Re-visiting the Rhizosphere Eco-system for Agricultural Sustainability (Rhizosphere Biology)

The present book entitled, “Re-visiting the Rhizosphere Eco-system for Agricultural Sustainability” written by experts in the field, provides a comprehensive and consolidated state-of art overview of various aspects of rhizosphere biology, ecology and functioning. The role of rhizosphere microbial diversity in enhancing plant health and plant-microbe beneficial symbioses is discussed. Main topics include the diversity of plant-associated microbes in the rhizosphere, below-ground communication among the plant, soil, insects and microbes, rhizosphere ecosystem functioning, rhizosphere engineering, recruitment of microorganisms in the rhizosphere, mycorrhizal fungal symbiosis, positive interaction of the plants with the beneficial soil microorganisms for inducing the plant growth, conferring abiotic and biotic stress tolerance and modulating several pathways of the plants for the proper establishment and revitalization in the degraded and contaminated soils or negative likes the host-pathogen interactions leading to the disease development in plants. Further chapters focus on the role of signaling during the different stages of the plant-microbe coexistence, in symbiotic or pathogenic relationships, in quorum sensing, microbial signaling and cross-talk, bio-film formation, and antimicrobial peptides. The book also discusses the application of microbes in biodegradation of xenobiotic contaminants, bioremediation of heavy metals, sustainable agriculture and soil health, biological control of insect pests and plant pathogens, and the latest tools of omics which offer pioneering approaches to the exploration of microbial structure and function, secretome, holobiome, below-ground interaction, and microbial cooperation for sustainable food production and enhanced resource acquisition. Descriptions of cutting-edge techniques and novel approaches make this book unique in the area of rhizosphere biology. This is a useful reading material for researchers and students of microbiology, agriculture, ecology, and rhizosphser studies. Preface Contents Editors and Contributors 1: Evolution of the Knowledge and Practice of Endophytic Microorganisms for Enhanced Agricultural Benefit and Environmental Su... 1.1 Introduction 1.2 History and Concepts of Microbial-Plant Interactions 1.3 Benefits to Plants 1.3.1 Control of Plant Diseases and Pests, and Alleviation of Abiotic Stress 1.3.2 Improvements in Photosynthesis 1.3.3 Enhanced Nutrition 1.3.4 Enhanced Plant Growth and Yield 1.4 Improvements in Soil Health and Sustainability 1.5 Conclusion References 2: Mycorrhizosphere Revisited: Multitrophic Interactions 2.1 Introduction 2.2 Major Mycorrhizal Types 2.2.1 Arbuscular Mycorrhiza 2.2.2 Ectomycorrhiza 2.3 Rhizosphere 2.3.1 Soil as a Natural Support for All Living Organisms 2.3.2 Difference Between Rhizosphere and Non-Rhizosphere 2.3.3 Microbial Interactions 2.4 Mycorrhizosphere 2.4.1 Mycorrhiza Helper Bacteria 2.4.2 Interactions of Mycorrhizal Fungi with Beneficial Microflora 2.4.3 Interactions of Mycorrhizae with Pathogenic Microorganisms 2.4.4 Interactions of Mycorrhizae with the Stressed Soil Environment 2.5 Perspectives of Mycorrhizosphere for Sustainable Agriculture 2.5.1 Mycorrhizosphere