocarbon pollutant bioavailability (Souza et al., 2014). Thus, the use of biosurfactants is a promising approach for enhancing the bioavailability of POPs, especially polycyclic aromatic hydrocarbons (PAHs) (Gupta et al., 2016). Hydrophobicity and surfactant activity supports the dealings between microbes and insoluble substrates, overcoming diffusion limitations during substrate transportation to cells. It is well known that the competence of microbial consortia composed of PAH-degrading bacteria is significantly higher when using surfactants. Nevertheless, Owsianiak et al. (2009) found that two different surfactants altered the hydrophobicity of the cell surface of the consortia by means of increasing hydrophilic and decreasing hydrophobic cultures. Their result indicates that in surfactant-mediated biodegradation, the efficacy of surfactants relies on the speciation of microorganisms, but not on the form of the surfactant. Other critical factors that affect the bioremediation efficiency of microorganisms include soil structure, air/oxygen availability, redox potentials, dissolved oxygen, availability and solubility of nutritional contents, nutrient diffusion, mass transfer, moisture content, water-solubility, chemical composition, and concentrations of heavy metals.

10.7 Conclusion and future prospects Microorganisms exhibit different strategies to reduce the toxicity of heavy metals. Wide spectrums of microbial-assisted heavy metal detoxification mechanisms are applied in different settings for the reclamation of contaminated sites. Microbes are the best living entities used in bioremediation as they have high tolerance or resistance to the higher concentration of heavy metals. Using microorganisms as natural bioremediating agents is an eco-friendly approach and exhibits a less expensive strategy to remediate metal-contaminated soil. Furthermore, intensive research is needed to decipher the molecular mechanism behind heavy metal resistance in different groups of microorganisms. The improvement of genetically engineered microbial strains is also required to complete the detoxification of heavy metals from their contaminated sites.

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9.

CHAPTER

Omics approaches to pesticide biodegradation for sustainable environment

11

Saurabh Gangola1, Samiksha Joshi1, Geeta Bhandari2, Pankaj Bhatt3, Saurabh Kumar4 and Satish Chandra Pandey5,6 1

School of Agriculture, Graphic Era Hill University, Bhimtal, Uttarakhand, India 2Department of Biosciences, Himalayan School of Biosciences, Swami Rama Himalayan University, Dehradun, Uttarakhand, India 3Department of Agriculture and Biological Engineering, Purdue University, West Lafayette, IN, United States 4ICAR-Research Complex for Eastern Region, Patna, Bihar, India 5Cell & Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University Campus, Almora, Uttarakhand, India 6Center for Advanced Biotechnology Research, Absolute, Gurugram, Haryana, India

11.1 Introduction Scarcity of agricultural land (due to industrialization), burgeoning human population, loss of food products (due to natural calamities and pest infestation), and water crisis are some of the major factors that restrict the financial and economic development of developing countries. It is difficult to increase crop yields in the future under such constraints (Gangola, Bhatt et al., 2022). To achieve the food targets farmers have adopted various advanced technologies, such as the use of hybrid seeds, systematic irrigation, and application of chemical fertilizers and pesticides (Foley et al., 2011). Advancement in agriculture has resulted in various environmental threats, such as decreased fertility of the soil, increased acidification of the soil, increased nitrate leaching, enhanced resistance in weed species toward common weedicides, and decreased biodiversity of the soil (Tilman, Cassman, Matson, Naylor, & Polasky, 2002; Verma, Verma, & Sagar, 2013). Pesticides are a diverse group of organic and inorganic chemicals such as insecticides, herbicides, fungicides, nematicides, and soil fumigants, which are not only used to control pests but also as preservatives in households. During agricultural practices these pesticides are used in excess by farmers to increase crop productivity as well as improve the quality of food products. By preventing pest attacks farmers are able to maximize their economic returns. In general pest infestations in agriculture produce (pre- and postharvest conditions) deplete annual food production by 45% on average (Abhilash & Singh, 2009). To control pests and disease vectors, chemical pesticides are used, which increase agricultural productivity significantly and decrease the spread of insect-borne diseases in humans (e.g., malaria, dengue, encephalitis, filariasis, etc.) (Bhatnagar, 2001; Rekha Naik & Prasad, 2006). In tropical regions, effective management of pests is necessary for the maintenance of crop yield because in these areas high temperature and humidity facilitate the rapid growth and fast reproduction of pests, which severely exert crop losses Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00010-7 © 2023 Elsevier Inc. All rights reserved.

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(Lakshmi, 1993). Out of 3 billion kilograms of pesticides produced annually, more than 75% is used in agricultural practices globally (Moore, Lizotte Jr, Knight, Smith Jr, & Cooper, 2007). The first generation of pesticides introduced over 40 years ago included organochlorine (OC) and organophosphorus (OP) compounds. Manufacturers started producing large amounts of synthetic pesticides in the late 1940s, and their use became widespread with time (Daly, Doyen, & Ehrlich, 1978). First-generation pesticides included inorganic compounds (lead, mercury, arsenic) and botanicals (nicotine, pyrethrum, rotenone), which were used to kill pests. Second-generation pesticides (synthetic pesticides) like DDT (synthesized in 1873 by Paul Muller) were used in World War II to control body lice. Currently, thousands of synthetic pesticides made up of 1000 different chemicals and compositions are being manufactured. Third-generation pesticides include insect pheromone, insect growth regulators, chitin synthesis inhibitors, juvenile hormones, and Bacillus thuringiensis (toxin). However, nonjudicial use of pesticides affects the entire ecosystem as they enter the food chain (through residues) and contaminate the soil, air, ground, and surface water. These xenobiotic chemicals have also been shown to be hazardous for health. Pesticides are responsible for serious environmental, health, and safety problems due to their improper storage conditions, mishandling, spillage, and other related mismanagements. Pesticides also affect the diversity of microbial communities in soil and water and disturb metabolic activity, reproducibility, and growth of microorganisms. Exposure to pesticides can change the nature of organisms and alter their population size (Odukkathil & Vasudevan, 2013). Owing to the negative impact of pesticides on organisms, the European Food Safety Authority (EFSA) has changed the expression “pesticide” with the new term “plant protective product (PPP).”

11.2 Biodegradation Methods such as pyrolysis, recycling, filling of contaminated land, and incineration are used to minimize soil pollution and toxication from agricultural fields (Wang, Niu, & Cui, 2005). These physicochemical methods are neither cheap nor adequate enough to remediate the environment (Jain et al., 2005). The use of microbiological agents would be one of the promising methods of exploiting microbial ability for cleaning contaminants from polluted sites. This alternative bioremediation strategy could be more effective, economical, less hazardous to the organisms, and ecofriendly (Stoytcheva, 2011). Biodegradation is the “Chemical dissolution of any complex organic compound into simpler substances such as carbon dioxide, water, and ammonia with the help of any biological means.” The biochemical reaction of degradation is mediated by intracellular and extracellular microbial system-associated enzymes. In the biodegradation process, generally, oxidation of organic compounds occurs (loses electrons) by an electron acceptor, which itself is reduced. Under an aerobic environment, microbial oxygenases play a key role and add oxygen molecules to the xenobiotic structure, making them susceptible to the degradation process. The incorporation of oxygen acts as an electron acceptor. During aerobic respiration the oxidized organic compounds couple with the reduction of molecular oxygen. While in anaerobic conditions, organic chemicals or inorganic ions are used by the microbial system as an alternative electron acceptor. Anaerobic biodegradation can occur under fermentative, denitrifying, iron-reducing, sulfate-reducing, or methanogenic conditions.

11.3 Parameters affecting biodegradation of pesticides

193

Biodegradation, carried out with the help of algae, fungi, bacteria, and actinomycetes, (Finley, Broadbelt, & Hatzimanikatis, 2010) is a natural phenomenon (Kosaric, 2001) that does not produce any kind of noxious intermediate metabolites (Furukawa, 2003) and is an effective technique for removing toxic substances (Minsheng & Xin, 2004; Wang et al., 2005). Diverse groups of microorganisms present in various habitats, such as fresh and marine water, sewage, and soils, have the capacity to metabolize xenobiotic compounds and convert them into natural minerals for further utilization by plants. Therefore microbes perform a major role in developing pesticidecontamination-free agricultural soil. Due to continuous exposure to contaminated or stress environments, microorganisms, especially bacteria, develop a modified genetic system to adapt and survive in those conditions (Parsek, McFall, & Chakrabarty, 1995). Microorganisms living in contaminated environments utilize pollutants as a source of carbon and nitrogen for obtaining energy. Hence, microorganisms are supposed to be the best tool for the bioremediation of pesticides present in soil or water (Table 11.1).

11.3 Parameters affecting biodegradation of pesticides 11.3.1 Pesticide structure The structure of a pesticide molecule determines its physical and chemical properties and inherent biodegradability (Fig. 11.1). Minor modifications in the structure frequently lead to radical changes Table 11.1 List of common pesticide-degrading microorganisms. Types of microorganisms

Genus

Pesticides

Bacteria

Pseudomonas

Aldrin, chlorpyrifos, coumaphos DDT, diazinon, endosulfan, endrin, hexachlorocyclohexane, monocrotophos, parathion Chlorpyrifos, coumaphos, DDT, diazinon, dieldrin, endosulfan, endrin, glyphosate, methyl parathion, monocrotophos, parathion, polycyclic aromatic hydrocarbons Chlorpyrifos, endosulfan, diazinon, glyphosate, methyl parathion, parathion Aldrin, carbofuran, chlorpyrifos, diazinon, diuron Alachlor, aldicarb, atrazine, carbofuran, chlordane, chlorpyrifos, DDT, diuron, endosulfan, esfenvalerate, fenitrothion, fenitrooxon, fipronil, heptachlor epoxide, lindane, malathion, metalaxyl, pentachlorophenol, terbuthylazine, 2,4-D Phorate, parathion, atrazine, fenvalerate, DDT, patoran

Bacillus

Alcaligenes, Flavobacterium Actinomycetes Fungi

Micromonospora, Actinomyces, Nocardia, Streptomyces White rot fungi, Rhizopus, Cladosporium, Aspergillus fumigatus, Penicillium, Aspergillus, Fusarium, Mucor, Trichoderma spp, Mortierella sp.

Algae

Chlamydomonas, genus of diatoms

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Chapter 11 Omics approaches to pesticide biodegradation

FIGURE 11.1 Factors affecting pesticide persistence in soil and their biodegradation.

in the susceptibility of a substrate to biodegradation and bioremediation. The introduction of OH, COOH, and NH2 in the substrate structure may help to provide a site of attack for biotransformation. The addition of a halogen or alkyl group makes the substrate more resistant to biotransformation (Cork & Krueger, 1991).

11.3.2 Pesticide concentration Pesticide concentration during application in the field is an important factor for the determination of the rate of biodegradation. Degradation kinetics of most pesticides follow the first-order reaction and roughly in proportion to the residual pesticide concentration the rate of degradation also decreases (Gangola, Sharma, et al., 2022; Topp, Vallaeys, & Soulas, 1997).

11.3.3 Pesticide solubility Pesticides having minimum solubility in water tend to be more resistant to microbial transformation compared with compounds having more solubility in water. Microorganisms prefer to utilize the dissolved fraction of substrate from their environment. Therefore the rate of biodegradation also depends on the solubility of the compound in the environment (Cork & Krueger, 1991).

11.3 Parameters affecting biodegradation of pesticides

195

11.3.4 Soil types Soil provides optimum environmental conditions, such as soil organic matter (SOM), clay content, pH, etc., for the growth of degradative microorganisms influencing the degradation rate of pesticides (Gupta & Gajbhiye, 2002). Soil particles can absorb pesticides, regulate their bioavailability, and influence their persistence.

11.3.5 Soil moisture Moisture (water) influences the rate of metabolism/degradation of contaminants because it affects the kind and amount of soluble materials available for degradation. The amount of water in the pore spaces of the soil also affects the exchange of oxygen. Under saturated conditions, oxygen can be consumed faster than it is replenished in the soil vapor space and the soil can become anaerobic. An anaerobic state of the soil can retard the rate of biodegradation and may cause major changes in the metabolic activities of microbes. Conversely, soil moisture content should be between 25% and 85% of the water-holding capacity, and a range of 50%
80% is optimal for biodegradation. Water acts as a solvent for pesticide movement and diffusion. It is also essential for microbial activities (Gupta & Gajbhiye, 2002).

11.3.6 Temperature Temperature directly influences the rate of biodegradation by controlling the rates of enzymecatalyzed reactions. The rate of biodegradation decreases roughly by one-half for each 10 C decrease in temperature. The rate of biodegradation is generally exceedingly low at 0 C, which may vary seasonally, and the microbial metabolic activity itself can increase soil temperature (Topp et al., 1997).

11.3.7 Soil pH Although biodegradation may occur under a wide range of pH, a pH of 6.5
8.5 is generally found optimal for biodegradation in most terrestrial and aquatic systems. The availability of nutrients depends on soil pH. Phosphorus, which is a crucial nutrient for biological systems, shows its maximum solubility at a pH value of 6.5 and decreases with the up and down of this pH value. Soil pH may affect pesticide adsorption and abiotic/biotic degradation processes (Burns, 1975).

11.3.8 Soil organic matter The behavior of pesticides may change due to the presence of organic matter in the soil. Soil organic matter may either decrease the microbially mediated pesticide degradation efficiency by stimulating pesticide adsorption processes or increase microbial activity by cometabolism (Perucci, Dumontet, Bufo, Mazzatura, & Casucci, 2000; Yoshida, 1978). Soil amended with farm yard manure, hen manure, and bagasse enhances the degradation (up to 99%) of endosulfan and imidacloprid under the treatment of Aspergillus oryzae and Trichoderma longibrachiatum (Gangola, Khati, & Sharma, 2015; Gangola, Pankaj, Srivastava, & Sharma, 2015).

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11.3.9 Soil microbial biomass Microbial biomass is that portion of soil organic matter that comprises live microorganisms including bacteria, actinomycetes, algae, and protozoa. It is a significant characteristic of soil quality and an ecologically vital parameter (Doran & Parkin, 1994). Pesticides result in qualitative and quantitative alteration of the nature of the soil microbial population (Bhatt et al., 2021; Matsumura & Boush, 1971). Negi, Srivastava, and Sharma (2014) also reported that soil bacteria (Bacillus, Pseudomonas, Exiguobacterium, Microbacterium, Chromobacterium, and Stenotrophomonas sp.) isolate and degrade 88% of endosulfan, imidacloprid, and carbendazim (100
200 μg/mL).

11.4 Proteomics of pesticide biodegradation Enzymes play a central role in the biodegradation of several pesticides. In situ activation of various pesticides occurs due to the action of several enzymes. Pesticides also target specific enzymes playing a vital role in physiological functions (Scott, Jensen, Philoge`ne, & Arnason, 2008). Analysis of protein expression under particular stress conditions is called proteomics, and the study can be done with several traditional and advanced tools of protein biochemistry. Analysis of proteins on the basis of molecular weight is possible by SDS-PAGE, whereas more reproducible and correct analysis is possible with 2D gel electrophoresis of proteins. On the basis of isoelectric point and molecular weight, proteins can be separated in a gel more easily. Furthermore, matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) analysis helps in the interpretation of the exact protein responsible for the pesticide biodegradation (Fig. 11.2) (Bhatt et al., 2019; Breugelmans et al., 2010; Meng, Zhang, Chen, Cao, & Shang, 2014). To date very few reports on pesticidedegrading proteomics using bacterial strain are available; however, some reports are available with resistant insects (Pandey, Tripathi, Tripathi, Pandey, & Gangola, 2019).

11.5 Molecular basis of pesticide degradation Several molecular and proteomic approaches are used to determine the expression of a particular protein crucial for the removal of pesticides (Widada, Nojiri, & Omori, 2002). Under normal environmental conditions, bacterial cells produce different enzymes for the utilization of carbon/nitrogen sources from the surroundings to fulfill their nutritional requirements, whereas under stressed conditions the expression of genes is changed. In recent years, advancements in the field of genomics, metagenomics, proteomics, bioinformatics, and high-throughput analyses have enabled detailed exploration of ecologically significant microflora, thus recognizing vital pesticide biodegradation pathways and the capability of microbes for adaptation in unfavorable environments (Arora, Mohanta, Srivastava, Bae, & Singh, 2014). For examining the molecular basis of pesticide biodegradation and the involvement of catabolic genes, implementation of recombinant DNA technology has been described by Widada et al. (2002). Several pesticide-degrading catabolic genes and plasmids have been characterized from various microorganisms. Most catabolic genes are situated on the chromosomes; however, certain degradative genes have also been reported in plasmids or transposons. Current advancement in metagenomics and whole genome

11.5 Molecular basis of pesticide degradation

197

BIODEGRADATION

CLASSICAL METHODS

ADVANCED METHODS

Collection of sample from contaminated site Metabolic analysis (GC-MS) Isolation and Biochemical characterization(Bacteria/Fungi)

Microorganism tolerance

Degradation(Minimal medium/Soil)

Identification of pesticide degrading gene and sequencing/Gene cloning/Reconbinen DNA technology

Proteomic analysis (PAGE/2DE/LCMS, MALDI-TOF/Protein sequencing)

Spectroscopic analysis/GC/HPLC Metagenomics analysis Molecular characterization

FIGURE 11.2 Fundamental to advanced approach for the complete study of pesticide biodegradation.

sequencing have created new opportunities for searching for novel catabolic genes and their regulatory mechanisms in culturable and nonculturable microbes in various ecosystems. Exploration of molecular mechanisms of pollutant biodegradation by microbes and their interactive action with the environment are significant for the successful employment of these techniques for in situ remediation studies. Microbial enzymes, such as organophosphorus hydrolase (OPH; coded by the opd gene) capable of hydrolyzing pesticides have been reported by Li, He, and Li (2007). The opd gene is present in chromosomes/plasmids and can help microbes to metabolize various organophosphate pesticides. The opd gene consisting of 996 nucleotides, a typical promoter sequence (TTGCAA N17 TATACT), has been obtained from Escherichia coli. Plasmids containing biodegradation-specific genes show substantial genetic diversity, however, the opd gene is a highly conserved region. Methyl-parathion hydrolase (MPH encoded by the mpd gene), has been reported from Pseudaminobacter, Ochrobactrum, Achrobacter, and Brucella (Zhongli, Shunpeng, & Guoping, 2001). Several studies reported cypermethrin-degrading genes from bacteria using molecular cloning. The main enzyme for the degradation of cypermethrin is pyrethroid hydrolase. Various types of pyrethroid hydrolases have been reported in Ochrobactrum, Bacillus, and Sphingobium sp. (Ruan et al., 2013).

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Esterase is another vital hydrolase possessing the capability of metabolizing a wide range of compounds, such as carbamates, organophosphates, and pyrethroids containing the ester group. Some pyrethroid-degrading genes, such as estP, pytH, pye3, pytH, and pytZ, have been described by Ruan et al. (2013). Examination of expression and occurrence of catabolic genes is vital for bioremediation studies for a better understanding of the biotransformation mechanism in comparison to 16S rDNA sequencing. A direct positive correlation exists between the abundance of catabolic genes and the potential for degradation, thus the more catabolic genes the more will be degradation (Rogers, Ong, Kjartanson, Golchin, & Stenback, 2002). Thus there has been an increased emphasis on quantifying the levels of mRNA to characterize bioremediation genes. Often increased mRNA concentration can be, at least qualitatively, associated with higher rates of contaminant degradation. Analysis of the mRNA level for gene expression other than those directly involved in bioremediation might yield additional insight into the mechanisms that control the rate and extent of bioremediation (Lovley, 2003). The recombinant DNA studies have enabled the development of DNA and RNA probes for the identification of microorganisms from different ecosystems with the distinct capability of pollutant biodegradation (Kumar, Mukerji, & Lai, 1996).

11.6 Metagenomic analysis It is essential to investigate the impact of the application of pesticides on soil microorganisms because microbial functions play an important role in crop production, nutritional quality of crops, and soil sustainability (Topp, 2001). Thus existing structural diversity of soil microflora and their diverse metabolic activities are significant in this regard. Soil microflora also correlates with the mobile pool of elements vital to life and therefore their existence is crucial for biogeochemical cycling (Adesemoye & Kloepper, 2009). Thus the quantitative structural and functional parameters of soil microbes can be employed as indicators for examining the influence of pesticides on soil ecosystems and assessing their biological status (Joshi et al., 2021). Various agricultural inputs also affect the structural diversity of soil microbial communities. Mineral fertilizers impact plant growth by enhancing soil biological activity via an increase in system productivity, crop residue return, and soil organic matter. A very little hazardous effect of essential herbicides on the soil microbes have been reported, however deleterious effects of insecticides and fungicides are more prevalent (Bhandari, Bhatt, Gangola, Srivastava, & Sharma, 2021). The two problems that need to be dealt with are improvement in monitoring the response of soil microflora to pesticide application and their related ecological implications. Monitoring can be done by reliable assessment and quantification, of the correlation between the exposure of the pesticide to the soil ecosystem and the structural parameter of the soil microbial community. The other problem can be addressed through the generation of novel strategies for elaborating and understanding the magnitude and diversity of soil microbial responses to pesticides (Allison, Czimczik, & Treseder, 2008).

11.6.1 Cultivation-independent methods The major setback of culturable methods is that only a small fraction of the diverse soil microflora can be cultivated in the laboratory, and thus available for examination (Gangola, Joshi, Kumar,

11.7 Conclusion

199

Sharma, & Sharma, 2021; Schloss & Handelsman, 2006; Zengler, 2008). Contrarily, the molecular cultivation-independent processes are more sensitive and highly informative due to dependence on the DNA sequence information (Guo et al., 2009). However, several other biochemical biomarkers can also be employed for assessing the change in the microbial community structure. Fatty acids also enable the generation of vital insights of significant parameters of soil microbial communities, such as viable biomass, community structure, nutritional status, and physiological stress responses (Demoling, Ba˚a˚th, Greve, Wouterse, & Schmitt, 2009). Other potential techniques being employed include proteomics of environmental samples (Bastida, Moreno, Nicolas, Hernandez, & Garcia, 2009; Schneider et al., 2010) for a specific review of soil (metaproteomics) and metabolic analysis (metabolomics) (Liebeke, Bro¨zel, Hecker, & Lalk, 2009). To date, the specific use of these nonDNA-based “meta” approaches for characterizing pesticide impact on soil microflora have not yet been reported. However, in the near future, it is very likely to happen with improved benchmarking of experimental protocols in this rapidly evolving field. A majority of DNA-dependent methods rely on the polymerase chain reaction (PCR) and on taxonomic information given by the conserved 16S rRNA gene, which can be amplified by PCR with the help of universal oligonucleotide primers from environmental DNA (Wilmes, Simmons, Denef, & Banfield, 2008). Widely known PCR-dependent methods consist of DNA fingerprinting of amplified DNA fragments using amplified ribosomal DNA restriction analysis (RISA, ARISA) (Kumari, Srivastava, Bhargava, & Rai, 2009), denaturing gradient gel electrophoresis (DGGE) (Feris, Hristova, Gebreyesus, Mackay, & Scow, 2004), and terminal restriction fragment length polymorphism (T-RFLP) (Schu¨tte et al., 2008). These approaches have found wide applications in the analysis of bacterial responses in the soil following pesticide contamination (Ferreira, Dusi, Costa, Xavier, & Rumjanek, 2009; Joynt, Bischoff, Turco, Konopka, & Nakatsu, 2006). The development of novel sequencing technologies (Morales & Holben, 2011) has completely modified the nature of the examination of microbial diversity and functional studies in soil ecosystems. The current techniques of nucleic acid isolation, sequencing accuracy, and data management and analysis however still limit our capacity of sampling an important and representative part of the microbial diversity of soils (Vogel et al., 2009), thus creating a great setback by preventing full exploration of metagenomic and novel sequencing techniques (Chaudhary et al., 2021). Indeed, recent estimates suggest that bacterial biodiversity may range between 104 and 107 phylotypes per gram of pristine soil with 1 g of soil containing as many as 1010 bacteria (Gangola, 2019). To our knowledge, studies utilizing next-generation sequencing technologies to investigate the detailed structure of bacterial populations in soil ecosystems and their response to contamination with pesticides have not been described yet. However, it seems clear that such studies hold a substantial potential to probe soil ecosystem responses and their timecourse with unprecedented sensitivity (Gangola, 2019; Gangola, Sharma, Bhatt, Khati, & Chaudhary, 2018).

11.7 Conclusion To increase crop yields farmers are using various technologies like use of chemical fertilizers and pesticides. The excessive utilization of such chemicals in agriculture has caused many environmental problems. These pollutants affect microbes, animals, humans, insects, water animals as well as soil fertility. The physiochemical remedial strategies are not adequate enough, thus the biological

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method that utilizes the capability of microbes for detoxification of contaminants has shown to be an effective approach: Bioremediation can be considered as an effective, nonhazardous, economic, eco-friendly, and versatile approach.

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981. Odukkathil, G., & Vasudevan, N. (2013). Enhanced biodegradation of endosulfan and its major metabolite endosulfate by a biosurfactant producing bacterium. Journal of Environmental Science and Health, Part B, 48(6), 462
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19. Rogers, S. W., Ong, S. K., Kjartanson, B. H., Golchin, J., & Stenback, G. A. (2002). Natural attenuation of polycyclic aromatic hydrocarbon-contaminated sites. Practice Periodical of Hazardous, Toxic, and Radioactive Waste Management, 6(3), 141
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CHAPTER

Microbial consortia and their application for environmental sustainability

12

Prasenjit Debbarma1, Rashmi Sharma1, Nidhi Luthra2, Satish Chandra Pandey3,4 and Shiv Vendra Singh1 1

School of Agriculture, Graphic Era Hill University, Dehradun, Uttarakhand, India 2Department of Soil Science, Indian Agricultural Research Institute, New Delhi, Delhi, India 3Cell & Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University Campus, Almora, Uttarakhand, India 4Center for Advanced Biotechnology Research, Absolute, Gurugram, Haryana, India

12.1 Introduction Industrialization, globalization, intensification of agriculture, and extensive and overuse of chemical pesticides have led to environmental pollution in the agroecosystems, contaminating water bodies, degraded soil, and subsequently causing loss of biodiversity by killing beneficial microbes, animals, insects, and other aquatic animals (Devarinti, 2016; Kughur, Otene, & Audu, 2015). The microbial communities existing in the ecosystem follow the rule of coexistence exhibiting interspecies and interkingdom relations for their abundance. These microbial communities exhibit highly interspecific complex metabolic communications and perform numerous activities to manage metabolic load for survival. Due to their unique properties, varied metabolic capacities, and ability to coexist, they can maintain environmental sustainability. An enhanced microbial biodiversity can stabilize the working of agroecosystems and improve the resilience to climate change. The applicability of microbes in organic and inorganic pollutant degradation and in reducing or transforming heavy metals make them an eco-friendly tool to be used in environmental bioremediation (Li et al., 2021; Pacheco, Moel, & Segre`, 2019). One of the most challenging issues being faced by government and nongovernment organizations is the proper discarding of waste materials, which are generated due to different human activities. The application of microbes, including bacteria, fungi, algae, etc., is one of the most successful and widely explored ways of contending with the hazard of waste disposal. Agricultural systems based on organic farming improve biodiversity and the composition of soil microorganisms. The application of organic substances in agriculture is being promoted to attain good quality food, environment protection, alongside improving microbial diversity (Paredes, Vald´es, & Nuti, 2020). To benefit from the immense capabilities of soil microbiomes, understanding the spatial and temporal distribution and composition of microbial communities becomes important (Baquerizo, et al., 2016). The larger diversity of microorganisms in the soil system interact with greater functionality, making the soil healthy. This helps in producing food with higher nutritional quality. In this chapter, we have tried to cover the applicability of various microbiomes as an eco-friendly Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00012-0 © 2023 Elsevier Inc. All rights reserved.

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approach to treating hazardous wastes, which are harmful to the environment and human beings. This chapter also deals with the understanding of efficient soil-plant-microbe interaction that contributes considerably to restoring environmental sustainability.

12.2 Microbial bioremediation of pollutants 12.2.1 Potential microbial candidates A large number of microorganisms, that is, bacteria, fungi, and algae, including versatile species of aerobes as well as anaerobes along with plants and some animals, are involved in the bioremediation process and to the reclamation of the contaminated environment (Fig. 12.1).

12.2.1.1 Bacteria 12.2.1.1.1 Aerobic Many bacteria can degrade contaminants and use them as a source of carbon or energy in the presence of oxygen (Negi, Kapri, Zaidi, Satlewal, & Goel, 2009). Carbon dioxide and water molecules are released after the complete disintegration/mineralization of contaminants (Kumar, Bisht, Joshi, & Dhewa, 2011). Aerobic bacteria having such degradation abilities are Acidovorax sp., Pseudomonas sp., Alcaligenes sp., Sphingomonas sp., Rhodococcus sp., Bacillus sp., Rhodococcus sp., Moraxella sp., Mycobacterium sp., etc. According to previous surveys, these microbes are reported to degrade pesticides, hydrocarbons, aromatic compounds, heavy metals, radioactive substances, etc. (Singleton, Guzm´an Ramirez, & Aitken, 2009). Pollutant 1 O2 -CO2 1 H2 O 1 biomass 1 residueðsÞ

FIGURE 12.1 Candidate domains with bioremediation potential.

