Soil Microbiomes for Sustainable Agriculture: Functional Annotation

Description

This book encompasses current knowledge of soil microbiomes and their potential biotechnological application for plant growth, crop yield, and soil health under the natural as well as harsh environmental conditions for sustainable agriculture. The microbes are ubiquitous in nature. The soil is a natural hotspot of the soil microbiome. The soil microbiome plays a critical role in the maintenance of global nutrient balance and ecosystem functioning. The soil microbiomes are associated with plant ecosystems through the intense network of plant–microbe interactions. The microbes present in bulk soil move toward the rhizospheric region due to the release of different nutrients by plant systems. The rhizospheric microbes may survive or proliferate in rhizospheric zone depending on the extent of influences of the chemicals secreted into the soil by roots. The root exudates contain the principal nutrients factors (amino acids, glucose, fructose, and sucrose). The microbes present in rhizospheric region have capabilities to fix atmospheric nitrogen, produce different phytohormones, and solubilize phosphorus, potassium, and zinc. The plant systems take these nutrients for their growth and developments. These soil and plant associated microbes also play an important role in protection of plants from different plant pathogenic organisms by producing different secondary metabolites such as ammonia, hydrogen cyanide, siderophores, and hydrolytic enzymes. The soil microbiomes with plant growth-promoting (PGP) attributes have emerged as an important and promising tool for sustainable agriculture. The soil microbiomes promote the plant growth and enhance the crop yield and soil fertility via directly or indirectly different plant growth-promoting mechanism. The soil microbes help the plant for adaptation in extreme habitats by mitigating the abiotic stress of high/low temperatures, hypersalinity, drought, and acidic/alkaline soil. These PGP microbes are used as biofertilizers/bioinoculants to replace the harmful chemical fertilizers for sustainable agriculture and environments. The aim of the book “Soil Microbiomes for Sustainable Agriculture” is to provide the recent advances in mechanisms of plant growth promotion and applications of soil microbiomes for mitigation of different abiotic stresses in plants. The book is useful to scientists, researchers, and students related to microbiology, biotechnology, agriculture, molecular biology, environmental biology, and related subjects. Foreword by Davinder Singh Foreword by Amrik Singh Ahluwalia Preface Contents Editor and Contributors 1 Plant Growth-Promoting Soil Microbiomes: Beneficial Attributes and Potential Applications 1.1 Introduction 1.2 Plant and Soil Microbiomes 1.2.1 Diversity and Composition 1.2.2 Factors Affecting the Soil Microbiomes 1.3 Scientific Techniques for Plant–Soil Microbiome Profiling 1.4 Beneficial Attributes of Soil Microbiomes 1.5 Biotechnological Applications in Agriculture 1.6 Presence of Soil Microbiomes and Management Practices 1.7 Towards Synthetic Symbiosis: Bioengineering Plant–Soil Microbiomes 1.8 Perspectives in Sustainable Agriculture and Food Security 1.9 Recent Trends and Outcome in Plant–Soil