Tailoring with AM Fungi and N-Fixers 2.5.2 Mycorrhizosphere Tailoring with AM Fungi and P-Solubilizers 2.5.3 Mycorrhizosphere Tailoring with AM Fungi and PGPR 2.5.4 Mycorrhizosphere Tailoring with Microbial Consortia 2.6 Conclusion References 3: Conservation Strategies for Rhizobiome in Sustainable Agriculture 3.1 Introduction 3.2 Importance of Rhizobiome in Agriculture 3.3 Understanding the Rhizosphere Ecology, Biology, and Microzone 3.4 Assessing the Rhizobiome in Different Ecosystems 3.5 Effect of External Parameters on the Rhizobiome 3.5.1 Overview of Rhizobiome Structure in Agricultural Fields 3.5.2 Factors Related to the Development of Rhizobiome 3.5.2.1 Effect of Vermicompost on Rhizobiome 3.5.2.2 Effect of Biochar on Rhizobiome 3.5.2.3 Effect of Chemical Pesticides on Rhizobiome 3.6 Conservation Strategies for Enriching the Soil with Useful Rhizobiome 3.6.1 Conservation Through Manipulation of Rhizospheric pH 3.6.2 In Situ Conservation of Rhizobiome 3.6.3 Ex Situ Conservation of Rhizobiome 3.7 Impact of Rhizobiome on Soil Enrichment Along with Plant Growth and Development 3.8 Future Aspects References 4: Exploring the Rhizosphere Microbiome for Sustainable Agriculture Production 4.1 Introduction 4.2 Modulators of the Rhizosphere Microbiome 4.3 Root-Associated Microbiome 4.4 Mycorrhiza and Plant Growth-Promoting Rhizobacteria (PGPR) 4.5 Key Mechanisms Adopted by Host for Recruiting Microbial Diversity 4.6 Mechanism of Action of PGPR 4.7 The Direct Mechanism of Action 4.7.1 Fixation of Atmospheric Nitrogen 4.7.2 Phosphorus Solubilization 4.7.3 Siderophore Production 4.7.4 ACC Deaminase Activity 4.7.5 Signaling of Phytohormones 4.8 Indirect Mechanism of Action 4.8.1 Induced Systemic Resistance 4.8.2 Biological Control and Plant Protection 4.9 Quorum-Sensing and Biofilm Formation 4.10 Metagenomics Tools for Plant Microbiome Analysis 4.11 Future Perspectives and Concluding Remarks References 5: From Rhizosphere to Endosphere: Bacterial-Plant Symbiosis and Its Impact on Sustainable Agriculture 5.1 Introduction 5.2 PGPRs and Their Recruitment Inside Plants (Bacterial-Plant Symbiosis) 5.3 Bacterial Endophytes in Plant Growth Promotion and Stress Tolerance 5.4 Functionality of Seed-Inhabiting Bacterial Endophytes in Modern Agricultural Practices 5.5 Conclusion References 6: Arbuscular Mycorrhizal Fungal Symbiosis for Mutual Benefit: More Than Expectation 6.1 Introduction 6.2 Mycorrhiza 6.3 Intracellular Accommodation of AMF 6.4 Exchange of Benefits in AMF Symbiosis 6.5 Significance of AMF for Plants in Natural and Agroecosystems 6.6 Functional Specificity in AMF Interactions with Host Plant 6.7 Benefit of AMF to Natural and Agroecosystems 6.7.1 AMF Association for Mitigation of Biotic Stress in Cropland Ecosystem 6.7.2 Effects of AMF on Plant Defence and Disease Resistance 6.7.3 Mechanism of Plant Disease Reduction by AMF 6.7.4 AMF Association for Mitigation of Abiotic Stress in Cropland Ecosystem 6.8 Significance of AMF in the Managed Ecosystems of Different Climatic Zones 6.9 Commercialization of AMF References 7: Rhizodeposits: An Essential Component for Microbial Interactions in Rhizosphere 7.1 Introduction 7.1.1 Rhizosphere: A Dynamic Ecological Niche Space for Complex Microbial Interactions 7.2 Rhizodeposits: A Vital Component for Plant-Soil Linkage 7.2.1 