12.2 Microbial bioremediation of pollutants

207

12.2.1.1.2 Anaerobic Anaerobic bacteria are able to utilize pollutants as a nutrient source in the absence of oxygen. The occurrence of anaerobes is not as frequent as aerobic bacteria for pollutant removal in nature. The end products of anaerobic degradation are methane and water molecules. Anaerobic bacteria have gained considerable attention from the scientific community for further exploration. They are used for the bioremediation of chlordane, polychlorinated biphenyls (PCBs), pentachlorophenol, and reductive dechlorination of chlorinated solvents such as trichloroethene (TCE), trichloroethane (TCA), carbon tetrachloride (CT), and chloroform. Pollutant 1 CO2 -CH4 1H2 O 1 biomass 1 residueðsÞ

It is reported that anaerobic degradation of explosives like TNT and other xenobiotics is preceded by Clostridium sp., Desulfovibrio sp., and archaebacteria, such as Methanococcus sp., Syntrophobacter sp., Pelatomaculum sp., Dehalobacterium sp., etc. (Ederer, Lewis, & Crawford, 1997; Sinha et al., 2009).

12.2.1.1.3 Methanotrophs Aerobic bacteria that utilize methane as the main source of carbon and energy are called methylotrophs. The very first enzyme in their pathway for aerobic degradation is methane monooxygenase (MMO), which has a broad substrate range and is active against a wide range of compounds, including chlorinated aliphatic trichloroethylene and 1,2-dichloroethane (Pandey, Singh, Singh, & Singh, 2014).

12.2.1.2 Ligninolytic fungi White rot fungi such as Phanerochaete chrysosporium and Stropharia species have the ability to degrade an extremely diverse range of recalcitrant or toxic environmental pollutants, such as polycyclic aromatic hydrocarbons, pentachloro-biphenyls, fluoroquinolone antibiotics (Christian, ˇ Shrivastava, Shukla, Modi, & Vyas, 2005; Cvanˇ carov´a, Kˇresinov´a, Filipov´a, Covino, & Cajthaml, 2012; Tortella, Dur´an, Rubilar, Parada, & Diez, 2015). This group also releases extracellular enzymes, with a low substrate-specificity, so they can also act upon various pollutant molecules (Rhodes, 2014).

12.2.1.3 Algae Algae are the alternative biological agents abundantly present in nature as a potential sink for the removal of toxic substances from the surroundings. An array of microalgae species, such as Aurosira sp., Scenedesmus bijuga, Oscillatoria sp., Chlorococcum sp., and Dunaliella sp., have been used to remediate noxious heavy metals from the soil. They are also potent in cleaning wastewater in water treatment facilities (Abdel-Raouf, Al-Homaidan, & Ibraheem, 2012). Other species, such as Chlamydomonas, Euglena, Chlorella, Selenastrum sp., etc., are reported to perform bioaccumulation and biotransformation of various aromatic chlorinated compounds like DDT, lindane, phenol, etc. (Semple, Cain, & Schmidt, 1999). Scenedesmus quadricauda, Monoraphidium braunii, and Chlamydomonas reinhardtii degrade fungicides, bisphenols, and herbicides, respectively (Dosnon-Olette, Trotel-Aziz, Couderchet, & Eullaffroy, 2010; Gattullo, Ba¨hrs, Steinberg, & Loffredo, 2012; Jin, Luo, Zhang, Zheng, & Yang, 2012).

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12.2.1.4 Animals Animals are rarely considered for bioremediation purposes due to some ethical issues. Nonetheless, the literature survey reveals that pearl oysters (Pinctada imbricata), mussels (Dreissena polymorpha), clams, fish, polychaetes (Sabella spallanzanii and Branchiomma luctuosum), bivalve mollusc, oligochaetes, and sponge (Chondrilla nucula) are suitable bioremediators for different pollutants, such as heavy metals, polymeric waste, hydrocarbons, etc., and are thus, considered as bioindicators (Lyytika¨inen, Pehkonen, Akkanen, Leppa¨nen, & Kukkonen, 2007; Martinez, Vera, & BobadillaFazzini, 2015; Zhou, Zhang, Fu, Shi, & Jiang, 2008).

12.2.1.5 Plants Another means for reclamation of the toxic environment are the plants. Phytoremediation is another perspective of bioremediation that uses plants for the treatment of contaminated soils. It is suitable when the pollutants cover a wide area and when they are within the root zone of the plant (Garbisu & Alkorta, 2003). Phytoremediation of heavy metal polluted soils can be achieved via different mechanisms of phytoextraction, phytostabilization, phytodegradation, phytostimulation, and phytovolatilization, which are discussed in detail in the chapter (Table 12.1).

12.2.2 Bioremediation: potential and sustainable process for environmental cleanup Bioremediation is based on the exploitation of different biological agents in various processes for the removal of unwanted, hazardous pollutants present in the environment. It includes in situ or ex situ experimentations using different microorganisms to clean up a contaminated site (Pande, Pandey, Sati, Pande, & Samant, 2020; Das & Adholeya, 2012). Two basic principles are involved: immobilization and mobilization in different manners.

12.2.2.1 Immobilization It confers the reduction in mobility of pollutants by altering their physical or chemical properties with the help of microorganisms. The various types of approaches that come under this category are solidification, stabilization, and precipitation (Hytiris, Fotis, Stavraka, Bennabi, & Hamzaoui, 2015). The stabilization and solidification technique is achieved by mixing the contaminated material with appropriate amounts of stabilizer material and water. The predominant mechanism by which metals are immobilized is by precipitation of hydroxides. The mobility and toxicity of metals are reduced when it is reduced to a lower redox state (Violante, Cozzolino, Perelomov, Caporale, & Pigna, 2010). These techniques can be both in situ (for volatile or semivolatile organics) and ex situ (for surface or shallow contamination).

12.2.2.2 Mobilization It imparts mobility to the metal pollutants through heterotrophic and autotrophic leaching, chelation by microbial metabolites and siderophores, methylation, and redox transformations (Akhtar, Chali, & Azam, 2013). Heterotrophic leaching of phosphate and sulfate-containing materials leads to the release of nutrients, making it better than autotrophic leaching and solubilization (Gadd, 2010). Siderophores are specific iron chelating legends that are able to bind to other metals. Methylation involves the formation of metalloids by enzymatic transfer of methyl groups. Reduction and

12.2 Microbial bioremediation of pollutants

209

Table 12.1 Different types of microbes, animals, and plants cleaning up various pollutants. Candidate domains

Types of pollutants

References

BacteriaSphingomonas sp., Bacillus sp., Pseudomonas sp., Acidovorax sp., Pseudomonas sp. Streptomyces sp.

Azo dyes, chromium, polycyclic aromatic hydrocarbons, crude oil Carbonyl

Stolz (2001); Khan and Ahmad (2006); Singleton et al. (2009); Mulet et al. (2011) Selvam and Vishnupriya (2013)

Chromium, engine oil

Isikhuemhen, Anoliefo, and Oghale (2003); Adenipekun (2008);

Mytilus edulis, Crassostrea virginica, Chione fluctifraga

Lead, zinc, organic and inorganic waste

E. fetida, L. terrestris

Arsenic, titanium oxide, chlortetracycline, chromium, copper

Gifford, Dunstan, O’Connor, Roberts, and Toia (2004), Martı´nez-Co´rdova, Lo´pezElı´as, Leyva-Miranda, Armenta-Ayo´n, and Martinez-Porchas (2011) Button et al. (2010); Bigorgne et al. (2011); Lin, Zhou, Xu, Chen, and Li (2012); Klobuˇcar et al. (2011)

Fungi Glomus intraradices, Pleurotus tuberregium Animals

Plants Lolium perenne, Pisum sativum, Arabidopsis thaliana, Transgenic tomato, Zea mays, Allium sativum, Triticum aestivum

Zinc, arsenic, 2,4,6 trinitrotoluene, cadmium

Bonnet, Camares, and Veisseire (2000); Doncheva, Stoynova, and Velikova (2001); Strand et al. (2002); Jiang, Yang, and Zhang (2007); Wang, Zou, Duan, Jiang, and Liu (2007); Ahmad, Akhtar, Zahir, and Jamil (2012)

Radioactive (uranium, radium) Chromium, nickel, selenium, petroleum waste

Edgington, Gordon, Thommes, and Almodovar (1970) Parameswari, Lakshmanan, and Thilagavathi (2010); Mane, Kadem, and Chaudhari (2013); Aditi, Kumar, and Suneetha (2015)

Microalgae Cystoseira indica Anabaena variabilis, Westiellopsis sp., Spirogyra sp, Nostoc sp, Fucus vesiculosus

oxidation process can also mobilize metals, metalloids, and other organo-metallic compounds (Wuana & Okieimen, 2011). Such processes tend to dissolve insoluble metallic compounds and minerals in soil (Martinez et al., 2015). Key environmental and biological factors affecting bioremediation (Jain et al., 2011) 1. 2. 3. 4. 5.

Population density of microorganisms having degradation potential Nutrient availability Temperature pH Water potential

210

6. 7. 8. 9. 10. 11.

Chapter 12 Microbial consortia and their application for environmental

Presence and absence of oxygen depending on the type of microbe Bioavailability of pollutants Composition of pollutants Moisture Organic matter Salinity

12.2.3 Mechanisms involved in bioremediation 12.2.3.1 Adsorption Effectiveness of bioremediation technologies is dependent on the adsorption of contaminants and it is often the principal limiting factor. Microbes can adsorb heavy metals at binding sites, which are present in their cellular structure. The adsorption capacity is dependent on the geochemistry of the system and the total biomass of the microbes (Dixit et al., 2015).

12.2.3.2 Biosorption In this mechanism, the affinity of a biosorbent toward metal ions is higher and continues till the point of equilibrium. The transformation of the heavy metals from toxic to nontoxic form takes place during the process (Dixit et al., 2015). It also involves aerobic or anaerobic microbial activities.

12.2.3.3 Molecular approach: genetically engineered microorganisms Genetic engineering is a modern technology involving the formation of microorganisms targeting specific contaminants (Wasilkowski, Swe˛dzioł, & Mrozik, 2012). The genes of microorganisms are altered to cause the desired effect. A literature survey reveals that genetically engineered microorganisms are able to degrade specific compounds (Table 12.2). There are at least four principal approaches to genetically engineered microorganism development for bioremediation application (Menn, Easter, & Sayler, 2008): Table 12.2 Genetically modified microorganisms degrading various organic compounds. Genetically modified microorganisms

Organic compounds

References

Escherichia coli AtzA

Atrazine

Pseudomonas fluorescens HK44 Pseudomonas putida Burkholderia cepacia, Hybrid poplar Comamonas testosteroni, SB3 Alcaligenes eutrophus

Naphthalene

Strong, McTavish, Sadowsky, and Wackett (2000) Sayler and Ripp (2000)

Naphthalene Toluene, trichloroethylene; carbon tetrachloride 3-Chloroaniline Chromium

Filonov et al. (2005) Taghavi et al. (2005); James, Xin, Doty, and Strand (2008) Bathe, Schwarzenbeck, and Hausner (2009) Srivastava, Jha, Mall, and Singh (2010)

12.2 Microbial bioremediation of pollutants

• • • •

211

Modification of enzyme specificity and affinity Pathway construction and regulation Bioprocess development, monitoring, and control. Bioaffinity bioreporter sensor applications for chemical sensing, toxicity reduction, and endpoint analysis.

12.2.4 Enzymes for bioremediation Enzymes being biological catalysts lower the activation energy along with the conversion of substrates into products under optimum conditions(Pandey, Tripathi, Tripathi, Pandey, & Gangola, 2019)(Gangola, Joshi, Kumar, & Pandey, 2019). Two important classes of enzymes reported for bioremediation are oxidoreductases and hydrolytic enzymes.

12.2.4.1 Microbial oxidoreductases Oxidoreductases belong to group 1 of the enzyme class and may further be classified according to the type of bond oxidized or reduced. Bacterial oxidoreductases are an important group of enzymes that play an essential role in the biotransformation of many environmental pollutants like xenobiotic and radioactive compounds and azo dyes (B´artı´kov´a et al., 2015). They are further classified as oxygenases, laccases, and peroxidases.

12.2.4.1.1 Microbial oxygenases They utilize FAD/NADP/NADPH to transfer oxygen from molecular oxygen to reduced substrate. They also increase the reactivity and solubility of organic compounds. They are further classified as monooxygenases and dioxygenases (Karigar & Rao, 2011). Monooxygenases incorporate one oxygen molecule. Dioxygenases carry out the oxidation of a wide range of substrates.

12.2.4.1.2 Microbial laccases They catalyze the oxidation of reduced phenolic and aromatic substrates. Laccases occur in multiple isoenzyme forms where each form is encoded by a separate gene. (Chandra & Chowdhary, 2015). The activity of the laccase enzyme is dependent on the pH and the presence or absence of inhibitors like azide, cyanide, and hydroxide.

12.2.4.1.3 Microbial peroxidases They speed up the oxidation of lignin and phenolic compounds. Hydrogen peroxide oxidoreductase is the donor. They can be heme and nonheme proteins. They are further classified into lignin, manganese, and versatile peroxidases (Karigar & Rao, 2011).

12.2.4.2 Microbial hydrolytic enzymes Microbial hydrolytic enzymes reduce the toxicity of a molecule by disrupting the chemical bonds. They belong to group 3 of the enzyme class. Enzymes such as amylase, protease, and lipase used in the food and chemical industries (S´anchez-Porro, Martin, Mellado, & Ventosa,2003). Cellulase and hemicellulase find application in biomass degradation (Kuhad, Gupta, & Singh, 2011; Mathew,

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Chapter 12 Microbial consortia and their application for environmental

Sukumaran, Singhania, & Pandey, 2008). The hydrolytic enzymes are further classified as lipases, cullulases, and proteases.

12.2.4.2.1 Microbial lipases Lipases degrade lipids derived from a variety of plants, animals, and microorganisms. Research illustrates that lipase activity reduces hydrocarbons, thus finding application in the bioremediation of oil spills (Balaji, Arulazhagan, & Ebenezer, 2014). The production cost of lipase is higher, which restricts its use in the industrial sector.

12.2.4.2.2 Microbial cellulases Cellulases can convert waste cellulose material into food. Cellulases are usually a mixture of endoglucanase, exoglucanase, and β-glucosidase (Bennett, 2002).

12.2.4.2.3 Microbial proteases Proteases hydrolyze the breakdown of proteins. They hydrolyze several proteinaceous substances which are released into the atmosphere. They are divided into endopeptidases and exopeptidases. Exopeptidases act near the terminal while endopeptidases act on the inner regions of the peptide chain. The enzyme activity is reduced by the presence of free amino and carboxyl-terminal (Karisgar & Rao, 2011) (Table 12.3). Table 12.3 Different types of enzymes working at a molecular level in the reclamation of pollutants. Source of enzymes

Class of enzymes

Pollutants

References

Psychrotrophic microbe

Dioxygenase

Whyte, Greer, and Inniss (1996)

Fungus Phanerochaete, Chrysosporium, Pyricularia oryzae Microbe (polluted water)

Lacasses, manganese, and lignin peroxidases

Aromatic compound, 2,3 catechol phenolic azo dyes

Textile and synthetic dye, xenobiotic 2,4 dichlorophenol

Husain (2006)

Hydrocarbons/ organic Triolein

Prasad and Manjunath (2011)

(a) Oxidoreductases

Plant Minced Shepherd’s purse rot

Oxidoreductase Oxidoreductase

Chivukula and Renganathan (1995), Rubilar, Diez, and Gianfreda (2008)

Park, Park, and Kim (2006)

(b) Hydrolytic enzymes Bacteria

Lipases

Fungus, Candida rugosa

Lipase

Karigar and Rao (2011)

12.2 Microbial bioremediation of pollutants

213

12.2.5 Major bioremediation strategies/techniques and their types 12.2.5.1 Bioremediation It is a biological process whereby organic wastes are biologically degraded under controlled conditions. For bioremediation to be effective, microorganisms must enzymatically attack contaminants and convert them to harmless products. The different types of in situ and ex situ bioremediation (Sharma, 2012) are discussed as follows.

12.2.5.1.1 In situ It involves the treatment of contaminated material at the site. The following are different technologies under in situ bioremediation: 1. Biosparging: In this process, an indigenous microorganism biodegrades the pollutants in the saturated zone. The air (or oxygen) and nutrients are injected into the saturated zone to increase the biological activity of the indigenous microorganisms. 2. Bioventing: In this process, an indigenous microorganism biodegrades the pollutants in the unsaturated zone. Bioventing systems deliver air from the atmosphere into the soil above the water table through injection wells placed in the ground where the contamination exists. 3. Biostimulation: The term biostimulation is often used to describe the addition of electron acceptors, electron donors, nitrogen, oxygen, and carbon to stimulate native microbial populations. 4. Bioaugmentation: In this, selected (standardized) bacteria are added to an area that has been polluted by any unwanted material.

12.2.5.1.2 Ex situ It involves the treatment of contaminated material elsewhere from the main site. The different technologies under ex situ bioremediation are discussed as follows. 1. Solid phase: Solid-phase bioremediation is a process that treats soils over the ground areas equipped with large collection systems to prevent escaping of any contaminant from the treatment. Moisture, heat, nutrients, or oxygen are controlled for the application of this treatment to enhance biodegradation. Solid-phase systems are relatively simple to operate and maintain, requiring a large amount of space, and cleaning up and more time to complete than slurry-phase processes. Solid-phase soil treatment processes include landfarming, soil biopiles, and composting. a. Landfarming: In this relatively simple technique, contaminated soils are excavated and spread on a pad with a built-in system to collect any leachate or contaminated liquids that seep out of contaminant-soaked soil. The soils are periodically turned over to mix air into the waste. Moisture and nutrients are controlled to enhance bioremediation. In general, this practice is limited to 20
30 cm of soil. It has received much attention as a disposal alternative because of its potential to reduce monitoring and maintenance costs. b. Soil biopiles: Contaminated soil is piled in heaps several meters high over an air distribution system. Aeration is provided by pulling air through the heap with a vacuum pump. Moisture and nutrient levels are maintained at levels that maximize bioremediation. The soil heaps

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Chapter 12 Microbial consortia and their application for environmental

can be placed in enclosures. Volatile contaminants are easily controlled since they are usually part of the air stream being pulled through the pile. c. Composting: Biodegradable waste is mixed with a bulking agent such as straw, hay, or corn cobs to make it easier to deliver the optimum levels of air and water to the microorganisms. Three common designs are static pile composting (compost is formed into piles and aerated with blowers or vacuum pumps), mechanically agitated in-vessel composting (compost is placed in a treatment vessel where it is mixed and aerated), and windrow composting (compost is placed in long piles known as windrows and periodically mixed by tractors or similar equipment). 2. Slurry phase: bioreactors: In a large containment vessel (bioreactor), contaminated soil is mixed with water and other additives to keep the native microorganisms in contact with the pollutants in the soil. Nutrients and oxygen are added, and conditions in the bioreactor are controlled to create the optimum environment for the microorganisms to degrade the pollutants. After completion of the treatment, the solids are dehydrated, which are disposed of or treated further if they still contain pollutants. This type of biological treatment can be a relatively quick process compared with other biological treatment processes, particularly for contaminated clays. The success of the process is highly dependent on the specificity of the soil and chemical composition and characteristics of the contaminated material. This technology is particularly useful where rapid remediation is in high demand.

12.3 Rhizospheric soil-plant-microbe interactions The importance of soil and its dynamic functioning is irrefutable. It is the efficient soil-plantmicrobe interaction that contributes considerably in restoring environmental sustainability. Rhizospheric microbes have expansive ability of governing nutrient transformation, fixation, solubilization, mobilization, and enhancing their use efficiency, thereby contributing to soil, plant, and environmental sustainability. The term rhizosphere, coined by Lorenz Hiltner in 1904, denotes the environment under the influence of roots. The root surface is termed the inner rhizosphere (10
500 microns) and the area embracing the immediate adjacent part of the roots is termed the outer rhizosphere (500
5000 microns). Compared with the nonrooted bulk soil, the rhizospheric soil contains a much larger population of microbes because of the root exudates, viz., carbohydrates, organic acids, vitamins, flavonoids, nucleotides, enzymes, hormones, etc., which leads to the positive rhizosphere effect (Kumar, Maurya, Raghuvanshi, Meena, & Islam, 2017).

12.3.1 Plant growth-promoting rhizobacteria A group of root colonizing, plant life-supporting soil microorganisms, enhancing plant growth and yield by various mechanisms is known as plant growth-promoting rhizobacteria (PGPR), or probiotic rhizobacteria, or plant probiotic microorganisms (PPMs) (Picard, Baruffa, & Bosco, 2008). The role of PGPR may be summarized as follows.

12.3 Rhizospheric soil-plant-microbe interactions

215

12.3.1.1 Direct mechanisms • • • •

Biological nitrogen fixation Nutrient solubilization and translocation Phytosiderophores production, which increases iron availability and suppresses plant pathogens. Phytohormones production, which enhances the growth of plants

12.3.1.2 Indirect mechanisms• • •

Induced resistance system Disease suppression Abiotic stress tolerance

12.3.2 Nitrogen-fixing microbes Biological nitrogen fixation (BNF) is the most crucial biochemical reaction for sustaining life. BNF reduces the inert nitrogen gas (N2) of the atmosphere to reactive ammonia that is taken up by plants and microbes through the nitrogen cycle. Nitrogen-fixing rhizobacteria fix nitrogen symbiotically (Rhizobium) and nonsymbiotically (Azotobacter, Azospirillum, Beijerinckia, etc.). Symbiotic nitrogen fixation is of paramount importance from ecological and economical point of view as it reduces the dependency on external inputs. Symbiotic nitrogen fixers can be nodule forming or nonnodule forming legumes or nonlegumes, stem nodulating, or root nodulating. Broadly two major groups of nitrogen-fixing bacteria, that is, Rhizobia and Frankia have been tested. Rhizobia can supply a major part of nitrogen requirement in most of the cropping systems that includes legumes and ensure sufficient nitrogen supply (Gupta, 2004). Frankia is an actinomycetes mainly associated with woody group plants. Alnus, Myrica, Casuarina are widely known to have symbiotic relationship with Frankia (Tilak et al., 2005).

12.3.3 Nutrient-solubilizing microbes Some nutrients, though adequately present in the soil, are unavailable to the plants. These nutrients are present in an insoluble form that can be solubilized by certain microorganisms, such as phosphorus-solubilizing microbes (Bacillus, Pseudomonas) solubilize the insoluble and precipitated tricalcium phosphate, hydroxyapatite, etc.; potassium-solubilizing rhizobacteria (Bacillus mucilaginosus, Pseudomonas) solubilize the insoluble potassium and make them available for plants (Shekhar et al., 2000). These nutrient solubilizing microbes secrete organic acids, which reduces the pH in their vicinity and aids in the dissolution of the fixed form of nutrients in soil by chelation and ion-exchange reactions (Shivran, Kumar, & Kumari, 2013). Potassium-solubilizing bacteria can stimulate plant growth and increase the nutrient concentration in plants (Basak & Biswas, 2009; Lin, Rao, Sun, Yao, & Xing, 2002).

12.3.4 Nutrient-mobilizing microbes Modern agricultural practices are exceedingly dependent on chemical fertilizers obtained from nonrenewable resources. Overuse of these nonrenewable resources may lead to a sustainability crisis,

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Chapter 12 Microbial consortia and their application for environmental

which can be avoided by using nutrient-mobilizing microbes that can facilitate nutrient acquisition from the soil itself. One such association is mycorrhizal association. The association between fungi and roots of higher plants is commonly termed as mycorrhizal association. The mycorrhizae are of two types, namely ectomycorrhizae and endomycorrhizae. Ectomycorrhizae (Amanita, Boletus) grow intercellularly and form a sheath like structure around the root surface known as hartig net, which is usually 80
100 cm thick. While endomycorrhizae (Glomus, VAM) can grow both interand intracellularly. They grow intercellularly with dichotomous branching known as arbuscules. At the terminal end they form storage organs known as vesicles, which store nutrients and lipids.

12.3.4.1 Role of mycorrhizal association • • •

Alteration in the root morphology and increment in the root surface, hence high nutrient absorption. Production of phosphatase enzymes, which releases insoluble nutrients Increase in nutrient mobility

12.3.5 Arbuscular mycorrhizal fungi The mycorrhizal association allows for a complex multispecies underground network between soil fungus and plants (Heijden, Martin, Selosse, & Sanders, 2015). Among the underground soil microorganisms, arbuscular mycorrhizal fungi (AMF) form a symbiotic composite association with 93% of terrestrial plant families, including multiple agricultural crops. They belong to the subphylum Glomeromycotina, containing Archaeosporales, Diversisporales, Glomerales, and Paraglomerales (Spatafora, et al., 2016). The AMF symbiosis receives carbohydrates and lipids from plants. AMF have structures like arbuscules and vesicles, which allow the exchange of nutrients with plants. The beneficial aspects of the association for plants are related to increased nutrient uptake
promoting phosphorus, iron, and zinc uptake by plants (Rich, Nouri, Courty, & Reinhardt, 2017); crop growth and yield; reduced fertilizer needs in agricultural systems (Smith, Jakobsen, Grnlund, & Smith, 2011), improved soil structure, water retention (Cavagnaro et al., 2015); and resistance to biotic stresses (Cameron, Neal, van Wees, & Ton, 2013). The positive aspects of arbuscular mycorrhizae are clubbed with a sustainable and organic agriculture system to get quality food and at the same time reducing environmental impairment (Sa¨le et al., 2015; Silva-Flores, Bueno, & Neira, 2019). Such AMF association can be an excellent alternative to overcome the biotic or abiotic stress in soils under the agricultural system.

12.4 Conclusion Diverse microorganisms and their vast physiological activities offer tremendous opportunities in environmental cleanup and sustainability. The nature and mechanism to accomplish the overall synergy may vary with different ecosystems in which they are being employed or augmented. These microorganisms are not only efficient in bioremediation of xenobiotics but they are also the most important components of the agricultural system. Therefore identification and characterizing of the molecular basis of these potential candidates are very important in enhancing their ability for environmental sustainability for a long term.

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150.

CHAPTER

Recent advances in in silico approaches for removal of environmental pollutants

13

Tushar Joshi1, Shalini Mathpal1, Priyanka Sharma2, Satish Chandra Pandey3,4, Priyanka Maiti5, Mahesha Nand6 and Subhash Chandra7 1

Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India 2Department of Botany, Kumaun University, Nainital, Uttarakhand, India 3Center for Advanced Biotechnology Research, Absolute, Gurugram, Haryana, India 4Cell & Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University Campus, Almora, Uttarakhand, India 5Centre for Environmental Assessment and Climate Change, G.B. Pant National Institute of Himalayan Environment (GBP-NIHE), Kosi-Katarmal, Almora, Uttarakhand, India 6ENVIS Centre on Himalayan Ecology, G.B. Pant National Institute of Himalayan Environment (GBP-NIHE), KosiKatarmal, Almora, Uttarakhand, India 7Computational Biology & Biotechnology Laboratory, Department of Botany, SSJ University, Almora, Uttarakhand, India

13.1 Introduction The idea of the environment is as old as the idea of nature itself. The word environment has a broad meaning that refers to the conditions in which creatures made up of air, water, food, sunlight, and other elements thrive and serve as living sources of life for all living and nonliving species, including plants. However, the increasing use of xenobiotics is liable to create dangers to human health, destruction to living resources and ecological systems, damage to structures or amenities, or interference with lawful uses of the environment (Appannagari, 2017). Xenobiotics are those chemical compounds that are not normally generated or anticipated to be present within organisms. Hence these xenobiotic chemicals come into the environment from the overuse of a variety of industries in metropolitan areas (Pande, Pandey, Sati, Pande, & Samant, 2020; Mishra et al., 2021). The xenobiotics are released into the environment as a waste product from factories, resulting in heavy metal pollution and posing a serious hazard to human health and the ecosystem. The heavy metals also pollute the soil and water, which are mostly anthropogenic in nature. Although certain heavy metal ions are necessary, the majority of them are hazardous at low concentrations. Heavy metal treatment generates sludge, which cannot be destroyed or changed, and releases nonbiodegradable chemicals (Nies, 1999). Even at low concentrations, heavy metals are cytotoxic, carcinogenic, and mutagenic (Salem, Eweida, & Farag, 2000). Textile manufacturing is one of the sectors that pollute the environment. Textile mills and their wastewater have been growing in tandem, resulting in a huge environmental concern throughout the world. Two-thirds of the dyestuff market is accounted for by the textile sector. Approximately 10%
15% of the colors used are discharged into the wastewater during the dyeing process. The textile sector is widely acknowledged as the primary source of pollution in the environment (Pande et al., 2019; Samchetshabam, Hussan, Choudhury, & Gita, 2017). Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00011-9 © 2023 Elsevier Inc. All rights reserved.

