Microbiological Activity for Soil and Plant Health Management

Description

Plants and the soil they grow in, are confronted with severe biotic and abiotic stresses viz. nutrient starvation, salt stress, drought, flooding, xenobiotic contamination, in order to sustain in an ecosystem. They also shape the microbial composition in their vicinity by modulating their secretions. This book discusses the pressing demand for novel and potential microorganisms to support an environment-friendly and cost-effective way of stress management in the plants. The book summarizes the processes and mechanisms involved in microbe-assisted plant and soil stress management. It discusses the challenges and opportunities in the application of microbial interactions in plant health. It describes in detail the nutrient dynamics of different soil systems. It includes important topics like agriculturally important genes and enzymes, rhizosphere modeling & engineering, genetically engineered bio-inoculants etc. It also talks about the application of next-generation technologies, omics and nano-based technologies. In the recent years, more than 50% of agricultural production relies on chemical fertilizers, leading to serious health issues and environmental concerns. This book provides natural solutions to these environmental concerns. This book is useful for researchers and students in the field of microbiology, agriculture, soil biology and plant sciences. Preface Contents About the Editors 1: Agriculturally Important Microbes: Challenges and Opportunities 1.1 Introduction 1.2 Azotobacter 1.2.1 Action Mechanism of Plant Growth-Promoting Rhizobacteria 1.2.2 Azotobacter as Biofertilizers and Biocontrol Agents 1.3 Serratia spp. 1.3.1 Action Mechanism as Plant Growth-Promoting Rhizobacteria 1.3.2 Serratia as Biocontrol Agents 1.3.3 Serratia in Abiotic Stress Tolerance 1.4 Bacillus spp 1.5 Pseudomonas 1.6 Challenges to the Use of Agriculturally Important Microbes 1.6.1 Screening of Microbes and Poor Shelf Life of Bioformulation 1.6.2 Lack of Field Reproducibly of PGPR Performance 1.6.3 Skewed Perception 1.6.4 Challenges in Product Commercialization 1.6.5 Challenges in Products Registration and Patent Filing 1.7 Future Aspects References 2: Agriculturally Important Microorganism: Understanding the Functionality and Mechanisms for Sustainable Farming 2.1 The Concept of Plant Microbiome and the Rhizobiome 2.2 Agriculturally Important Microorganisms (AIMs) 2.3 Diversity and Functionality of AIMs 2.3.1 Diversity and Interrelationship 2.3.2 Diversity and Functionality 2.3.2.1 Biocontrol Agents (BCA) 2.3.2.2 Plant Growth-Promoting Rhizobacteria (PGPR) 2.3.2.3 Plant Growth-Promoting Fungi (PGPF) 2.3.2.4 Arbuscular Mycorrhizal Fungi (AMF) 2.3.2.5 Endophytes 2.3.2.6 Actinomycetes 2.4 Mechanisms Involved in Plant and Soil Health Improvement 2.4.1 Direct Mechanism 2.4.1.1 Biological Fixation of the Atmospheric Nitrogen 2.4.1.2 Solubilization of Phosphates by Microorganisms 2.4.1.3 Production of Siderophores by Microorganisms 2.4.1.4 Production of Phytohormones 2.4.2 Indirect Mechanism 2.4.2.1 Induction of Resistance in Host Plants by AIMs 2.5 Molecular Signaling in the Rhizosphere and Beyond: The Cross Talk 2.5.1 Microbe Triggered Immunity 2.5.2 Microbial Signaling 2.6 Current and Future Challenges 2.7 Conclusion References 3: Microbial Diversity of Different Agroecosystems: Current Research and Future Challenges 3.1 Introduction 3.2 Microbial Diversity