Phytomicrobiome Interactions and Sustainable Agriculture

AMIT VERMA is Assistant Professor in the Department of Biochemistry, S.D. Agricultural University, India. JITENDRA KUMAR SAINI is Assistant Professor in the Department of Microbiology at Central University of Haryana, India. ABD EL-LATIF HESHAM is Professor of Microbial Genetics and Environmental Meta-Genome Biotechnology at Genetics Department, Faculty of Agriculture, Beni-Suef University, Egypt. HARIKESH BAHADUR SINGH is Professor of Excellence, Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India.

• List of Contributors xiiPreface xviAbout the Editors xviii1 Plant Root Exudate Analysis: Recent Advances and Applications 1Shulbhi Verma and Amit Verma1.1 Introduction 11.2 Root Exudates Composition: Collection and Analysis 31.3 Role of Root Exudates in Shaping Rhizospheric Microbiomes 51.4 Applications of Root Exudation 61.5 Conclusion and Future Prospects 7References 102 Phytoproteomics: A New Approach to Decipher Phytomicrobiome Relationships 15Prachie Sharma and Kapila Kumar2.1 Introduction 152.2 Phytomicrobiome 162.3 Phytomicrobiome: The Communication via Signaling 182.4 Proteomics 192.4.1 Gel-Based Protein Separation Techniques 212.4.2 Non-Gel Protein Separation Techniques 212.5 Analysis of Phytomicrobial Interactions Using Proteomics Approaches 222.6 Conclusion and Future Prospects 26References 283 Metagenomics: An Approach to Unravel the Plant Microbiome and Its Function 32Ravindra Soni, Deep Chandra Suyal, Balram Sahu, and Suresh Chandra Phulara3.1 Introduction 323.2 Metagenomics 333.3 Metagenomics of Plant Rhizosphere 333.4 Metagenomics of Plant Phyllosphere 353.5 Metagenomics of Plant Endosphere 363.6 In-silico Tools for Metagenome Analysis 373.6.1 Mothur 373.6.2 Quantitative Insights into Microbial Ecology (QIIME) 373.6.3 MEta Genome Analyzer (MEGAN) 383.7 Recent Progress in Metagenomic Studies of Plant Microbiome 383.8 Conclusion and Future Prospects 38References 384 Combating the Abiotic Stress Through Phytomicrobiome Studies 45Hemant S. Maheshwari, Abhishek Bharti, Richa Agnihotri, Ajinath Dukare, B. Jeberlin Prabina, Saurabh Gangola, and Mahaveer P. Sharma4.1 Introduction 454.1.1 Abiotic Stress and Phytomicrobiome 454.1.2 Role of Signaling in Phytomicrobiome Interactions 464.2 Phytomicrobiome Signaling Compounds 474.2.1 Root Exudates and Plant Volatiles Compounds 474.2.2 Microbial Volatile Organic Compounds 474.2.3 Quorum Sensing 484.2.4 Underground Phytomicrobiome Signaling 484.3 Mechanisms of Phytomicrobiome Associated with Abiotic Stress Tolerance 494.3.1 Drought Stress Alleviation 504.3.2 Salinity Stress Mitigation 534.3.3 Heavy Metal Toxicity 554.3.4 Low-Temperature Stress 564.3.5 Nutrient Deficiency 564.3.6 Flooding or Water Submergence 564.4 Importance of Phytomicrobiome Engineering for Crop Stress Alleviation 574.5 Omics Strategies in Phytomicrobiome Studies 584.6 Conclusion and Future Prospects 59Acknowledgments 59References 605 Microbial Diversity of Phyllosphere: Exploring the Unexplored 66Rakhi Dhankhar, Aparajita Mohanty, and Pooja Gulati5.1 Introduction 665.2 Origin of Phyllosphere Microflora 675.3 Tools to Study Phyllomicrobiome 685.3.1 Conventional Methods 695.3.2 Microscopic Techniques 695.3.3 First-Generation Molecular Techniques 705.3.4 Next-Generation Sequencing Methods 705.3.5 Omics and Bioinformatics Approaches 765.3.6 Other Molecular Methods 775.4 Biodiversity of Phyllosphere 775.5 Microbial Adaptation to Phyllosphere 785.5.1 Adaptation to Abiotic Stresses 795.5.2 Adaptation to Biotic Stresses 805.5.3 Adaptation to Nutrient Scarcity 815.6 Interaction of Phyllomicrobiota with Plants 815.6.1 Positive Interactions 825.6.2 Negative Interactions 835.7 Significance of Phyllomicrobiome Studies 835.8 Conclusion and Future Prospects 84References 856 Rhizosphere Engineering: An Effective Approach for Sustainable Modern Agriculture 91Reema Mishra, Tripti Grover, Pooja Gulati, and Aparajita Mohanty6.1 Introduction 916.2 Natural Plant–Microbe Interactions in Rhizosphere 926.3 Molecular Mechanisms in Plant–Microbe Interactions in Rhizosphere 936.4 Biochemical Components in