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Paper industries generate a wide range of pollutants by releasing partly treated effluents into the environment (Majumdar et al., 2019). Partially or poorly treated paper mill effluents contain a variety of complex chlorinated organic and phenolic compounds as well as contaminants such as sulfur-containing compounds (Latorre, Rigol, Lacorte, & Barcelo´, 2005). All of these chemicals constitute a growing danger to biodiversity in terms of environmental safety due to their hazardous character. Apart from these sectors, numerous other sectors, including power, cement, iron and steel, chloralkali processes, pharmaceuticals, fertilizers, refineries, pesticides, distilleries, sugar, and tanneries, emit substantial amounts of pollutants in the form of air and water emissions. These pollutants must be controlled to safeguard the ecosystem and environment. Bacteria play an important role in the biodegradation of industrial pollutants, thereby helping to reduce pollution in the environment (Pande, Pandey, Sati, Bhatt, & Samant, 2022). They operate on complex contaminants and either break them down into the simplest molecule or reduce their toxicity by changing their chemical makeup by converting them (Chandra, Raj, Yadav, & Patel, 2009). Chlorinated and phenolic contaminants have a long half-life in the environment and are seldom destroyed in natural settings or by other traditional techniques. Bacterial-derived enzymes can break down complex and chlorinated chemicals via chemical processes, using contaminants as a substrate to break them down to their most basic form. Although bacterial-mediated bioremediation has the greatest bioremediation rate, screening bacteria for appropriate enzymes that act on the target pollutant is a time-consuming and labor-intensive procedure, and it is difficult to run several biodegradation experiments in the wet lab at the same time (Thouand, 2014). Techniques used in the wet lab for the biodegradation process are shown in Fig. 13.1. The in silico bioremediation technique is recognized for its ability to mitigate this problem since it is performed on specialist computer systems; nevertheless, this approach merely simplifies the problem and requires additional in vitro and in vivo activities (Aukema et al., 2017). For toxicity assessment and biodegradation of environmental contaminants, in silico approaches are used in a variety of domains. In silico bioremediation employs a variety of computer-aided approaches to gain insight into the biodegradation process and to better understand the mechanism of enzyme
pollutant interaction at the atomic level (Cheng et al., 2012). In silico bioremediation is a computer-based method that uses and also depends on a variety of disciplines of research, including genomics, computational biology, proteomics, bioinformatics, molecular modeling, molecular dynamics simulation (MDS), and a specialized algorithm for route prediction (Ding et al., 2018). In silico bioremediation techniques provide a simultaneous degradation of a variety of contaminants by predicting potential degradation routes and enzymatic systems (Kleinman et al., 2014). Hence as an emerging alternative or computational method, in silico approaches are being used for the bioremediation of complex pollutants. Thus this chapter will draw the attention of researchers to various computational approaches to find new solutions to control pollution, giving new ideas to take initiatives to control pollution.

13.2 In silico approaches The in silico bioremediation method is a novel multidisciplinary approach that deals with the breakdown of chemical compounds or contaminants by investigating their structure and binding characteristics. In silico bioremediation uses computer-based technologies that combine multiple computational

13.3 In silico approach for toxicity analysis of pollutants

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FIGURE 13.1 A schematic illustration of bioremediation approach using in vitro conditions.

methodologies to reduce hazardous chemicals by anticipating their probable degradation routes and changing characteristics. The most current technique for discovering new ways and efforts to improve the conventional treatment of hazardous chemicals with microorganisms is multidisciplinary research on bioremediation processes. The quantity of bioremediation research has steadily risen in recent years. The bioremediation approach employs in silico methods, mathematical models, metabolic engineering, genomics, proteomics, and biodegradation pathways to provide accurate biodegradation findings. Currently, scholarly interest is focused on in silico bioremediation as a means of reducing environmental contaminants that are resistant to traditional bioremediation (Huang et al., 2013). In recent years, system biology has been integrated into research for improved microbial degradation studies, where degradation study is created based on prior involvements and materials obtained via earlier research (Akhter, Tasleem, Alam, & Ali, 2017). Before the confirmation of computer-projected findings in real time under wet lab conditions for the investigation of specific pollutants degradation, an in silico bioremediation approach might be utilized to manage a cost-effective solution of bioremediation.

13.3 In silico approach for toxicity analysis of pollutants Many methods have been created for the environmental cleaning of hazardous chemicals by microorganisms; however, they cannot be entirely effective without knowing the toxicity level of the

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compounds, as toxicity influences the survival of the degradative strains (Copley, 2009). Thus, before putting a lot of work into developing in silico bioremediation technology for any chemicals, in silico techniques must be used to estimate their toxicity levels. Quantitative structure
activity relationships (QSARs) are an in silico approach for determining a QSAR model based on experimental or computed data (Schultz, Cronin, Walker, & Aptula, 2003) (Fig. 13.1). A combined approach with techniques like 3D-QSAR, docking, local binding energy (LBE), and GRID can be used to estimate the toxicity of allele-chemicals such as pesticides (Fratev, Lo Piparo, Benfenati, & Mihaylova, 2007). OSIRIS Property Explorer is an in silico tool for determining the toxicity of any chemical molecule. The toxicological profile of known poisons will serve as a foundation for determining the toxicity of an unknown chemical. Another technique that can be used to detect the concentration of chemicals and toxic levels in the tissue is pharmacokinetic (PK) models. PK model relates chemical concentration in tissues to time, estimates the number of chemicals in different parts of the body, and quantifies ADME (absorption, distribution, metabolism, and excretion) processes (Jack, Wambaugh, & Shah, 2013; Sung et al., 2014). In PK, toxicokinetic models are used to relate chemical concentration in tissues to the time of toxic responses. In the study carried out by McRobb et al. (2014), they identified aquatics models like Danio rerio, Pimephales promelas, Takifugu rubripes, Xenopus laevis, and Xenopus tropicalis which have toxicity targets similar to human targets. Through in silico study, they analyzed the conservation of human toxicity and endocrine disruption targets in aquatic species which are generally caused by endocrinedisrupting chemicals (EDCs) and adverse drug reactions. Further, they selected an animal model for toxicity testing whose sequence identity is often reliant between human proteins and their animal ortholog. They compared the ligand-binding sites of 28 human “side-effect” targets to their corresponding ortholog subpockets involved in protein interactions with specific chemicals. In a recent study, Hemmerich and Ecker (2020) predicted certain hazardous elements, such as mutagenic or organ toxicity, based on the computational model through in silico techniques.

13.4 Molecular docking approach for bioremediation In the in silico bioremediation process, molecular docking techniques are employed as a methodology for predicting and investigating binding characteristics of the ligand (pollutants) and protein that are involved in the process. Docking is a computational approach that uses specialized algorithms to discover the optimum ligand-binding site for a protein or enzyme’s binding site or active site (Repasky, Shelley, & Friesner, 2007). Docking is used to anticipate the optimal interaction between receptors and ligands to produce a stable complex while lowering the binding energy of the complex. The receptor molecule or enzyme binds to the substrate or pollutant to create a stable complex with favorable ligands or pollutants binding conformations in the cavity or active site of an enzyme during the docking process. The docking methods determine the energy scores for the best fitting or conformations of the ligand by computing the active site characteristics of proteins and enzymes and attempting to fit the ligand into the active site. The molecular docking method is used in in silico bioremediation to screen contaminants for enzyme binding (Gupta, Sharma, & Kumar, 2018). By binding into a best-fit active site and calculating energy scores, pollutant binding affinity can predict how enzymes break down or catalyze the pollutant (Srinivasan

13.4 Molecular docking approach for bioremediation

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et al., 2019). A molecular docking algorithm is a sophisticated computer software that analyzes and inspects the protein sequence and calculates the active site or binding pockets that might also occur. The technique calculates the best-fit pollutant location as a binding site in an enzyme’s surface structure and predicts the posture computationally. The software reviews the computations after docking and returns a few best-fitted energy scores and the lowest energy, which is referred to as best-fitting or docked energy (Srinivasan & Sadasivam, 2018). Many docking methods have been developed for biological molecules such as enzymes, organic pollutants, and protein
protein, DNA
DNA, and protein
DNA binding or interactions. The docking technique is used in computational or in silico bioremediation to screen contaminants for binding and catalytic interaction, and to forecast the optimal docking score or comprehend the degradation of pollutants with their suitable degrading enzyme (Fig. 13.2) (Liu et al., 2018). Many studies are available where researchers used molecular docking techniques for the bioremediation of pollutants and chemical substances. The study by Akhter et al. (2017) used in silico approach for the bioremediation of arsenic by structure prediction and they further used docking studies to understand bioremediation to eliminate toxic metal arsenic in water, air, and soil by arsenite oxidase (AO); and bacterial enzymes from Pseudomonas stutzeri TS44. In another study, Wang et al. (2016) used a molecular docking

FIGURE 13.2 Schematic graphical overview of in silico bioremediation approach flow; from the screening of pollutants to degradation pathway prediction using databases, molecular docking, and molecular dynamics simulation techniques.

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study to show that phenol was a valid inhibitor for cyclin E in the cell cycle and cell metabolism. On the basis of these studies, we can say that molecular docking techniques can be used to remove chemical substances from the environment. We can also give a brief introduction about those particular enzymes where chemical and toxic substances can bind and cause harmful effects in the living body.

13.5 Molecular dynamics simulation approach for bioremediation Molecular dynamics simulation (MDS) is another approach that gives insights into the activity of proteins and ligands or pollutant bindings. MDS is a method of computing the dynamics of a macromolecule in a particular time interval ranging from a picosecond to a microsecond. MDS gives information on the changes and conformational aberrations that occur in a protein-ligand complex or enzyme pollutants over a defined time frame in a specific format (Zhang, Dong, Bedrov, & van Duin, 2019). The MDS technique is based on Newton’s second law of motion, F 5 ma, where F is the force applied to the particle, m is its mass, and a is the acceleration. MD is based on computer methods and has become indispensable for evaluating the corporeal basis of protein or enzyme structure as well as their biological properties in a live system. MDS of enzymes and pollutants investigates the dynamics of all atoms in enzymes or protein molecules, capturing the behavior of molecules and events like ligand binding and releases from the active site of enzymes (Hollingsworth & Dror, 2018). The MDS approach often employs a three-dimensional structure of proteins or other macromolecules, such as ligands, which are based on experimental limitations from NMR spectroscopy or X-ray crystallography. MDS, when run on a high-performance computer with a specialized graphics processing unit, allows for the virtual study of biomolecular interactions across time scales equivalent to those found in real cell systems. On a supercomputer, an enzyme simulation of molecular dynamics for B2500 ns for a molecule with 25,000 atoms and less than B150 ns for a 700,000 atomic composition may be completed in less than an hour. However, in a single day, a typical computer system with a high-end graphics processing unit may perform up to a few nanoseconds. Process enzymes are promising biological agents for removing or reducing complicated contaminants from the environment in bioremediation. Using the MDS method, in silico bioremediation has been used to tackle environmental pollutant-related concerns in a short amount of time. During the interplay of enzyme and pollutant catalytic behaviors, the MDS method offers the dynamicity of an enzyme on a given time scale. By presenting a protein-ligand RMSD trajectory map for a given time scale, MDS of an appropriate time scale investigates the enzyme pollutants degrading nature as a binding activity or catalytic activity of ligands or pollutants (Fig. 13.2) (Chen et al., 2011). In many studies, researchers used MDS techniques to check the interaction between proteins of bacteria and pollutants or chemical substances. Bhatt et al. (2021) used MDS to understand the molecular mechanism of microbial degradation of glyphosates. In their study, they used glyphosate oxidoreductase (GOX) and C
P lyase enzymes to get knowledge of the interaction with glyphosate degradation. Another recent study (Pande et al., 2021) used MDS techniques to get information about the role of laccase enzymes of microbes on dye and their intermediate metabolite degradation. These studies show that MDS techniques can be used to get information on biodegradation.

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13.6 Biodegradation pathway prediction Biodegradation pathway prediction is a relatively new computer approach for predicting potential pollutant degradation routes (Cardona & Su´arez, 2010). Paper mills discharge a wide range of contaminants into the environment, which can affect biodiversity in a variety of ways. Some are extremely sophisticated and cannot be degraded in nature. The scientific community is very much concerned about the complexity of contaminants in terms of their component nature and resistance to degradation. Route prediction may be able to tackle this challenge by predicting the probable degrading pathways for pollutants of concern that can be broken down from their complicated structure to their simplest forms through specific transformation phases. A biodegradation pathway prediction website comprises data obtained from microbial enzymatic system reactions, which might be used to forecast the transformation routes of environmental contaminants, xenobiotics, chemical compounds, and other substances (Moriya et al., 2010). The data is uploaded to the server in the form of a chemical descriptor (SMILES). The server uses the provided data associated with individual reactions to predict metabolic pathways, and the database or server’s predicted results, presented in 2D graphical forms, contain transformed compounds in the simplest form possible by processing and applying rule-based enzyme reactions (Wackett, 2013). In in silico bioremediation, biodegradation pathway prediction is a recent trend. It is a timesaving and cost-effective approach that predicts routes on computer systems and exposes potential transformation pathways of worry contaminants, which can then be confirmed in a wet lab.

13.7 Metabolic pathway simulation of biodegradation The EAWAG-BBD database provides data on microbial biochemical catalysis processes, such as biodegradation routes for different chemicals and xenobiotics. The EAWAG-BBD website produces and delivers sets of data based on catalytic reactions of microbial enzymes; they give significant insights about pollutant degradation by anticipating catalytic pathways on a standard computer system. In recent decades, the production of a wide range of synthetic compounds has increased, and to investigate the toxicological impacts on the environment, nearly 10 million synthetic chemicals are utilized in industries to manufacture novel materials. Therefore this database can be used to collect information on the toxicity of chemical compounds through catalytic pathways. (The EAWAG Biocatalysis/Biodegradation Database, which includes the EAWAG-BBD pathway prediction system, may be accessed by forwarding the web URL http://eawag-bbd.ethz.ch to the EAWAG-BBD pathway prediction system.)

13.8 Bioremediation using proteomics The expression of proteins in the cells of an organism changes depending on the environment. Adaptive reactions to diverse environmental stimuli, such as the presence of hazardous

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substances in the environment, may cause variations in physiological responses. Proteomics has enabled thorough analysis of global changes in protein composition or abundance, as well as the identification of essential proteins implicated in microorganism response to a specific physiological condition. Several studies have identified groups of proteins that are up or down-regulated in response to particular contaminants. Natural and genetically modified microbes have been used for partial bioremediation of polycyclic aromatic hydrocarbons (PAHs) in situ and ex situ. The physiological changes in an organism during bioremediation may be studied using a proteomics method to learn more about bioremediation-related genes and their control. The proteome of membrane proteins is of great importance in bioremediation, particularly in the biodegradation of PAHs. Souza-Neto et al. (2014) identified bacteria that degrade crude oil and did a proteomic analysis of isolates that grow in the presence of that pollutant to evaluate the profile of protein expression.

13.9 Bioremediation using genomics Genomic is a sophisticated computer technology that uses the whole DNA sequence of an organism to study the structure and function of all genes in that organism. A nonmolecular technique, or in silico, is a treatability research in which samples of the polluted environment are incubated in the laboratory and the rates of contaminant breakdown or immobilization are documented. The technique is now the most widely used microbiological examination of bioremediation processes. Such investigations offer an estimate of the microbial community’s potential metabolic activity, but they reveal nothing about the microorganisms responsible for bioremediation or why certain modifications that may be assessed for designed bioremediation applications promote or do not promote activity. When bioremediation processes are studied in more depth, it is common to try to identify the species that are involved. For the development and interpretation of molecular investigation, the extraction and characterization of pure cultures have been and will continue to be vital. Isolates, representative of microorganisms involved in bioremediation processes, can be extremely valuable because they allow researchers to investigate not only their biodegradation reactions but also other aspects of their physiology that are likely to control their growth and activity in contaminated environments. Before the application of molecular techniques in bioremediation, it was unclear if the isolated species were important in bioremediation in situ or weeds that grew quickly in the lab but were not the main organisms responsible for the environmental response of interest. Using genetics, we can identify which organisms are vital for biodegradation. Researchers can also utilize genetics to modify organisms at the gene level by determining which genes are critical in the biodegradation process; these organisms are known as genetically modified organisms (GMOs). Toxic chemicals, xenobiotics, and pesticide substances are being remedied using GMOs in environmental biotechnology (Malla et al., 2018). Understanding natural microbial communities is necessary for designing a synthetic colony (Schloss & Handelsman, 2008). It is difficult to tell which species are involved in bioremediation in a natural population (Grosskopf & Soyer, 2014). As a result, estab-

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lishing an artificial microbial community with function-specific species for bioremediation goals using a synthetic microbial community is a promising strategy. These communities could serve as a controlled model system for the study of functional, ecological, and structural aspects. Based on their interactions and functions, Grosskopf and Soyer (2014) defined synthetic communities as the cultivation of two microbial species under well-specified conditions (Bruggeman & Westerhoff, 2007). Genomic techniques are very useful and researchers are using these techniques to identify the group of families in bacteria that will be effective for biodegradation. Morales et al. (2017) predicted a total of 11,195 protein-coding genes including a diverse group of gene families from Scedosporium apiospermum involved in hydrocarbon degradation pathways like dioxygenases and cytochrome P450. A recent study by Li et al. (2019) examined the metabolic capacity of microorganisms in contaminated (CMS) and pristine (PMS) mangrove sediments at subtropical and tropical coastal sites. Through comparison of CMS with PMS, they discovered that the former had a reduced diazotroph abundance and nitrogen-fixing capability, but had an enhanced metabolism that is linked to the production of microbial greenhouse gases through greater methanogenesis and sulfate reduction.

13.10 Systems biology methods The development of genomic technology and systems biology offers new ways to biological processes that are now uncontrollable and at the core of significant environmental issues. The biological destiny of the roughly eight operons implicated in this process is a significant task in this regard. The University of Minnesota’s biodegradation database identified thousands of novel chemical compounds that are prevalent in contemporary Organic and Industrial Chemistry. A vast range of microbial strains can thrive on contaminants in the environment (about 800 today). Bioremediation has been studied from a molecular biology perspective, characterizing chemical reactions and genes; the University of Minnesota has made a pioneering effort in compiling nearly all of our current knowledge on biodegradation pathways and developing systems to deal with that data, such as learning rules for predicting biodegradative features. However, the majority of information on microbial biodegradation of xenobiotics and refractory compounds in the literature focuses on duos consisting of one pollutant versus one strain, leaving out important elements of realistic situations like gene exchange and metabolic cooperation. This community-based approach to genomes and functionomes (as opposed to organism-based approaches) is leading to the sequencing of genomes of communities and ecosystems, rather than single species. These circumstances highlight the need to qualify and represent information in biodegradation databases in a way that allows the entire known biodegradative potential of the microbial world to be crossed with the entire collection of compounds known to be partially or completely degraded (mostly) by bacteria (Kitano, 2002). For bioremediation objectives, it is vital to characterize cellular processes, microbial community composition, and metabolic activity in the presence of stress caused by toxic substances that modify the microbial community’s regular behavior (McGenity, Timmis, & Fernandez, 2016).

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Furthermore, the ultimate goal of bioremediation research is to eliminate or detoxify dangerous chemical compounds, and bioremediation effectiveness necessitates a thorough understanding of all environmental elements that influence microbial cellular processes and cell-cell interactions (Noble, Pro¨schel, & Mayer-Pro¨schel, 2011). Nowadays systems biology approaches are being used by researchers (Iman et al., 2017); for example, in a study, scientists used the systems biology approach to biodegradation for the largest and most important groups of industrial chemical nitro aromatics.

13.11 Removal of environmental pollutants through artificial intelligence Artificial intelligence (AI) refers to the emulation of human intelligence processes by computers. Obtaining information, creating rules for using information, drawing approximate or accurate conclusions, and self-correcting are all part of the process. AI has lately emerged as a critical component of the medical sector. AI applications like machine learning and deep learning allow systems to learn and develop on their own without having to be explicitly programmed. The goal of machine learning is to create computer systems that can access data and utilize it to learn (Fig. 13.3). Half-lives established in simulation experiments under marine environmental circumstances are suitable data to be utilized in regulatory assessments of persistence (marine water or sediments). This is because a chemical’s persistence represents not only the possibility of long-term exposure of organisms but also the possibility of the material reaching the marine environment and being transferred to distant locations. Because such data is rarely available, extrapolation from other types of available information, such as simulation test data obtained under freshwater conditions, or the results of biodegradation screening tests or estimation models, is frequently used to assess potential persistence in the marine environment. There are two types of screening tests: ready biodegradability and intrinsic biodegradability. If a chemical Kpasses6 the test criteria, it is deemed biodegradable; if it Kfails6 the test criteria, it is termed nonbiodegradable. Unfavorable (stringent) circumstances are used in a ready biodegradation test. If a chemical passes the ready test, it will likely biodegrade quickly in the environment. In contrast, just because a chemical fails the ready test does not mean it will not deteriorate in the environment. The circumstances for an intrinsic biodegradation test are favorable (nonstringent). As a result, if a chemical fails the intrinsic test, it is likely that it will not biodegrade quickly in the environment. In a recent study, Ahmad et al. (2020) used machine learning programming for aerobic biodegradation of azo dyes and hexavalent chromium (SBAHC). In this study, machine learning programming was used to simulate the dyes, which included gene expression programming, random forest, support vector regression, and support vector regression-fruit fly optimization technique.

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FIGURE 13.3 Schematic graphical overview of artificial intelligence techniques (deep and machine learning) from the screening of pollutant compounds from databases by using a mathematical algorithm to molecular docking, and molecular dynamics simulation techniques.

13.12 Conclusion A clean environment is essential for human beings, animals, and plants to survive. However, the indiscriminate use of synthetic chemicals and compounds in industrial areas is spreading pollution

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and creating a negative impact on the environment. To reduce the level of pollution new techniques, apart from in vitro and in vivo, using computer programs and software have been introduced, known as in silico techniques. The field of in silico has been introduced as a new method for saving time in research. In silico methods can also be used for toxicology prediction of any chemical compounds before using in in vitro conditions. Sometimes in silico methods work well for some toxic chemicals but may not perform well for others. When utilized correctly to determine the toxicity of compounds, in silico technologies can be highly useful. In silico approaches are also being used by researchers for biodegradation prediction using molecular docking and dynamics techniques. Genomics and proteomics techniques are also used for searching many types of bacterial genes useful for biodegradation. If these techniques are used on a large scale, they can save money and time in research.

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Significance of nanoscale in macroscale in various sectors such as agriculture, environment, and human health

Priyanka Basera1, , Shuchishloka Chakraborty2, , Meeta Lavania1 and Banwari Lal1 1

Environmental and Industrial Biotechnology Division, The Energy and Resources Institute, New Delhi, Delhi, India 2 Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India

14.1 Introduction In general, technology is defined as the technique that simplifies human tasks for a better livelihood. Advancement in technology is a growing and fascinating area for researchers. Nanotechnology is one such emerging technique with multiple applications in various sectors. In the 20th century, in the year 1959, the concept of nanotechnology was introduced by Nobel Laureate and American physicist Richard Phillips Feynman. Feynman delivered a novel and thought-provoking concept through his famous lecture line: “There’s plenty of room at the bottom,” which was later proven, and thus he came to be known as the father of nanotechnology (Bayda, Adeel, Tuccinardi, Cordani, & Rizzolio, 2019). In 1974 Japanese scientist Norio Taniguchi coined the term “nanotechnology” by referring to semiconductor-like materials in thin film deposition and ion beams in nanoscales (Taniguchi, 1974). A plethora of nanoscience research and engineering were conducted with time, and their breakthroughs were well documented. Nanotechnology is a zooming field for research involving characterization, designing, fabrication, and wide application of nanoparticles. A material is considered “nano” when at least one of its dimensions lies in a 1
100 nm scale (Williams, 2008). Nanomaterials are physically and chemically different from their bulk materials due to their unique surface area and volume ratio. This chapter tries to comprehend the importance of nanoscience in the field of agriculture and environment. Although nanotechnology serves multiple purposes in various sectors, one cannot neglect its adverse effects on the environment and human health. Chemical elements in nanoparticles have small sizes and complex structures, facilitating environmental accumulation. Further, it can enter the food chain, resulting in free radical production in living organisms. Nanoparticles in aerosol form can induce lung infection and heart ailments when inhaled by humans and animals. This chapter portrays the benefits and detrimental effects of the latest research in nanotechnology in agriculture and environmental sciences. 

Priyanka Basera and Shuchishloka Chakraborty have equally contributed to this chapter.

Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00016-8 © 2023 Elsevier Inc. All rights reserved.

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14.2 Nanomaterials in agriculture sector Agriculture is considered to be the backbone of developing countries. The agriculture sector plays the primary source of income, and more than half of the population depends on it for their livelihood. According to the Food and Agriculture Organization (FAO), India is placed as the largest producer of many fruits and the second-largest producer of wheat and rice in the world agriculture statistics. As the world population rises, it is essential to use modern technologies like nanotechnology in agricultural sectors. Fig. 14.1 illustrates the growing research trend toward agriculture nanotechnology.

FIGURE 14.1 Term occurrence network visualization of trending research in nanotechnology showing agriculture and environment as concerns: a chronological overview of terms based on average publication year. Each node in the map represents a term that occurred at least 50 times, and the size of the node of a term is proportional to the number of occurrences of that term. Bigger node size is related to a higher occurrence rate of the keyword, and shorter distance indicates a closer correlation of indicated terms. The cool-warm color trend presents the shift in the average publication per year, indicating the current topic of interest.

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Nanotechnology is a rising technique; the prefix “nano” suggests that the study belongs to the nanoscale when the proportion of surface area relative to the volume becomes significant. The agricultural sector suffers from many challenges such as climate change, soil fertility reduction (especially deficiency in macro- and micronutrients), and misuse/overuse of chemical fertilizers and pesticides. In terms of research concerning nanotechnology in the agricultural sector, Scopus data indicates India’s topmost position, followed by China and the United States of America (Fig. 14.2). The discovery of nanotechnology is an advantage for the agriculture industries where nanoparticles can act as “nano-mystic bullets” carrying chemicals, pesticides, or genes for the selected plant. For example, nanocapsules can release their content in a controlled and uniform manner to the cuticles and tissues of the plant (P´erez-de-Luque & Rubiales, 2009). Nanotechnology has varied applications, and in the agriculture sector, it can be a boon and also a bane depending on its applications (Fig. 14.3).

14.2.1 Crop enhancement: use of nanofertilizers Nanotechnology is revolutionizing the agriculture industry by innovating new techniques, like nanofertilizers. Due to the higher surface area and minimal size of these nanofertilizers, they have high reactivity with other compounds in soil, threading to environmental toxicity. It is reported that fertilizer alone can contribute 50% to crop production (Singh, Ravisankar, & Prasad, 2017).

FIGURE 14.2 Worldwide scenario of publication of agriculture in nanotechnology.

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FIGURE 14.3 Positive and negative impact of nanotechnology in agriculture sector.

Current fertilizers are bulk fertilizers with comparatively low efficiency, as they are majorly lost by volatilization and leaching (Seleiman et al., 2020). Loss of fertilizers has severe environmental consequences such as eutrophication. However, nanofertilizers facilitate the slow and steady release of nutrients, thereby reducing the loss of nutrients and enhancing nutrient use efficiency. Nanofertilizers can be divided into the following categories: (1) nanomaterials made of macronutrients, and (2) nanomaterials made of micronutrients, where nutrients are in the form of nanomaterials. Micronutrients like zinc and boron are necessary for the development of plants. Zinc acts as a cofactor for most enzymes and proteins and is reported to regulate auxins and provide protection from several harmful pathogens (Broadley, White, Hammond, Zelko, & Lux, 2007; Noreen, Fatima, Ahmad, Athar, & Ashraf, 2018). On the other hand, boron helps in the synthesis of the plant cell wall and promotes plant growth (Zulfiqar, Navarro, Ashraf, Akram, & Munn´e-Bosch, 2019). Therefore, it is necessary to supply adequate zinc and boron nanofertilizers in plants to achieve maximum yield. It was documented that plants required a low concentration of micronutrients; for instance, pomegranate trees (Punica granatum cv. Ardestani) attained a 30% increase in the fruit yield after being supplied with boron and zinc in the range of 34 and 636 mg/tree, respectively (Navarro-Leo´n, Albacete, de la Torre-Gonz´alez, Ruiz, & Blasco, 2016). In addition to this, zinc nanomaterial played an imperative role in the growth of cucumber seedlings, rice, maize, wheat, potato, sugarcane, sunflower, and pearl millet (Navarro-Leo´n et al., 2016). Another application of nanomaterial is in controlling biotic and abiotic stress, such as nanosilicon is found to be quite effective in the mitigation of salinity stress (Meghana, Wahiduzzaman, & Vamsi, 2021)

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Macronutrients such as nitrogen (N), phosphorus (P), and potassium (K) are considered the primary nutrient content for proper growth and development of plants. Nano forms of these macronutrients are developed through nanotechnology as it has been seen that there is an upsurge in the utilization of NPK as macronutrients in agriculture (Wang, Lombi, Zhao, & Kopittke, 2016). Nitrogen and potassium nanofertilizers can be carried by zeolite, which helps improve plant productivity through its controlled nutrient delivery mechanism (Karaca, 2004; Liu & Lal, 2015). It was reported that when blended with humus, zeolite compounds improve crop production. In a recent development, it was observed that the use of zeolite nanocomposites consisting of NPK, micronutrients, mannose, cadmium, iron, and zinc, yielded healthy crop growth (Elemike, Uzoh, Onwudiwe, & Babalola, 2019). Thus, the dawn of nanotechnology has shed numerous opportunities in agriculture industries. Nanoparticles produced with the help of nanotechnology can be employed to re-revolutionize the agricultural sector.