Microbiome Research 1.10 Conclusion and Future Prospects References 2 Microbes Associated with Crops: Functional Attributes for Crop Productivity 2.1 Introduction 2.2 Microbes Linked with Crops 2.2.1 Rhizospheric Microbiomes 2.2.2 Epiphytic Microbiomes 2.2.3 Endophytic Microbiomes 2.3 Mechanisms of Increasing Crop Productivity and Yield 2.3.1 Phosphate Solubilization 2.3.2 Siderophores 2.3.3 Phytohormones 2.3.4 N2 Fixation 2.3.5 ISR and ASR 2.3.6 ACC Deaminase 2.3.7 Lytic Enzymes 2.3.8 Nanoparticles 2.3.9 Biofilms 2.3.10 Antibiotics 2.4 Beneficial Effects on Crop Production and Yield 2.4.1 Seed Germination Enhancement 2.4.2 Stimulation of Plant Growth 2.5 Resistance to Abiotic Stress 2.5.1 Bioremediation 2.5.2 Plant Disease and Pest Control 2.6 Factors Affecting Crop Productivity and Yield 2.7 Conclusion and Future Prospects References 3 Soil Microbes with Multifarious Plant Growth Promoting Attributes for Enhanced Production of Food Crops 3.1 Introduction 3.2 Soil 3.2.1 Actinomycetes 3.2.2 Fungi 3.2.3 Algae 3.2.4 Protozoa 3.2.5 Viruses 3.2.6 Nematodes 3.2.7 Bacteria 3.3 Bacteria that Stimulate the Growth of Plants 3.3.1 The Mechanism of Action of Growth-Stimulating Bacteria 3.3.2 The Influence of PGPR Bacteria on System Architecture and Root Structure 3.4 The Most Important Plant Growth-Promoting Bacteria 3.4.1 Azospirillum 3.4.2 Azotobacter 3.4.3 Phosphobacter 3.4.4 Bacillus 3.4.5 Pseudomonas in Biological Control 3.5 Conclusion References 4 Phosphorus Solubilization: Mechanisms, Recent Advancement and Future Challenge 4.1 Introduction 4.2 Importance of Phosphorus for Agriculture 4.3 Phosphate Resources and Reserves 4.4 Soil Phosphorus Cycle 4.5 Different Strategies to Increase Soil Soluble Phosphate Requirement 4.6 Environmental Problems of Chemical Fertilizers 4.7 Phosphate-Solubilizing Microorganisms 4.7.1 Phosphate-Solubilizing Fungi 4.7.2 Phosphate-Solubilizing Bacteria (PSB) 4.7.3 Phosphate-Solubilizing Actinobacteria 4.8 Mechanism of P-Solubilization 4.8.1 Inorganic P-Solubilization 4.9 Organic P-Solubilization 4.10 Plant Growth Promotion by P-Solubilizing Microorganisms 4.11 Genetic Manipulation of PSMs 4.12 Industrial Production of PSMs as Biofertilizers and Their Application 4.12.1 Isolation of PSMs 4.12.2 Scaling up of PSMs 4.12.3 Methods of Microbial Biofertilizers Application 4.13 Future Challenges in PSMs Application 4.14 Conclusion References 5 Potassium Solubilization: Mechanism and Functional Impact on Plant Growth 5.1 Introduction 5.2 Potassium in Soil 5.3 Potassium Requirement for Plant Growth: Function and Deficiency 5.4 Potassium Solubilizing Microbes 5.5 PGPR for Sustainable Agriculture 5.6 Mechanism of Potassium Solubilization by Microorganisms 5.7 Conclusions and Future Perspectives References 6 Fe Chelation and Zinc Solubilization: A Promising Approach for Cereals Biofortification 6.1 Introduction 6.2 Key Problems Associated with Micronutrient Malnutrition 6.3 Iron Uptake 6.4 Molecular Components Involved in the Uptake of Micronutrients in Cereals 6.5 Zinc Solubilization 6.6 Mechanism of Zinc Solubilization by PGPR 6.7 Biofortification 6.7.1 Agronomic Biofortification 6.7.2 Breeding Approach Toward Biofortification 6.7.3 Biofortification Through Genetic Engineering 6.7.4 Molecular Breeding Techniques for