Rhizosphere Signaling 946.5 Tools and Techniques in Rhizosphere Engineering 966.5.1 Stable Isotope Probing (SIP) 966.5.2 DNA Arrays 976.5.3 Fluorescence In Situ Hybridization (FISH) 976.5.4 Bioreporters 976.5.5 Genomics 986.5.6 Transcriptomics 986.5.7 Proteomics 996.5.8 Metabolomics 996.6 Rhizosphere Components Amenable to Engineering 1006.6.1 Soil Modification 1006.6.2 Plant Amendment 1006.6.2.1 Root Exudate Modification 1006.6.2.2 Root Architecture Modification 1016.6.2.3 Enhancing Abiotic Stress Tolerance in Plants 1016.6.2.4 Enhancing Biotic Stress Tolerance in Plants 1036.6.2.5 Engineering Metabolic Pathways in Plants 1056.6.3 Engineering Microbial Populations 1076.7 Conclusion and Future Prospects 107Acknowledgment 108References 1087 Plant Communication with Associated: Its Components, Composition and Role in Maintaining Plant Homeostasis 118Dibyajit Lahiri, Moupriya Nag, Sayantani Garai, Bandita Dutta, and Rina Rani Ray7.1 Introduction 1187.2 Biofilm and Rhizospheric Interactions 1197.3 Biofilm Formation at the Root Rhizosphere 1207.3.1 The Components of Biofilm Matrix 1217.3.2 Bacterial Quorum Sensing 1227.4 Genetic Features Responsible for Bacterial Cell Adhesion to Plant System 1257.4.1 Chemotaxis Motility 1257.4.2 Substrate Utilization and Transport 1257.4.3 Lipopolysaccharide and Membrane Proteins 1267.4.4 Plant Cell Wall Modification 1277.4.5 Adhesion and Biofilm Formation 1287.4.6 Stress Protection 1287.4.7 Bacterial Secretion System 1297.4.8 Transcriptional Regulators and Sensor Proteins 1307.5 Nutrient Interactions 1387.5.1 Release and Activation of Minerals 1387.5.2 Nutrient Recycling 1387.5.3 Nitrogen Dynamics 1387.5.4 Ionic Modification 1397.6 Biotic Interaction 1407.6.1 Symbiosis 1407.6.2 Synergy 1407.6.3 Competition 1407.6.4 Antagonism 1417.6.5 Pathogenesis 1427.7 Conclusion and Future Prospects 142References 1438 Phytomicrobiome: Synergistic Relationship in Bioremediation of Soil for Sustainable Agriculture 150Nimmy Srivastava8.1 Introduction 1508.2 Phytoremediation 1518.2.1 Process of Phytoremediation 1518.2.2 Strategies for Phytoremediation 1518.3 Phytomicrobe Interactions and Rhizomediation 1528.3.1 Principle of Phytomicrobiome Interaction During Rhizomediation 1528.3.2 Removal of Inorganic Contaminants 1548.3.3 Removal of Organic Pollutants 1548.3.4 Factors Affecting Rhizomediation 1578.4 Conclusion and Future Prospects 157References 1589 Rhizospheric Biology: Alternate Tactics for Enhancing Sustainable Agriculture 164Kalpana Bhatt and Pankaj Bhatt9.1 Introduction 1649.2 Engineering the Rhizosphere 1659.2.1 Rhizosphere and Rhizobia 1659.2.2 Root Exudates: Chemical Nature and Types 1679.2.3 Factors Affecting Root Exudate 1689.3 Engineering Soil Microbial Populations and Plant–Microbe Interactions 1699.3.1 Microorganisms in Soil 1699.3.2 Soil Modification: Altering Microbial Populations 1709.4 Plant Growth-Promoting Rhizobacteria: Mechanisms, Potential, and Usages 1709.4.1 Direct Mechanisms 1719.4.1.1 Biological N2 Fixation 1719.4.1.2 Phosphate Solubilization 1739.4.1.3 Zinc Solubilization 1749.4.1.4 Siderophore Production 1749.4.1.5 Production of Phytohormones 1749.4.1.6 ACC (1-Aminocyclopropane-1-Carboxylate) Deaminase Activity 1759.4.2 Indirect Mechanisms 1759.5 Plant–Microbe Interaction 1769.6 Biofertilizers and its Applications 1779.7 Plant Genetic Engineering 1779.8 Conclusion and Future Prospects 178Acknowledgments 178References 17910 Application of Inorganic Amendments to Improve Soil Fertility 187Sunita Chauhan and Shweta Kulshreshtha10.1 Introduction 18710.2 Impact of Bhoochetna Movement in Southern India 18810.3 Sustainable Agriculture 18810.3.1 Healthy Soil and Soil Quality 18910.3.2 Soil Quality 18910.3.3 Soil Quality Indicator 19010.3.4 Soil Quality Index 19110.4 Factors to Be Considered While Selecting a Soil Amendment 19210.5 Advantages of Soil Amendments 19410.6 Land Modeling 19410.7 Major Applications of Soil Amendments 19510.7.1 Phyto-Stabilization in Polluted or Contaminated Soils 19510.7.2 Restoration of Soil 19610.7.2.1 Soil Acidity/pH Soil Amendments 19610.7.2.2 Mineral Soil Amendments and Conditioners 19610.7.2.3 