Root Exudates: A Multifunctional Compound of the Rhizosphere Microzone 7.2.2 Factors Influencing Root Exudation Pattern 7.2.3 Mechanism of Root Exudation and Genes Involved 7.3 Root Exudates Mediating Belowground Interactions 7.3.1 Root Exudates Mediating Plant-Microbe Interactions 7.3.1.1 Root Exudates: An Essential Chemoattractant for Microbial Host Root Colonization 7.3.1.2 Root Exudates as Signalling Molecules Rhizobia Frankia Arbuscular Mycorrhizal Fungi (AMF) 7.3.1.3 Root Exudates as Carbon Cycling Activator and Nitrification Inhibitor 7.3.1.4 Role of Root Exudates in Nutrient Deficiency 7.3.2 Other Novel Functions of Root Exudates 7.4 Conclusion and Future Perspectives References 8: Rhizospheric Microbial Diversity: Organic Versus Inorganic Farming Systems 8.1 Introduction 8.1.1 Plant-Microbe Relationship and Rhizosphere 8.1.2 Rhizosphere Exudates and Nutrient Availability 8.2 Microbial Diversity in Different Land Systems 8.3 Inorganic Versus Organic Microbial Shifting References 9: Rhizomicrobes: The Underground Life for Sustainable Agriculture 9.1 Introduction 9.2 Modern Techniques to Explore Rhizomicrobes 9.3 Techniques to Introduce PGP Microbes in Agriculture 9.4 Importance of Rhizomicrobes 9.4.1 Biofertilization 9.4.1.1 Phosphate Solubilization 9.4.1.2 Nitrogen Fixation 9.4.1.3 Siderophore Production 9.4.2 Biostimulation 9.4.3 Biocontrol 9.5 Conclusions References 10: Synthetic Biology Tools in Cyanobacterial Biotechnology: Recent Developments and Opportunities 10.1 Introduction 10.2 Development of BioBricks for Tailoring Cyanobacterial Genome 10.2.1 Inducible and Constitutive Promoters 10.2.2 Optimizing RBS Modifications 10.2.3 Riboswitches Mediated Regulation of Gene Expression 10.2.4 Small RNA (sRNA) as Functional Tools 10.2.5 Utilization and Function of Reporter Genes 10.3 Advancing Cyanobacterial Transformation Through the CRISPR-Cas System 10.4 Genome-Scale Metabolic Models 10.5 Development of Modular Cloning Suite for Cyanobacterial Transformation 10.6 Engineering Cyanobacteria for Enhancing Abiotic Stress Tolerance 10.7 Frontline Approaches for Modifying Cyanobacterial Genome 10.8 Conclusion and Future Direction References 11: The Potential of Rhizobacteria for Plant Growth and Stress Adaptation 11.1 Introduction 11.2 Rhizobacterial Functions in Plant Growth and Development 11.3 Enhanced Nutrient Uptake 11.4 Tolerance to Abiotic Stress 11.4.1 Heavy Metals 11.4.2 Salinity 11.4.3 Drought 11.4.4 Temperature 11.5 Biotic Challenges 11.5.1 Disease Suppressive Soils 11.5.2 Fighting Plant Diseases 11.5.3 Plant Defensive Reactions 11.5.4 Quorum-Sensing-Mediated Antagonistic Activity 11.6 Perspectives References 12: Mycoremediation: An Emerging Technology for Mitigating Environmental Contaminants 12.1 Introduction 12.1.1 Benefits of Bioremediation 12.1.2 Drawbacks of Bioremediation 12.2 Fungi as Bioremediators 12.2.1 Biosorption Mechanism 12.3 Enzymes Used by Fungi in the Remediation Process 12.3.1 Ligninolytic Fungal Enzymes 12.3.2 Non-ligninolytic Fungal Enzymes 12.4 Mycoremediation of Polycyclic Aromatic Hydrocarbons 12.5 Mycoremediation of Heavy Metals 12.6 Mycoremediation of Plastics 12.7 Mycoremediation of Dyes and Agricultural Contaminants 12.8 Advances in Mycoremediation Technology 12.9 Conclusion and Prospects References 13: Exploration of Plant Growth-Promoting Rhizobacteria (PGPR) for Improving Productivity and Soil Fertility Under Sustainable... 