Biofortification 6.8 Biofortification of Wheat for Fe and Zn 6.8.1 Utilization of ph1b Mutant 6.8.2 Utilization of Mono 5B Line 6.8.3 Radiation-Induced Gene Transfer 6.9 Conclusion References 7 Soil Microbes in Plant Growth Promotion and for Mitigation of Abiotic Stress of Drought 7.1 Introduction 7.2 Drought Stress and Plant Performance 7.3 Microbes-Mediated Drought Tolerance in Plants 7.4 Mechanism of Drought Tolerance by Soil Microbiome 7.4.1 Alteration of Phytohormones Production in Plants 7.4.2 Functions of Volatile Compound 7.4.3 Modification in Root Morphology 7.4.4 AMF-Mediated Drought Tolerance 7.4.5 By Altering Root Morphology 7.4.6 AMF-Mediated Water and Nutrient Uptake 7.4.7 Challenges to Use Microbial Bio-inoculants 7.5 Conclusion and Future Prospects References 8 Thermotolerant Soil Microbes and Their Role in Mitigation of Heat Stress in Plants 8.1 Introduction 8.2 Plant Responses to Heat Stress 8.2.1 Heat Stress on Plant Physiology 8.3 Heat Stress Impacts on Crops 8.3.1 Cereals 8.3.2 Pulses 8.3.3 Oilseeds 8.3.4 Cotton 8.3.5 Sugarcane 8.3.6 Vegetables 8.4 Thermotolerant Soil Microbes 8.5 Role of Thermotolerant Soil Microbes in the Mitigation of Heat Stress 8.5.1 Heat Stress in Plants and the Thermotolerant Microbiome 8.5.2 Heat Shock Proteins and Heat Shock Transcription Factors Mediated Heat Tolerance 8.5.3 Plant Growth Regulator Mediated Heat Tolerance 8.5.4 Microbial Mediation of ROS 8.5.5 EPS or Biofilm-Based Defense 8.5.6 Protective Molecules Moderation 8.5.7 Nutrient and Water Uptake 8.6 Use of Thermotolerant Soil Microbes for Agricultural Sustainability 8.7 Conclusion References 9 Microbiomes of Hypersaline Soils and Their Role in Mitigation of Salt Stress 9.1 Introduction 9.2 Adaptations to High Salinity by Halophytes 9.3 Hypersaline Soil Microbiome 9.4 Role of Hypersaline Soil and Halophyte Microbiomes in Salinity Tolerance 9.4.1 Phytohormones Production 9.4.2 Mineral Solubilization 9.4.3 Biological Nitrogen Fixation 9.4.4 ACC Deaminase Production 9.4.5 Siderophores and Hydrogen Cyanide Production 9.4.6 Exopolysaccharides Matrix 9.4.7 Halocins 9.4.8 Polyamines and Volatile Organic Compounds 9.5 Conclusion and Future Prospects References 10 Psychrotrophic Soil Microbes and Their Role in Alleviation of Cold Stress in Plants 10.1 Introduction 10.2 Isolation and Inoculation of Psychrotrophic Bacteria in Maize 10.3 Effect of Cold Stress on Physiological Response of Plants 10.3.1 Effect of Psychrotrophic Bacteria Nutrient Availability for Plant in Maize Under Cold Stress 10.3.2 Effect of Psychrotrophic Bacteria on Photosynthetic Parameters in Maize Under Cold Stress 10.3.3 Effect of Psychrotrophic Bacteria on Membrane Permeability–Electrolyte Leakage and Malondialdehyde Content 10.3.4 Effect of Psychrotrophic Bacteria on Phytohormones Modulation Under Cold Stress 10.3.5 Effect of Psychrotrophic Bacteria on Osmotic Stress Management of Plants Under Cold Stress 10.3.6 Effect of Psychrotrophic Bacteria on ROS Scavenging Activity in Plants Under Cold Stress 10.4 Conclusion References 11 Strategies for Abiotic Stress Management in Plants Through Soil Rhizobacteria  11.1 Introduction 11.2 Abiotic Stresses in the Plants 11.3 Mitigation of Abiotic Stresses 11.4 Salinity, Alkali Stress, and Acidic Stress 11.5 Drought Stress 11.6 Cold Stress 