of Agroecosystems 3.2.1 Temporal and Spatial Distribution 3.2.2 Diversity in Different Agroecosystems 3.2.2.1 Jhum Agroecosystem 3.2.2.2 Microbial Diversity in Sundarbans 3.2.2.3 Agroecosystem of North Western Himalayas 3.2.2.4 Thar Agroecosystem 3.2.2.5 Coffee Shade Tree Agroecosystem 3.2.2.6 Apatani Wet Rice Agroecosystem 3.2.2.7 Agroecosystem of Leh Ladakh 3.2.2.8 Effect of Changing Environment on Microbial Diversity 3.3 Role of Microorganisms in Ecosystem Functioning 3.3.1 Nutrient Cycling 3.3.2 Soil Formation and Weathering 3.3.3 Waste Recycling 3.4 Effect of Changing Environment on Microbial Diversity 3.4.1 Soil Biodiversity, Resistance, and Resilience 3.4.2 Nitrogen Deposition 3.4.3 Elevated Carbon Concentration 3.5 Mitigation Strategies 3.5.1 Soil Biodiversity and Sustainable Agricultural Practices 3.5.2 Soil Biodiversity and Restoration Ecology 3.5.3 Agroecosystem Management with Core Microbiomes 3.6 Conclusion References 4: Soil Microbial Biomass asan Index of Soil Quality and Fertility in Different Land Use Systems of Northeast India 4.1 Introduction 4.2 Role of Soil Microbes in an Ecosystem 4.3 Soil Microbial Biomass 4.4 Land-Use Types of Northeast India 4.5 Soil Nutrient Status of Different Land-Use Types of Northeast India 4.6 Changes in Microbial Biomass C, N, and P Due to Land-Use Types 4.7 Microbial C:N:P Stoichiometry in Different Land-Use Types of Northeast India 4.7.1 Microbial C:N Ratio 4.7.2 Microbial C:P Ratio 4.7.3 Microbial N:P Ratio 4.8 Soil Nutrient Fractions in Microbial Biomass of Different Land Uses of Northeast India 4.9 Conclusion References 5: Microbes and Plant Mineral Nutrition 5.1 Introduction 5.2 An Overview of Soil Microorganisms for the Availability of Nutrients in Plants 5.3 Soil Microbes Induced Nitrogen Uptake by Plants 5.4 Soil Microbes Induced Phosphate Uptake by Plants 5.5 Soil Microbes Induced Potassium Uptake by Plants 5.6 Soil Microbes Mediated Micronutrient Acquisition in Plants 5.6.1 Iron 5.6.2 Zinc 5.7 Copper 5.7.1 Manganese 5.8 Future Perspectives and Challenges in Plant Microbe Based Agro-Inputs 5.9 Conclusion References 6: Drought Stress Alleviation in Plants by Soil Microbial Interactions 6.1 Introduction 6.2 Stresses, Soil Structure and Their Effect on Microbial Colonization 6.3 Microbes: As Protective Companion to Plants 6.3.1 Bacteria 6.3.2 AM Fungi 6.3.3 Actinomycetes 6.3.4 Virus 6.4 Drought Stress Management 6.4.1 Growth, Biomass, and Photosynthesis 6.4.2 Mineral Uptake and Mobilization 6.4.3 Redox Homeostasis and Membrane Stabilization 6.4.4 Osmolytes Regulation 6.4.5 Hormonal Regulation and Volatiles 6.5 Conclusion and Future Prospective References 7: Role of Nitrogen-Fixing Microorganisms for Plant and Soil Health 7.1 Introduction 7.2 Biological Nitrogen Fixation 7.2.1 Symbiotic Nitrogen Fixation 7.2.2 Invasion and Infection 7.2.2.1 Release of Flavonoids 7.2.2.2 Nod Factor 7.2.2.3 Nod Factor Perception 7.2.2.4 Responses to Nod Factor 7.2.2.5 Root Hair Curling 7.2.2.6 Nodule Organogenesis 7.2.3 Regulation of Nitrogen Fixation 7.2.4 Free Living and Associative Nitrogen Fixation 7.2.4.1 Free-Living Diazotrophs 7.2.4.1.1 Azotobacter vinelandii 7.2.4.1.2 Cyanobacteria 7.2.4.2 Associative Diazotrophs 7.3 Application in Management Practices 7.4 Conclusions References 8: Serendipita indica Mediated Drought and Heavy Metal Stress Tolerance in Plants 8.1 Introduction 8.2 Role of S. indica in Heavy Metal Stress Tolerance 8.3 Drought Stress Tolerance Mediated by