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