11.6.1 Mechanisms of Bacterial Cold Adaptations 11.6.2 Membrane Adaptation in Psychrophiles 11.6.3 Transcription and RNA Degradation/stabilization Under Cold Stress 11.6.4 Translational Regulations Under Cold Stress 11.6.5 Protein Adaptation to the Cold 11.7 Heavy Metal Stress 11.8 Omics Strategies 11.9 Genomics and Metagenomics 11.10 Transcriptomics 11.11 Proteomics 11.12 Metabolomics 11.13 Phenomics 11.14 Conclusion References 12 The Omics Strategies for Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants 12.1 Introduction 12.2 Abiotic Stress Response in Plants 12.2.1 Salinity Stress 12.2.2 Drought Stress 12.2.3 Submergence and Flood Stress 12.2.4 Heat Stress 12.2.5 Low Temperature Stress 12.2.6 High Light Stress 12.2.7 Soil Acidity Stress 12.2.8 Heavy Metal Stress 12.3 Physiological and Molecular Response of Plants Against Stress 12.4 Role of Microbiomes in Plant Defense and the Immune System Against Stress 12.5 Omics Approaches for Mitigation of Abiotic Stress 12.5.1 Genomics 12.5.2 Metagenomics 12.5.3 Transgenomics 12.5.4 Proteomics 12.5.5 Metabolomics 12.5.6 Transcriptomics 12.5.7 Lipidomics 12.5.8 Micromics 12.6 Conclusion References 13 Plant Probiotics: Technical Challenges and Emerging Solutions for Enhancing Food Crops 13.1 Introduction 13.2 Overview of Plant Probiotics 13.2.1 Origin of Plant Probiotics 13.2.2 Classification of Plant Probiotics 13.3 Mechanism of Action of Plant Probiotics 13.3.1 Direct Mechanism of Action 13.3.2 Indirect Mechanism 13.4 Plant Probiotics and Plant Nutrient Content 13.5 Plant Growth Promoting Probiotics and Omics Technologies 13.6 Perspectives and Challenges of PGPB Applications 13.6.1 The Global PGPB Market 13.6.2 Challenges with Commercial Application of PGPB Products 13.6.3 Challenges in Product Registration 13.6.4 Antibiotic Resistance of PGPB 13.7 Conclusion and Future Prospects References 14 Biofertilizers: Microbes for Agricultural Productivity 14.1 Introduction 14.2 Fertilizers as Plant Growth Boosters 14.2.1 Chemical Fertilizers 14.2.2 Organic Fertilizers 14.2.3 Biofertilizers 14.3 Making Nutrient Available for Plants 14.3.1 Fixation of Nitrogen 14.3.2 Phosphate Solubilizing Activity 14.3.3 Potassium Solubilizing Activity 14.3.4 Zinc Solubilization 14.3.5 Iron Sequestration 14.3.6 Production of Volatile Organic Compounds 14.3.7 Production of Hydrolytic Enzymes 14.3.8 Production of Hormones 14.4 Environmental Stress Relief 14.5 Factors Influencing the Efficiency of Biofertilizers 14.5.1 Effect of the Plants on the Efficacy of Biofertilizers 14.5.2 Effect of Soil Conditions on the Efficacy of Biofertilizers 14.5.3 Effect of Interaction of Soil Microorganisms with Autochthonous on the Efficacy of Biofertilizers 14.5.4 Effect of Farmers’ Practices on the Efficacy of Biofertilizers 14.5.5 Other Factors Affecting the Efficacy of Biofertilizers 14.6 Production Process 14.7 Fermentation Process 14.8 Biofertilizer Formulation 14.8.1 Peat Formulations 14.8.2 Liquid Formulations 14.8.3 Granule Formulations 14.8.4 Freeze-Dry Formulations 14.8.5 Cell Immobilization Formulations 14.9 Advances in Formulation 14.10 Packaging and Quality Control 14.11 Conclusion and Future Prospects References 15 Biopesticides: Microbes for Agricultural Sustainability 15.1 Introduction 15.2 Classification of Biopesticides 