14.2.2 Crop protection Nanotechnology provides a powerful tool for better plant cultivation. Smart sensors have been developed, which aid in detecting and controlling pathogens (Scott & Chen, 2013). Nanoscale sensors can sense viruses, bacteria, and even a minute amount of contaminants in the plants. In the case of pathogen detection, the receptors/sensors on the nanosensors interact with the antibodies or specific ligands present on the bacterial surface (Chen, Andler, Goddard, Nugen, & Rotello, 2017). According to a study conducted by Lin, Huang, Lu, Kuo, and Chau (2014), cymbidium mosaic virus and odontoglossum ringspot virus were detected by gold nanorods, even in low concentrations. Similarly, immunosensors of Fe3O4/SiO2 showed promising results in tracking ringspot virus in tomatoes, pot mottle virus in beans, and Arabis mosaic virus, even at significantly low concentrations (Zhang, Chen, et al., 2013; Zhang, Yang, Tang, & Xu, 2013). The importance of nanoparticles was also mentioned in the research by Ghidan, Al-Antary, Salem, and Awwad (2017), explaining the vital role of zinc oxide (ZnO) nanoparticles from Punica granatum peel extract, affecting the role of green peach aphids. In addition to this, a similar study was conducted by Ghidan, Al-Antary, Awwad, and Ayad (2018) in the following year. They revealed the critical role of magnesium oxide in various concentrations against green peach aphids. Nanosensors play a significant role in agriculture as it is a great tool for tracking pathogens. Nanosensors are well known for their sensitivity against plant pathogens like Xanthomonas axonopodis pv. Vesicatoria, which causes bacterial spots in peppers and tomatoes, can be easily identified by fluorescent silica nanoparticles conjugated with antibody molecules (Yao et al., 2009). Gold nanoparticles carry tremendous potential due to their fluorescence-quenching ability. Gold nanorods were able to detect cymbidium mosaic virus (48 pg/mL) and odontoglossum ringspot virus (42 pg/mL) (Lin et al., 2014).

14.2.3 Crop improvement The stream of nanotechnology has multiple domains in agriculture, where crop improvement is an active research area that demands exponential exploration. Nanotechnology presents effective results in crop improvement, as it helps in enhancing the crop/food shelf life and nutrients. In addition to this, it also aids in keeping food fresh for a long duration for the best quality food

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consumption. It also increases micronutrient and antioxidant absorption (Kanjana, 2015). Nanomaterials firmly release materials to transfer the proper amount to the target material within sufficient time for the reaction. There are plenty of routes for introducing nanoparticles in the plant, such as seeds, roots, pollens, isolated cells, and protoplasts along with nanoparticles or by foliar spraying, irrigation with nanoparticles, direct injection, and hydroponic treatment (Singh, Tiwari, Pandey, Lata, & Singh, 2021). Nanoparticles can also enter the plant system through the root epidermis or apoplastic and symplastic routes (Wang et al., 2016; Zahedi, Karimi, & Teixeira da Silva, 2020). It is documented that plants’ enhanced yield and shelf life were obtained after absorbing beneficial nanoparticles (Chen, Cen, et al., 2013; Chen, Roco, et al., 2013). Nanotechnology helps create nanoparticles from bulk inorganic and organic compounds, increasing food durability. For instance, nanoparticles of chitosan, silicon (Si), silver (Ag), and ZnO were used as a coating agent, which proved valuable in improving short-lived food items like Chinese bayberry and strawberry (Li, Ye, Jiang, & Luo, 2017; Wang et al., 2010). In addition, nanoparticles of titanium dioxide (TiO2) were predicted to be supportive of nitrogen fixation and photosynthesis. In the photosynthesis process in spinach, increased plant growth efficiency was noted at a TiO2 concentration of less than 4% (Zheng, Hong, Lu, & Liu, 2005).

14.2.4 Fate of nanomaterial in soil Nanomaterials/nanoparticles, when released into the soil environment, experience changes in their physical, chemical, and biological nature, which leads to alteration in their physicochemical properties. Soil easily holds nanoparticles, which significantly affects soil properties such as pH, ionic strength, and organic matter. It is suggested that unutilized nanoparticles present in the soil remain accumulated and alter soil properties. For instance, the 6.6 nm diameter of Zea mays root cells makes it challenging to translocate 30 nm TiO2 nanoparticles, eventually accumulating in the root cells (Asli & Neumann, 2009). A study conducted by Du et al. (2011), illustrated that the root of wheat plants absorbed a small fraction of TiO2 nanoparticles, rendering the rest unattended, which resulted in modifying the beneficial soil enzymes and leading to toxicity in the soil environment.

14.3 Nanomaterial in environmental sector Nanotechnology has paved its way in most industries and sectors. In the environmental sector, nanomaterials promise to provide efficient strategies for removing biological and anthropogenic contaminants, draw simplicity and position in agriculture, and serve as an energy source and storage. Environmental application of incipient nanotechnology can be a sustainable approach; however, nanotechnology also has adverse environmental effects. Thus, the environmental application of nanotechnology requires the safe designing of nanomaterials with plausible environmental benefits and advancements in sustainable development (Bhatt et al., 2021). Nanotechnology is a nascent multidirectional technique and has gained rapid importance (Fig. 14.4). More notably, the concept of environmental nanotechnology has received full recognition recently. Data retrieved from

14.3 Nanomaterial in environmental sector

245

FIGURE 14.4 Emerging trend of environmental nanotechnology.

Scopus, using the search term “nanotechnology” limited the subject area to “Environmental science,” demonstrating that the application of nanotechnology into the environmental sector gained extreme attention since the 1990s (Fig. 14.1). Bibliometric data was analyzed by term occurrence network for reviewing, using VOSviewer (1.6.17) (Bodnariuk & Melentiev, 2019; VanEck & Waltman, 2010). It demonstrates the trending research in nanotechnology, showing agriculture and environment as concerns in nanotechnology, based on average publication year. The graphical representation of term occurrence network analysis of the keywords from the retrieved publications from Scopus shows the shift in the research trend in the application of nanotechnology in the environmental area (Fig. 14.1). Among the prospects of nanotechnology that have environmental applications, water treatment remediation, environmental sensing, and alternative energy sources have considerable potential benefits (Fig. 14.5). Some common nanomaterials that have been studied for environmental application are listed in Table 14.1

14.3.1 Wastewater and water remediation Nanotechnology advancements for water and wastewater remediation involve removing pollutants from wastewater using nanoparticles that belong to three categories: nano adsorbents, nanocatalysts, and nanomembranes.

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FIGURE 14.5 Application of nanotechnology in the field of environment.

14.3.1.1 Nanoadsorbents Compared with conventional adsorbents, nanoadsorbents offer many active adoption sites due to their larger surface area (Qu, Alvarez, & Li, 2013). These are efficiently used in removing organic compounds and metal ions, and their sensitivity can be increased by functionalization. Among all nanoparticles, the size and absorption efficacy of nanoscale metal oxides and carbon nanotubes (CNTs) are primarily employed for efficient remediation technology (Chen, Duan, & Zhu, 2007). Nanoscale metal oxides form a complex with the pollutants and undergo a one-electron oxidation reaction under visible irradiation. This technique is implemented in the treatment of heavy metals and organic compounds (Lu, Chiu, & Liu, 2006).

14.3.1.2 Nanomembranes The nanomembrane process has confirmed its effectiveness in higher separation. It is a simple process involving minimal chemical addition, thermal input, and effluent regeneration (Balamurugan,

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Table 14.1 Application of nonmaterial in environmental remediation of contaminants. Materials

Applications

References

Metal-based nanomaterials Ag nanoparticles/Ag ions TiO2 nanoparticles/ metal-doped TiO2

Titanate nanotubes

Antibacterial activity Antibacterial activity, photocatalytic degradation

Binary mixed oxide Iron-based

Supports both photo-catalyst and thermocatalyst oxides Photocatalytic activity Competitive adsorption

Bimetallic nanoparticles

Remediation from chlorine and bromine contamination and disinfection

Xiu, Zhang, Puppala, Colvin, and Alvarez (2012); Pal, Tak, and Song (2007) Alizadeh Fard, Aminzadeh, and Vahidi (2013); Bessa da Silva, Abrantes, Nogueira, Gonc¸alves, and Pereira (2016); Sreeja and Vidya Shetty (2016) Chen, Cen, et al. (2013); Chen, Roco, et al. (2013) Rasalingam, Peng, and Koodali (2014) Guo, Weng, Wang, and Chen (2017); Han and Yan (2016); Mystrioti, Xanthopoulou, Tsakiridis, Papassiopi, and Xenidis (2016) Nagpal, Bokare, Chikate, Rode, and Paknikar (2010); Xie, Fang, Cheng, Tsang, and Zhao (2014)

Silica nanomaterials Amine modified xerogels Amine functionalized aluminosilicates and porous silica Carboxylic acid functionalized silica Amino functionalized silica

Adsorption of acidic gas (CO2 and H2S)

Huang, Yang, Chinn, and Munson (2003)

Adsorption of gases, aldehydes, ketones

Thiol functionalized silica

Adsorption of heavy metals

Drese, Talley, and Jones (2011); Choi, Drese, Eisenberger, and Jones (2011); Nomura and Jones (2013) Tsai, Chang, Saikia, Wu, and Kao (2016); Bruzzoniti et al. (2007) Repo, Warchoł, Bhatnagar, Mudhoo, and Sillanpa¨a¨ (2013); Hern´andez-Morales et al. (2012) Rostamian, Najafi, and Rafati (2011); Hakami, Zhang, and Banks (2012); Walcarius and Delacoˆte (2005)

Adsorption of dyes and heavy metals Adsorption of heavy metals

Graphene-based nanomaterial Pristine graphene Graphene oxide

ZnO-graphene/ cadmium sulfidegraphene TiO2-graphene

Adsorption of water contaminants (fluoride) Intercalation, adsorption, and antibacterial effects of water/gaseous pollutants SOx, H2, NH3, heavy metals, pesticides, pharmaceuticals Photocatalytic activity to remediation of heavy metals Photocatalysis for selective oxidation for removal of gaseous contaminants

Li et al. (2011) Guo et al. (2017); Deng et al. (2017)

Zhang, Chen, et al. (2013); Zhang, Yang, et al. (2013) Zhang, Jia, Lv, Deng, and Xie (2010); Zhang, Tang, Fu, and Xu (2010); Yang, Zhang, and Xu (2013) (Continued)

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Table 14.1 Application of nonmaterial in environmental remediation of contaminants. Continued Materials

Applications

References

Polymer-based nanomaterial Amphiphilic polyurethane nanoparticles PAMAM dendrimers Amine modified PDLLA PEG Polyamine-modified cellulose Polymer nanocomposites

Adsorption of polynuclear aromatic hydrocarbons for soil remediation

Tungittiplakorn, Lion, Cohen, and Kim (2004)

Enhances ultrafiltration of wastewaters to recover heavy metals Capturing volatile organic compounds

Diallo, Christie, Swaminathan, Johnson, and Goddard (2005) Guerra, Campbell, Whitehead, and Alexis (2017) Brummel et al. (2021), Guerra, Campbell, Attia, Whitehead, and Alexis (2018) Khare, Yadav, Ramkumar, and Verma (2016); Mittal, Maity, and Ray (2015)

Capturing volatile organic compounds Adsorption of metal ions and dyes from wastewater

Sundarrajan, & Ramakrishna, 2011; Buonomenna, 2013). Incorporation of nanomaterials into membranes is mostly done in two ways, by surface grafting or by adding new functionality, such as better permeability, catalytic reactivity, contaminant degradation, self-cleaning (Pendergast & Hoek, 2011), and controlled membrane fouling (Vatanpour et al., 2012). Based on the membrane structure, nanomembranes are categorized into nanofibrous membranes (composed of ultra-fine fibers using various materials), nanocomposite membranes (thin film composite structures made by interfacial polymerization on ultrafiltration substrates), and osmotic membranes (utilization of nanoparticles to functionalize the active layer to expand the thin film composite membrane applications) (Lau, Ismail, Misdan, & Kassim, 2012).

14.3.1.3 Nanocatalysts Nanocatalysts demonstrate improved catalytic activities, and thus they are broadly used for water treatment degradation of organic compounds. In wastewater treatment, Fe2O3 nanoparticles have been used for methylene blue dye degradation (Dutta, Maji, & Adhikary, 2014), nano nickel-zinc ferrite catalysts for 4-chlorophenol degradation (Kurian & Nair, 2015), and platinum nickel nanoalloys for water treatment (Ma, Wang, & Na, 2015). TiO2 and ZnO nanoparticles with photocatalytic mechanisms are primarily used to degrade organic pollutants in air and water (Keller, Keller, Ledoux, & Lett, 2005) and are also known to be antimicrobial agents (Pathakoti, Huang, Watts, He, & Hwang, 2014).

14.3.2 Remediation The role of nanomaterials in environmental remediation includes using bimetallic nanoparticles, nanoscale zeolites, nanoscale zerovalent iron, semiconducting nanoparticles, magnetic nanoparticles, dendrimers, aerogel, and solid adsorbents.

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249

14.3.2.1 Metallic nanoparticles Nanoscale zerovalent iron (nZVI nanoparticles) (10
100 nm in diameter) have good surface adaptability, remarkable magnetic properties, and better biocompatibility (Xu et al., 2012), which make them suitable for environmental remediation. The core of nZVI nanoparticles produces suitable reactants such as Fe(II), H/H2, and iron hydroxides and oxides (Noubactep, 2009), accountable for reducing pollutants. Elemental iron or other metals combined with a metal catalyst form bimetallic nanoparticles that are applied to remediate contaminants in soil and groundwater, and among all, palladium and Fe bimetallic nanoparticles are widely available for dehalogenation (Alonso, Beletskaya, & Yus, 2002). However, these nanoparticles are limited by short lifetimes in the subsurface due to surface passivation (Schrick, Blough, Jones, & Mallouk, 2002) and decreased reactivity due to structural changes (Zhu & Lim, 2007).

14.3.2.2 Semiconducting nanoparticles and dendrimers Semiconducting nanoparticles and dendrimers consist of complex structures. Semiconducting nanoparticles are known for photocatalytic remediation. They are made of TiO2 and yield an electronhole pair when irradiated with light (Kołodziejczak-Radzimska & Jesionowski, 2014). They can transfer charge to organic pollutants and induce their oxidation to less harmful residual products. Dendrimers are highly structured polymer molecules comprising a central core and protruding branches. Dendrimers have interior voids suitable for entrapping small gas molecules and low molecular weight organic compounds (Zeng & Zimmerman, 1997). Semiconducting nanoparticles aid in degrading a range of herbicides, insecticides, and pesticides (Konstantinou, 2003). TiO2based nanotubes are also reported to degrade chlorinated compounds effectively. Poly(amidoamine) (PAMAM) dendrimers are stated to remove Cu(II) from aqueous solutions (Diallo et al., 1999) and augment the elimination and recovery of Cu(II) from water by ultrafiltration (Diallo et al., 2005).

14.3.2.3 Carbon capture The consumption of petrochemical products has significantly escalated, increasing the demand for CO2 capture (Shin, Song, An, Seo, & Park, 2014). Carbon capture technologies involve adsorption and regeneration techniques. The techniques encompass sorption, cryogenics, and membranes (Aaron & Tsouris, 2005). Nanoparticles accelerate the rate of CO2 absorption into amine solvents (Seo, Lages, & Kim, 2020; Zhang, Tian, & Fu, 2018). Adsorbents contain activated carbon, zeolites, silica adsorbents, metal nanoparticles, and CNTs (Seo et al., 2020). Moreover, adsorbents like functionalized single-walled CNTs and multiwalled CNTs have received attention for CO2 capture owing to their distinctive characteristics, such as high thermal and chemical stability (Hsu, Lu, Su, Zeng, & Chen, 2010; Lu, Bai, Wu, Su, & Hwang, 2008).

14.3.3 Sources of energy Green energy can be made using nanotechnology to produce solar and fuel cells as probable sources of commercially available alternative clean energy sources.

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14.3.3.1 Solar cells Third-generation solar cells are based on nanocrystals and nanoporous materials. Based on nanotechnology, solar cells are categorized as dye-sensitized solar cells (Chang et al., 2011; O’Regan & Gra¨tzel, 1991), hybrid organic solar cells (Kamat, 2010; Tyagi, Rahim, Rahim, Jeyraj, & Selvaraj, 2013), and quantum dot solar cells (Kamat, 2008; Sablon et al., 2010; Shalom, Buhbut, Tirosh, & Zaban, 2012). The conversion of light energy and capture in solar cells is empowered by changing a nanostructured semiconductor capture interface with a dye, conjugate polymer, or semiconductor nanocrystal. The significant components of dye-sensitized solar cells (DSSC) are a dye-sensitized photoanode, a counter electrode, and a redox electrolyte. The principle of DSSC is the formation of electron-hole pairs in the dye molecules under light illumination followed by the transfer of electrons to the conduction band of TiO2 and leaving the hole behind in the oxidized dye molecules. The oxidized dye is regenerated by a surrounding redox electrolyte (normally iodide/triiodide), which acts as a mediator (Adachi et al., 2004; Chang et al., 2011; Ramiro-Manzano et al., 2007), significantly increasing their competence. Hybrid organic photovoltaic or solar cells comprise thin films (less than 100 nm) of organic semiconductor materials to translate solar energy into electrical energy. Among most carbon nanostructures, graphene is used chiefly to fabricate carbon-based organic photovoltaic cells (Kamat, 2010; Liu et al., 2009; Wang, Gao, et al., 2014; Wang, Shoji, Baba, Ito, & Ogata, 2014). Properties of quantum dots (QDs) like size-dependent band gap, substantial dipole moments, photostability, and high optical absorption coefficients, make them good candidates for photovoltaic cells (Sablon et al., 2010). These can be structured into solar or photovoltaic cells in three different ways, namely: (1) metals semiconductor junction QD solar cells or Schottky solar cells (Johnston et al., 2008); (2) semiconductor nanostructure polymer solar cells (Kamat, 2008); and (3) solar cells based on QD sensitization (Shalom et al., 2012).

14.3.3.2 Fuel cells Semiconductors such as cadmium sulfide, silicon carbide, copper indium selenide, and TiO2 have been used for photocatalytic water splitting. This technique is used by fuel cells for hydrogen production by artificial photosynthesis (Karthik Pandiyan & Prabaharan, 2020; Kudo & Miseki, 2009; Maeda & Domen, 2010). However, using TiO2 has some limitations due to its large bandgap and rapid recombination of photogenerated electron/hole pairs (Ni, Leung, Leung, & Sumathy, 2007).

14.3.4 Environmental sensing Environmental biosensors have gradually emerged through an operative integration of specific biorecognition elements and electrochemical sensors. This high selectivity of bio-recognition elements can be used for multicomplex detection and work without complex processing. Hence, the electrochemical sensors and biosensors have shown great potential for laboratory-based and on-site analysis of environmental contaminants. The materials used in these sensors comprise conducting polymers, metal-based nanoparticles, CNT, graphene, and metal-organic frameworks. The sensors are mainly used to detect environmental contaminants such as heavy metals, phenolic compounds, polyaromatic hydrocarbons, xenobiotics, pesticides, pathogens, and gas pollutants.

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251

14.3.4.1 Gas sensors Vapor-sensitive polymers, semiconductor metal oxides, and other porous materials such as silicon are incorporated into gas or chemical sensors (Rittersma, 2002). SnO2, WO3, ZnO, In2O3, and Nb2O5 are widely considered for gas sensor applications (Chen, Crittenden, Hackney, Sutter, & Hand, 2005; Diallo et al., 1999) due to their enhanced sensitivity, stability, and low cost (Han ¨ zgu¨r et al., 2005; Wang, Gao, et al., 2014; Wang, Shoji, et al., 2014). Gold nanopartiet al., 2016; O cle functionalized nanomaterials have been used for environmental sensing recently. It has been identified that the functionalization of the noble metal affects their overall energetics and catalytic activity, regulating the number of carriers (electrons and holes) of semiconductors (Barreca et al., 2011; Guo, Zhang, Gong, Ju, & Cao, 2016). Additionally, reduced graphene oxide (rGO) and metal oxide nanoparticles are likely to be promising nanomaterials for gas-sensing applications due to their enhanced sensing properties (Huang et al., 2013; Liu, Lin, Sun, Zhou, & Cui, 2016). CNTs can also be fused into other sensing materials such as metal oxide semiconductors to expand their sensitivity (Keat, Zeng, & Grimes, 2002).

14.3.4.2 Heavy metal ion sensors Environmental sensors can detect heavy metal geogenic and anthropogenic contamination in the environment. Sensing systems employing nanomaterials use an extensive range of detection techniques (optical, electrical, ion-exchange, semiconducting metal oxides, and conductive polymers), which have enhanced the activity of sensors concerning their sensitivity, reproducibility, the limit of detection and quantification (LOD), and field portability (Aragay, Pino, & Merkoc¸i, 2012; Huang & Choi, 2007). Metal sensing systems are critically developed by immobilizing the specific onto an immobilizing/transducing platform and function on optical, electrochemical, magnetic, or miscellaneous principles (Aragay, Pons, & Merkoc¸i, 2011).

14.3.4.3 Optical sensing Optical detection of heavy metals is usually done on the principle of analyte-induced alterations in the physicochemical properties of a fluorophore, which is related to the charge/energy charge/ energy transfer process (Arshadi, Faraji, & Amiri, 2015). Most commonly, QDs, gold nanoparticles, nanometalorganic frameworks, and carbon dots are used for the optical detection of heavy metal ions. Various optical sensors include fluorescent, colorimetric, surface plasmon resonance (SPR), and surface-enhanced Raman scattering (SERS) sensors.

14.3.4.4 Electrochemical sensing Electrochemical sensing is done by compact systems that perceive the sensing signals through conducting wires. Some commonly used electrochemical sensors are specific anodic stripping voltammetry (electrochemically deposits the heavy metals at an endless potential to preconcentrate the analyte and strip the deposited analyte off the electrode surface). The electrode’s design involves nanoparticles that can be modified gold nanoparticles, gold/CFs, rod-like hydroxyapatite, or Nafion nanocomposites (Cao, Shi, Zhang, Zang, & Mak, 2015; Gooding, Shein, & Lai, 2009; Xu & Yan, 2016; Zeng, Ren, Shen, & Hu, 2016). Recently, single-walled nanotubes and functionalized singlewalled carbon nanohorns were used for the sensitive detection of microcystin-LR with a limit of 0.6 ppb (Wang et al., 2009; Zhang, Jia, et al., 2010; Zhang, Tang, et al., 2010).

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14.4 Negative aspects of nanotechnology Nanotechnology is an escalating field for researchers due to its multiple roles in various sectors. Although it has wide applications in various fields, it is still a challenging technology, and therefore risk assessment of nanomaterials is vital. The plethora of articles and the frameworks reviewed were published related to the hazardous effect of nanomaterials/nanoparticles. The toxic nature of nanomaterials depends on their size, surface activity, and aggregation. The toxic nature of nanomaterials has no direct correlation with their mass and concentration (Bodnariuk & Melentiev, 2019). As is well documented, nanotechnology provides improvement and enhancement in the agriculture sector. However, a tremendous amount of research is still required to assess the negative effect caused by nanomaterials as they have the potential to disturb the biological system of humans, animals, plants, environment, and even microorganisms (Fig. 14.6). Nanomaterials enter with the help of point or nonpoint sources, intentionally or unintentionally, into food and in our environment through air, soil, and water; it was reported that nanomaterials translocate between different trophic levels (Rienzie & Adassooriya, 2018). The deleterious effect of nanomaterials in plants can be studied with an example of Allium cepa species. Nanointeraction with the cells of A. cepa results in the generation of reactive oxygen species. In A. cepa, the size and dose of nanomaterials play an essential role in increasing lipid peroxidation and chromosome aberrations activity. In the case of roots, nanomaterials react with root hairs and damage the vegetal system (Rajeshwari, Suresh, Chandrasekaran, & Mukherjee, 2016).

FIGURE 14.6 Routes of nanomaterials through which nanoparticles can enter the human body.

References

253

Similarly, the toxicity of nanomaterials was observed in Arabidopsis thaliana and studies revealed that nanomaterials were responsible for poor root elongation, leaf expansion, and vegetative growth (Qian et al., 2013; Sosan et al., 2016). It has also been studied that nanomaterials are responsible for low crop yield as they affect the germination rate, reduce root and shoot length, fluctuate the photosynthesis process, and play a role in disturbing the nutritional content in crops (Gao et al., 2018; Ochoa et al., 2018; Rajput et al., 2009). An aerosol form of nanomaterial can effortlessly pass through the human circulatory system and lead to harmful effects. They are responsible for creating free radicals, which cause cellular distortion through lipid peroxidation, alteration of protein structure, DNA disruption, and gene mutation (Buzea, Pacheco, & Robbie, 2007; Rasalingam et al., 2014). It has also been reported that nanoparticles can migrate to cells and sites such as the cytoplasm and nucleus. In addition, they can show deleterious effects on the cell organelles or DNA and cause cell mortality with their cellular localization effect (Jeevanandam, Barhoum, Chan, Dufresne, & Danquah, 2018). Feng et al. (2013), reported that the relationship of nanomaterials with the soil-plant ecosystem is a complex topic. The microbial community that resides in the soil is considered the micro soil biota. Their presence in the soil indicates the health or fertility of the soil, which aid in the proper growth of crops and vegetables. According to Rienzie and Adassooriya (2018), soil bacteria show higher sorption capacity toward nanomaterials, and lead to accumulations. They can transfer it to the higher trophic level in plants to animals and humans through the food chain and can also have a lethal effect on soil microorganisms.

14.5 Conclusion With the rapid surge in the global population, the demand for food has fired up. Under such circumstances, nanotechnology seems to have great potential in transforming old technologies and using them in different areas of agriculture and the environment. Nanotechnology in agriculture provides promising results by enhancing crop and food quality, productivity, and shelf-life, and developing pest-resistant crops. In addition to this, nanotechnology plays a pivotal role in the environment sector by remediation, energy storage, and environmental sensing. However, the nanosize and high reactivity of these materials become perilous to human health. Proper risk assessment is a vital component in the study of nanotechnology. Therefore, nanotechnology has developed innovative and precise nanomaterials for various fields with both pros and cons.

