Soil Microbiomes for Sustainable Agriculture: Functional Annotation

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