Phytomicrobiome Interactions and Sustainable Agriculture Edited by Amit Verma S. D. Agricultural University Palanpur, Gujarat, India Jitendra Kumar Saini Central University of Haryana Mahendergarh, Haryana, India Abd El-Latif Hesham Beni-Suef University Beni-Suef, Egypt Harikesh Bahadur Singh GLA University Mathura, Uttar Pradesh, India This edition first published 2021 © 2021 John Wiley & Sons Ltd All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by law. Advice on how to obtain permission to reuse material from this title is available at http://www.wiley.com/go/permissions. The right of Amit Verma, Jitendra Kumar Saini, Abd El-Latif Hesham and Harikesh Bahadur Singh to be identified as the authors of the editorial material in this work has been asserted in accordance with law. 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Neither the publisher nor authors shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages. Library of Congress Cataloging-in-Publication Data Names: Verma, Amit, 1983- editor. Title: Phytomicrobiome interactions and sustainable agriculture / edited by Amit Verma, S.D. Agricultural University, Gujarat, India, Jitendra Kumar Saini, Central University of Haryana, Mahendergarh, India, Abd El-Latif Hesham, Beni-Suef University, Egypt, Harikesh Bahadur Singh, GLA University, Mathura, India. Description: First edition. | Hoboken, NJ : Wiley-Blackwell, 2021. | Includes bibliographical references and index. Identifiers: LCCN 2020051129 (print) | LCCN 2020051130 (ebook) | ISBN 9781119644620 (hardback) | ISBN 9781119644811 (adobe pdf) | ISBN 9781119644828 (epub) Subjects: LCSH: Plant-microbe relationships. | Agricultural microbiology. | Plants–Microbiology. | Plants–Effect of stress on. | Sustainable agriculture. Classification: LCC QR351 .P525 2021 (print) | LCC QR351 (ebook) | DDC 579/.178–dc23 LC record available at https://lccn.loc.gov/2020051129 LC ebook record available at https://lccn.loc.gov/2020051130 Cover Design: Wiley Cover Image: © Catherine MacBride/Getty Images Set in 9.5/12.5pt STIXTwoText by SPi Global, Pondicherry, India 10 9 8 7 6 5 4 3 2 1 To my father and mother v Contents List of Contributors xii Preface xvi About the Editors xviii 1 Plant Root Exudate Analysis: Recent Advances and Applications 1 Shulbhi Verma and Amit Verma 1.1 Introduction 1 1.2 Root Exudates Composition: Collection and Analysis 3 1.3 Role of Root Exudates in Shaping Rhizospheric Microbiomes 5 1.4 Applications of Root Exudation 6 1.5 Conclusion and Future Prospects 7 References 10 2 Phytoproteomics: A New Approach to Decipher Phytomicrobiome Relationships 15 Prachie Sharma and Kapila Kumar 2.1 Introduction 15 2.2 Phytomicrobiome 16 2.3 Phytomicrobiome: The Communication via Signaling 18 2.4 Proteomics 19 2.4.1 Gel-Based Protein Separation Techniques 21 2.4.2 Non-Gel Protein Separation Techniques 21 2.5 Analysis of Phytomicrobial Interactions Using Proteomics Approaches 22 2.6 Conclusion and Future Prospects 26 References 28 3 Metagenomics: An Approach to Unravel the Plant Microbiome and Its Function 32 Ravindra Soni, Deep Chandra Suyal, Balram Sahu, and Suresh Chandra Phulara 3.1 Introduction 32 3.2 Metagenomics 33 vi Contents 3.3 Metagenomics of Plant Rhizosphere 33 3.4 Metagenomics of Plant Phyllosphere 35 3.5 Metagenomics of Plant Endosphere 36 3.6 ­In-silico­Tools for Metagenome Analysis 37 3.6.1 Mothur 37 3.6.2 Quantitative Insights into Microbial Ecology (QIIME) 37 3.6.3 MEta Genome Analyzer (MEGAN) 38 3.7 Recent Progress in Metagenomic Studies of Plant Microbiome 38 3.8 Conclusion and Future Prospects 