S. indica 8.4 Conclusion References 9: Role of Rhizosphere and Endophytic Microbes in Alleviation of Biotic and Abiotic Stress in Plants 9.1 Introduction 9.2 Biotic and Abiotic Stress and Their Impacts on Crop Production 9.3 Diversity and Consortium of Rhizosphere and Endophytic Microbes 9.4 Environmental and Host Influence on the Rhizosphere and Endophytic Microbes 9.4.1 Environmental Effects 9.4.2 Effects of Agronomic Practices 9.4.3 Influence of Host Plants 9.5 Role of Rhizosphere and Endophytic Microbes in Agriculture 9.5.1 Plant Growth Promotion by Increasing Nutrient Availability 9.5.2 Plant Growth Promotion by Hormone Production 9.5.3 Defend Plants Against Biotic Stress 9.5.4 Increase Abiotic Stress Tolerance in Plants 9.6 Molecular Mechanisms of Stress Alleviation 9.6.1 Microbe-Mediated Induced Systemic Tolerance to Abiotic Stress 9.6.1.1 Amelioration of Nutrient Deficiency 9.6.1.2 Water, Temperature and Salinity Stress Tolerance 9.6.1.3 Tolerance of Stress Due to Heavy Metal and Herbicide Toxicity 9.6.2 Microbe-Mediated Induced Systemic Resistance to Biotic Stresses 9.6.3 Defence Mechanisms of Rhizosphere and Endophytic Microbes Against Biotic Stresses 9.6.4 Defence Against Phytopathogens 9.6.5 Defence Against Phytophagous Insects 9.7 Influence of Rhizosphere and Endophytic Microbes on Product Quality 9.8 Biotechnological Approaches for Enhancing the Effectiveness of Rhizosphere and Endophytic Microbes 9.9 Conclusion and Future Perspective References 10: Augmentation of Plant Salt Stress Tolerance by Microorganisms 10.1 Introduction 10.1.1 Impact of Soil Salinization on Plants 10.1.2 Plant Growth-Promoting Bacteria 10.1.3 Mycorrhizal and Endophytic Fungi 10.2 Molecular Mechanism Involved in Salt Tolerance 10.2.1 General Mechanisms of Augmenting Salt Tolerance in Plants 10.2.2 Specific Mechanisms in Regulating Salt Tolerance by Microorganisms 10.3 Microbial Stimulation of Salt Tolerance 10.3.1 Salt Tolerance by Bacteria 10.3.2 Salt Tolerance by Fungi 10.4 Combinatorial Benefits of PGPB and Mycorrhizal Fungi 10.5 Conclusion and Future Perspective References 11: Impact of Plant Exudates on Soil Microbiomes 11.1 Rhizosphere 11.2 Root Exudate 11.2.1 Rhizodeposition 11.2.2 Root Exudate and Organic Acid 11.3 Plant Interaction with Microbes 11.4 Root Exudate Impact References 12: Global Climate Change and Microbial Ecology: Current Scenario and Management 12.1 Introduction 12.2 Microbial Functions in the Environment 12.3 Applications in Agriculture 12.3.1 Nutrient Recycling 12.3.2 Sustaining Optimal Soil Structure for Agriculture 12.3.3 Mineralization and Humification 12.4 Role of Soil Enzymes in Decomposition of Organic Matter 12.4.1 Amylase 12.4.2 Arylsulfatase 12.4.3 β-Glucosidase 12.4.4 Cellulose 12.4.5 Chitinase 12.4.6 Dehydrogenase 12.4.7 Phosphatase 12.4.8 Proteases 12.5 Pollutants Mitigation 12.6 Bioremediation 12.7 Impact of Climate Change on the World´s Agriculture 12.7.1 Effects of Temperature 12.7.2 Moisture Fluctuations 12.7.3 Significance of Terrestrial and Aquatic Ecosystems 12.8 The Relevance of the Microbial World to the Problem 12.9 Role of Terrestrial Microbes 12.9.1 Production of Carbon Dioxide and Methane 12.9.2 The Issue of Agricultural Lands 12.10 Role of Aquatic Microbes 12.11 Microbial Adaptations to Cope with Climate Change 12.12 Plant-Microbe Interactions in Managing Stressed Agriculture 12.13 Climate Change Impacts on the Soil Microbiome 12.13.1 Soil Warming 12.13.2 Elevated Carbon