13.1 Introduction 13.2 Rhizosphere 13.3 Plant Growth-Promoting Rhizobacteria (PGPR) 13.3.1 Functional Attributes of PGPR for Sustainable Agriculture 13.3.1.1 Biofertilizer 13.4 Mechanisms of PGPR 13.4.1 Biological Nitrogen Fixation (BNF) 13.4.2 Phosphate Solubilization 13.4.3 Potassium Solubilization 13.4.4 Siderophore Production (Iron Chelation) 13.4.5 Zinc Solubilization 13.4.6 Plant Growth Regulators (PGRs) 13.4.6.1 Indole-3-Acetic Acid (IAA) 13.4.6.2 Cytokinin 13.4.6.3 Gibberellin 13.4.6.4 Abscisic Acid 13.4.7 Biocontrol Agents 13.5 PGPR for Stress Management 13.6 Future Perspective and Challenges 13.7 Conclusions References 14: Rhizosphere Engineering for Systemic Resistance/Tolerance to Biotic and Abiotic Stress 14.1 Introduction 14.1.1 An Insight into the Rhizosphere and Its Components 14.2 Rhizosphere Engineering and Different Approaches 14.2.1 Soil Amendments 14.2.2 Plant as a Management Tool 14.2.3 Microbe Engineering 14.2.4 Plant-Microbes Interaction Engineering 14.3 3Rhizosphere Engineering to Confer Abiotic Stress Tolerance to Plants 14.3.1 Temperature Extreme 14.3.1.1 Redesigning the Plant Metabolism 14.3.1.2 Introduction of Synthetic Microbial Communities 14.3.2 Drought 14.3.3 Rhizosphere Engineering for Tolerance to Salinity 14.3.3.1 Halophiles in Salinity Stress Tolerance 14.3.3.2 PGPR in Salinity Stress Tolerance Case Study 1 14.3.3.3 Fungi in Salinity Stress Tolerance 14.3.3.4 Synthetic Consortia of Microbes in Salinity Stress Tolerance 14.3.3.5 ``Plant-Fungal-Bacterial ́ ́ Symbiosis in Salinity Stress Tolerance 14.3.4 Rhizosphere Engineering for Tolerance to Xenobiotic Compounds 14.3.4.1 What Are the Mechanisms of Tolerance by Plants against Xenobiotics? 14.3.4.2 What Rhizosphere Engineering Can Do Extra to the Tolerance-Either by Bioremediation and/or by Phytoremediation 14.4 Rhizosphere Engineering to Confer Biotic Stress Tolerance/Systemic Resistance to Plants 14.5 Conclusions and Future Prospects References 15: Understanding the Microbiome Interactions Across the Cropping System 15.1 Introduction 15.2 Plant-Associated Microbial Communities in Cropping System 15.3 Plant Selection for the Rhizosphere Microbial Communities 15.4 Endosphere-A Niche for Intimate Friends 15.5 Microbial Groups Living in the Phyllosphere 15.6 Microbial Interaction Across the Cropping Systems 15.7 Soil Fertilization 15.8 Cover Crops 15.9 Tillage 15.10 Chemical Control and Bioremediation of Farmland 15.11 Understanding and Exploiting Plant Beneficial Microbes 15.12 Nitrogen Fixation 15.13 Balancing Action of Lodgepole Pine 15.14 Microbial Cocktail 15.15 Advancement Required for Improving Microbiome in Future 15.16 Conclusions References 16: Role of Rhizosphere Microorganisms in Endorsing Overall Plant Growth and Development 16.1 Introduction 16.2 Microbial-Based Fertilizers 16.3 Role of Rhizosphere Microorganisms in Nutrient Acquisition and Assimilation (N, P, K, Zn) 16.3.1 Biological Nitrogen Fixers 16.4 Phosphorus-Solubilizing Microorganisms 16.5 Potassium-Solubilizing Microorganisms 16.6 Zinc-Solubilizing Microorganisms 16.7 Role of Rhizosphere in Root Development and Defining Root System Architecture 16.8 Rhizosphere-Mediated Amelioration of Biotic and