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CHAPTER

Recent advances in biofilm formation and their role in environmental protection

15

Shobha Upreti1,2, Vinita Gouri1,2, Veni Pande3,4, Diksha Sati2,3, Garima Tamta5, Satish Chandra Pandey3,6 and Mukesh Samant3 1

Cell and Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University, Almora, Uttarakhand, India 2Department of Zoology, Kumaun University, Nainital, Uttarakhand, India 3Cell & Molecular Biology Laboratory, Department of Zoology, Soban Singh Jeena University Campus, Almora, Uttarakhand, India 4 Department of Biotechnology, Sir J.C. Bose Technical Campus, Bhimtal, Kumaun University, Nainital, Uttarakhand, India 5 Department of Chemistry, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India 6 Center for Advanced Biotechnology Research, Absolute, Gurugram, Haryana, India

15.1 Introduction Biofilms are heavy growths of microorganisms that aggregate to form colonies, which further attach to the surface consisting of a slime layer for protection and survival of the microbial cell. Biofilms, produced by both gram-positive and gram-negative bacteria, are found in almost all environments (biotic and abiotic), and have a range of environmental applications (Arnaouteli, Bamford, Stanley-Wall, & Kov´acs, 2021; Li, Li, Wang, & Wang, 2010; Manickam, Misra, & Mayilraj, 2007). Biofilm is developed through the production of an extracellular matrix, which is mainly composed of sticky extracellular polysaccharides (EPS) and proteins produced by the microbial cell (Branda, Vik, Friedman, & Kolter, 2005). The biofilm formation occurs through a series of events: adhesion of individual microbial cells to a surface area, cell proliferation and aggregation into microcolonies, extracellular matrix production, and cell detachment (Fig. 15.1) (Arnaouteli et al., 2021). Environmental pollution is also increasing rapidly with the increase in environmental pollutants, viz., hydrocarbons, polyethylene heavy metals, and industrial waste, along with the human population (Puhakka et al., 1995; Song, 2009; Yong & Zhong, 2013). The presence of these toxic pollutants in the environment can affect ecosystems and ultimately human health. Biofilmassociated bacteria play an important role in protecting the environment from such threats (Ferrer, Golyshin, & Timmis, 2003; Hunter, Ekunwe, Dodor, Hwang, & Ekunwe, 2005; Kang & Park, 2010; Malik & Grohmann, 2012). Many biofilm-forming bacterial species potentially provide a suitable microenvironment for efficient bioremediation processes to naturally and artificially overcome these environmental constraints (Huang et al., 2013). Aquatic contaminants are generally characterized by their toxicity to living organisms and the environment. Biofilm-mediated wastewater and sewage treatment processes in industries are the most efficient techniques because of their distinct advantages over conventional methods (Rinaudi et al., 2006). Moreover, bacteria physically interact with the surface of the plant root system and further stabilize the plant-associated habitat. Hence rhizobia biofilms act as an economically important Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00001-6 © 2023 Elsevier Inc. All rights reserved.

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FIGURE 15.1 Stages in biofilm formation: (1) primary cell adhesion to the surface; (2) extracellular exopolysaccharide matrix production; (3) biofilm architecture in its early stages; (4) development of biofilm structure; (5) bacterial cell dispersal from the biofilm.

root colonizer, fixing atmospheric nitrogen into ammonia (Crueger, Crueger, Brock, & Brock, 1990). Therefore, the present chapter deals with the events involved in biofilm formation, the important role of biofilms in environmental protection, and the role of biofilm formation for health. Various bacteria and their role in environmental protection have been depicted in Table 15.1.

15.2 Biofilm formation Biofilm formation occurs in a series of phases. The biofilm gets more securely adhered at each phase, protecting the bacteria within it from the action of disinfectants and sterilizers (Garrett, Bhakoo, & Zhang, 2008). Bacteria must be able to get close enough to a surface to develop a biofilm. There are five stages in biofilm formation. In the first stage, the attachment of bacterial cells to the surface occurs through van der Waals forces (Hey, Richards, & Seymour, 2016). Cell attachment is rescindable until Stage 1. Stronger physical or chemical shear pressures can be tolerated by the irreversibly adhered biofilms (Sutherland, 2001). Flagella and Type IV pili-based motilities are essential for the early stages of attachment. Attached cells can consolidate and form microcolonies due to the twitching motilities facilitated by Type IV pili. According to Toole, George, and Kolter (1998), P. aeruginosa mutants lacking flagella and Type IV pili were unable to settle on the

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265

Table 15.1 Role of various bacterial species in environmental protection S. No.

Bacterial species

1

Serratia liquefaciens

2

Pseudomonas aeruginosa Sphingobium fuliginis

3

Gram stain

Significance

References

Polycyclic aromatic hydrocarbons degradation Phenol, polyethylene, and phenanthrene degradation Polycyclic aromatic hydrocarbons degradation Polycyclic aromatic hydrocarbons and p nitrophenol degradation Nitrobenzene, toluene, polycyclic aromatic hydrocarbons, phenol, and 2,4dichlorophenol degradation Polycyclic aromatic hydrocarbons degradation Hexachlorocyclohexane bioremediation Pyrene and benzopyrene degradation Polychlorinated biphenyl degradation Hexadecane degradation

Song (2009)

Polyethylene degradation

Nowak, Paja˛k, Drozd-Bratkowicz, & Rymarz (2011)

Gramnegative

Polyethylene degradation

2,4,6-Trichlorophenol, 2,3,4,6tetrachlorophenol, and pentachlorophenol degradation Cresol, naphthalene, phenol, and 1,2,3-trimethylbenzene degradation Carbon tetrachloride

Awasthi, Srivastava, Singh, Tiwary, & Kumar Mishra (2017) Singh et al. (2006)

Gramnegative Gramnegative Gramnegative Gramnegative

4

Stenotrophomonas maltophilia

5

Pseudomonas putida

Gramnegative

6

Sphingomonas sp.

7

Xanthomonas sp.

8

Bacillus subtilis

9

Burkholderia cepacia

10

Acinetobacter sp.

11

Staphylococcus cohnii, Rhodococcus ruber, and Microbacterium paraoxydans Klebsiella pneumonia

Gramnegative Gramnegative Grampositive Gramnegative Gramnegative Grampositive

12

13

Pseudomonas sp. and Rhodococcus sp.

Gramnegative

14

Pseudomonas fluorescens

Gramnegative

15

Providencia stuartii and Pseudomonas cepacia

Gramnegative

Yong and Zhong (2013) Huang et al. (2013) Juhasz, Stanley, and Britz (2000) Li et al. (2010); Singh, Paul, Rakesh, and Jain (2006)

Yong and Zhong (2013) Manickam et al. (2007) Hunter et al. (2005) Ferrer et al. (2003) Kang and Park (2010)

Singh et al. (2006)

Singh et al. (2006)

surfaces or form microcolonies. The peptidoglycan on the cell wall is covalently attached to the microbial surface components that recognize sticky matrix molecules and are dependent on adhesions. The attachment of human pathogens, Staphylococcus epidermidis and Staphylococcus aureus, to human matrix proteins such as fibrinogen (Fg), vitronectin (Vn), fibronectin (Fn), and others is

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the first step in the formation of biofilms. The peptidoglycan on the cell wall is covalently attached to the components of the microbial surface that recognizes sticky matrix molecules that are adhesion-dependent. There are more than 20 components, so the microbial surface recognizes adhesive matrix molecule genes in S. aureus, but only 12 in S. epidermidis RP62A (Otto, 2008). Autolysin-mediated noncovalent adhesions may also help in the early stage of biofilm attachment (Heilmann, Hussain, Peters, & Go¨tz, 1997). In Stage 2, cells bind themselves more firmly by producing an exopolymer material, a compound that is strongly adhesive. Thus, the irreversible phase of bacterial adhesion to a surface is marked by the formation of the EPS matrix. Because of the function that P. aeruginosa biofilms play in cystic fibrosis progression, the EPS matrix of P. aeruginosa has been extensively investigated. Alginate, a significant polysaccharide element of P. aeruginosa EPS matrix, is formed in greater numbers by bacteria adhered to a surface compared with the planktonic cells (Davies, Chakrabarty, & Geesey., 1993). Stage 3 involves the formation of microcolonies, and the maturation of the biofilm also begins here. Cells of the identical species or some different species are attracted to the biofilm from the bulk fluid as soon as the initial layer of the biofilm has been made. Biofilms develop into a mushroom or tower shape as it expands from a thin layer. Bacteria are grouped in a thick biofilm of more than 100 layers, as per their metabolism and aero tolerance. To avoid being exposed to oxygen, anaerobic bacteria, for example, prefer to live in deeper strata. In Stage 4, further maturation occurs, and the biofilm transforms into a 3-D structure with clusters of cells and channels flowing between them. Bacteria in biofilm communities communicate with one another and perform specialized activities. As the biofilm further develops, the bacteria entrapped secretes other biofilm scaffolds, namely DNA, proteins, polysaccharides, and so on. Finally, the biofilm disperses cells in Stage 5, following the formation of the structure, bacteria are released into the liquid media, allowing the biofilm to spread throughout the surface so that they might progress to the production of new biofilms (Hall-Stoodley & Stoodley, 2005; Stoodley, Sauer, Davies, & Costerton, 2002). Biofilms disseminate for a variety of reasons, including nutrient deficiency, severe competition, population outgrowth, and so forth. Dispersal can happen across the entire biofilm or only a portion of it. Planktonic bacteria release encourages the formation of additional biofilms at other locations. It is to be noted that cell division is rare in mature biofilms. Biofilm cells, in their mature stage, primarily consume energy to generate exopolysaccharides, which are utilized by cells for nutrition (Watnick & Kolter, 2000).

15.2.1 Events of signaling in biofilm formation The association between environmental stimuli and the microorganism’s response to the relevant signaling events is required for biofilm formation. The environmental stimuli can be integrated into signaling pathways through several sensing systems. The extracytoplasmic function signaling pathway (ECF), quorum sensing (QS), and two-component systems (TCS), events can all be triggered by these sensing systems. Biofilm development is also triggered by secondary messengers, viz. cdi-GMP (cyclic guanosine monophosphate) (Jonas, Melefors, & Ro¨mling, 2009). A progressively synchronized system of gene expression is essential for the formation of biofilm. As a result, these signaling events play an essential part in the development of microbial biofilms by producing adaptive reciprocation toward internal and external stimuli (Bordi & de Bentzmann, 2011). Histidine kinase (HK) and response regulator (RR) proteins make up a two-component signaling pathway. A sensor protein with an N-terminal ligand-binding domain and a C-terminal kinase domain is

15.3 Role of biofilms in environmental protection

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known as HK. The phosphoryl group transfer from adenosine triphosphate to a particular conserved histidine residue in HK causes signal transduction. Following that, HK moves the phosphoryl group from histidine to RR’s aspartate residue (Stock, Robinson, & Goudreau, 2000). RR, a transcriptional regulator, is activated by this phosphate. In general, for the production of P. aeruginosa biofilms, GacS (HK)/GacA (RR) (two-component systems) are involved (Rasamiravaka, Labtani, Duez, EI, & Jaziri, 2015). The rsm gene expression, which codes for RsmY and RsmZ, responsible for the regulation of the transition among planktonic and sedentary forms, is induced by this system (Brencic et al., 2009). For the formation of biofilm, Quorum-sensing (QS) systems are used by bacteria to synchronize their gene expression. QS appears to be a process through which bacteria manage collective activities and monitor cell density (Lyon & Muir, 2003). It is a bacterial communication method through which they coordinate their expression of genes through the production of a variety of intercellular signals known as autoinducers or pheromones. For example, in the case of gram-negative bacteria, acyl-homoserine lactones are the autoinducer and thus facilitate QS; however, in gram-positive bacteria, oligopeptides, that is, small peptides, are the autoinducer that regulates QS. These molecules congregate on the cell surface, and when the microbial population reaches a particular threshold, these autoinducers can control the gene expressions involved in the formation of biofilm and virulence (Bordi & de Bentzmann, 2011). Biofilm formation has been regulated by QS in numerous bacteria (Irie & Parsek, 2008). AHL QS systems are responsible for eDNA release and biofilm building in the PAO1 strain of P. aeruginosa. The QS system controls the generation of PEL exopolysaccharides in the PA14 strain (Sakuragi & Kolter, 2007). Besides these pathways, a high concentration of the secondary messenger c-di-GMP stimulates the production of bacterial biofilm (Bordi & de Bentzmann, 2011). A high level of c-di-GMP is thought to be a stimulant for microbial biofilms formation by the production of extracellular polymeric substance (EPS) or by the formation of alginate polymer, or pili (Rasamiravaka et al., 2015).

15.3 Role of biofilms in environmental protection Biofilms have been reported to be beneficial in different areas, viz., bioremediation, remediation of heavy metals and hydrocarbons, wastewater treatment, biodegradation of polyethylene, role in health, etc.

15.3.1 Bioremediation The rapid expansion of refineries over the last decades has caused severe environmental degradation as a result of the toxic waste released from these industries (Paul, Pandey, Pandey, & Jain, 2005). The perseverance of these chemical pollutants and their effect on the environment has raised public awareness regarding the risk of long-term natural calamities (Pandey & Jain, 2002). Hence, numerous techniques and extensive research is in progress for the development of a sustainable environment (Singh et al., 2006). Microorganisms have been utilized to remove the natural contaminants in situ, a process known as bioremediation. The biological techniques used for treating harmful effluents are more economically efficient and effective than any physical or synthetic method (Paul et al., 2005). Hence, the ability of biofilm networks for the process of bioremediation

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Chapter 15 Recent advances in biofilm formation

has been recently taken into account. Moreover, there have been studies that suggest that biofilmmediated bioremediation is a more prospective and secure option in contrast to planktonic microorganism-mediated bioremediation since cells in a biofilm have higher endurance and increased chances of variations as they are surrounded by a framework of biofilms (Decho, 2000; Singh et al., 2006). Understanding the interactions between the organic pollutants, microorganisms, and aquifers or soil are essential for successful bioremediation. Physiological features of microbes, viz., chemotaxis and biosurfactant synthesis, augment the bioavailability and, consequently, the breakdown of hydrophobic substances (Pandey & Jain, 2002; Paul et al., 2005). Microbes that form biofilm on the hydrocarbon surfaces and secrete polymers can sequester compounds as they have higher microbial biomass and are capable of sequestering the mobilization of different compounds by bioaccumulation (increased accumulation of microbes under influence), biosorption, and biomineralization (formation of insoluble precipitates by interactions with biological matter). Hence biofilms are suitable for treating recalcitrant pollutants, or compounds that are slow-degrading (Barkay & Schaefer, 2001). The exclusive architecture and controlled passage of fluid within the biofilm help it to support a higher biomass density, which aids mineralization by maintaining appropriate pH, redox potential around the cells’ immediate environment, and localized concentrations of the solute (Flemming, 1995; Horn & Morgenroth, 2006). Biofilm reactors are also one of the crucial techniques used in bioremediation. The methods used by the primary biofilm reactors are classified as up-flow sludge blanket (USB), internal circulation (IC), biofilm fluidized bed (BFB), biofilm airlift suspension (BAS), and expanded granular sludge blanket (EGSB). These biofilm-based reactors are often used to treat enormous amounts of industry wastewater and municipality effluents (Nicolella, Van Loosdrecht, & Heijnen, 2000a,b; Singh et al., 2006).

15.3.2 Heavy metal remediation Biofilms play a vital role in the remediation of heavy metals and radionuclides (Barkay & Schaefer, 2001; Lloyd, 2002). The variety of microorganisms in the contaminated sites, and their distribution, along with the genes encoding for the phenotypes that are crucial for metalmicroorganism associations, are vital components in the bioremediation of radionuclides and metals (Pande, Pandey, Sati, Bhatt, & Samant, 2022; Pande, Pandey, Sati, Pande, & Samant, 2020). Heavy metal bioremediation can be accomplished by immobilizing, concentrating, and partitioning the heavy metals into a natural compartment, consequently limiting the expected dangers (Barkay & Schaefer, 2001; Lloyd, 2002; Singh et al., 2006). There have been studies where sulfate-reducing biofilms from bacteria were grown in a consistent culture and were presented to a medium consisting of 20
200 mM copper. As a result, these bacterial biofilms were found to accumulate copper as copper sulfides (White & Gadd, 2000). Moreover, an instantaneous expansion in the biofilm’s EPS (extracellular polymeric substances) content was observed, which insinuated the importance of biofilms and EPS for entrapping the metal precipitates (White & Gadd, 2000). The formation of ZnS, that is sphalerite, by the aerotolerant desulfo bacteria has been observed in the biofilm (Labrenz et al. 2000). Moreover, 84% removal of metals like Cd21, Cu21, and Zn21 have been reported in wastewater by utilizing the rotating biological contactor with substituting desorption and sorption cycles (Costley & Wallis, 2001). The physiological responses associated with the biofilms during the absorption of organic or inorganic solutes and water can also influence the fate of

15.3 Role of biofilms in environmental protection

269

various compounds present in their surroundings, which can be crucial for bioremediation (Flemming, 1995; Singh et al., 2006).

15.3.3 Remediation of hydrocarbons Recalcitrant chemicals, such as chlorinated aromatic compounds, belong to a class of chemicals that can travel swiftly through soils and are found in a variety of chemicals. These are among the most common groundwater and soil pollutants, which can cause cancer at very low doses (Kargi & Eker, 2005; Puhakka et al., 1995). There have been studies where a rotating perforated tube biofilm reactor with the activated sludge of microbial biomass and P. putida were utilized in the degradation of DCP (2,4-dichlorophenol) , to confiscate DCP from synthetic wastewater. This process has been reported to remove about 100% of DCP (Kargi and Eker, 2005). Bacteria modified to adhere to the polyaromatic hydrocarbons (PAHs), aid in the degradation of PAHs, such as in the case of diclofop-methyl, methyl 2-[4-(2,4-dichloro phenoxy)] phenoxyl pyruvate, adsorption and accumulation of this pesticide was observed on the surface of the biofilms, which was further digested by the biofilm community (Johnsen, Wick, & Harms, 2005; Juhasz et al., 2000). Moreover, nitroaromatic compounds also belong to the xenobiotics group. These compounds are utilized in the industries involved in the development of pesticides, explosives, and pharmaceuticals. The nitroaromatic compounds consist of a nitro group in their structure, which prevents them from degradation, and often when these compounds are acted upon by the microbes, their conversion results in the formation of toxic metabolites (Gisi & Stucki, 1997; Juhasz et al., 2000; Lendenmann, Spain, & Smets, 1998). There have been studies where compounds like isomeric dinitro toluene or DNT were degraded by utilizing a fluidized bed biofilm reactor. In a study, the reactor was supplied with a solution consisting of 2,4-DNT at a concentration of 40 mg/L and 2,6-DNT at a concentration of 10 mg/L, and the degrading efficiency was reported to be .98% in the case of 2,4 DNT and 94% in the case of 2,6-DNT for all the loading rates (Gisi & Stucki, 1997). Moreover, altering the biochemical pathways, along with the different enzymes involved in these pathways, could further promote bioremediation through bacterial biofilms.

15.3.4 Wastewater treatment Biofilms have been involved in wastewater treatment for a long time now, with the first being in 1893 in England, where biofilms were utilized in trickling filters (Lohmeyer, 2022). Despite being detrimental to the environment, biofilms are still employed in degrading complex contaminants. The use of biofilms in depollution is cheaper and more efficient compared with the planktonic microbes, as biofilms are more resistant to stress and have a better survival rate. Biofilm-forming microbes are, in fact, fierce competitors for oxygen and nutrients (Asri, Elabed, & Koraichi, 2020). Moreover, they have also been able to withstand and overcome severe hydrodynamic forces and stressful circumstances. Hence, they are ideal candidates for bioremediation. Moreover, to surmount environmental challenges, biofilms have been reported to utilize EPS matrix to form a range of structures (Das, Khan, Guha, Das, & Baran Mandal, 2012; Kreft & Wimpenny, 2018; Miqueleto, Dolosic, Pozzi, Foresti, & Zaiat, 2010). The utilization of biofilms for the immobilization, adsorption, and degradation of a range of contaminants has also been reported (Quintelas, Bruna, Figueiredo, & Teresa, 2010). These biofilm processes have been utilized to remove various organic

270

Chapter 15 Recent advances in biofilm formation

and inorganic contaminants from the aqueous system (Chen, Sun, & Chung, 2008; Hai, He, Wang, & Li, 2014; Quintelas, Pereira, Kaplan, & Tavares, 2013). Microbial biofilms have been successfully involved in the remediation of a range of pollutants, viz. pesticides, petroleum, heavy metals, and dyes (Mitra & Mukhopadhyay, 2016). The biofilm mode in microbial cells results in the immobilization of these cells inside a self-synthesized matrix, which helps resist the predatory protozoans and protects the microbial cells from stress and various pollutants (Quintelas, da Silva, Silva, Figueiredo, & Tavares, 2011). The planktonic form of microbial cells differs from the biofilm mode in the expression of various genes. A range of metabolic pathways can be observed due to the congregation of different microbial species in the biofilm; hence degradation of a range of pollutants can occur separately or collectively by the biofilm (Horemans, Breugelmans, Hofkens, Smolders, & Springael, 2013). Several microbial forms, including bacteria, yeast, fungi, and algae, have been successfully used as biofilm forms for the management of wastewater (Abzazou, Araujo, Auset, & Salvado´, 2016; Nhi Cong, Ngoc Mai, Thanh, Nga, & Minh, 2014). Hence, for the development and scaling up of efficient management systems, these investigations are very crucial.

15.3.5 Biofilms in agriculture The exudates from plant roots induce a range of bacteria to accumulate in its surroundings and as a result influence the rhizosphere. Factors such as the development of microcolonies and cell adhesion are crucial for the establishment of rhizobacteria on the plant roots. Moreover, microbes such as Paenibacillus, Burkholderia, Pseudomonas, and Bacillus have also been reported to display beneficial interaction with plant roots (Jung, Hong, Park, Chul Kim, & Shin, 2018; Vardharajula, Ali, Grover, Reddy, & Bandi, 2011). Other factors, including water, nutrient availability, and the association between different bacterial strains, can induce the formation of biofilms on the roots of plants ´ ˜ iga, Donoso, Ruiz, Ruz, & Gon´zalez, 2017). The properties of the root show diversity all along (Zun the length of the root, and the nutrients and chemicals released by the plant roots at various regions aid in the development of biofilms. In contrast to the sparsely populated mature root zone and root hairs, the root cap and cell division zone are the major areas for the colonization of bacteria (Timmusk, Grantcharova, Gerhart, & Wagner, 2005). The roots of the plant Arabidopsis thaliana consist of an intricate bacterial consortium, which involves bacteria forming biofilms that improve the growth and productivity of the plant (Hassani, Dur´an, & Hacquard, 2013). The chemical constituents of root exudates directly influence the bacterial group present in the rhizosphere. For example, the exudates secreted from the roots of cucumber stimulated Bacillus subtilis N11, while fumaric acid secreted from the roots of bananas stimulated B. amyloliquefaciens SQR9, induced biofilm formation (Mhlongo, Piater, Madala, Labuschagne, & Dubery, 2018). The bacteria in the biofilm framework further enhance the growth of plants along with protecting the plants against phytopathogens, a phenomenon commonly known as biocontrol (Bogino, De las Mercedes Oliva, Sorroche, & Giordano, 2013). Moreover, plant growth promoting rhizobacteria (PGPR) play a vital role in increasing growth in plants (Seneviratne et al., 2010). This is mostly accomplished via biofilm formation in the rhizosphere. Reports suggest that in vitro development of biofilmed PGPR have been exploited to boost agricultural yield (Seneviratne et al., 2010). Biofilmed PGPR can also be utilized as biofertilizers by augmenting their capacity for nitrogen fixation along with the adsorption of macro- and micronutrients (Leifert et al., 1995). Hence a deeper understanding of this area can result in the advancement of the agricultural sector (Leifert et al., 1995).

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15.3.6 Polyethylene degradation Polyethylene is a nonbiodegradable material, making its degradation extremely challenging even after they are suppressed in a landfill for many years (Yong & Zhong, 2013). Moreover, when kept in damp soil for 12
32 years, polyethylene showed very little or no degradation at all (Otake, Kobayashi, Asabe, Murakami, & Ono., 1995). The nonbiodegradable nature of polyethylene is due to the nature of its molecular structure, making it insoluble and hydrophobic (Restrepo-Flo´rez, Manuel, Bassi, & Thompson, 2014; Webb, Arnott, Crawford, & Ivanova, 2013). Studies involving the biodegradation of polyethylenes include LDPE (low-density polyethylene) and HDPE (highdensity polyethylene) (Restrepo-Flo´rez et al., 2014). Ethylene was polymerized under high pressure for the production of LDPE. LDPE has been reported to have low density due to its branched-chain structure. Moreover, at room temperature, LDPE has been reported to be highly stable. However, reports suggest that LDPE can be degraded over time by the action of certain solvents and some oxidizing agents, consequently resulting in the softening and swelling of LDPE. LDPE can withstand temperatures of about 95 C for a short span and can withstand temperatures of about 80 C for long durations. Various forms of polyethylenes have been demonstrated to be degraded by a range of bacterial strains, viz., Stenotrophomonas, Acinetobactor, Klebsiella, Pseudomonas, Ralstonia, etc. (Ghatge, Yang, Ahn, & Hur, 2020; Nowak et al., 2011; Rajandas, Parimannan, Sathasivam, Ravichandran, & Yin, 2012; Restrepo-Flo´rez et al., 2014). The majority of these bacteria can degrade the texture of polyethylene or create a biofilm on the surface of polyethylene. The ability of Pseudomonas to digest and metabolize plastic polymers by extracellular oxidation or by the action of hydrolytic enzymes aids in the uptake and decomposition of polymeric fragments and regulates the biofilm-polymer interaction (Wilkes & Aristilde, 2017). Polyethylene can also be completely degraded in water via the action of P. fuorescens in the presence of biosurfactants, implying their relevance in the degradation and oxidation of polymers (Arkatkar, Juwarkar, Bhaduri, Veera Uppara, & Doble, 2010). Moreover, the degradation of HDPE has also been reported via the action of Klebsiella pneumoniae following thermal treatment (Awasthi et al., 2017). This strain was observed to adhere firmly to the surface of HDPE, consequently leading to an elevation in the thickness of the HDPE biofilm by 18.4% and a decline in the mass, along with the tensile strength by 18.4%. SEM images have proved that the action of biofilms caused cracks and corrosion on the surface of HDPE (Awasthi et al., 2017).

15.3.7 Biofilm formation for health Biofilms are especially essential for human health because they are accountable for a variety of contagious diseases connected with inert materials, such as medical equipment for interior or exterior usage (Bordi & de Bentzmann, 2011). Biofilms are created by both gram-positive and gramnegative bacteria on internally placed medical equipment. Bacteria that commonly create biofilms are Burkholderia cenocepacia, Clostridium difficile, Escherichia coli, Enterococcus faecalis, K. pneumoniae, P. aeruginosa, Proteus mirabilis, S. aureus, S. epidermidis, and Streptococcus viridans (Bielecki, Glik, Kawecki, & Martins Dos Santos, 2008; Donlan, 2001a; Rodney & Donlan, 2001b). Biofilm-forming microbes produce a variety of disorders, including cystic fibrosis, chronic bacterial prostatitis, native valve endocarditis, otitis media, and periodontitis. In humans, biofilmforming microbes are responsible for around 65% of all hospital infections (Costerton, Stewart, &

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Chapter 15 Recent advances in biofilm formation

Greenberg, 1999; Donlan, William Costerton, Donlan, & William Costerton, 2002; Donlan, 2001a, b; Douglas, 2003; Ramage, Martı´nez, & Lo´pez-Ribot., 2006) Due to their resistance to elimination by the body’s defense response and generated antimicrobials; biofilm diseases are notoriously hard to eliminate once developed (Trizna et al., 2015). Compared with the zooplanktonic cultures, biofilms are found to be 1,000 times more resistant to antibiotics (Gilbert, Allison, & McBain., 2002; Hoyle & Costerton, 1991; Mah & O’Toole, 2001). This increased strength of biofilm-forming microbes may be due to their genetic and phenotypic richness (Ehrlich, Hu, Shen, Stoodley, & Christopher Post, 2005). The complexity of the biofilm structure, including an exopolymeric matrix, may impede antibacterial agents from reaching the microorganism. Though the biofilm matrix is not completely impermeable, and other factors are also involved in their resistance to antimicrobials (Freeman, Woods, Welsby, Percival, & Cochrane, 2009). In response to changes in their surroundings, for example, nutrient depletion and waste product build-up, biofilm-forming microbes could also attain a slow-growth stage or starving stage (Chen, Yu, & Sun, 2013). While evaluating the resilience of biofilms against specific antimicrobial agents, the limited capacity of these agents to access the bacteria contained within the biofilm matrix is considered critical (Percival et al., 2011a,b). This could happen as a consequence of chemical interactions with exopolymeric matrix components or adsorption, to anionic polysaccharides (Percival et al., 2011a,b; Walters, Roe, Bugnicourt, Franklin, & Stewart, 2003). Bacteria within a biofilm may actively employ distinct mechanisms, including antibiotic sequestration in the periplasm to prevent them from reaching their target sites. Biofilm-forming microbes may employ various active processes, such as antibiotic retention in the periplasm, to inhibit antibiotics from accessing their target areas (Walters et al., 2003). Due to secretion or cell lysis, β-lactamase, the enzyme which blocks the action of β-lactam ring-containing antibiotics, can aggregate within the biofilm matrix. β-Lactamase has higher reaction kinetics; hence it can disintegrate β-lactam antibiotics within the biofilm outer layers quickly compared with their inward diffuse rate (Johnsen et al., 2005). Within the lowest portion of the biofilm structure, slow-growing bacteria with low metabolic activity are present due to limited access to vital nutrients and gaseous exchange (Davies, 2003; Percival et al., 2011a,b). As a consequence, the biofilm-anchored cells are metabolically quiescent and morphologically adapted to thrive in harsh settings (Anwar, Strap, Chen, & Costerton., 1992; Fux, Costerton, Stewart, & Stoodley, 2005; Rhoads, Wolcott, Cutting, & Percival, 2007). These are referred to as persister cells and comprise a limited, sluggishly-growing population inside the biofilm that has transitioned into a dormant but extremely protected condition (Lewis, 1985; Percival et al., 2011a,b; Roberts & Stewart, 2005). Persister cells are a kind of altruistic cells that limit the transcription of genes involved in ATP production and biosynthesis (Lewis, 1985). This subset of cells accounts for only around 0.1%
10% of the total cells in a biofilm and is capable of re-synthesizing the microfilm after any antimicrobial encounter (Harrison et al., 2005; Roberts & Stewart, 2005). Device-related infections were the first biofilm-based medical infections to be documented, suggesting that the host inflammatory response can enhance biofilm formation by facilitating adhesion to the device’s surface (Hall-Stoodley, William Costerton, & Stoodley, 2004). Biofilms linked with clinical equipment were originally reported in the 1980s when microbial build-up on the interface of internally placed devices was proven, such as central venous catheters, urinary catheters, peritoneal dialysis catheters, contact lenses, mechanical heart valves, pacemakers, prosthetic joints, and voice prostheses (Donlan et al., 2002; Jacqueline & Caillon, 2014). The biofilm build-up on clinically implantable devices has resulted in the definition of a novel contagious illness known as chronic

References

273

polymer-associated infection (Go¨tz, 2002). Biofilm-based illnesses can lengthen hospitalization by two to three days and add to $1 billion in additional costs each year (Archibald et al., 1997). As a result, there is an immediate requirement to uncover efficacious, prophylactic, and curative solutions to implant-based infections in the living systems.