Dioxide 12.13.3 Microbial Biochemical Pathways and Climate Change 12.14 Plant, Microbe, and Climate Change 12.14.1 Direct Impacts of Climate Change on Soil Communities and Plants 12.14.2 Indirect Effects of Climate Change on Plants and Soil Microbiome 12.14.3 Interactions Between Climate Change and Microbial Ecosystems in Terrestrial Regions 12.14.4 Soil and Agriculture 12.14.5 Freshwater 12.15 Conclusion References 13: Biotic Stress Management by Microbial Interactions in Soils 13.1 Introduction 13.2 Important SoilBorne Diseases and Losses in Different Crops 13.3 Role of Soil Health in Plant Disease Incidence 13.4 Potential of Biological Agents for Disease Management 13.5 Mechanism of Action of Biocontrol Agents and Host-BCAs Interaction 13.6 Expression of Plant Defense Genes During Host-BCAs Interaction 13.7 Modification of Soil Environment to Manage Plant Diseases 13.8 Commercial Formulation of Biocontrol Agents in Market 13.9 Conclusion References 14: Interactions Between Plant Genotypes and PGPR are a Challenge for Crop Breeding and Improvement Inoculation Responses 14.1 Introduction 14.2 Plant Breeding and Rhizosphere Microorganisms 14.3 Plant Growth-Promoting Rhizobacteria and Sustainable Agriculture 14.4 PGPR and Rhizosphere Microbial Ecology 14.5 Biological Indicators of Soil Quality 14.6 Conclusion References 15: Significance of Microbial Enzyme Activities in Agriculture 15.1 Introduction 15.2 Principal Soil Enzymes in Sustainable Agriculture 15.2.1 Phosphatase Enzyme 15.2.2 Dehydrogenase Enzyme 15.2.3 Sulfatase and Arylsulfatase 15.2.4 Urease Enzyme 15.2.5 Cellulase 15.2.6 Chitinase Enzyme 15.3 Factors Influencing Enzyme Activity 15.4 Soil Enzymes as a Bioindicator of Soil Health 15.5 Conclusion References 16: Omics Technology for Plant Stress Management 16.1 Introduction 16.2 Insights into Omics Technologies Used in Plant Stress Management 16.3 Genomics 16.4 Transcriptomics 16.5 Proteomics 16.6 Metabolomics 16.7 Lipidomics 16.8 Proteogenomics 16.9 miRNA Omics 16.10 Prime-Omics 16.11 Bioinformatics 16.12 Ionomics 16.13 Phenomic 16.14 Integration of Omics Technologies 16.15 Conclusion References 17: Rhizosphere Modeling and Engineering for Agricultural and Environmental Sustainability 17.1 Introduction 17.2 Engineering Plants Through Plant Genetic Engineering 17.3 Manipulating Rhizosphere pH 17.4 Response of Plants to Aluminum Toxicity in Soil 17.5 Vacuole Nitrate Transporters, Malate Channels, and Metabolism 17.6 Multidrug and Toxic Compound Extrusion (MATE) 17.7 Enhancing Organic Anion Efflux from Roots 17.8 Acquisition of Phosphorus 17.9 Aluminum-Induced Secretion of Organic Acid Anions from Roots 17.10 Acquisition of Other Nutrients and Heavy Metals 17.11 Communications with Plant Growth-Promoting Microorganisms 17.11.1 Root-Released Organic Anions in Intercropping 17.11.2 The Encoding Genes that Enhance Organic Anion Efflux from Roots Rhizosphere 17.12 Conclusion and Future Direction References 18: Factors Affecting Soil Ecosystem and Productivity 18.1 Introduction 18.2 Abiotic Factors 18.2.1 Physical Factors 18.2.1.1 Soil Texture 18.2.1.1.1 Soil Compaction 18.2.1.1.2 Erosion 18.2.1.1.3 Infiltration and Bulk Density of Soil 18.2.1.1.4 Soil Depth and Plant Rooting 18.2.1.2 Soil Structure 18.2.1.2.1 Aggregation 18.2.1.3 Soil Water 18.2.1.4 Soil Temperature 18.2.2 Chemical Factors 18.2.2.1 Soil pH 18.2.2.1.1 Soil Acidification 18.2.2.1.2 Soil Salinity and Sodicity 18.2.2.2 Nutrients 18.2.2.2.1 Plant