Abiotic Stresses 16.9 Plant Health and Biocontrol 16.10 Drought 16.11 Temperature Stress 16.12 Salinity 16.13 Metal Toxicity 16.14 Phytostimulation Through Exudation and Hormones 16.15 Auxin 16.16 Ethylene 16.17 Gibberellins 16.18 Cytokinin 16.19 VOCs 16.20 Manipulating Phenological Traits (Flowering) and Heterosis 16.21 Conclusion References 17: Rhizospheric Microbial Community as Drivers of Soil Ecosystem: Interactive Microbial Communication and Its Impact on Plants 17.1 Introduction 17.2 Arbuscular Mycorrhizal Fungi 17.3 Nitrogen-Fixing Microbes 17.4 Symbiosis Between Plant and Rhizospheric Microbes 17.5 Signalling Between AM and Plants 17.6 Rhizobacteria-Mediated Nutrient Cycling in Soil and Soil Health 17.7 Engineered Nanoparticle Effect on PGPR 17.8 Microbial Signals in Plant Growth and Development 17.9 Important Research Gaps and Future Challenges 17.10 Conclusion References 18: Rhizospheric Microbes and Plant Health 18.1 Introduction 18.2 Composition, Structure and Function of the Rhizosphere 18.3 Plant Health and Rhizosphere Microorganisms 18.4 Role of Different Rhizospheric Microorganismsin Plant Growth and Development 18.4.1 Trichoderma Spp. 18.5 Mycoparasitism-Related Secondary Metabolites 18.6 Plant Growth Regulators 18.6.1 Plant Growth-Promoting Rhizobacteria (PGPR) 18.7 Abiotic Stress Tolerance 18.8 Siderophore Production 18.9 Major PGPR Involved in Plant Health 18.9.1 Bacillus spp. 18.9.2 Pseudomonas spp. 18.9.3 Rhizobium spp. 18.9.4 Azotobactor 18.10 Omics Approaches to Unravel the Rhizosphere Interactions and Function 18.11 Conclusion References 19: Omics Approaches to Unravel the Features of Rhizospheric Microbiome 19.1 Introduction 19.1.1 Present Scenario of the Rhizospheric Science 19.1.2 Multi-Omics Approach 19.2 Integration of Omics Approaches in Rhizosphere Studies: An Overview 19.3 Omics Techniques to Study the Rhizo-Microbiome Interface 19.3.1 Denaturing Gradient Gel Electrophoresis (DGGE) and Temperature Gradient Gel Electrophoresis (TGGE) 19.3.2 Terminal Restriction Fragment Length Polymorphism (T-RFLP) 19.3.3 Amplified rDNA Restriction Analysis (ARDRA) and Random Amplified Polymorphic DNA (RAPD) 19.3.4 DNA Cloning and Sanger Sequencing 19.3.5 NGS in Crop Improvement 19.4 Challenges Ahead for Themulti-Omics in the Field of Rhizospheric Science 19.5 The Future Prospect of Multi-Omics in the Rhizosphere Science 19.6 Conclusion References 20: Rhizo-Deposit and Their Role in Rhizosphere Interactions Among the Plant, Microbe and Other Ecological Components for Crop... 20.1 Introduction 20.2 Microorganisms as Biocontrol Agents 20.3 Phenomenon of Antagonism (Mechanism of Action) 20.4 Direct Action of Biocontrol Agents 20.4.1 Hyper-Parasitism 20.4.2 Antibiosis 20.4.3 Competition 20.5 Indirect Action of Biocontrol Agents 20.5.1 Induced Systemic Resistance (ISR) 20.5.2 Growth Promotion 20.5.3 Solubilization and Sequestration of Inorganic Plant Nutrients 20.5.4 Inactivation of Pathogen ́s Enzymes 20.6 T. harzianum Grown on Different De-Oiled Cakes and Composts May Have a Better Rhizosphere Competence 20.6.1 Effect on Vigour and Yield of Tomato 20.7 Application of Bioagents for Suppressing the Diseases in Plants 20.8 Application of Bioagents for Tolerance to Water Stress in Crops 20.9 Rhizosphere Application of Bioagents for Growth Promotion and