15.4 Conclusion Biofilms occur in both natural and artificial systems to provide a suitable environment for the growth and interaction of various bacterial species. The production of microbial biopolymers is responsible for the formation of mature biofilms that directly or indirectly protect the human population from environmental hazards. Biofilm plays an important role in the environment for cleaning up contaminated sites and industrial waste. In recent times, with increases in the accumulation of toxic compounds in the environment, biofilms have gained attention in order to minimize the toxic effects. The great versatility of microbes provides simple, economical, and more eco-friendly strategies to reduce environmental pollution, including bioremediation of industrial waste and hydrocarbons, along with wastewater or sewage treatment. Biofilms in agriculture provide a positive relationship between plants and bacteria and directly promote plant yield. Therefore beneficial aspects of bacterial-mediated biofilms will have great potential for developing new strategies to protect environmental well-being in the future. In addition, research can be carried out via the application of advanced techniques, and new regulation strategies in bacterial biofilm formation are expected to be discovered.

Acknowledgments The authors are thankful to the Department of Zoology, SSJ Campus, Almora, for providing a suitable research environment.

Conflict of interest The authors have declared no conflict of interest.

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CHAPTER

Antibiotics: action mechanism and modern challenges

16

Utkarsha Sahu1,2 and Prashant Khare1,2 1

Department of Microbiology, All India Institute of Medical Sciences, Bhopal (Madhya Pradesh), India 2Center for Advanced Biotechnology Research, Absolute, Gurugram, Haryana, India

16.1 Introduction Antibiotics are naturally occurring or synthetic antimicrobial molecules used against various microbial ailments. They are not effective against fungal or viral infections but are in high demand for disease treatment caused by various bacterial infections. They work by blocking some crucial processes in microbial cells selectively (Walsh, 2003). Paul Ehrlich’s work on the antibacterial effects of dyes can be defined as the beginning of the modern era of antimicrobial chemotherapy. Ehrlich wanted to develop stains for histological examination of tissues. He found out that some bacteria are unable to survive in the presence of some stains. He focused himself to look for the chemical compounds responsible for it. Ultimately, together with his team, he was successful in isolating an arsenic-based compound called salvarsan, which was very effective against Treponema pallidum, a causative agent for syphilis. This was the first chemical compound isolated that had significant antimicrobial properties (Gould, 2016). After this, the age golden of antibiotics started with the discovery of penicillin in the 1950s. Antibiotics are divided into different categories based on their origin (natural and synthetic), mode of action (β-lactam, quinolone, sulfa drugs, aminoglycosides), and based on responses (bactericidal and bacteriostatic) (Miller, 2002). Although, it is argued that antibiotic discovery is a big milestone in scientific history, the biggest challenge is the failure to develop a sustainable platform for antibiotic discovery. A few might blame the lack of efforts and/ or funding but in retrospect, substantial efforts were placed by pharmaceutical industries during the 1990s (Gwynn, Portnoy, Rittenhouse, & Payne, 2010). In addition, the accumulation of antibiotics in the environment is another problem for mankind. It is reported to adversely affect the human gut microbiome and plant growth along with other physical parameters. In this chapter, we have discussed the history of antibiotic discovery, the key events, their classification, mode of action, and the challenges faced due to antibiotic misuse. The discovery of new antibiotics is surely demanded in contemporary times but we also need to ensure that these antibiotics would not be misused to avoid resistance issues. An alternate approach to overcome the challenge of antibiotic resistance could be to focus on identifying new drug targets that are less prone to resistance caused due to mutations (Kapoor, Saigal, & Elongavan, 2017). Thus, sustainable use of antibiotics along with the discovery of new antibiotics is the need of modern medicine (Kapoor et al., 2017). Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00004-1 © 2023 Elsevier Inc. All rights reserved.

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16.2 History, classification, and mechanism of action of different antibiotics 16.2.1 History of antibiotics The first antibiotic to be discovered was salvarsan against syphilis by Sahachiro Hata, Paul Ehrlich, and Alfred Bertheim in 1909 (Vernon, 2019). This was followed by the discovery of neosalvarsan in 1912. Neosalvarsan was used to cure syphilis and had lesser side effects compared with salvarsan. In the 1920s, different azo dye-based chemical compounds were screened for their antimicrobial activity. K1730, also known as prontosil, was one such compound discovered by Josef Klarer, Gerhard Domagk, and Fritz Mietzsch. K1730 was very efficient against gram-positive bacteria, however, it was inefficient against gram-negative bacteria. Later in the year 1932, Protonsil derived sulfonamides came to the market for curing puerperal fever. Another milestone in the discovery of antibiotics was the observation made by Alexander Fleming. He discovered an antibacterial mold that was named Penicillin (Fleming, 2001). The first ever antibiotic to be tested in mice was tyrothricin, discovered by Ren´e Dubos in the year 1939. Tyrothricin was isolated from the soil and exhibited substantial antimicrobial properties (Honigsbaum, 2016). The word antibiotic was first used in the year 1941 by Selman Waksman (Clardy, Fischbach, & Currie, 2009). This was followed by the discovery of an aminoglycoside antibiotic named streptomycin, in 1943, by Albert Schatz and Selman Waksman (Sakula, 1988). Streptomycin proved to be very effective against tuberculosis. The first ever orally administered antibiotic was Penicillin V made in the year 1945. Although the work on penicillin started very early, the X-ray structure of penicillin was decoded in 1945 by Dorothy Hodgkin (Glusker, 1994). The first amphenicol, named chloramphenicol, was discovered in 1947 by Ehrlich. It was identified as a natural compound secreted by the bacteria Streptomyces venezuelae present in compost and soil (Ehrlich, Bartz, Smith, Joslyn, & Burkholder, 1947). The first tetracycline, chlortetracycline, was discovered in 1948 by Benjamin Duggar followed by the discovery of first macrolide-erythromycin in 1949 by A. Aguilar (Jeli´c & Antolovi´c, 2016). Erythromycin was administered to patients who were allergic to penicillin. In 1952, vancomycin, the first glycopeptide was discovered. It was isolated from the soil samples (Levine, 2006). This was followed by the chemically synthesized penicillin by J.C. Sheeman in 1957, which led to the development of different chemical variants such as carbenicillin and ampicillin (Blum, Deaguero, Perez, & Bommarius, 2010; Butler et al., 1973). In 1957, a crude extract of the plant Nocardia mediterranei was chemically modified to create rifampicin, a crucial anti-TB drug (Chakraborty & Rhee, 2015). In the same year kanamycin was isolated by a Japanese group. Kanamycin was capable of killing both streptomycin and penicillin resistant bacteria (Umezawa, 1958). A separate group of β-lactam antibiotics known as carbapenems were discovered by Merk in the year 1976. These antibiotics were capable of killing other β-lactam resistant bacteria (Fair & Tor, 2014). In the year 1999, a new class of antibiotics termed streptogramin was discovered, which restricted protein synthesis in bacteria (Mast & Wohlleben, 2014). In 2001 another group of synthetic antibiotics, known as oxazolidinones, was introduced (Zurenko et al., 2001) (Table 16.1).

16.2 History, classification, and mechanism of action of different antibiotics

283

Table 16.1 Timeline of antibiotic discovery. S. No.

Antibiotics

1 2 3 4

Salvarsan Neosalvarsan Penicillin Prontosil derived sulfonamides Tyrothricin Streptomycin Penicillin V Chlortetracycline

5 6 7 8 9 10 11 12 13 14 15

Erythromycin Vancomycin Chemically synthesized penicillin Kanamycin β-Lactam antibiotics Streptogramin Oxazolidinones

Year of discovery

Targeted infections

1909 1912 1928 1932

Syphilis Syphilis Broad range infections Puerperal fever

1939 1943 1945 1948

Antimicrobial properties Tuberculosis Broad range infections Diseases caused by Rickettsiae, Chlamydiae, and Mycoplasmas Infection of respiratory tract, nose, skin, and throat. Respiratory and urinary tract infection Broad range of infections

1949 1952 1957 1957 1976 1999 2001

Broad range of infections Broad range of infections Against multidrug-resistant infections Skin/soft tissue infections, pneumonia, infections caused by gram positive bacteria

16.2.2 Classification of antibiotics Antibiotics are classified into different groups based on different criteria such as origin, mode of action, and target (Fig. 16.1).

16.2.2.1 Natural and synthetic antibiotics Based on their origin, antibiotics are divided into two categories: Natural and Synthetic.

16.2.2.1.1 Natural antibiotics Antibiotics produced by the secondary metabolism pathway of bacteria are classified as natural antibiotics. They are formed only when required and are not crucial for the existence of bacteria. Natural antibiotics are often produced by bacterial cells to kill other bacteria utilizing their debris as a food source. Common examples of naturally occurring antibiotics include chlortetracycline, penicillin, gramicidin, and streptomycin. The major part of natural antibiotic secreting bacteria is isolated from the soil. Natural antibiotics have certain advantages over synthetic antibiotics in terms of lesser side effects.

16.2.2.1.2 Synthetic antibiotics As the field of antibiotic study flourished with a better understanding of the mechanism of action of antibiotics the chemical synthesis of new antibiotics accelerated. In the past 30 years, various

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FIGURE 16.1 Classification of antibiotics.

types of antibiotics were synthesized. Many of these were approved for disease treatment. Some examples of synthetic antibiotics are fluorocyclines, 6-aminopenicillanic acid, linezolid, meropenem, and cephalosporin C. Synthetic antibiotics are more toxic to pathogens and act faster than natural antibiotics (Upmanyu & Malviya, 2020).

16.2.2.2 Bactericidal and bacteriostatic antibiotics Based on the putative targets, antibiotics are further divided into two categories, namely bactericidal antibiotics and bacteriostatic antibiotics.

16.2.2.2.1 Bactericidal antibiotics The mode of action of these antibiotics is killing bacteria in different ways (Pankey & Sabath, 2004). Common examples of bactericidal antibiotics include lipoglycopeptides, glycopeptides, aminoglycosides, quinolones, lipopeptides, cephalosporins, penicillin, monobactams, etc. (Patil & Patel, 2021).

16.2.2.2.2 Bacteriostatic antibiotics These antibiotics limit bacterial infection by arresting microbial growth and blocking their cell division. However, this process is concentration-dependent. Once the concentration of antibiotics decreases, the bacteria can resume their division. An interesting feature of these antibiotics is that

16.2 History, classification, and mechanism of action of different antibiotics

285

they may behave as bactericidal for a few bacteria and as bacteriostatic for other bacteria (Patil & Patel, 2021).

16.2.2.3 Aminoglycosides and tetracyclines, β-lactams, sulfa drugs, and quinolones Based on their mechanism of action, antibiotics can be further divided into four categories: aminoglycosides and tetracyclines, β-lactams, sulfa drugs, and quinolones (Kapoor et al., 2017).

16.2.2.3.1 Aminoglycosides and tetracyclines Aminoglycosides and tetracycline group of antibiotics act by targeting the 30S ribosome. Tetracyclines limit the presence of aminoacyl-tRNAs for the ribosome whereas the aminoglycoside (kanamycin, streptomycin, framycetin, gentamicin, tobramycin, etc.) and aminocyclitol group of antibiotics bind to the 16s rRNA. On the other hand, spectinomycin disrupts the steadiness of peptidyl-tRNA. It targets the 30s ribosomal subunit and limits protein synthesis (Krause, Serio, Kane, & Connolly, 2016). The only naturally occurring bactericidal antibiotics are the aminoglycoside class of antibiotics. Streptogramins, macrolides, chloramphenicol, and tetracycline are generally bacteriostatic. However, these can also work as bactericidal antibiotics during particular treatment or in specific species.

16.2.2.3.2 β-Lactams A major component of the bacterial cell wall is peptidoglycan (PG). It comprises a covalent crosslinked polymer of β-(1,4)-N-acetyl hexosamine. The PG layer provides mechanical strength to the bacterial cells. This mechanical strength is helpful for the survival of bacterial cells in stress conditions such as osmotic pressure. Enzymes such as transpeptidase and transglycosylase help in maintaining the PG layer by adding disaccharide pentapeptides (Salton & Horne, 1951). β-Lactams and glycopeptides are antibiotics that restrict the biosynthesis of the cell wall by targeting the crucial protein function necessary for this function. Common examples of β-lactams are carbapenems, cephalosporins, monobactams, and penicillins (Periti & Nicoletti, 2013). Inhibitors targeting the cell wall synthesis can also alter the shape and size of the cell creating cellular stress leading to cell death (Yocum, Waxman, Rasmussen, & Strominger, 1979). The common antibiotics of this class limit the reaction for peptide bond formation catalyzed by transpeptidases, thereby preventing the cross-linking of PG subunits. β-Lactam drugs behave as the substrate of transpeptidases and inactivate the enzyme (Bugg & Walsh, 1992; Kohanski, Dwyer, & Collins, 2010). Experimental evidence suggests that Streptococcus pneumoniae strain with reduced or no amidase activity resisted higher concentrations of β-lactam. The strain exhibited bacteriostatic characteristics against bactericidal concentrations of β-lactam after antibiotic treatment. It is also verified that amalgamation of β-lactam antibiotics can inhibit murein hydrolases and the synthesis of PG, inducing cell death (Novak, Charpentier, Braun, & Tuomanen, 2000)

16.2.2.3.3 Sulfa drugs Also called sulfonamides, this class of antibiotics has different clinical usages. They are being used since the1930s and are among the first antibiotics to be used in clinical practices. Sulfa drugs are bacteriostatic and their mode of action involves inhibition of folic acid biosynthesis that is required for cell growth in sulfa-sensitive bacteria (Fukaya, 1990). Sulfa drugs possess a wide antimicrobial activity range against both gram-negative and gram-positive bacteria. However, bacterial resistance

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to sulfa drugs is now very common and that is why their use has now decreased. However, they are still used for limiting infections in the urinary tract along with other drugs. In addition, they are also used in combination with other drugs to limit malaria and parasitic diseases (Garg, Gogtay, & Kshirsagar, 1996). Sulfonamides possessing 5-aminosalicylic acid are organizational apparatuses of sulfasalazine used for chronic treatment of inflammatory bowel disease. The amalgamation of pyrimethamine and sulfadoxine is used as an alternative treatment option for chloroquine-resistant malaria (Sulfadoxine-Pyrimethamine, 2017). Currently, sulfa drugs are primarily used in combination with dihydrofolate reductase (DHFR) inhibitors known as trimethoprim (TMP). A combination of TMP and sulfamethoxazole (SMX) called cotrimoxazoles is the most prescribed combination for several bacterial infections, such as bronchitis, urinary tract infections (UTI), methicillin-resistant staphylococcus aureus (MRSA) infections, and traveler’s diarrhea (Griffith et al., 2018). In addition, cotrimoxazole prophylaxis is also used in the prevention of Pneumocystis jirovecii infection in patients with immunocompromised conditions.

16.2.2.3.4 Quinolones These molecules are structural derivatives of quinoline that gained its name from the oily substance obtained after quinine distillation (Gerhardt, 1842). Ever since the isolation of quinine in 1811 from the Cinchona bark, various other derivatives of quinoline have been isolated from different natural resources. Particularly, 4-hydroxyquinoline and 2-hydroxyquinoline principally occur as 4 (1H)-quinolone and 2(1H)-quinolone, respectively (Heeb et al., 2011). Numerous other bacterial and animal species also produce quinolone compounds that differ in various heteroaromatic and carbocyclic ring substitutions but also have additional rings merged with the quinolone nucleus (Michael, 2008). The first-generation quinolones, such as nalidixic acid, were introduced around the 1960s for treating UTIs. These are rarely used in the present scenario due to their toxicity. Later Ciprofloxacin (second-generation), levofloxacin (third-generation), and gemifloxacin (fourth-generation) quinolones were discovered and differentiated on the basis of their chemical structure and mode of action (Drlica & Zhao, 1997). The quinolone group of antibiotics mainly target the topoisomerase involving reactions, thereby disrupting crucial cellular processes such as cell division, transcription of mRNA and DNA replication (Michael, 2008). Two different type II topoisomerases, namely topoisomerase IV and gyrase, are encoded by most species of bacteria. These enzymes are crucial for controlling the DNA winding levels, removing knots from chromosomes, and modulating the topological state of the DNA by making negative supercoils. Altogether, topoisomerases are required for the chromosome modulation of bacteria, and by targeting them, the quinolone antibiotics hinder the process causing cell death (Heeb et al., 2011; Michael, 2008).

16.2.3 Antibiotics in the environment: modern challenges and future perspectives Molecules possessing antibiotic properties, formed by various microbes, existed long before humans identified their role in the treatment and prevention of bacterial infections (Larsson, 2014).

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287

Bacteria were exposed to prolonged antibiotic selection pressure in due course of time. During the 20th century, mankind started producing large-scale antibiotics including the synthetic byproducts of natural antibiotics and sole synthetic antibiotics. As a result of which, the whole bacterial community was exposed to the unparalleled selection pressure of antibiotics leading to the development of antibiotic resistance (Polianciuc, Gurz˘au, Kiss, Georgia S¸tefan, & Loghin, 2020). Apart from the risk of selection pressure-induced antibiotic resistance, antibiotics can be absorbed by plants leading to interference with physiological processes and ecotoxicological effects. To determine the extent of this damage several acute and chronic toxicity tests have been carried out in plants, which indicated the effect of antibiotics on mitochondria (oxidative stress response in plants) and photosynthesis (chloroplasts gene expression and cell proliferation) (Wang, Ryu, Houtkooper, & Auwerx, 2015). In addition, the antibiotic concentrations in agricultural soil reduced biomass production and delayed seed germination. Altogether, these changes affect the crop yield in farmland exposed to contaminated manure (Minden, Deloy, Volkert, Leonhardt, & Pufal, 2017). The possible negative effects of antibiotic intake by plants, crops, and humans have been well established (Kang et al., 2013; Pan, Wong, & Chu, 2014). However, the influence of antibiotics on plants, specially, noncrop plants is not fully elucidated. Different studies highlight the role of antibiotics in plant growth and performance. Furthermore, the response to these factors can be in a dose-dependent manner such as toxic effects at increased concentrations and growth at lower concentrations. (Liu et al., 2013; Migliore, Rotini, Cerioli, Cozzolino, & Fiori, 2010). Plant roots are the most affected parts of plants due to antibiotic accumulation resulting in adverse effects on root length, elongation and water uptake, and lateral root numbers (Migliore et al., 2010; Piotrowicz-Cie´slak, Adomas, Nałae¸cz-Jawecki, & Michalczyk, 2010). In addition, different studies have also reported that antibiotic accumulations can change the production of biomass, leaf number, shoot length, branching patterns, root/shoot ratio, internode length, fresh/dry weight, etc. (Bradel, Preil, & Jeske, 2000; Liu et al., 2009; Michelini, Reichel, Werner, Ghisi, & Thiele-Bruhn, 2012; Yang et al., 2010). Different physiological traits altered by antibiotics include chloroplast synthase activity, photosynthetic rate, abscisic acid (ABA) synthesis, transpiration rate, and stomatal conductance (Kasai, Kanno, Endo, Wakasa, & Tozawa, 2004; Werner et al., 2007). Altogether, these studies validate that the accumulation of different antibiotics in plant tissues affects plant growth and other functional traits. In addition, we are also concerned for the microbial communities residing in and/or on our bodies that are prone to direct selection pressure. Other environments, however, might also be exposed to antibiotic selection via different routes. Thus, there is a major concern that augmented selection pressure from antibiotic considering that the environment can facilitate the conscription of resistance from the environment to human pathogens (Kapoor et al., 2017; Larsson, 2014). Furthermore, antibiotics can change the human microbiome leading to health discrepancies like allergic reactions and disturbance in the digestive system. Once entering the environment these antibiotic residues impart adverse effects on human health and biota in various trophic levels (Patangia, Anthony Ryan, Dempsey, Paul Ross, & Stanton, 2022). The adverse reaction to antibiotics in humans can be of two different types. A drug dose-independent reaction that does not involve an immunity-based reaction is known as antibiotics side effects (Granowitz & Brown, 2008). On the other hand, an immune system-based hypersensitivity associated with IgE antibodies causes angioedema and anaphylaxis resulting in upregulated antibody concentration in the blood due to poor elimination and

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decreased metabolism. This situation is termed as an allergic reaction. The prediction of these adverse effects caused due to antibiotics is warranted. However, these effects might vary from patient to patient (Granowitz & Brown, 2008). Antibiotic resistance is a great threat to mankind today, and regulatory, scientific, and economic barriers together contribute to this. Different approaches to reawaken R&D are needed that include the identification of innovative antibiotic scaffolds and altering our thinking about the treatment of infections. For instance, focusing on disarming the pathogen instead of modulating the host immune response or killing the microbe (Spellberg, 2014). The future economic approaches are most likely to target the push incentives presented by private-public partnerships and increase the price by concentrating the development on areas with unmet needs. These factors can also aid to prevent the overuse of new antibiotics after marketing (Spellberg, 2014). In addition, regulatory reforms are also needed to confirm meaningful and feasible antibiotic pathways for creating restricted-use pathways. The pathways should mainly focus on extremely resistant infections. Thus, although we need new antibiotics to target new and previously established resistant microbes, we have to also ensure that those newly discovered antibiotics are not misused to prevent further drug resistance. For breaking the current resistance cycle strong approaches challenging the age-old dogma are required.

16.2.4 Discussion For many years humans were prone to different types of pathogenic infections that often reached epidemic proportions and killed millions of individuals. During this time humans thought about the causes of these infectious diseases. But, due to a lack of knowledge, the search for approaches to prevent, heal, and fight these communicable diseases was ineffective for a while (Mohr, 2016). Only after the discovery of antibiotic-producing molds, the disapproval of the abiogenesis theory, and the question about the nature of infectious diseases was answered, an array of new discoveries started due to which bacterial isolation, culture, and identification were possible (Mohr, 2016). Simultaneously, the first antibiotics of synthetic origin developed. Later, several synthetic compounds and soil-borne fungi and bacteria were screened by different labs for their bioactivity. By the start of the 20th century, several diseases that previously reached an endemic status, such as plague, syphilis, cholera, and tuberculosis, could be fought with recently discovered antibiotics (Walsh, 2003). However, with advancements in antibiotic discovery mankind failed to limit the misuse of antibiotics resulting in selection pressure on microbes causing antibiotic resistance. In addition, the accumulation of antibiotics in the environment adversely affected plant growth, root development, shoot length, transpiration rate, etc. (Liu et al., 2013; Migliore et al., 2010). Also, antibiotic overuse can alter the species of plants in natural fields that can have unknown consequences on the environment (Minden et al., 2017). In addition, it also affected the human gut microbiota and the digestive tract (Migliore et al., 2010; Piotrowicz-Cie´slak et al., 2010). Assuming that there is a comparative lack of success in developing effective synthetic antibiotics the best hope for sustainable antibiotic development could be to find contemporary microbial natural products as these are unparalleled in chemical diversity and effectiveness. This should also be accompanied by the sustainable use of newly developed antibiotics to avoid the selection pressure-induced drug resistance in microbes.

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Drug resistance in pathogenic species of Candida

17

Neha Jaiswal and Awanish Kumar Department of Biotechnology, National Institute of Technology, Raipur, Chhattisgarh, India

17.1 Introduction Many microorganisms live in the human body in small amounts, fungi are one of them. One of the types of fungi is Candida species, which lives in the human body without causing any harm. However, when a favorable environment arises, they grow in large amounts and cause infections in the human body. Candidiasis is a yeast infection caused by Candida species. It majorly causes infection in an immunocompromised body. Candida can cause infection in the oral and vaginal part of the body, and sometimes it infects other parts of the body like the skin, belly, etc. Candidiasis infections are of two types: oral infection (thrush) and vaginal infection (yeast infection). Oral candidiasis is most commonly caused by Candida species like C. albicans, C. glabrata, C. guilliermondii, C. krusei, C. parapsilosis, C. pseudotropicalis, C. stellatoidea, and C. tropicalis. In oral candidiasis, white plaque is generated on the surface of the tongue and when removed an erythematous area remains known as an antibiotic sore mouth. In vaginal candidiasis, symptoms like itching, burning rashes, fever, and white discharge (cottage cheese like) from the vagina are seen. Fungal infections have become a worldwide problem, a million people die every year due to invasive fungal infections and 75% of women get infected by vulvovaginal candidiasis once in their lifetime (Brown et al., 2012). The mortality rate of fungal infection is increasing because of the difficulty in diagnosing, which reaches up to 50% in many cases (Ko¨hler, Casadevall, & Perfect, 2014). It is clear that there is an urgent need for medical devices for the diagnosis of fungal infections accurately. For the treatment of candidiasis, generally antibiotics are used, unlike other infections. For fungal infections mainly three classes of antibiotics are taken: azoles, echinocandin, and polyenes (Berman, Krysan, 2020). Azoles generally bind with Erg11 and an cause interruption in ergosterol synthesis, which is the main sterol component of the cell membrane; echinocandins target the cell wall of Candida by disrupting β-1,3-D-glucan synthase; while polyenes target the cell membrane by binding with ergosterol and forming pores on the cell membrane of Candida, leading to osmotic disbalance (Berman, Krysan, 2020). These antibiotics are fungicidal causing fungal cell death, or fungistatic arresting cells from proliferation. However, Candida cells become drug resistant due to mutation. Drug resistance can be devastating and limits the number of available drugs for treatment. The development of antifungal resistance depends on multiple host and microbial factors (White, Marr, & Bowden, 1998). The host immune system plays an important role in the Advanced Microbial Techniques in Agriculture, Environment, and Health Management. DOI: https://doi.org/10.1016/B978-0-323-91643-1.00014-4 © 2023 Elsevier Inc. All rights reserved.

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drug resistance of Candida species since immunocompromised patients are more likely to fail the therapy (Ben-Ami, Lewis, & Kontoyiannis, 2008). Medical devices, such as indwelling catheters, artificial heart valves, and other surgical devices, mediate the transfer of infection and the establishment of biofilms that resist antifungal drug action (d’Enfert, 2006; Bonhomme & d’Enfert, 2013). Over 10 years (1997
2007) of data from 142 institutions in 41 countries, identified 31 species of Candida pathogenic of which 5 species are mainly responsible for 92% of infection cases (Pfaller et al., 2010). The five species most common for candidiasis infection are C. albicans (65.3%), C. glabrata (11.3%), C. tropicalis (7.2%), C. parapsilosis (6.0%), and C. krusei (2.4%) (Pfaller et al., 2010). Historically the number of infections is rising but C. albicans remains the most common species. In 2009 a novel species of Candida, Candida auris, was isolated in Japan. Candida auris is an emerging fungal pathogen associated with nosocomial infections (Satoh et al., 2009; Sabino, Verı´ssimo, Pereira, & Antunes, 2020). A significant role played by its gene in central metabolism allows it to survive in diverse environments (Chowdhary, Sharma, & Meis, 2017). Virulence factors like enzyme secretion, nutrient acquisition, siderophore-based iron acquisition, tissue invasion, twocomponent histidine kinase system, and pathways involved in cell wall modeling are common in all species (Sharma, Kumar, Pandey, Meis, & Chowdhary, 2016). C. auris can challenge the immune system by evading neutrophil attacks and innate immune responses (Johnson, Davis, Huttenlocher, Kernien, & Nett, 2018). Biofilm formation is the major strain for drug resistance in Candida species. Biofilms allow drug confiscation in the extracellular matrix, which facilitates drug tolerance in many Candida species (Mitchell et al., 2015). ATP-binding cassette (ABC) and major facilitator superfamily (MFS) are also major factors of drug resistance. The ability of drug resistance and causing infections to several host niches are supported by virulence factors of Candida species, with immunodeficiency of the host being one of the factors. For the past 10 years the rise in incidences of candidiasis and its drug resistance exacerbates the need for new drugs for treatment. Antifungal resistance is a major problem in certain populations, especially in HIVpositive patients. It is studied that 33% of HIV patients infected with oral thrush had drug-resistant Candida species (Law et al., 1994). The development of a novel antifungal drug is important to kill biofilms and inhibit Candida infections. The eukaryotic nature of the fungi is the reason for slow drug development. Bioavailability, transmission of drugs through the membrane, and limitation of interest of the pharmaceutical industries are challenges for novel drug development. In fact, since mid-2000 not a single antifungal drug has entered clinical practice. In this review, we will focus on the pathogenic yeast Candida species and the factors and mechanisms associated with their drug resistance. The biology, epidemiology, pathogenicity, and therapeutic challenges are discussed in this chapter. We also address some in-depth knowledge about Candida drug resistance sites, molecular mechanisms, and genes responsible for the drug resistance property.

