Current Trends in Microbial Biotechnology for Sustainable Agriculture

Preface
Acknowledgements
Contents
Editors and Contributors
About the Editors
Contributors
1: Soil Microbiomes for Healthy Nutrient Recycling
	1.1	 Introduction
	1.2	 Soil Health and Sustainability
	1.3	 Soil Quality
	1.4	 Soil Quality Indicators
	1.5	 Potential Role of Microbes for Soil Health
		1.5.1	 Soil as a Microbial Habitat
		1.5.2	 Soil Microbes and Agro-Ecosystem Stability
		1.5.3	 Microorganisms and Soil Functions
	1.6	 Role of Microorganisms in Nutrient Cycling
		1.6.1	 Organic Matter Decomposition
		1.6.2	 Carbon Cycling
		1.6.3	 Nitrogen Cycle
		1.6.4	 Siderophores Production
		1.6.5	 Hormones Production
		1.6.6	 Phosphate Solubilization
		1.6.7	 Manganese (Mn) Solubilizers
		1.6.8	 Iron Solubilizers
		1.6.9	 Soil Enzymes
	1.7	 Conclusion and Future Perspectives
	References
2: Soil Microbial Diversity: Calling Citizens for Sustainable Agricultural Development
	2.1	 Introduction
	2.2	 Soil Microbial Diversity
		2.2.1	 The Indian Biodiversity Scenario
	2.3	 Soil Microbial Diversity and Its Impacts on Ecosystem Function
	2.4	 Soil Biodiversity and Its Role in Coping with Stress and Disturbances
		2.4.1	 Abiotic Stress and Disturbance
		2.4.2	 Biotic Stress and Disturbance
	2.5	 Dynamics of Microbial Communities in Metal-Polluted Areas
	2.6	 Bioinformatics in Soil Microbial Research
		2.6.1	 Biodiversity Database
		2.6.2	 Bacteria
		2.6.3	 Fungi
		2.6.4	 Viruses
		2.6.5	 Genetics
		2.6.6	 General All Biota
	2.7	 Some Specific Opportunities
		2.7.1	 Modernizing the Biological Library
		2.7.2	 Digitizing the Biological Legacy
		2.7.3	 Multidimensional Observation and Recording
		2.7.4	 Mobile Computing
	2.8	 Managing the Soil Biodiversity: Priorities
	2.9	 Bioaugmentation Assisted Phytoextraction Mediated Through Microbes
	2.10	 Metal Extraction and Its Mechanism from Soil by Microorganism-Assisted Plant
	2.11	 Significant Metal Accumulation by Plants
		2.11.1	 Bioavailability of Metals
		2.11.2	 Metal Extraction by Plants
	2.12	 Plant-Associated Microbes Improve Heavy Metal Mobilization/Immobilization
	2.13	 Metal Reduction and Oxidation
	2.14	 Biosorption
	2.15	 Conclusion and Prospects
	References
3: Metagenomics in Deciphering Microbial Communities Associated with Medicinal Plants
	3.1	 Introduction
	3.2	 Habitat-Based Diversity of Plants and Associated Microbes
		3.2.1	 Hydrophytes
		3.2.2	 Hygrophytes
		3.2.3	 Halophytes
		3.2.4	 Mesophytes
		3.2.5	 Xerophytes
	3.3	 Microbes Associated with Medicinal Plants
		3.3.1	 Taraxacum
		3.3.2	 Ginkgo Bilboa
		3.3.3	 Curcuma longa
		3.3.4	 Oenothera biennis
		3.3.5	 Linum usitatissimum
		3.3.6	 Melaleuca alternifolia
		3.3.7	 Echinacea
		3.3.8	 Vitis vinifera
		3.3.9	 Lavandula
		3.3.10	 Matricaria chamomilla
	3.4	 Metagenomics
	3.5	 Approaches in Metagenomics
	3.6	 Metagenomics and Diversity of Medicinal Plants
		3.6.1	 Cannabis Microbiome
		3.6.2	 Ocimum sanctum Microbiome
		3.6.3	 Maytenus spp. Microbiome
		3.6.4	 Centella asiatica Microbiome
		3.6.5	 Crocus sativus L (Saffron) Microbiome
		3.6.6	 Ficus deltoidea Microbiome
		3.6.7	 Tinospora crispa Microbiome
		3.6.8	 Anoectochilus roxburghii Microbiome
		3.6.9	 Dendrobium officinale Microbiome
	3.7	 Conclusion
	3.8	 Terminologies
	References
4: Role of Metagenomics in Deciphering the Microbial Communities Associated with Rhizosphere of Economically Important Plants
	4.1	 Introduction
	4.2	 Achievements with Metagenomics in Economic Important Plant and Microbial Interactions
		4.2.1	 Medicinal Plants
		4.2.2	 Plants Producing Cereals
		4.2.3	 Leguminous Plants
		4.2.4	 Essential Oil-Bearing Plants
	4.3	 Insight on Plant Growth-Promoting Rhizobacteria
	4.4	 Biotechnological Impact of Next-Generation Sequencing Technologies
	4.5	 Conclusion and Future Prospects
	References
5: Plant–Microbe Association for Mutual Benefits for Plant Growth and Soil Health
	5.1	 Introduction
	5.2	 Plants–Microbes Association
		5.2.1	 Endophytic Microbiome
			5.2.1.1	 Bacterial Endophytes
			5.2.1.2	 Fungal Endophytes
		5.2.2	 Plant Growth-Promoting Rhizobacteria
		5.2.3	 Breeding Microbe-Optimized Plants
		5.2.4	 Engineering Microbiome, Plant-Optimized Microbiomes