Nutrient Depletion 18.3 Biotic Factors 18.3.1 Soil Organic Matter (SOM) 18.3.2 Soil Biota 18.3.2.1 Soil Fauna 18.3.2.1.1 Earthworms 18.3.2.1.2 Formicidae (Ants) 18.3.2.1.3 Termitidae (Termites) 18.3.2.1.4 Nematodes 18.3.2.2 Soil Flora 18.3.2.2.1 Soil Microbes 18.3.2.2.2 Bacteria 18.3.2.2.3 Fungi 18.3.2.2.4 Algae 18.3.3 Plant-Microbe Interactions: Key Player of Agricultural Sustainability 18.4 Recent Trends and Future Perspectives 18.5 Conclusion References 19: Microbial Genes, Enzymes, and Metabolites: To Improve Rhizosphere and Plant Health Management 19.1 Introduction 19.2 Importance of Different Microbial Populations Associated with the Plant 19.3 The Role of Microorganisms in Soil Protection 19.4 The Role of Microorganisms (Biofertilizers) in Sustainable Agriculture 19.5 The Role of Genetic Engineering in the Use of Microbial Genes in Agriculture 19.5.1 The Role of WRKY Gene Family in Bacterial Resistance 19.5.2 The Role of pthA Gene in Developing Resistance to Chancre 19.5.3 The Role of Beta-Lactam Gene in Reducing the Toxicity of Antibiotics 19.5.4 The Role of PR5 Gene Family in Responding to Stressful Situations 19.5.5 Bt gene and Concern Management in Transgenic Crops 19.5.6 The Role of rol Gene Family in Increasing the Sensitivity of Plants to Certain Hormones 19.5.7 PA Gene Expression of Bacillus anthracis in Plants 19.5.8 The Role of Gene Encoding the Enzyme Asr in Production of Glucose Biopolymers 19.5.9 The Role of Food Coloring Phycocyanin 19.5.10 The Role of Alpha-toxin Gene in Creating Immunity Against Gas Gangrene 19.5.11 The Role of BPDO Genes in Reducing Environmental Pollution 19.5.12 The Role of Laccases (Such as CotA) in Environmental Detoxification 19.5.13 The Role of Flavodexin (Fld) Gene in Tolerance to Abiotic Stresses 19.5.14 The Role of Bacterial merA Gene in Environmental Purification 19.5.15 The Role of Chitinase Gene in Production of Biological Fungicides and Insecticides 19.6 The Role of Microorganisms in Dissolving Phosphate 19.6.1 Dissolution of Mineral Phosphate 19.6.1.1 The Most Important Genetic Factors Involved in the Dissolution of Mineral Phosphate 19.6.2 Mineralization of Organic Phosphorus 19.6.2.1 The Most Important Genetic Factors Involved in the Dissolution of Organic Phosphorus 19.6.2.1.1 Phosphatases 19.6.2.1.2 Phytases 19.7 The Role of Different Microbial Genes in the Synthesis of Bioethanol 19.8 Use of Microbial Genes in Plant Genome Editing 19.8.1 Overview of the CRISPR/Cas9 System Mechanism 19.9 Conclusion References 20: Recent Trends in Organic Farming 20.1 Introduction 20.2 Roles of Microorganism as the Potential Rejuvenator of Polluted Soil, Soil Health Promoter, and Plant Growth Stimulator 20.3 Features of Organic Farming 20.4 Benefits of Organic Farming 20.4.1 Environment 20.5 Production Requirements in Organic Farming 20.6 Crop Requirements 20.7 Effects on Soil Quality 20.8 Advantages of Organic Farming 20.8.1 Sustainability 20.8.2 Ecological Services 20.8.3 Biodiversity 20.9 Challenges Faced in Organic Farming 20.10 Role of PGPR as Biotechnological Tool for the Achievement of Sustainable Agriculture and Environment 20.11 Specific Samples of Beneficial Microorganisms that Could Lead to Sustainable Agriculture and the Environment 20.11.1 Rhizobium spp 20.11.2 Azospirillum spp 20.11.3 Bacillus spp 20.11.4 Serratia spp 20.11.5 Pseudomonas spp 20.11.6 Stenotrophomonas spp 20.12 Specific Examples of Beneficial Microorganism Involved in the Maintainaece of Soil