17.2 Epidemiology Over the past decades, candidiasis is the most common clinically relevant infectious disease compared with other bacterial or viral infections (Cortegiani et al., 2018). This trend is attributable to the increasing number of immunocompromised patients and the increasing use of medical devices. Invasive infections caused by Candida have become an emerging problem in some populations,

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introducing a notable diagnosis and therapeutics challenge to researchers and resulting in major attention on the epidemiology of Candida infection. Several Candida species can cause infections on the skin and the mucosal surface of host people. Candidemia is a bloodstream infection caused by Candida, and it is the most common invasive infection. Critically ill or immunocompromised people are more susceptible to invasive candidiasis, which can become life-threatening (Hasan, Xess, Wang, Jain, & Fries, 2009). Oral candidiasis is most common in HIV-positive patients, which leads to malnutrition and slow absorption of antibiotics (Fidel, 2006; Hasan et al., 2009). Further Candida can cause an invasive infection (bloodstream infection) known as candidemia, which has a high mortality rate leading to serious health challenges and costs (Almirante et al., 2005; Lai, Wang, Liu, Huang, & Hsueh, 2012). Candidiasis has become a major fungal infectious disease due to an increment in non-albican species. However, in a study of major North American medical centers in 2019, most of the nonalbican species (C. glabrata and other non-C. albicans species) were observed, and C. albicans were most frequent in candidiasis patients. In European countries, candidemia is mostly caused by C. albicans and some non-albicans such as 14% for C. glabrata and C. parapsilosis, 7% for C. tropicalis, and 2% for C. krusei (Tortorano et al., 2006). This change in epidemiology was also observed in some American countries, which can be associated with the immunocompromised status, frequent use of antibiotics, and old age of patients. In Chile, an increment in non-albican species was observed, where C. parapsilosis, C. tropicalis, and C. glabrata most frequently showed antifungal resistance properties (Ajenjo et al., 2011). According to a study, in Brazil, 40% of candidemia was caused by C. albicans, 20% by C. tropicalis, 20% by C. parapsilosis, and the rest by C. glabrata species. In Ireland, C. dubliniensis was isolated from the oral cavity of HIV-positive patients. The genome of the species lacking the hypha-related virulence gene limits hyphal transmission, decreasing the potential of invasive infections (Moran, Coleman, & Sullivan, 2012). In some regions of Spain and Latin America, C. parapsilosis became an emerging species of candidemia. It was recognized as the second most frequent bloodstream infectious species after C. albicans (Colombo et al., 2007). C. guilliermondii and Candida rugosa are very rare species but in some cases, C. rugosa (1%) causes oral infections in some diabetic patients (Pires-Gonc¸alves et al., 2007). C. glabrata is one of the species causing candidemia infection by showing resistance to fluconazole (Nucci, Queiroz-Telles, Tobo´n, Restrepo, & Colombo, 2010). The rise in non-albicans infection and antifungal resistance modify the epidemiology of candidiasis. Some non-albicans species show less susceptibility for antifungal than albican species. C. tropicalis are less susceptible to fluconazole; however, C. albicans show more susceptibility to fluconazole. In 2009 C. auris, a new species of Candida, was found in Japan. It shows resistance to all available antifungals and creates a global emergence. In a record from March 2020, there were 1092 cases of C. auris in the United States. C. auris has the ability to form dry biofilms, which are difficult to eradicate and provide very high resistance to azoles, amphotericin B, and echinocandin (Sherry et al., 2017) (Alfouzan et al., 2020). This species has a very high mortality rate (75%) and can frequently colonize medical devices and host surfaces (Mathur et al., 2018). All these characteristics allow it to spread the infection from person to person. Since the 19th century the discovery of new antifungals has increased. Due to the increased availability of antifungals in the environment microorganisms, they consequently get resistant to drugs. Although much knowledge exists about the epidemiology of candidiasis, many questions still arise (particularly, in the context of countries like Japan and South Korea with a high percentage of elderly population): Will the rate of Candida infection change with the

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age of the population? Will the increased use of drugs lead to the emergence of drug resistance or the emergence of new species? There are many aspects to know in epidemiology. However, in this decade the epidemiology of Candida remains stable but will continue to change in the decades to come.

17.3 Overview of molecular mechanisms of drug resistance Over the past few decades, drug resistance has been a major issue in our science community. There are many cases where antimicrobial drugs are becoming ineffective for infectious diseases. This issue of drug resistance is particularly concerning fungal pathogens, which can cause invasive infections and spread the emergence of multidrug resistance. Resistance can be simply defined as the reduction in the effectiveness of a particular drug for the treatment of a disease. In other words, the strain is with increased minimal inhibitory concentration (MIC) value for the drug relative to its control (Berman, Krysan, 2020). Drug tolerance is another word that means the strain has the ability to survive in the presence of antibiotics at a concentration above the MIC (Berman, Krysan, 2020). In Candida species, both drug resistance and tolerance are observed. C. auris is one of the species that shows drug resistance and tolerance for all available antifungals (azole, echinocandin, and amphotericin B). There are multiple mechanisms for drug resistance adaptation including stress response, overexpression, alteration of the target gene, upregulation of multidrug transporter, genome modifications, etc. All these mechanisms provide drug-resistance properties to Candida strains and this particular component or site is known as the resistance site. There are multiple resistance sites like ERG11, UPC2, TAC1, MMR1, FKS1, FKS2, and ABC, which are all target sites that convert into resistance sites by mutation and overexpression.

17.3.1 ERG genes In Candida, ERG is a gene encode for lanosterol demethylase, which is a target of antifungals. Alteration in the target gene is a common mechanism of resistance. Amino acid substitution in ERG11 leads to drug resistance by decreasing the binding affinity of the lanosterol demethylase enzyme (Revie, Iyer, Robbins, & Cowen, 2018; Lamb et al., 1997). In C. albicans 140 amino acid substitution associates resistance toward azoles (Morio, Loge, Besse, Hennequin, & Le Pape, 2010). Mutation in ERG11 shows fluconazole resistance in C. auris (Flowers, Colon, Whaley, Schuler, & Rogers, 2015). In the study of whole genome sequencing of C. auris indicated the substitution of three hot-spot amino acids Y132F, K143R, and F126L implicates azole resistance in C. albicans (Lockhart, 2019; Lockhart et al., 2017). Although overexpression of ERG11 is controlled by zinc cluster transcription factor (UPC2), it results in higher concentration of ergosterol, which generates azole resistance in C. albicans and non-albicans. It also contributes in lowering the drug susceptibility (Robbins, Caplan, & Cowen, 2017; Revie et al., 2018). In polyene, mutations in ERG2 (Jensen et al., 2015), ERG3 (Martel et al., 2010a, 2010b), ERG5 (Martel et al., 2010a, 2010b), and ERG11 (Sanglard, Ischer, Parkinson, Falconer, & Bille, 2003) decreases amphotericin B susceptibility of C. albicans. On other hand, in C. glabrata, ERG2 (Hull et al., 2012), ERG6 (Vandeputte et al., 2008), and ERG11 (Hull et al., 2012) reported polyene resistance.

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The higher expression of ERG genes in the ergosterol biosynthesis pathway show amphotericin B resistance for C. auris (Munoz et al., 2018). The loss of function of ERG genes can also generate azole resistance (Kelly et al., 1997). A missense mutation in ERG3 leads to the loss of function, which encodes Δ-5,6-desaturase, and blocks the cellular accumulation of 14-α methyl-3,6-diol, which if incorporated in the cell membrane allows the replication and growth of fungi in the presence of azole (Morio, Pagniez, Lacroix, Miegeville, & Le Pape, 2012).

17.3.2 ATP-binding cassette In Candida species the first main azole resistance efflux pump is an ATP-binding cassette (ABC). Overexpression of CDR1 and CDR2 in ABC transporter leads to azole resistance (Revie et al., 2018). The transcriptional activator of CDR1, known as the transcriptional factor (Tac1), promotes the regulation of CDR1 and CDR2 by binding with cis-acting drug response elements (DREs) (Coste et al., 2006; Garcia-Effron, Katiyar, Park, Edlind, & Perlin, 2008). Overexpression of both CDRs generates azole resistance. Drug resistance property by this site is also seen in C. glabrata (Sanglard, Ischer, & Bille, 2001). In C. auris, CDR1 plays an important role in drug resistance (Kim et al., 2019). The upregulation of CDR1 and major facilitator (MF) increases fluconazole sensitivity (Kean et al., 2018). Mutation in TAC1 gives rise to higher fluconazole resistance for C. auris. Similarly, for polyene drugs, the efflux pump plays the majority of amphotericin B resistance in C auris (Rybak et al., 2020). Since membrane transporter resistance is not so clear, this requires further analysis.

17.3.3 FKS genes FKS genes are the essential genes of Candida species. Mutation in FKS genes generates antifungal resistance. There are two hotspot (HS) regions in the FKS gene, the HS1 region (641
649) and the HS2 region (1357
1364). Mutation in these region links with echinocandin resistance (Perlin, 2007). Mutation in FKS1 genes has more to contribute to drug resistance than FKS2 and FKS3 genes (Garcia-Effron, Lee, Park, Cleary, & Perlin, 2009; Garcia-Effron, Park, & Perlin, 2009; Park et al., 2005). In C. albicans, the higher transcription of the FKS1 gene shows lower echinocandin susceptibility (Suwunnakorn, Wakabayashi, Kordalewska, Perlin, & Rustchenko, 2018). C. auris shows higher FKS1 transcription while C. glabrata have both FKS1 and FKS2 transcription. The echinocandin resistance of C. auris is due to FKS1 mutation meanwhile FKS2 mutation generates resistance in C. glabrata (Chowdhary et al., 2018). In clinically isolated C. glabrata species S629P/ T and S663P/F/A are the most observed amino acid substitutions in HS1 of FKS1 and FKS2, showing high MIC values (Arastehfar et al., 2020). In C. albicans, S456P/F and Ser641P/F are the most prevalent resistance-associated mutations leading to HS1 and HS2 mutation (Perlin, 2007). C. tropicalis and C. auris have mutations in HS1 of FKS1 by the substitution of S645P and S639P/F/Y, showing echinocandin resistance. (Arastehfar et al., 2020). Due to polymorphism, P660A in the HS1 of FKS1 of clinically isolated C. parapsilosis shows a higher MIC value against echinocandin compared with other Candida species (Garcia-Effron et al., 2008).

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17.4 Factors facilitating antifungal drug resistance Evolution is a nature of any organism to survive in the environment. Microorganisms evolve according to surviving conditions. Drug resistance is one of the techniques of survival for microorganisms. The frequent use of antimicrobial drugs leads to increased drug resistance. Drug resistance has become a major problem in treating the disease. C. albicans most predominantly shows multidrug resistance to infection. The drug resistance property of this fungi is facilitated by many factors such as genomic alteration, environmental state, over-prescription of antifungal drugs, immunocompromised stage of hosts, etc. The major factor is the genomic alteration of Candida, in which the antifungal targets became drug sustainable and show drug resistance. The structural status of Candida is also an important factor, such as biofilm formation, which protects it from the host immune system and antifungal drugs. However, human behavior is also a major factor like skipping prescribed drugs or overdoses, lack of therapeutic knowledge, or patient demand. Genome alteration is mutations in the genes of an organism. The genomic plasticity, which is a major characteristic of the Candida species, helps them to adapt to extreme conditions (Selmecki, Forche, & Berman, 2010). Because of exposure to high antifungals, the adaptation of stressed conditions in cells gets stronger (Henry, Nickels, & Edlind, 2000). Eventually, mutations in alleles confer high resistance. Mutations for drug resistance are generally two types: alteration in drug targets and expression of drug efflux pumps (Shapiro, Robbins, & Cowen, 2011). There are mainly three classes of antifungal drugs: azoles, echinocandins, and polyenes. Resistance toward azoles involves multiple mechanisms like change in sterol biosynthesis, alteration in the target gene sequence, and overexpression of the efflux pump (Lupetti, Danesi, Campa, Del Tacca, & Kelly, 2002). In Candida, point mutations in the ERG11 gene leads to drug resistance toward azoles (Xiang et al., 2013). Overexpression of drug efflux pump includes multidrug resistance gene (MDR1) or Candida resistance gene CDR (Morschha¨user et al., 2007; Coste, Karababa, Ischer, Bille, & Sanglard, 2004). Upregulation of these pumps can be attributed to at least 17 different mutations in their transcriptional regulator TAC1. In C. parapsilosis mutation in transcriptional factor genes, MMr1 and EGR11, and overexpression of CDR1 and MDR1 govern azole resistance (Silva et al., 2011). Resistance toward echinocandins is seen in the hotspot region of FKS1 genes in C. albicans mutation and in the FKS2 hotspot region for C. glabrata mutation (Arendrup, Perlin, 2014). The mutation in the target gene results in low binding affinity of antifungals. Although resistance to amphotericin B is still rare in Candida, C. auris is one species that shows antifungal resistance toward most of the drugs.

17.5 Conclusion and future prospects Candida is a growing clinical threat and drug resistance is an emerging problem. In the past years, there has been a 20%
30% increase in candidemia infection showing resistance to azoles and echinocandins. Naturally C. albicans is susceptible to all drugs but mutation and evolutionary changes of species have converted them to drug-resistant. The drug resistance of Candida species is due to many mechanisms. The emergence of dangerous species like C. auris is a constant threat, which shows multidrug resistance, and a pathogenic threat for the near future. Understanding the

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mechanism of antifungal drug resistance and its key principles would help to develop new antifungals and effective strategies for treating emerging fungal species. Limited antifungal drugs and increasing drug resistance should direct our effort toward drug discovery, and identification of new classes of drugs and new targets. Collective mining of natural antifungals, the discovery of new target sites, and renewed interest of pharmaceuticals can provide good hope to challenge the drug resistance problem helping in the development of novel therapeutics.

Acknowledgments Authors are grateful to the National Institute of Technology, Raipur (CG), India.

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Index Note: Page numbers followed by “f” and “t” refer to figures and tables, respectively.

A ABA. See Abscisic acid (ABA) ABC. See ATP-binding cassette (ABC) Abiotic stress, 4
5, 24, 67
68, 83 agricultural application of stress-tolerant microorganisms, 73 microbial effects on crop productivity under stress conditions, 72
73 microbial resources for alleviation of, 68
72 biotic stress mitigation, bacterial-assisted, 71
72 cold stress mitigation, bacterial-assisted, 71 drought mitigation, bacterial-assisted, 69 heavy metal stress mitigation, bacterial-assisted, 70
71 salinity mitigation, bacterial-assisted, 69
70 role of beneficial microbes in, 11 Abscisic acid (ABA), 34
35 Actinomycetes, 8 beneficial role of, 7t Acyl homoserine lactones (AHLs), 23
24, 57 application of, 61 plant response to, 59 signaling molecules, 59
60 Adsorption, 177, 210 Aerobic bacteria, 206 Agricultural/agriculture contaminants affecting, 135f environmental pollutants’ impact on, 133
142 dyes from textile industries, 142, 143f electronic waste, 137
138 metals and metalloids, 134
137 nanoparticles, 138
139 particulate matter, 141
142 pharmaceuticals and personal care products, 139
140 plastics, 138 radioactivity/nuclear reactors, 139 remediation for removal of chemical contaminants, 142
143 sewage wastewater and sludge, 140
141 land, scarcity of, 191 in mountainous areas, 99
100 role of biofilms in environmental protection in, 270 role of microorganisms in, 84 biofertilizers, 84 biopesticides, biofungicides, and bioinsecticides in agroecosystem, 84
85 plant
microbial interaction, 85 sustainability, 90f

Agrochemicals in agriculture, 39
40 Agroecosystem, 1
2, 205 biofungicides in, 84
85 bioinsecticides in, 84
85 biopesticides in, 84
85 functioning of, 3 sustainable, 3 AHLs. See Acyl homoserine lactones (AHLs) Air pollution, 141
142 Algae, 207 Ambient temperature, 182 AMCs production. See Antimicrobial compounds (AMCs) production AMF. See Arbuscular mycorrhizal fungi (AMF) AMF-based biofertilizers, 101 1-Aminocyclopropane-1-carboxylic acid (ACC) deaminase production, 31
32 ethylene biosynthesis pathway depicting, 32f use of microorganisms with, 31
32 Aminoglycosides, 285 Ampicillin, 282 AMPs. See Antimicrobial peptides (AMPs) Anaerobic bacteria, 207 Animals, 208 types of, 209t Anionic polysaccharides, texture of, 271
273 Antibiotic production, 36
38 Antibiotic resistance genes (ARGs), 140
141 Antibiotics, 281, 288 adverse reaction to, 287
288 categories of, 281 classification of, 283
286, 284f aminoglycosides and tetracyclines, 285 bactericidal antibiotics, 284 bacteriostatic antibiotics, 284
285 natural antibiotics, 283 quinolones, 286 ß-Lactams, 285 sulfa drugs, 285
286 synthetic antibiotics, 283
284 discovery, 283t in environment, 286
288 history of, 282 intake, negative effects of, 287 malnutrition and slow absorption of, 294
295 misuse of, 288 of synthetic origin, 288 Antifungal drug action, 293
294

305

306

Index

Antifungal drug resistance, factors facilitating, 297 Antimicrobial compounds (AMCs) production, 37
38 Antimicrobial peptides (AMPs), 36
38 Antimicrobials, production of, 36
37 Antimony, 179 AO. See Arsenite oxidase (AO) Aquatic contaminants in agriculture, 263
264 Aquatic ecosystem, 140
141 Arabidopsis thaliana, 60 Arbuscular mycorrhizal fungi (AMF), 6
7, 7t, 100, 216 Archaeosporales, 6
7 ARGs. See Antibiotic resistance genes (ARGs) Arsenic, 179 Arsenite oxidase (AO), 226
228 Artificial intelligence (AI), 232, 233f Associative symbiotic nitrogen-fixing biofertilizers, 106 Atmospheric nitrogen into ammonia, 263
264 ATP-binding cassette (ABC), 35
36, 180, 293
294, 296 Augmentation control, 120
121 Autoclaving, 161 Auxin, 33
34 biosynthesis, 33f Azoles, 293
294, 298 Azotobacter chroococcum, 26
28 Azotobacter strains, 72
73 Azotobacter vinelandii, 26
28

B Bacillus, 71 antimicrobial compounds produced by, 37f B. amyloliquefaciens, 39 B. brasiliensis, 26
28 B. cepacia, 41 B. subtilis, 71
72 B. thuringiensis, 128 Bacteria, 206
207 aerobic, 206 anaerobic, 207 culture of, 101 methanotrophs, 207 potential microbial candidates, 206
207 utilization of, 86 Bacterial antagonists, 40t Bacterial communication, 57 Bacterial-derived enzymes, 224 Bacterial endosymbionts, 125 Bacterial infections, treatment and prevention of, 286
287 Bacterial secreted osmolytes, 69 Bacterial strains, 33
34, 69 Bactericidal antibiotics, 284 Bacteriostatic antibiotics, 284
285 Beneficial microbes, 11
12 Beneficial microorganisms, 11
12, 40
41, 85t

Beneficial rhizospheric bacteria, 33
34 ß-Lactams, 282, 285 Bioaccumulation, redox status of, 177 Biocontrol agent, 11
12 augmentation control, 120
121 and biofertilization with microorganisms for sustainable agriculture bacterial endosymbionts and endophytes, 125 endophytic fungi, 123 microbes of various environments, 125
126 mycorrhizal fungi, 123
124 plant growth-promoting rhizobacteria (PGPR), 121
122 rhizobia, 123 rhizospheric fungi, 124
125 viruses, 126
127 classical biological control, 120 conservative biological control, 121 of cotton bollworm, 127
128 description of, 119
120 seasonal biological control, 121 of sugarcane Pyrilla, 127 types of, 120
121 of water hyacinth, 128 of white woolly aphid, 128
129 of woolly apple aphid, 128 Biodegradation, 192
193 databases, 231 metabolic pathway simulation of, 229 pathway prediction, 229 Biodegraders, 87t Biodiversity, 205
206 Biofertilization with microorganisms bacterial endosymbionts and endophytes, 125 endophytic fungi, 123 microbes of various environments, 125
126 mycorrhizal fungi, 123
124 plant growth-promoting rhizobacteria (PGPR), 121
122 rhizobia, 123 rhizospheric fungi, 124
125 viruses, 126
127 Biofertilizers, 11, 43, 84, 126t in agroecosystems, 86t carrier, 113 challenges of commercialization, 110
113 biofertilizer carrier, 113 biological constraints, 112 field-level constraints, 113 marketing constraints, 112 regulatory constraints, 112 technical constraints, 112 characteristics of, 100 commercially available, 111t definition of, 98
99

Index

description of, 97
98 development, 101 encapsulated bioformulations, 105 foliar application, 109 implication of, 98 iron-solubilizing, 108 liquid bioformulation, 104 mass production of, 44 in mountainous ecosystems, 99
100 need for, 99
100 nitrogen-fixing biofertilizers, 105
106 associative symbiotic nitrogen-fixing biofertilizers, 106 free-living nitrogen-fixing biofertilizers, 106 symbiotic nitrogen-fixing biofertilizers, 105
106 phosphate-mobilizing biofertilizers, 107 phosphate solubilizing biofertilizers, 106
107 potassium-solubilizing biofertilizers, 107 preparation of, 100
101 proportion in, 101 quality of, 43 seed treatment, 110 soil treatment, 110 solid bioformulation, 102
104 dried powder (dust), 102
103 granules, 102
103 wettable powders, 102
103 wettable/water-dispersible granules, 102
103 types of, 105
109 bioformulations, 102
105 zinc-solubilizing biofertilizer, 108
109 Biofilm-based illnesses, 271
273 Biofilm-mediated wastewater, 263
264 Biofilms development of, 266
267, 270 in environmental protection, 267
273 in agriculture, 270 bioremediation, 267
268 formation for health, 271
273 heavy metal remediation, 268
269 polyethylene degradation, 271 remediation of hydrocarbons, 269 wastewater treatment, 269
270 formation of, 264
267, 270, 293
294 events of signaling in, 266
267 stages in, 264
266, 264f framework of, 267
268 maturation of, 264
266 utilization of, 269
270 Bioformulation development technologies, 100 dried, 102
103 encapsulated, 105 preparation, 102, 102f types of, 102
105, 103t

307

Biofungicides, 84
85, 87t Bioinsecticides, 87t Bioleaching, 177
178 Biological constraints, 112 Biological molecules, conformational modification in, 170
171 Biological nitrogen fixation (BNF), 25
28 plant growth promoting rhizobacteria with, 27t Biomass production, 287 Biopesticides, 11, 84
85 Bioremediation, 163, 208
210, 213
214, 267
268 aerobic methods, 163 anaerobic methods, 163 candidate domains with, 206f definition of, 267
268 environmental and biological factors affecting, 209
210 enzymes for, 211
212 microbial hydrolytic enzymes, 211
212 microbial oxidoreductases, 211 microbial proteases, 212 ex situ, 213
214 function-specific species for, 230
231 immobilization, 208 mobilization, 208
210 molecular docking approach for, 226
228 molecular dynamics simulation approach for, 228 objectives, 231
232 of pesticides, 98
99 processes, 230
231 in situ, 213 using genomics, 230
231 using in vitro conditions, 225f using proteomics, 229
230 Biosorption, 177, 210 Biosurfactants bioavailability of, 183
184 production, 38 Biosynthesis, 271
273, 285
286 Biosynthetic genes, 69 Biotechnology, productive and sustainable agro-environmental growth description of, 83 genetic engineering and sustainable agriculture, 83
84 nanotechnology in agriculture, 89
91 in food industry, 91 for improved soil quality, 91 nanofertilizers, 89 nanopesticides, 90 role of microorganisms in agriculture, 84 biofertilizers, 84 biopesticides, biofungicides, and bioinsecticides in agroecosystem, 84
85 plant
microbial interaction, 85

308

Index

Biotechnology, productive and sustainable agro-environmental growth (Continued) stress conditions, 83 Biotic stress, 67
68, 71
72, 83 agricultural application of stress-tolerant microorganisms, 73 bacterial-assisted drought mitigation, 69 bacterial-assisted heavy metal stress mitigation, 70
71 bacterial-assisted salinity mitigation, 69
70 description of, 67
68 microbial effects on crop productivity under stress conditions, 72
73 microbial resources for alleviation of, 68
72 cold stress mitigation, 71 drought mitigation, 69 heavy metal stress mitigation, 70
71 mitigation, 71
72 salinity mitigation, 69
70 BNF. See Biological nitrogen fixation (BNF) Bradyoxetin production, 61 Bradyrhizobia, 61 Burkholderia phytofirmans, 71

C Cadmium, 134
135, 181 depositions, 181 Candida cell membrane of, 293
294 characteristic of, 298 description of, 293 drug resistance of, 298
299 epidemiology, 293
294 factors facilitating antifungal drug resistance, 297 molecular mechanisms of drug resistance, 294
295 ATP-binding cassette, 296 ERG genes, 295
296 FKS genes, 296
297 structural status of, 298 virulence factors of, 293
294 Candidemia, 294
295 Capacity of microorganisms in contaminated (CMS), 231 Carbamates, 197
198 Carbenicillin, 282 Carbon atoms, 57 Carbon capture, 249 Carcinogenesis, 158 Catabolic genes, 196
197 Cell differentiation, 11 Ceratovacuna lanigera, 128
129 CERK1. See Chitin elicitor receptor kinase 1 (CERK1) Chemical-based fertilizers, 68 Chemical contaminants, remediation for removal of, 142
143 Chemical degradation, 161
162

Chemical disinfection, 161 Chemical exposure, health consequences due to, 158 Chemical fertilizers, 1, 22, 85
86, 98 application of, 6
7 excessive use of, 99
100 Chemical mixtures, 158 Chemical pesticides, 11
12 Chemical phosphate fertilizers, 28
29 Chemical phosphatic fertilizer, 101 Chemical remediation, 174 Chitin elicitor receptor kinase 1 (CERK1), 41
42 Chloramphenicol, 286
288 Chlortetracycline, 282 Chronic polymer-associated infection, 271
273 Classical biological control, 120 Classification of antibiotics, 283
286, 284f aminoglycosides and tetracyclines, 285 bactericidal antibiotics, 284 bacteriostatic antibiotics, 284
285 natural antibiotics, 283 quinolones, 286 ß-Lactams, 285 sulfa drugs, 285
286 synthetic antibiotics, 283
284 Climate change, 1
2 CMS. See Capacity of microorganisms in contaminated (CMS) Cobalt, 180 Coenzymes, 25 Cofactor pyrroloquinoline quinones (PQQ), 32
33 Cold stress mitigation, 71 Colletotrichum gloeosporioides, 71
72 Commercial biocontrol agents, 126t Commercialization, challenges of biofertilizer carrier, 113 biological constraints, 112 field-level constraints, 113 marketing constraints, 112 technical constraints, 112 Commercial-waste products, 170 Contaminants complexity of, 229 soil, 173 vegetation, 156 Contamination, form of, 155 Conventional breeding, 1 CopABCD genes, 180
181 Copper, 180
181 Cotton bollworm, 127
128 Crops bioinoculation of, 73 enhancement, 241
243 improvement, 243
244

Index

protection, 1
2, 243 yield, loss of, 68 Cucumis sativus, 60 Cultivation-independent methods, 196 Cypermethrin-degrading genes, 197
198 Cytokinin, 34

D Dalbergia sissoo, 24 Deep-well injection, 160 Defense-related enzymes, 71
72 Device-related infections, 271
273 Diversisporales, 6
7 DNA-dependent methods, 199 Docking methods, 226
228 Dried bioformulation, 102
103 Dried powder (dust), 102
103 Drought, 68 mitigation, 69 stress on plant growth and development, 69 Drug efflux pump, overexpression of, 298 Drug resistance, 293
294 adaptation, 296 antifungal, 297 molecular mechanisms of, 294
295 ATP-binding cassette, 296 ERG genes, 295
296 FKS genes, 296
297 types of, 298 Drug tolerance, 296