38 References 38 4 Combating the Abiotic Stress Through Phytomicrobiome Studies 45 Hemant S. Maheshwari, Abhishek Bharti, Richa Agnihotri, Ajinath Dukare, B. Jeberlin Prabina, Saurabh Gangola, and Mahaveer P. Sharma 4.1 Introduction 45 4.1.1 Abiotic Stress and Phytomicrobiome 45 4.1.2 Role of Signaling in Phytomicrobiome Interactions 46 4.2 Phytomicrobiome Signaling Compounds 47 4.2.1 Root Exudates and Plant Volatiles Compounds 47 4.2.2 Microbial Volatile Organic Compounds 47 4.2.3 Quorum Sensing 48 4.2.4 Underground Phytomicrobiome Signaling 48 4.3 Mechanisms of Phytomicrobiome Associated with Abiotic Stress Tolerance 49 4.3.1 Drought Stress Alleviation 50 4.3.2 Salinity Stress Mitigation 53 4.3.3 Heavy Metal Toxicity 55 4.3.4 Low-Temperature Stress 56 4.3.5 Nutrient Deficiency 56 4.3.6 Flooding or Water Submergence 56 4.4 Importance of Phytomicrobiome Engineering for Crop Stress Alleviation 57 4.5 Omics Strategies in Phytomicrobiome Studies 58 4.6 Conclusion and Future Prospects 59 Acknowledgments 59­ References 60 5 Microbial Diversity of Phyllosphere: Exploring the Unexplored 66 Rakhi Dhankhar, Aparajita Mohanty, and Pooja Gulati 5.1 Introduction 66 5.2 Origin of Phyllosphere Microflora 67 5.3 Tools to Study Phyllomicrobiome 68 5.3.1 Conventional Methods 69 5.3.2 Microscopic Techniques 69 5.3.3 First-Generation Molecular Techniques 70 5.3.4 Next-Generation Sequencing Methods 70 5.3.5 Omics and Bioinformatics Approaches 76 5.3.6 Other Molecular Methods 77 5.4 Biodiversity of Phyllosphere 77 Contents vii 5.5 Microbial Adaptation to Phyllosphere 78 5.5.1 Adaptation to Abiotic Stresses 79 5.5.2 Adaptation to Biotic Stresses 80 5.5.3 Adaptation to Nutrient Scarcity 81 5.6 Interaction of Phyllomicrobiota with Plants 81 5.6.1 Positive Interactions 82 5.6.2 Negative Interactions 83 5.7 Significance of Phyllomicrobiome Studies 83 5.8 Conclusion and Future Prospects 84 References 85 6 Rhizosphere Engineering: An Effective Approach for Sustainable Modern Agriculture 91 Reema Mishra, Tripti Grover, Pooja Gulati, and Aparajita Mohanty 6.1 Introduction 91 6.2 Natural Plant–Microbe Interactions in Rhizosphere 92 6.3 Molecular Mechanisms in Plant–Microbe Interactions in Rhizosphere 93 6.4 Biochemical Components in Rhizosphere Signaling 94 6.5 Tools and Techniques in Rhizosphere Engineering 96 6.5.1 Stable Isotope Probing (SIP) 96 6.5.2 DNA Arrays 97 6.5.3 Fluorescence In Situ Hybridization (FISH) 97 6.5.4 Bioreporters 97 6.5.5 Genomics 98 6.5.6 Transcriptomics 98 6.5.7 Proteomics 99 6.5.8 Metabolomics 99 6.6 Rhizosphere Components Amenable to Engineering 100 6.6.1 Soil Modification 100 6.6.2 Plant Amendment 100 6.6.2.1 Root Exudate Modification 100 6.6.2.2 Root Architecture Modification 101 6.6.2.3 Enhancing Abiotic Stress Tolerance in Plants 101 6.6.2.4 Enhancing Biotic Stress Tolerance in Plants 103 6.6.2.5 Engineering Metabolic Pathways in Plants 105 6.6.3 Engineering Microbial Populations 107 6.7 Conclusion and Future Prospects 107 Acknowledgment 108 References 108 7 Plant Communication with Associated: Its Components, Composition and Role in Maintaining Plant Homeostasis 118 Dibyajit Lahiri, Moupriya Nag, Sayantani Garai, Bandita Dutta, and Rina Rani Ray 7.1 Introduction 118 7.2 Biofilm and Rhizospheric Interactions 119 7.3 Biofilm Formation at the Root Rhizosphere 120 7.3.1 The Components of Biofilm Matrix 121 viii Contents 7.3.2 Bacterial Quorum Sensing 122 7.4 Genetic Features Responsible for Bacterial Cell Adhesion to Plant System 125 7.4.1 Chemotaxis Motility 125 7.4.2 Substrate Utilization and Transport 125 7.4.3 Lipopolysaccharide