Sustainable Agriculture Reviews 60: Microbial Processes in Agriculture

Preface
Brief Synopsis of the Book
Contents
About the Editors
Contributors
Chapter 1: The Perpetual Battle of Bacteria and Phages
1.1 Introduction
1.2 Bacterial Anti-phage Strategies
1.2.1 Blocking of Adsorption
1.2.2 Blocking of Phage DNA Injection
1.2.3 Phase Variations of Bacteria
1.3 Restriction-Modification System
1.4 Abortive Infection
1.4.1 Abi System in L. lactis
1.4.2 Abi System in E. coli
1.5 The Clustered Regularly Interspaced Short Palindromic Repeats System
1.6 Bacteriophage Exclusion
1.7 Conclusion
References
Chapter 2: Orchestration of the Plant Microbiome for Enhanced Agriculture
2.1 Introduction
2.2 Plant-Associated Microbiome
2.3 Utilization of the Soil Microbiome by Proper Management Techniques
2.4 Bacterial Mechanisms of Plant Growth Promotion
2.5 Rhizosphere Contribution to Crop Yields
2.5.1 Exopolysaccharides to Promote Soil Aggregation
2.5.2 Improving Soil Microbes for Stress Alleviation in Crops
2.5.3 Enhancing Nutrient Uptake by Plant Using the Microbiome
2.5.4 Microbiome for Efficient Nitrogen Fixation
2.6 Plant–Microbiome Interactions to Improve Phytoremediation
2.7 Disease-Induced Assemblage of Plant-Beneficial Bacterial Consortia
2.8 Microbes to Enhance Root Growth
2.9 Metabolic Potential of Endophytic Bacteria
2.10 Conclusion
References
Chapter 3: Plant Growth Promoting Rhizobacteria to Mitigate Biotic and Abiotic Stress in Plants
3.1 Introduction
3.2 Major Abiotic Stresses Limiting Agricultural Production
3.2.1 Drought
3.2.2 Salinity
3.2.3 Flooding
3.2.4 Metal Contaminants
3.2.5 Extreme Temperatures
3.3 Biotic Stress
3.4 Plant Growth Promoting Rhizobacteria
3.5 Stress Tolerance Mechanisms of Plant Growth Promoting Rhizobacteria
3.5.1 Production of Phytohormones
3.5.2 Production of Volatile Compounds
3.5.3 Production of Osmolytes
3.5.4 Production of Exopolysaccharides
3.5.5 Antioxidant Defence
3.5.6 Production of 1-Aminocyclopropane-1-Carboxylate Deaminase
3.5.7 Phytoremediation and Tolerance to Metal Toxicity
3.5.8 Production of Antibiotics
3.5.9 Production of Antifungal Metabolites Such as Hydrolytic Enzymes
3.5.10 Enhancement of Plant Defensive Response by Induced Systemic Resistance
3.5.11 Siderophore Production for Acquisition of Iron
3.6 Conclusion
References
Chapter 4: Ecology and Mechanisms of Plant Growth Promoting Rhizobacteria
4.1 Introduction
4.2 Applications and Mechanisms
4.2.1 Direct Mechanisms
4.2.1.1 Facilitating Resource Acquisition
4.2.1.2 Modulating Phytohormone Levels
4.2.2 Indirect Mechanisms
4.2.2.1 Antibiotics and Lytic Enzymes
4.2.2.2 Siderophores
4.2.2.3 Competition
4.2.2.4 Ethylene
4.2.2.5 Induced Systemic Resistance
4.3 Ecology of Interactions of Plant Growth-Promoting Rhizobacteria
4.3.1 Symbiotic Organisms
4.3.2 Other Microorganisms
4.3.3 Soil Fauna
4.3.4 Host Rhizospheric and Endophytic Relationships
4.4 Improving Rhizobacterial Potential by Genetic Modification
4.5 Commercialization of Plant Growth Promoting Rhizobacteria
4.6 Perspective
4.7 Conclusion
References
Chapter 5: Diversity and Evolution of Nitrogen Fixing Bacteria
5.1 Introduction
5.2 Diversity of Nitrogen-Fixing Bacteria
5.2.1 Diversity of Free-Living Nitrogen-Fixing Bacteria
5.2.2 Diversity of Symbiotic Nitrogen-Fixing Bacteria
5.2.3 Diversity of Associative Nitrogen Fixing Bacteria