Different Types of Inorganic Amendments 19710.8 Combination Strategy for Soil Quality Improvement 20210.9 Conclusion and Future Prospects 203References 20311 Improved Plant Resistance by Phytomicrobiome Community Towards Biotic and Abiotic Stresses 207Neha Trivedi11.1 Introduction 20711.2 Microbes and Plants 20711.2.1 Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants 20811.2.2 Microbial-Induced Response to Stresses 20811.3 Response of Abiotic Response on Plant 20911.3.1 Induced Systemic Tolerance (IST) 20911.3.2 Metabolic Changes in Plants Induced by Microbes During Stress 20911.3.2.1 Metabolic Cross-Talk in Plants After Stress Induction 21011.3.2.2 Activation of Antioxidant Mechanism 21011.3.2.3 Activation of Systemically Induced Resistance 21011.4 Role of Phytohormones in Increasing Abiotic and Biotic Stress Tolerance 21111.5 Gene Transfer in Plants 21211.6 Conclusion and Future Prospects 212References 21212 Bioprospecting: At the Interface of Plant and Microbial Communities 217Madan L. Verma, Varsha Rani, Reena Kumari, Deepka Sharma, Sanjeev Kumar, and Rekha Kushwaha12.1 Introduction 21712.2 Plant-Associated Microbial Communities 21812.3 Beneficial Effects of Plant-Associated Microbial Communities 22212.3.1 Rhizoremediation 22312.3.2 Plant Growth–Promoting Rhizobacteria (PGPR) 22312.3.3 Biotic and Abiotic Stress Resistance 22412.3.4 Signalomics 22612.4 Role of Microbial Processing (Signals) in Facilitating Plant Growth 22612.5 Conclusion and Future Prospects 230Acknowledgments 230References 23113 Advances in Omics and Bioinformatics Tools for Phyllosphere Studies 240Hina Bansal13.1 Introduction 24013.2 Recent Trends and Approaches 24113.3 Computing for Biology 24313.4 Bioinformatics in Microbial Research 24313.5 Phyllosphere Microbiome Studies Based on Genome-Wide Association 24513.6 Omics Strategies and Their Integration 24613.6.1 Metagenomics 24613.6.2 Metatranscriptomics 24613.6.3 Metabolomics 24713.6.4 Proteomics 24713.7 Conclusion and Future Prospects 248References 24814 Microbial Mediated Zinc Solubilization in Legumes for Sustainable Agriculture 254Pawan Saini, Sharon Nagpal, Pooja Saini, Arun Kumar, and Mudasir Gani14.1 Introduction 25414.2 Chronological Events of Zinc Biology 25514.3 Role of Zinc in Living System 25614.3.1 Essentiality of Zinc in Humans 25614.3.2 Essentiality of Zinc in Plants 25714.4 Zinc Deficiency vs. Zinc Toxicity in Crop Plants 25914.5 Availability of Zinc in Soil Environment 26014.6 Factors Affecting Zinc Availability to Plants 26114.7 Response of Legume Crops to Zinc 26214.8 Microbial Mediated Zinc Solubilization in Legume Crops 26314.8.1 Zinc-Solubilizing Bacteria (ZnSB) 26414.8.2 Zinc-Solubilizing Fungi (ZnSF) 26514.9 Conclusion and Future Prospects 266References 26615 Composition and Interconnections in Phyllomicrobiome 277Meghmala Waghmode, Aparna Gunjal, Neha Patil, and Sonali Shinde15.1 Introduction 27715.2 Significance of Phyllospheremicrobiota 27915.3 Phyllosphere Microorganisms as Plant Growth Regulator 28015.3.1 Plant Growth Hormones Production by Phyllosphere Microorganisms 28015.3.2 Phosphorus Solubilization by Phyllosphere Microorganisms 28015.3.3 Siderophores Production by Phyllosphere Microorganisms 28015.3.4 Phyllosphere Microorganisms as Biocontrol Agents Against the Phytopathogens 28015.3.5 Phyllosphere Microorganisms to Reduce Biotic and Abiotic Stress 28115.3.6 Synthesis of 1-Aminocyclopropane-1-Carboxylate Deaminase (ACC) 28215.3.7 Phyllosphere Microorganisms in Nitrogen-Fixation 28215.3.8 Frost Injury and Frost Control by Altering the Phyllosphere Microbiota 28215.3.9 Remediation of Toxic Pollutants 28315.3.10 Plant Probiotics 28315.3.11 Role of Phyllosphere Microorganisms in Climate Change 28415.3.12 Phyllosphere Microorganisms in Nutrient Yield and Increase of Plant Growth 28415.3.13 Plant Hormones as Colonization Mediators of the Plant Leaves 28415.4 Plant–Pathogen Interactions Mediated by Phyllosphere Microbiome 28515.4.1 Interaction Dependent on the Ionome 28515.4.2 Role of Secretory Systems and Secretory Products 28515.4.3 Quorum Sensing 28615.5 Conclusion and Future Prospects 286References 286