and Membrane Proteins 126 7.4.4 Plant Cell Wall Modification 127 7.4.5 Adhesion and Biofilm Formation 128 7.4.6 Stress Protection 128 7.4.7 Bacterial Secretion System 129 7.4.8 Transcriptional Regulators and Sensor Proteins 130 7.5 Nutrient Interactions 138 7.5.1 Release and Activation of Minerals 138 7.5.2 Nutrient Recycling 138 7.5.3 Nitrogen Dynamics 138 7.5.4 Ionic Modification 139 7.6 Biotic Interaction 140 7.6.1 Symbiosis 140 7.6.2 Synergy 140 7.6.3 Competition 140 7.6.4 Antagonism 141 7.6.5 Pathogenesis 142 7.7 Conclusion and Future Prospects 142 References 143 8 Phytomicrobiome: Synergistic Relationship in Bioremediation of Soil for Sustainable Agriculture 150 Nimmy Srivastava 8.1 Introduction 150 8.2 Phytoremediation 151 8.2.1 Process of Phytoremediation 151 8.2.2 Strategies for Phytoremediation 151 8.3 Phytomicrobe Interactions and Rhizomediation 152 8.3.1 Principle of Phytomicrobiome Interaction During Rhizomediation 152 8.3.2 Removal of Inorganic Contaminants 154 8.3.3 Removal of Organic Pollutants 154 8.3.4 Factors Affecting Rhizomediation 157 8.4 Conclusion and Future Prospects 157 References 158 9 Rhizospheric Biology: Alternate Tactics for Enhancing Sustainable Agriculture 164 Kalpana Bhatt and Pankaj Bhatt 9.1 Introduction 164 9.2 Engineering the Rhizosphere 165 Contents ix 9.2.1 Rhizosphere and Rhizobia 165 9.2.2 Root Exudates: Chemical Nature and Types 167 9.2.3 Factors Affecting Root Exudate 168 9.3 Engineering Soil Microbial Populations and Plant–Microbe Interactions 169 9.3.1 Microorganisms in Soil 169 9.3.2 Soil Modification: Altering Microbial Populations 170 9.4 Plant Growth-Promoting Rhizobacteria: Mechanisms, Potential, and Usages 170 9.4.1 Direct Mechanisms 171 9.4.1.1 Biological N Fixation 171 2 9.4.1.2 Phosphate Solubilization 173 9.4.1.3 Zinc Solubilization 174 9.4.1.4 Siderophore Production 174 9.4.1.5 Production of Phytohormones 174 9.4.1.6 ACC (1-Aminocyclopropane-1-Carboxylate) Deaminase Activity 175 9.4.2 Indirect Mechanisms 175 9.5 Plant–Microbe Interaction 176 9.6 Biofertilizers and its Applications 177 9.7 Plant Genetic Engineering 177 9.8 Conclusion and Future Prospects 178 Acknowledgments 178 References 179 10 Application of Inorganic Amendments to Improve Soil Fertility 187 Sunita Chauhan and Shweta Kulshreshtha 10.1 Introduction 187 10.2 Impact of Bhoochetna Movement in Southern India 188 10.3 Sustainable Agriculture 188 10.3.1 Healthy Soil and Soil Quality 189 10.3.2 Soil Quality 189 10.3.3 Soil Quality Indicator 190 10.3.4 Soil Quality Index 191 10.4 Factors to Be Considered While Selecting a Soil Amendment 192 10.5 Advantages of Soil Amendments 194 10.6 Land Modeling 194 10.7 Major Applications of Soil Amendments 195 10.7.1 Phyto-Stabilization in Polluted or Contaminated Soils 195 10.7.2 Restoration of Soil 196 10.7.2.1 Soil Acidity/pH Soil Amendments 196 10.7.2.2 Mineral Soil Amendments and Conditioners 196 10.7.2.3 Different Types of Inorganic Amendments 197 10.8 Combination Strategy for Soil Quality Improvement 202 10.9 Conclusion and Future Prospects 203 References 203 x Contents 11 Improved Plant Resistance by Phytomicrobiome Community Towards Biotic and Abiotic Stresses 207 Neha Trivedi 11.1 Introduction 207 11.2 Microbes and Plants 207 11.2.1 Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants 208 11.2.2 Microbial-Induced Response to Stresses 208 11.3 Response of Abiotic Response on Plant 209 11.3.1 Induced Systemic Tolerance (IST) 209 11.3.2 Metabolic Changes in Plants Induced by Microbes During Stress 209 11.3.2.1 Metabolic Cross-Talk in Plants After Stress