Disease Management 20.10 Conclusions References 21: Effects of Irrigation with Municipal Wastewater on the Microbiome of the Rhizosphere of Agricultural Lands 21.1 Introduction 21.2 Municipal Sewage and Treatment 21.3 Results of Biological Treatment 21.4 The Fungi of the Rhizosphere Microbiome 21.5 Polymerase Chain Reaction (PCR) 21.6 AM Fungi and Raw Sewage Used in Irrigation 21.7 Effect of Secondary Sludge Amendments to the Soil on AM Fungi 21.8 AM Fungi and Irrigation Using Biologically Treated Municipal Wastewater 21.9 Risks Associated with Irrigation with Biologically Treated Municipal Wastewater 21.10 Conclusions 21.11 Future Perspectives References 22: Plant-Rhizospheric Microbe Interactions: Enhancing Plant Growth and Improving Soil Biota 22.1 Introduction 22.2 The Rhizosphere 22.3 Natural Interactions Between Microorganisms and Plant 22.4 Biocontrol Potential 22.5 Disease-Suppressive Soil Microbes 22.5.1 Biocontrol Agents 22.5.2 Plant Growth-Promoting Microorganisms (PGPM) 22.6 Effect of Below-Ground Microbial Interactions on Above-Ground Microbes 22.7 Antagonism 22.8 Amensalism 22.9 Parasitism 22.10 Symbiotic Interaction 22.11 Negative and Positive Interactions and Their Influence on Microbial Diversity 22.12 Effect of Environment on Plant-Microbe Interaction 22.13 Effect of Agricultural Practices on Soil Microbiota 22.14 Below-Ground Microbes and Agricultural Sustainability 22.15 Future Endeavors References 23: Microbes-Mediated Rhizospheric Engineering for Salinity Stress Mitigation 23.1 Introduction 23.2 Global Distribution of Salinity 23.3 Effect of Soil Salinity on Crop Production 23.4 Osmoregulation in Salinity Stress 23.5 Rhizospheric Microbiome of Salt Tolerance 23.5.1 Modification in Phytohormonal Content 23.5.2 Interplay of Ethylene, IAA and ACC Deaminase in Salinity Stress 23.6 Mechanisms of Salt-Tolerant Microbiome 23.7 Prospects and Conclusion References 24: Metatranscriptomics of Plant Rhizosphere: A Promising Tool to Decipher the Role of Microorganisms in Plant Growth and Deve... 24.1 Metatranscriptomics 24.2 Methods to Study Metatranscriptomics 24.3 Identification of Novel Genes and/or Function in Rhizosphere 24.4 Metatranscriptomics in Microbial Diversity Analysis 24.5 Metatranscriptomics in Bio-Control of Phytopathogens 24.6 Metatranscriptomics in Plant Growth Promotion 24.7 Metatranscriptomics in Abiotic Stress Tolerance 24.8 Challenges 24.9 Conclusion References 25: Rhizospheric Engineering for Sustainable Production of Horticultural Crops 25.1 Introduction 25.2 Rhizosphere 25.3 Rhizospheric Microbes and Their Interactions with Plants 25.4 Plant Growth-Promoting Rhizobacteria 25.4.1 Types and Underlying Mechanisms of Plant Growth-Promoting Rhizobacteria 25.5 Effects of Plant Growth Promoting Rhizobacteria 25.5.1 Biological Nitrogen Fixation 25.5.2 Solubilisation of Phosphorus 25.5.3 Production of Stimulants of Plant Growth 25.5.4 Antagonistic Activity and Biocontrol Agents 25.5.5 Induced Systemic Resistance and Systemic Acquired Resistance 25.5.6 Industrial Applications of Plant Growth-Promoting Rhizobacteria 25.6 Rhizosphere Engineering 25.7 Benefits of Rhizosphere Engineering 25.7.1 Drought Resistance 25.7.2 Disease Resistance 25.7.3 Rhizoremediation 25.7.4 Regulation of Flowering 25.7.5 Rooting of Cuttings 25.8 Conclusion References