5.3 Importance of Nitrogen Fixing Microbes
5.3.1 Maintenance of Soil Health
5.3.2 Environmental Sustainability
5.3.3 Economic Importance
5.4 Evolution of Nitrogen-Fixing Bacteria
5.5 Evolution of Nitrogen-Fixing Endosymbiosis
5.6 Conclusion
References
Chapter 6: Encapsulation of Biofertilizers, Biopesticides and Biocontrol Agents
6.1 Introduction
6.2 Encapsulation
6.2.1 Advantages of Encapsulation
6.2.2 Microcapsule Structure
6.2.2.1 Coating Material
6.2.2.2 Common Natural and Synthetic Polymers
6.3 Techniques for Formulation of Microbial Inoculants
6.3.1 Microencapsulation Phase
6.3.1.1 Extrusion Method or Droplet Method
6.3.1.2 Emulsion Technique
6.3.2 Drying of Encapsulated Cultures
6.3.2.1 Spray Drying
6.3.2.2 Spray Chilling
6.3.2.3 Coacervation
6.3.2.4 Freeze Drying
6.3.2.5 Vacuum Drying
6.3.2.6 Fluid-Bed Agglomeration and Coating or Fluidized Bed Drying
6.3.2.7 Co-crystallization
6.4 Encapsulation of Plant Growth Promoting Microorganisms
6.5 Conclusion
References
Chapter 7: Induced Systematic Resistance and Plant Immunity
7.1 History of Resistance
7.2 Plant Systemic Immunity
7.3 Systemic Acquired Resistance Versus Local Acquired Resistance
7.4 Induced Systemic Resistance
7.5 Molecular Mechanism of Induced Systemic Resistance
7.5.1 Induction
7.5.2 Priming of Infected Plants
7.5.3 Signalling in Beneficial Microbe-Induced Systemic Resistance
7.5.4 Expression of Induced Systemic Resistance
7.6 Is Salicylic Acid Necessary for Induced Systemic Resistance?
7.7 Role of Hormones in the Signaling of Induced Systemic Resistance
7.8 Genes Involved in the Induced Systemic Resistance Mechanism
7.9 Controlling Crop Diseases Using Induced Resistance
7.10 Conclusion
References
Chapter 8: Microbial Elicitors for Priming Plant Defense Mechanisms
8.1 Introduction
8.2 Plant Immunity Against Harmful Microbes
8.3 Beneficial Microbes and Their Metabolites
8.3.1 Antibiotics
8.3.2 Siderophores
8.3.3 Microbial Volatile Organic Compounds
8.4 Conclusion
References
Chapter 9: Microbial Mitigation of Abiotic Stress in Crops
9.1 Introduction
9.2 Impact of Abiotic Stresses on Plant Metabolism and Growth
9.3 Role of Microorganisms in Abiotic Stress Alleviation
9.4 Mechanisms of Abiotic Stress Alleviation by Microorganisms
9.4.1 Production and Regulation of Phytohormones
9.4.2 Aminocyclopropane-Carboxylic Acid Deaminase Activity
9.4.3 Osmolyte Compounds in Stress Alleviation
9.4.4 Induction of Antioxidative Enzymes and Improved Antioxidant Status
9.4.5 Ion Homeostasis
9.4.6 Volatile Compounds
9.4.7 Production of Exopolysaccharides
9.4.8 Improving Plants Physiological Properties
9.4.8.1 Relative Water Content
9.4.8.2 Membrane Permeability and Lipid Peroxidation
9.4.8.3 Photosynthetic Activity
9.4.9 Improving Root Sytem Architecture
9.4.10 Nutrient Uptake
9.4.11 Induction of Stress-Related Genes Expression
9.5 Conclusion
References
Chapter 10: Microbial Alleviation of Abiotic and Biotic Stresses in Rice
10.1 Introduction
10.2 Plant Stress
10.3 Plant Growth-Promoting Microorganisms
10.4 Role of Microbes in Alleviating Abiotic Stresses in Rice
10.4.1 Drought Stress
10.4.2 Cold Stress
10.4.3 Heat Stress
10.4.4 Salinity Stress
10.4.5 Heavy Metal Stress
10.5 Biotic Stresses in Rice
10.5.1 Antibiotic-Mediated Suppression
10.5.2 Siderophore-Mediated Suppression
10.5.3 Enzymes and Phytohormones-Mediated Suppression
10.6 Conclusion
References