Induction 210 11.3.2.2 Activation of Antioxidant Mechanism 210 11.3.2.3 Activation of Systemically Induced Resistance 210 11.4 Role of Phytohormones in Increasing Abiotic and Biotic Stress Tolerance 211 11.5 Gene Transfer in Plants 212 11.6 Conclusion and Future Prospects 212 References 212 12 Bioprospecting: At the Interface of Plant and Microbial Communities 217 Madan L. Verma, Varsha Rani, Reena Kumari, Deepka Sharma, Sanjeev Kumar, and Rekha Kushwaha 12.1 Introduction 217 12.2 Plant-Associated Microbial Communities 218 12.3 Beneficial Effects of Plant-Associated Microbial Communities 222 12.3.1 Rhizoremediation 223 12.3.2 Plant Growth–Promoting Rhizobacteria (PGPR) 223 12.3.3 Biotic and Abiotic Stress Resistance 224 12.3.4 Signalomics 226 12.4 Role of Microbial Processing (Signals) in Facilitating Plant Growth 226 12.5 Conclusion and Future Prospects 230 Acknowledgments 230 References 231 13 Advances in Omics and Bioinformatics Tools for Phyllosphere Studies 240 Hina Bansal 13.1 Introduction 240 13.2 Recent Trends and Approaches 241 13.3 Computing for Biology 243 13.4 Bioinformatics in Microbial Research 243 13.5 Phyllosphere Microbiome Studies Based on  Genome-Wide Association 245 13.6 Omics Strategies and Their Integration 246 13.6.1 Metagenomics 246 13.6.2 Metatranscriptomics 246 13.6.3 Metabolomics 247 13.6.4 Proteomics 247 13.7 Conclusion and Future Prospects 248 References 248 Contents xi 14 Microbial Mediated Zinc Solubilization in Legumes for Sustainable Agriculture 254 Pawan Saini, Sharon Nagpal, Pooja Saini, Arun Kumar, and Mudasir Gani 14.1 Introduction 254 14.2 Chronological Events of Zinc Biology 255 14.3 Role of Zinc in Living System 256 14.3.1 Essentiality of Zinc in Humans 256 14.3.2 Essentiality of Zinc in Plants 257 14.4 Zinc Deficiency vs. Zinc Toxicity in Crop Plants 259 14.5 Availability of Zinc in Soil Environment 260 14.6 Factors Affecting Zinc Availability to Plants 261 14.7 Response of Legume Crops to Zinc 262 14.8 Microbial Mediated Zinc Solubilization in Legume Crops 263 14.8.1 Zinc-Solubilizing Bacteria (ZnSB) 264 14.8.2 Zinc-Solubilizing Fungi (ZnSF) 265 14.9 Conclusion and Future Prospects 266 References 266 15 Composition and Interconnections in Phyllomicrobiome 277 Meghmala Waghmode, Aparna Gunjal, Neha Patil, and Sonali Shinde 15.1 Introduction 277 15.2 Significance of Phyllospheremicrobiota 279 15.3 Phyllosphere Microorganisms as Plant Growth Regulator 280 15.3.1 Plant Growth Hormones Production by Phyllosphere Microorganisms 280 15.3.2 Phosphorus Solubilization by Phyllosphere Microorganisms 280 15.3.3 Siderophores Production by Phyllosphere Microorganisms 280 15.3.4 Phyllosphere Microorganisms as Biocontrol Agents Against the Phytopathogens 280 15.3.5 Phyllosphere Microorganisms to Reduce Biotic and Abiotic Stress 281 15.3.6 Synthesis of 1-Aminocyclopropane-1-Carboxylate Deaminase (ACC) 282 15.3.7 Phyllosphere Microorganisms in Nitrogen-Fixation 282 15.3.8 Frost Injury and Frost Control by Altering the Phyllosphere Microbiota 282 15.3.9 Remediation of Toxic Pollutants 283 15.3.10 Plant Probiotics 283 15.3.11 Role of Phyllosphere Microorganisms in Climate Change 284 15.3.12 Phyllosphere Microorganisms in Nutrient Yield and Increase of Plant Growth 284 15.3.13 Plant Hormones as Colonization Mediators of the Plant Leaves 284 15.4 Plant–Pathogen Interactions Mediated by Phyllosphere Microbiome 285 15.4.1 Interaction Dependent on the Ionome 285 15.4.2 Role of Secretory Systems and Secretory Products 285 15.4.3 Quorum Sensing 286 15.5 Conclusion and Future Prospects 286 References 286 Index 293