15.2.1 Microbial Pesticides 15.2.2 Biochemical Biopesticides 15.2.3 Botanical Biopesticides 15.3 Improvement of Biocontrol Agents 15.4 Safety, Detectability and Fate in the Applied Ecosystem 15.5 Commercialization of Microorganisms as Biocontrol Agents 15.6 Conclusion and Future Prospects References 16 Mycorrhiza: Plant Growth-Promoting and Biocontrol Agent Ability Under the Abiotic Stress Conditions 16.1 Introduction 16.2 Evolutionary History: Fossil Evidence 16.3 Fungal Symbionts 16.4 Mycorrhiza 16.5 Virtual Soil Diorama 16.6 Abiotic Stresses 16.7 Mycorrhizal Fungi as Biocontrol Agent 16.8 Plant Growth-Promoting Mycorrhiza Impact on Plant’s Health 16.9 Characteristics of Arbuscular Mycorrhizal Symbiosis 16.10 Mycorrhiza Cope with Abiotic Stresses 16.11 Arbuscular Mycorrhiza as Biocontrol Agent 16.12 Mycorrhizae-Mediated Biocontrol Mechanisms 16.12.1 High Nutrient Uptake 16.12.2 Competition for Nutrients and Space 16.12.3 Phytoalexins and Phytoanticipins 16.12.4 Hydrolases, Antibiosis, and Antioxidant Enzymes 16.13 Conclusion 16.13.1 Prospective Research References 17 Entomopathogenic Soil Microbes for Sustainable Crop Protection 17.1 Introduction 17.2 Background of Entomopathogenic Microbes 17.3 Entomopathogenic Microbes 17.3.1 Entomopathogenic Bacteria 17.3.2 Entomopathogenic Fungi 17.3.3 Entomopathogenic Viruses 17.3.4 Entomopathogenic Nematodes 17.3.5 Entomopathogenic Protozoan 17.4 Entomopathogenic Microbes and Their Modes of Action 17.5 Mass Production of Entomopathogenic Microbes 17.5.1 Mass Production of Bacteria 17.5.2 Mass Production of Fungi 17.5.3 Mass Production of Nematodes 17.6 Genetic Improvement in Entomopathogenic Microorganisms 17.6.1 Protoplast Fusion 17.6.2 Electroporation 17.6.3 Biolistic Transformation 17.6.4 Vector-Mediated Transformation 17.7 Effect of Entomopathogens in Combination with Other Microorganisms 17.8 Role in Sustainable Crop Protection 17.9 Limitations, Challenges and Opportunity 17.9.1 Limitation 17.9.2 Challenges 17.9.3 Opportunity 17.10 Conclusion and Future Prospects References 18 Global Scenario of Soil Microbiome Research: Current Trends and Future Prospects 18.1 Introduction 18.2 Soil Microbiome Research in the “Omics” Era 18.3 Different Sequencing Technologies in Soil Microbiome Research 18.3.1 “Gene-centric” Versus “Genome-centric” Metagenomics 18.3.2 Functional Potential of Soil Microbiomes to Environmental Changes/Disturbances 18.4 Limitations of Soil Metagenomics/Metatranscriptomics 18.5 Future Prospects in Soil Microbiome Research 18.5.1 Biodiversity and Biogeography 18.5.2 Sustainable Soil-Ecosystem Management 18.5.3 Rhizosphere Microbiome—Plant Health 18.5.4 Climate Change and Soil Microbiomes References 19 Functional Annotation and Biotechnological Applications of Soil Microbiomes: Current Research and Future Challenges 19.1 Introduction 19.2 Role of Soil Microbiomes in the Natural Ecosystem 19.3 Functional Annotation of Soil Microbiomes 19.3.1 Nutrients Acquisition 19.3.2 Release of Plant Growth Regulators 19.3.3 Amelioration of Biotic Stresses 19.3.4 Amelioration of Abiotic Stresses 19.3.5 Remediation of Environmental Pollutions 19.4 Biotechnological Application of Soil Microbiomes 19.4.1 Agriculture Applications 19.4.2 Environment 19.5 Conclusion and Future Propects  References