Chapter 11: Nutritional Biofortification of Crops by Microbes
11.1 Introduction
11.2 Biofortification of Crops with Micronutrients
11.2.1 Iron
11.2.2 Selenium
11.2.3 Zinc
11.2.4 Vitamins
11.2.5 Amino Acids
11.2.6 Fatty Acids
11.3 Arbuscular Mycorrhiza
11.4 Conclusion
References
Chapter 12: Microbial Rejuvenation of Soils for Sustainable Agriculture
12.1 Introduction
12.2 Constituents of Healthy Soils
12.3 Importance of Soil Health
12.4 Indicators of Soil Health
12.4.1 Essential Characteristics of Soil Health Indicators
12.4.2 Soil Health Parameters
12.4.2.1 Physical Parameters
12.4.2.2 Chemical Parameters
12.4.2.3 Biological Parameters
12.5 Factors Affecting Soil Properties
12.6 Soil Biology
12.7 Microbes for Improvement of Soil Health
12.8 Practices for Improving Soil Biology
12.9 Relation Between Soil Health, Microbes, and Sustainable Agriculture
12.9.1 Carbon Sequestration
12.9.2 Nutrient Cycling
12.9.3 Degradation of Xenobiotic Substances
12.9.4 Soil Suppressiveness
12.10 Conclusion
References
Chapter 13: Microbial Remediation of Agricultural Residues
13.1 Introduction
13.2 Residue Potential in India
13.3 Current Management Practices
13.3.1 Bedding and Feed for Animals
13.3.2 No-Tillage and Recycling of Crop Residues
13.3.3 Biochar Production
13.4 Microbes for Residue Management
13.5 Residue Management by Compost Preparation
13.6 Transforming Residues into Biofuel
13.6.1 Bioethanol Production
13.6.2 Biobutanol Production
13.6.3 Biohydrogen Production
13.6.4 Biogas Production
13.7 Residues for Feed and Food Production
13.7.1 Feed Production
13.7.2 Food Production
13.8 Conclusion
References
Chapter 14: The Biotechnological Story of Microbial Genes from Soil to Transgenic Plants
14.1 Introduction
14.2 Enhanced Abiotic Stress Tolerance
14.3 Enhanced Resistance Against Biotic Factors
14.4 Nutrient Availability
14.4.1 Nitrogen
14.4.2 Phosphorous
14.5 Conclusion
References
Chapter 15: Microbial Biosurfactants for Green Agricultural Technology
15.1 Introduction
15.2 Biosurfactants
15.3 Biosurfactants and Critical Micelle Concentration
15.4 Classification of Biosurfactants
15.5 Economics of Biosurfactants Production
15.6 Biosurfactants Favouring Bioremediation of Xenobiotic Compounds
15.6.1 Hydrocarbon Remediation
15.6.2 Heavy Metal Remediation
15.6.3 Pesticide Remediation
15.7 Biosurfactants as Virulence Factor Against Plant Pathogens
15.8 Plant Growth Promoting Activity of Biosurfactants
15.9 Biosurfactant with Multiple Characteristics
15.10 Future Challenges
15.11 Conclusion
References
Chapter 16: Role of Microbes in the Synthesis of Industrial Products from Lignocellulosic Materials
16.1 Introduction
16.2 Types and Composition of Lignocellulosic Biomass
16.3 Pretreatment and Hydrolysis of Lignocellulosic Biomass
16.3.1 Methods of Pretreatment
16.3.2 Factors Affecting the Pretreatment
16.3.3 Methods for the Hydrolysis of Pretreated Feedstock
16.4 Production of Industrial Products from Lignocellulosic Biomass
16.4.1 Production of Industrial Enzymes
16.4.2 Production of Bioethanol
16.4.3 Production of Xylitol
16.4.4 Production of Vinegar
16.4.5 Other Products
16.5 Improved Strategies for the Production of Industrial Products
16.5.1 Development of Genetically-Modified Strains
16.5.2 Immobilization Strategies
16.5.3 Computational Strategies
16.6 Current Status of the Green Technology
16.7 Conclusion
References