Health 20.12.1 Mycorrhizal Associations 20.13 Conclusion and Future Recommendation References 21: Advances in Microbial Applications in Safeguarding of Plant Health: Challenges and Future Perspective 21.1 Introduction 21.2 Diversity of Suitable Microbes for Plants 21.2.1 The Relation Between Plant and Microorganism 21.3 Application of Microbial Signaling in Plant Health 21.4 Microbial Role in Crop Improvement 21.5 Future Perspectives 21.6 Conclusion References 22: Rhizosphere Modelling and Nanotechnology: New Outlooks in Sustainable Agriculture 22.1 Introduction 22.2 Rhizosphere Modelling 22.2.1 Three-dimensional Root System Framework for Studying Nutrient and Water Uptake 22.2.2 Nutrient Uptake and Its Linkage with pH 22.2.3 Water Potential and Uptake Model 22.2.4 Role of Mycorrhizal Fungi on Phosphorous Uptake in Modelling Study 22.2.5 Circadian Rhythm Under Varying Abscisic Acid (ABA) Concentration 22.2.6 Modelling Game Theory 22.2.7 Combining Plant Models 22.2.8 Rhizosphere Study Via Carbon Flow 22.3 Nanotechnology Boosting Sustainable Agricultural Practices 22.3.1 Various Types of Nanoparticles and their Significance in Agriculture Box 22.1 Nano based materials and their rolein agriculture 22.3.2 Nano-fertilizers 22.3.3 Nanopesticides 22.3.4 Nanobiosensors 22.3.5 Nano-bioremediation 22.3.5.1 Nano-Bioremediation of Soil Pollution 22.3.5.2 Nano-Bioremediation of Organic Contaminants 22.3.5.3 Nanomaterial Assisted Remediation of Inorganic Contaminants 22.4 Hurdles to Overcome in Nanotechnology for Its Application in Plant Agriculture 22.4.1 Large-Scale Production 22.4.2 Safety Principles 22.5 Conclusion References 23: New Strategies for Commercialization of Microbial Technologies 23.1 Introduction 23.2 Advancements in Microbial Technologies 23.3 Steps of Commercialization of Microbial Product: Lab to Market 23.4 Current Scenario of Commercialization 23.5 Problems Associated with Commercialization of Microbial Products 23.6 Need of New Strategies 23.7 Future Prospects References 24: Techniques for Improving Microbial Inoculants as a Tool for Sustainable Development 24.1 Introduction 24.2 Techniques for Improving Microbial Inoculant Formulations 24.2.1 Solid Carrier Material as Inoculant Formulation 24.2.2 Liquid Carrier Material as Inoculant Formulation 24.2.3 Application of Cell Immobilization for Bio-inoculant Formation 24.2.3.1 Additives Effect on the Efficacy of Immobilized Inoculants 24.2.3.1.1 Other Additives Besides Starch and Sugars Humic Acid Protein Hydrolysate (PH) Glycerol Silicon 24.2.3.2 Metabolites 24.2.3.3 Bioencapsulation 24.3 Impact of the Gel-Forming Polysaccharides on Plant Health 24.4 Conclusion References 25: Bioinoculants for Agricultural Sustainability 25.1 Introduction 25.2 Problems Faced by the Farmers 25.3 Government Initiatives to Control Losses in the Crop Cultivation 25.4 Impact of Climate Variability on Agriculture 25.5 Biotic Factors and their Effects on Crop Production 25.5.1 Negative Effects 25.5.2 Positive Effects 25.5.2.1 PGPR 25.5.2.1.1 Production of Growth Regulators 25.5.2.1.2 Increased Uptake of Minerals and Soil Fertility 25.5.2.1.3 Induced Systemic Resistance (ISR) 25.5.2.1.4 Siderophore Production 25.5.2.2 Adaptation Strategies 25.6 Microbial Inoculants 25.7 Bioinoculated Crops 25.7.1 Soybean 25.7.2 Maize 25.7.3 Rice 25.7.4 Faba Beans 25.7.5 Vegetables 25.7.6 Legumes 25.8 Bioinoculant Formulations 25.8.1 Cell Immobilization 25.8.2 Encapsulation 25.9 Conclusion References