E EAWAG-BBD database, 229 ECF. See Extracytoplasmic function signaling pathway (ECF) Echinocandins, 298 resistance, 297 Ecological niches, multifaceted interplay of, 2 Ecological systems, 83 Ectomycorrhizal fungi, 6
7 EDCs. See Endocrine-disrupting chemicals (EDCs) Effective biofertilizer, 97 Effector triggered immunity (ETI), 41
42 Eichhornia crassipes, 128 Electrochemical sensing, 251 Electron acceptor, 192 Electronic waste, 137
138 Encapsulation, 160
161 bioformulations, 105 Endocrine-disrupting chemicals (EDCs), 225
226 Endophytes, 125 Endophytic fungi, 123 Endosphere, 2

309

Energy, sources of, 249
250 fuel cells, 250 solar cells, 250 Ent-kaurene-derived diterpenoid phytohormone., 34 Environmental pollutants on agriculture and food system description of, 133
142 dyes from textile industries, 142, 143f electronic waste, 137
138 metals and metalloids, 134
137 nanoparticles, 138
139 particulate matter, 141
142 pharmaceuticals and personal care products, 139
140 plastics, 138 radioactivity/nuclear reactors, 139 remediation for removal of chemical contaminants, 142
143 sewage wastewater and sludge, 140
141 contamination of food by, 133 removal of, 232 Environmental pollution, 8
9, 223, 263
264 Environmental protection in agriculture, 270 bacterial species in, 265t biofilm formation, 264
267 events of signaling in, 266
267 description of, 263
264 role of biofilms in environmental protection, 267
273 in agriculture, 270 biofilm formation for health, 271
273 bioremediation, 267
268 heavy metal remediation, 268
269 polyethylene degradation, 271 remediation of hydrocarbons, 269 wastewater treatment, 269
270 Environmental sensing, 250
251 electrochemical sensing, 251 gas sensors, 251 heavy metal ion sensors, 251 optical sensing, 251 Environmental stresses, 67
68 Environmental sustainability, 205 bioremediation, 208
210, 213
214 ex situ, 213
214 immobilization, 208 mobilization, 208
210 in situ, 213 description of, 205
206 enzymes for bioremediation, 211
212 microbial hydrolytic enzymes. See microbial hydrolytic enzymes microbial oxidoreductases. See microbial oxidoreductases mechanisms involved in bioremediation adsorption, 210

310

Index

Environmental sustainability (Continued) biosorption, 210 genetically engineered microorganisms, 210
211 microbial bioremediation of pollutants, 205
206 algae, 207 animals, 208 bacteria. See Bacteria ligninolytic fungi, 207 plants, 208 potential microbial candidates, 206
208 rhizospheric soil-plant-microbe interactions, 214
216 arbuscular mycorrhizal fungi (AMF), 216 plant growth-promoting rhizobacteria. See plant growthpromoting rhizobacteria (PGPR) Environment, hazardous compounds from, 84 Enzymatic system, 162
163 Enzymes and producing exopolysaccharides (EPS), 23
24 EPS. See Enzymes and producing exopolysaccharides (EPS) ERG genes, 295
297 Eriosoma lanigerum, 128 ETI. See Effector triggered immunity (ETI) Exposure dose, quantification of, 158 Ex situ bioremediation, 213
214 Extracellular enzymes, 70
71 Extracellular polysaccharides (EPS), 263
264 Extracytoplasmic function signaling pathway (ECF), 266
267 Extreme soil salinity, 68

F FAOSTAT, 1
2 Fatty acids, 38, 198
199 Field-level constraints, 113 FKS genes, 296
297 hotspot (HS) regions in, 297 Flagellin-sensitive 2 receptor (FLS2), 41
42 F-list, characteristics of, 154
155 FLS2. See Flagellin-sensitive 2 receptor (FLS2) Fly ash, 170 Foliar application, 109 Food contamination, 133
134 industry, 91 intakes, variety of, 139 oxidation process in, 91 processing industry, 91 quality of, 8
9 security, 11, 21
22, 91 system contaminants affecting, 135f description of, 133
142 dyes from textile industries, 142, 143f electronic waste, 137
138 metals and metalloids, 134
137

nanoparticles, 138
139 particulate matter, 141
142 pharmaceuticals and personal care products, 139
140 plastics, 138 radioactivity/nuclear reactors, 139 remediation for removal of chemical contaminants, 142
143 sewage wastewater and sludge, 140
141 Free-living heterotrophic diazotrophs, 26
28 Free-living nitrogen-fixing biofertilizers, 106 Fuel cells, 250 Fungal biocontrol agents, 123f Fungal infections, 293
294 Fungicides, 191, 198 Fungi, eukaryotic nature of, 293
294

G Gas sensors, 251 Genes, involved in determining resistance against, 178
181 antimony and arsenic, 179 cadmium, 181 copper, 180
181 mercury, 179 nickel and cobalt, 180 zinc, 181 Genetically modified microorganisms (GMMs), 84 Genetically modified organisms (GMOs), 83
84, 230
231 Genetically modified (GM) treatment and biofertilizers, 84 Genetic defects, 158 Genetic engineering, 83
84 Genome alteration, 298 Genomic, 230
231 techniques, 231 technology, 231 Gibberellins, 34 Glomerals, 6
7 Glomus versiforme, 7 Glycolipids, 38 Glyphosate oxidoreductase (GOX), 228 GMMs. See Genetically modified microorganisms (GMMs) GMOs. See Genetically modified organisms (GMOs) GOX. See Glyphosate oxidoreductase (GOX) Gram-negative bacteria, 181, 266
267 Granular bioformulation, 102
103 Greenhouse gases, 1
2 Gypsophila, phytohormones of, 59

H Hazardous pollutants, absorption of, 133
134 Hazardous Waste Identification Rules (HWIR), 158
159 Hazardous wastes (HWs) biological strategies, 162
163

Index

bioremediation. See Bioremediation enzymatic system, 162
163 land treatment, 162 biological treatment of, 162 bioremediation of waste materials, 162f characteristics of, 154 chemical strategies chemical degradation, 161
162 chemical disinfection, 161 classification of, 154
155 description of, 153
154 disposal sites, 156
157 factors governing human response to, 157f health consequences of exposure, 158 identification and monitoring of, 158
159 Indian scenario, 159 identification systems, 158
159 illegal trafficking, 164
165 and poor transportation facility, 164
165 impact of environment, 155
156 humans, 156
158 inadequate transfer of, 164
165 industrial sector, 153
154 mismanagement of, 164 modern hybrid technology, 163
164 physical strategies autoclaving, 161 deep-well injection, 160 encapsulation, 160
161 incineration, 159
160 inertization, 161 landfilling, 160 microwave irradiation, 161 solidification/stabilization, 160 transportation of, 164 Hazardous wastes management, 159
164 HCN. See Hydrogen cyanide (HCN) Health biofilm formation for, 263
264, 271
273 consequences of exposure, 158 hazards, caused by heavy metals, 137t Heavy metals adverse effects of, 172t agricultural source, 169 contamination, 136f description of, 167
168 domestic sources, 170 exclusion technologies, 167
168 factors affecting microbial remediation, 182
184 ambient temperature, 182 bioavailability of pollutants and biosurfactants, 183
184 condition of soil milieu, 183 pH, 182

substrate concentration, 183 substrate species, 182
183 genes involved in determining resistance against, 178
181 antimony and arsenic, 179 cadmium, 181 copper, 180
181 mercury, 179 nickel and cobalt, 180 zinc, 181 health hazards caused by, 137t industrial source, 168
169 ion sensors, 251 microbial remediation of, 175
178 adsorption, 177 bioleaching, 177
178 biosorption, 177 redox state change, 178 natural source of, 169 other sources of, 170 pollution, 173 redox status of, 178 remediation, 268
269 removal, 173
178 chemical remediation, 174 physical methods, 173 phytoextraction, 174 phytoremediation, 174
175 phytostabilization, 175 phytovolatilization, 174
175 rhizodegradation, 175 rhizofiltration, 175 in soil, plant, and fodder, 171t sources of, 168
170, 168f stress mitigation, 70
71 tolerance mechanisms, 70
71 toxicity on human and plant health, 170
172 Herbaspirillum, 26
28 Herbicides, 191 in agricultural activities, 140
141 Histidine kinase (HK), 266
267 History of antibiotics, 282 HK. See Histidine kinase (HK) Hormonal imbalance, 68 Host crops, 40t Host immune system, 293
294 HR. See Hypersensitive response (HR) Human industrial activity, 167
168 HWIR. See Hazardous Waste Identification Rules (HWIR) HWs. See Hazardous wastes (HWs) Hydrocarbons, remediation of, 269 Hydrogen cyanide (HCN), 36
37 Hypersensitive response (HR), 41
42

311

312

Index

I

L

Illegal trafficking, 164
165 and poor transportation facility, 164
165 Immobilization, 208 Incineration, 159
160 Induced systemic resistance (ISR), 71
72, 88 mediated by rhizobacteria, 42 pathway, 42 Industrial effluents, 177 Inertization, 161 Inoculated microbial strains, 31
32 Inorganic minerals, 70
71 Inorganic phosphate transporter (Pi), 7 Insecticides, 191, 198 In silico approaches for removal of environmental pollutants, 224
225 biodegradation metabolic pathway simulation of, 229 pathway prediction, 229 bioremediation molecular docking approach for, 226
228 molecular dynamics simulation approach for, 228 using genomics, 230
231 using proteomics, 229
230 description of, 223
224 removal of environmental pollutants through artificial intelligence, 232 schematic graphical overview of, 227f systems biology methods, 231
232 for toxicity analysis of pollutants, 225
226 In situ bioremediation, 213 Insoluble ferric oxides, 35 Integrated nutrient management (INM) systems, 43 Integrated pest management, 127
128 Invasive infections, 294
295 Ions, heavy metal consists of, 167
168 IROMPs. See Iron-regulated outer membrane proteins (IROMPs) Iron-regulated outer membrane proteins (IROMPs), 35
36 iron-solubilizing biofertilizers, 108 ISR. See Induced systemic resistance (ISR)

Land degradation, accelerated process of, 91 Landfilling, 160, 162 Land treatment, 162 Lanosterol demethylase, 296
297 Legume-rhizobia symbiosis, symbiotic association-dependent signals in, 62 Leguminous plants, rhizobial nodulation in, 69
70 Lethal heavy metals, 178
179 Ligninolytic fungi, 207 Lipopeptides, 38 Lipoproteins, 38 Liquid biofertilizers, 101 Liquid bioformulation, 104 Livestock, 156 LuxI type AHL synthase, 59
60 LuxR-type AHL synthase, 59
60

J Jasmonic acid (JA), 41
42

K Kinetin, 34 K-list, characteristics of, 154
155

M Macrolides, 286
288 Maize plants, physiological traits of, 69 Maize roots, inoculation of, 34 Major facilitator (MF), 297 Major facilitator superfamily (MFS), 35
36, 293
294 Marketing constraints, 112 Maximum residue levels (MRLs), 134
135 Medicago sativa, 39 Medicago truncatula, 59 Membrane proteins, proteome of, 230 Mercury, 179 Metagenomic analysis, 195 cultivation-independent methods, 196 Metagenomics, 196
198 Metal ion transporters (MIT), 181 Metallic nanoparticles, 249 Metalloids, 134
137 Metarhizium anisopliae, 128
129 Methane monooxygenase (MMO), 207 Methanotrophs, 207 Methicillin-resistant staphylococcus aureus (MRSA), 286 MFS. See Major facilitator superfamily (MFS) MIC. See Minimal inhibitory concentration (MIC) Microalgae, 88 Microbe-associated molecular patterns (MAMPs), 41
42 Microbes of various environments, 125
126 Microbial biofilms formation, 266
267 Microbial cells planktonic form of, 269
270 processes in, 281 Microbial cellulases, 212 Microbial consortium (MC), 43 Microbial diversity, 2

Index

Microbial interactions, 41
42 Microbial laccases, 211 Microbial lipases, 212 Microbial oxidoreductases, 211 Microbial oxygenases, 211 Microbial peroxidases, 211 Microbial proteases, 212 Microbial siderophores, 27t, 35
36 Microbiome, 2 Microorganisms, 22, 83, 98, 267
268 ability of, 24 applications of, 70
71 characteristics of, 100 diversity of, 88 on plant growth, 74t proficient colonization of, 98 species of, 71
72 variety of, 268
269 Microwave irradiation, 161 Mineral fertilizers, 198 Minimal inhibitory concentration (MIC), 296 Mitogen-activated protein kinases, 31
32 Mobilization, 10, 208
210 Modern hybrid technology, 163
164 Molecular docking approach, 226
228 Molecular dynamics simulation (MDS), 224, 228 Molecular mechanism, 196
197 MRSA. See Methicillin-resistant staphylococcus aureus (MRSA) Multidrug resistance, emergence of, 296 Mycorrhizae, plant growth-promoting, 89f Mycorrhizal association, 7, 216 Mycorrhizal fungi, 6
7, 86, 123
124 consortia of, 7 ecosystem functionality of, 6
7

N Nanoadsorbents, 246 Nanocatalysts, 248 Nanofertilizers, 89 development of, 89 Nanomaterials in agriculture sector, 240
244 crop improvement, 243
244 crop protection, 243 fate of nanomaterial in soil, 244 in soil, 244 Nanomembranes, 246
248 Nanoparticles, 138
139 long-term exposure to, 138
139 Nanoparticles (NPs), 89 presence of, 138
139 unregulated release of, 138
139

313

Nanopesticides, 90 development of, 89 Nanoscale in macro-scale description of, 239 nanomaterial in environmental sector, 244
251 carbon capture, 249 electrochemical sensing, 251 environmental sensing, 250
251 fuel cells, 250 gas sensors, 251 heavy metal ion sensors, 251 metallic nanoparticles, 249 nanoadsorbents, 246 nanocatalysts, 248 nanomembranes, 246
248 optical sensing, 251 remediation, 248
249 semiconducting nanoparticles and dendrimers, 249 solar cells, 250 sources of energy, 249
250 wastewater and water remediation, 245
248 nanomaterials in agriculture sector, 240
244 crop enhancement, 241
243 crop improvement, 243
244 crop protection, 243 fate of nanomaterial in soil, 244 negative aspects of nanotechnology, 252
253 Nanoscale science, 89 Nanotechnology, 138
139 in agriculture, 89
91, 90f in food industry, 91 for improved soil quality, 91 nanofertilizers, 89 nanopesticides, 90 Natural antibiotics, 283 Nematicides, 191 N-fertilizers, 25 Nickel, 180 Nitrogen fixation, 88 Nitrogen-fixing biofertilizers, 105
106 associative symbiotic nitrogen-fixing biofertilizers, 106 free-living nitrogen-fixing biofertilizers, 106 symbiotic nitrogen-fixing biofertilizers, 105
106 Nitrogen-fixing microbes, 215 nodD gene, 26 Nonbiodegradable chemicals, 223 Nonspecific acid phosphatases (NSAPs), 29 Novel antifungal drug, 293
294 Novel sequencing technologies, 199 NPs. See Nanoparticles (NPs) NSAPs. See Nonspecific acid phosphatases (NSAPs) Nutrient management, 1
2, 8
10 phosphorus solubilization, 10 potassium solubilization and mobilization, 10

314

Index

Nutrient-mobilizing microbes, 215
216 Nutrient-solubilizing microbes, 215 Nutritional imbalance, 68

O Optical sensing, 251 Oral infection (thrush), 293 Organic-based nutrient management, 91 Organic farming, 97 Organic pollutants, 156, 268 Organic substances, application of, 205
206 Organophosphates, 29 Osmolytes, 69 Osmotic balance, 167
168 Oxidative stress in human body cells, 138
139 Oxyhydroxides, 35

P PAHs. See Polyaromatic hydrocarbons (PAHs); Polycyclic aromatic hydrocarbons (PAHs) Paper industries, 224 Paraglomerales, 6
7 Parasitic nematodes, 98
99 Parasitoid, 119
120, 127
128 Particulate matter, 141
142 Pathogenic organisms, 11
12 Pathogens, variety of, 42 Pathway prediction, 229 PCB. See Polychlorinated biphenyl (PCB) Penicillin, 282 allergic to, 282 Penicillium oxalicum, 128
129 Peptidoglycan (PG), 285 Persistence, regulatory assessments of, 232 Personal care products, 139
140, 140t Pesticides, 1, 39
40 in agricultural activities, 140
141 biodegradation, 192
193, 196, 197f bioremediation of, 98
99 concentration, 194 degrading microorganisms, 193t description of, 191
192 metagenomic analysis, 195 cultivation-independent methods, 196 molecular basis of, 196
198 persistence in soil, 194f proteomics of, 196 removal of, 196
197 soil microbial biomass, 196 moisture, 195 organic matter, 195

pH, 195 types, 195 solubility, 194 structure, 193
194 temperature, 195 use of, 86 PG. See Peptidoglycan (PG) PGPB. See Plant growth promoting bacteria (PGPB) PGPF. See Plant growth promoting fungi (PGPF) PGPMs. See Plant growth-promoting microorganisms (PGPMs) Pharmaceuticals, 139
140, 140t Pharmacokinetic (PK) models, 225
226 Phaseolus vulgaris, 59 Phenazine-1-carboxylic acid (PCA), 36
37 Phosphate-mobilizing biofertilizers, 107 Phosphate solubilization, process of, 29 Phosphate solubilizing bacteria (PSB), 28
29 and application in different crops, 30t phosphate-solubilizing biofertilizers, 106
107 Phosphate solubilizing microorganisms (PSMs), 28
29 Phospholipids, 38 Phosphorous solubilization, 28
29 Phosphorus solubilization, 10 Phosphorus solubilizing microorganisms (PSMs), 10 Phosphorylation, 71
72 Phyllosphere, 2 Physical methods, 173 Phytoextraction, 174 Phytohormone production, 32
35 Phytopathogens, 39
40, 62 progression of, 71
72 Phytoremediation, 174
175 phytoextraction, 174 phytostabilization, 175 phytovolatilization, 174
175 rhizodegradation, 175 rhizofiltration, 175 Phytostabilization, 175 Phytovolatilization, 174
175 Planktonic bacteria release, 264
266 Plant growth promoting bacteria (PGPB), 4
5, 22
23, 41 for disease suppression, 40
41 siderophores of hydroxamates, 40
41 Plant growth promoting fungi (PGPF), 88 Plant growth-promoting microorganisms (PGPMs), 86 Plant growth promoting rhizobacteria (PGPR), 3
5, 22, 31
32, 59
60, 67
68, 72
73, 121
122, 214
215 abiotic stress tolerance, 39 beneficial role of, 5t as biocontrol agents and biofertilizers, 122t with biological control activity, 39
40 direct and indirect mechanisms, 24
25 direct mechanisms, 215

Index

disease suppression in, 36
37 exploited and studied, 25 germination of seeds, 4
5 indirect mechanisms, 215 interaction between plants and, 24 nitrogen-fixing microbes, 215 nutrient-mobilizing microbes, 215
216 nutrient-solubilizing microbes, 215 production, 44 of phytohormones by, 32
33 products, 43t role of mycorrhizal association, 216 and root exudates, 23
24 siderophore producing, 35
36 Plant
microbe interactions, 24, 62, 68, 85 Plant pattern recognition receptors (PRRs), 41
42 Plant roots, 287 soil zone of, 59 Plants, 208 acclimatization, 38
39 biomass, 24 body, 2 development, natural foundation for, 155
156 exudation patterns, 23
24 growth process of promoting, 40 and productivity of, 270 promoters, 87t regulators, production of, 10 regulatory hormone, 34 hormones, production of, 24
25 hyperaccumulation in, 134
135 pathogens, 4
5 biocontrol agents for, 124t protection agents, 135
137 toxic metal concentrations in, 170
171 types of, 209t Plastic, 138 bags, 138 P-list, 154
155 Pollutants, 21
22 bioavailability of, 183
184 toxicity analysis of, 225
226 Pollution in environment, 224 Polyaromatic hydrocarbons (PAHs), 269 Polychlorinated biphenyl (PCB), 135
137 Polycyclic aromatic hydrocarbons (PAHs), 133, 230 Polycyclic hydrocarbons, 141
142 Polyenes, 298 Polyethylene degradation, 271 texture of, 271 Polymeric surfactants, 38 Polymorphism, 297

Polyphenol oxidase (PPO), 41
42 Potassium solubilization, 10 Potassium-solubilizing biofertilizers, 107 Potential microbial candidates, 206
208 bacteria, 206
207 Potent microbes, application of, 100 PQQ. See Cofactor pyrroloquinoline quinones (PQQ) Priming, 42 Process enzymes, 228 Prokaryotes, 22 Prontosil, 282 Proteomics, 229
230 bioremediation using, 229
230 of pesticide biodegradation, 196 PRRs. See Plant pattern recognition receptors (PRRs) PSB. See Phosphate solubilizing bacteria (PSB) Pseudomonas, 59
60 P. koreensis, 24 P. mendocina, 39 Psychrotrophic bacteria, 99
100 Pyrilla perpusilla, 127 Pyrolysis, 192 Pythium aphanidermatum, 60

Q QQ. See Quorum quenching (QQ) QS. See Quorum sensing (QS) Quantitative structure
activity relationships (QSARs), 225
226 Quinolones, 286 Quorum quenching (QQ), 61 Quorum sensing (QS), 23
24, 266
267 bacterial compounds, 57
59 description of, 57 molecules produced by bacteria, 57, 58t in nitrogen-fixing rhizobia, 61
62 and plant disease protection, 60
61 in plant
microbe interactions, 59 in rhizobacterial community colonization, 59
60 in rhizosphere engineering, 62

R Radioactivity/nuclear reactors, 139 Radionuclides, 139 Ralstonia solanacearum, 41 Rampant agrochemicals, 67
68 Reactive oxygen species (ROS), 11, 38
39, 69 Redox state change, 178 Refineries, rapid expansion of, 267
268 Regulatory constraints, 112 Remediation, 248
249 carbon capture, 249

315

316

Index

Remediation (Continued) metallic nanoparticles, 249 semiconducting nanoparticles and dendrimers, 249 Reproductive (bud) dormancy, 34 Resistance, nodulation, and cell division (RND), 35
36 Resistance sites, 296 Response regulator (RR) proteins, 266
267 Rhizobacteria, 57
59 plant-beneficial properties of, 62 plant growth-promoting, 89f, 214
215 direct mechanisms, 215 indirect mechanisms, 215 nitrogen-fixing microbes, 215 nutrient-mobilizing microbes, 215
216 nutrient-solubilizing microbes, 215 role of mycorrhizal association, 216 Rhizobacteria-induced resistance (R-ISR), 41
42 Rhizobacteria in sustainable agriculture in abiotic stress remediation, 38
39 in biotic stress remediation, 39
41 commercialization of plant growth, 43
44 description of, 21
22 induced systemic resistance, 41
43 mechanisms of action, 24
38 ACC deaminase production, 31
32 antibiotic production, 36
38 biological nitrogen fixation, 25
28 biosurfactant production, 38 phosphorous solubilization, 28
29 phytohormone production, 32
35 siderophore production for iron acquisition, 35
36 zinc solubilizing bacteria, 30
31 and plant interaction, 22
24 Rhizobia, 62 Rhizobium, 25 Rhizobium leguminosarum, 61 Rhizoctonia solani, 71
72 rhizodegradation, 175 Rhizodeposit, 23
24 Rhizomicrobiomes, selection and growth of, 23
24 Rhizoplane, 2 Rhizoremediation, 59 Rhizosphere, 2, 4
12, 59, 270 biofilm formation in, 271 definition of, 88 fundamental mechanism of activities in, 59 microbial communities in, 22, 62 microorganisms in, 22
23 plant root growth in, 86 Rhizospheric bacteria, 33
34 Rhizospheric bacterial diversity, 22
23 Rhizospheric colonization, 59
60 Rhizospheric fungi, 124
125

Rhizospheric microorganisms, 21
22 Rhizospheric region, bacterial colonization in, 22
23 Rhizospheric strains, 10 Ribosomally synthesized peptides (RPs), 37
38 Root exudates, 31
32 Root exudation, 4 ROS. See Reactive oxygen species (ROS) RPs. See Ribosomally synthesized peptides (RPs) RR proteins. See Response regulator (RR) proteins

S Salinity mitigation, 69
70 Salt stress, loss of, 68 Sclerotium rolfsii, 41 Seasonal biological control, 121 Seed and bud dormancy, 34
35 germination, 72
73 treatment, 110 Semiconducting nanoparticles and dendrimers, 249 Sensing system, interruption of, 62 Serratia plymuthica, 60 Server in the form of a chemical descriptor (SMILES), 229 Sewage treatment processes, 263
264 wastewater, 140
141 Siderophores, 26
28, 71
72 categories, 35
36 formation of, 99
100 producing PGPR, 35
36 production for iron acquisition, 35
36 Sludge, 140
141 Soil-borne fungal diseases, 22 Soil-borne plant diseases, 36
37 Soil health, 43 Soils bacteria, 22
23, 36
37 characteristics, 169 contamination of, 139 fate of nanomaterial in, 244 fertility enhancement, 85
86 of hilly areas, 99
100 inorganic and organic pollutants in, 7 microbes, 21
22, 69
70, 162 microbial biomass, 196 milieu, condition of, 183 moisture, 195 negative impact on, 137
138 organic matter, 195 pH, 195 physical properties of, 138 quality, 3, 91 sustainability, 198

Index

treatment, 110 types, 195 Solar cells, 250 Solid bioformulation, 102
104 dried powder (dust), 102
103 granules, 102
103 wettable powders, 102
103 wettable/water-dispersible granules, 102
103 Solidification/stabilization, 160 Streptogramins, 286
288 Stress conditions, 74t, 83 responsive genes, 34
35, 67
68 tolerance, 38
39 tolerance capability in plants, 73 tolerant microorganisms, 73 Substrate concentration, 183 Substrate species, 182
183 Sugarcane Pyrilla, 127 Sulfa drugs, 285
286 Sulfa-sensitive bacteria, 285
286 Sulfonamides, 282, 285
286 Sustainable agricultural system, 3
4, 83
84 Sustainable agroecosystem, beneficial microbes for abiotic stress, 11 actinomycetes, 8 in agriculture, 2
3, 3f biocontrol agent, 11
12 biofertilizers and biopesticides, 11 description of, 1
2 mycorrhizal fungi, 6
7 nutrient management, 8
10 phosphorus solubilization, 10 potassium solubilization and mobilization, 10 plant growth promoting bacteria, 4
5 production of plant growth regulators, 10 rhizosphere, 4
12 for sustainable agricultural system, 3
4 Symbiotic nitrogen-fixing bacteria, 61 symbiotic nitrogen-fixing biofertilizers, 105
106 Synthetic antibiotics, 283
284, 288 Synthetic fertilizers, 85
86 and pesticides, use of, 86 Synthetic nitrogen fertilizer, production of, 1 Systems biology methods, 231
232

T TAC1 mutation, 297 TAL. See Tyrosine ammonia lysine (TAL) TCS. See Two-component systems (TCS) Technical constraints, 112 Temperature, 195

Tetracyclines, 282, 285
288 Textile industries, dyes from, 142, 143f Topoisomerase, 286 Toxicity analysis of pollutants, 225
226 Toxic substances, 193 Traditional bioremediation, 224
225 Transgenic crops, 85t Transgenic tomato plants, 59 Treated wastewater, 170 Trimethoprim (TMP), 286 Tryptophan, 30
33 Two-component systems (TCS), 266
267 Tyrosine ammonia lysine (TAL), 41
42 Tyrothricin, 282

U U-list, 154
155 Uncontaminated soil pollution, 173 Unicellular prokaryotic organisms, 57

V Vaginal candidiasis, 293 Vaginal infection (yeast infection), 293 van der Waals forces, 264
266 Vegetation diversity, 156 Viruses, 126
127

W Waste incineration facilities, 163 materials, 205
206 product, 223 special category of, 153 toxicity, and noxiousness of, 159
160 Wastewater treatment, 269
270 and water remediation, 245
248 nanoadsorbents, 246 nanocatalysts, 248 nanomembranes, 246
248 Water contamination, 155 hyacinth, 128 stress conditions, 4
5 Water-soluble humic materials (WSHM), 61 Wettable powders, 102
103 Wettable/water-dispersible granules, 102
103 White woolly aphid, 128
129 Woolly apple aphid, 128 WSHM. See Water-soluble humic materials (WSHM)

317

318

Index

X Xenobiotics, 223, 231

Y Yellow-green siderophores, 36
37

Z Zeatin, 34

Zinc, 181 concentration, 30
31 malnutrition, 30
31 solubilizing bacteria, 30
31 solubilizing biofertilizer, 108
109 stress, 70
71