		5.2.5	 Pairing Microbe-Optimized Plant Seed with the Optimal Microbiome
	5.3	 Current Scenario and the Need for Adopting of Biocontrol Agents in India
	5.4	 Plant–Microbe Interactions at the Post-genomic Era
	5.5	 Importance of Microbes in Agriculture Farming
		5.5.1	 The Direct Impact of PGP Microbes on Plant Nutritions
			5.5.1.1	 Nitrogen Fixation
			5.5.1.2	 Phosphorus Solubilization
			5.5.1.3	 Potassium Solubilization
			5.5.1.4	 Siderophores Production
		5.5.2	 The Indirect Impact of PGP Microbes on Plant Nutritions
			5.5.2.1	 Enzymes Production
			5.5.2.2	 Hydrogen Cyanide Production
			5.5.2.3	 Induced System Resistance
			5.5.2.4	 Emerging Biocontrol Strategies
				Implementation of Plant Exudates to Attract Beneficial Biocontrol Microbes
				Use of Substrates to Maintain Beneficial Biocontrol Microbes
				Phyllosphere Biocontrol
				Fungi as Biocontrol Agents
	5.6	 Conclusion and Future Prospects
	References
6: Deciphering and Harnessing Plant Microbiomes: Detangling the Patterns and Process—A Clean, Green Road to Sustainable Agriculture
	6.1	 Introduction
	6.2	 Plant Microbiomes
		6.2.1	 Rhizosphere Microbiome
		6.2.2	 Phyllosphere Microbiomes
			6.2.2.1	 Leaf and Stem Microbiomes
			6.2.2.2	 Floral Microbiomes
				Nectar Microbiome
			6.2.2.3	 Fruit Microbiomes
				Seed Microbiomes
	6.3	 Tools in Microbiome Analysis
	6.4	 Engineering Plant Microbiomes for Eco-Friendly, Sustainable Crop Production
	6.5	 Conclusion and Future Perspective
	References
7: Rhizosphere Biology: A Key to Agricultural Sustainability
	7.1	 Introduction
	7.2	 Plant–Microbe Interaction
	7.3	 Engineering of Rhizosphere
	7.4	 Plant Metabolism Through Rhizosphere Engineering
	7.5	 Genetic Modification of Rhizospheric Microbes
	7.6	 Molecular Mechanisms in the Rhizosphere
	7.7	 Role of Rhizospheric Microbes for Agricultural Sustainability
		7.7.1	 Mutual Plant–Microbe Interactions
		7.7.2	 Mitigation of Drought Stress
		7.7.3	 Mitigation of Salinity Stress
		7.7.4	 Mitigation of Heavy Metals Stress
		7.7.5	 Mitigation of Heat Stress
		7.7.6	 Combating Elevation CO2 Levels
	7.8	 Conclusion and Future Prospects
	References
8: Rhizosphere Microbiomes and Their Potential Role in Increasing Soil Fertility and Crop Productivity
	8.1	 Introduction
	8.2	 The Plant Microbiomes
	8.3	 The Rhizosphere of Plant Microbiomes
	8.4	 Plant Growth Promoting and Rhizospheric Microbiomes
		8.4.1	 Improving Soil Fertility
		8.4.2	 Phytohormones Producing Microbes
		8.4.3	 Abiotic Stress Resistance Microbes
		8.4.4	 Plant Pathogen Resistance
	8.5	 Conclusion
	References
9: Plant Growth-Promoting Rhizobacteria (PGPR): Current and Future Prospects for Crop Improvement
	9.1	 Introduction
	9.2	 Applications of PGPR in Agriculture
	9.3	 Mechanisms of Plant Growth Promotion by PGPR
		9.3.1	 Biofertilization
			9.3.1.1	 Nitrogen Fixation
			9.3.1.2	 Phosphate Solubilization
			9.3.1.3	 Potassium Solubilization
			9.3.1.4	 Exopolysaccharide Production
		9.3.2	 Stress Management
			9.3.2.1	 Abiotic Stress
			9.3.2.2	 Biotic Stress
			9.3.2.3	 Rhizoremediation
		9.3.3	 Biocontrol
			9.3.3.1	 Siderophores Production
			9.3.3.2	 Disease Resistance by Antibiotics
			9.3.3.3	 Induced Systemic Resistance
			9.3.3.4	 Protective Enzymes
		9.3.4	 PGPR as Plant Growth Regulators
	9.4	 Future Prospects and Perspective
	9.5	 Conclusion
	References
10: Beneficial Microbiomes for Sustainable Agriculture: An Ecofriendly Approach
	10.1	 Introduction
	10.2	 National Scenario
	10.3	 Common Nitrogen Fixers
		10.3.1	 Azotobacter
		10.3.2	 Rhizobium
		10.3.3	 Azolla
	10.4	 Need of Biofertilizers for Sustainable Management of Agroecosystem
	10.5	 Applications of the Biofertilizers
	10.6	 Potential Traits of Some Biofertilizers
		10.6.1	 Azospirillum
		10.6.2	 Azotobacter
		10.6.3	 Azolla and Blue Green Algae (Cyanobacteria)
		10.6.4	 Phosphate-Solubilizing Bacteria
		10.6.5	 Mycorrhiza
		10.6.6	 Zinc Solubilizers
	10.7	 Safeguards to Use Biofertilizers
	10.8	 Certain Problems Using Biofertilizers
	10.9	 Conclusion and Future Prospects
	References
11: Endophytic Microbiomes and Their Plant Growth-Promoting Attributes for Plant Health
	11.1	 Introduction
	11.2	 Endophytes
	11.3	 Ubiquity of Endophytes
	11.4	 Role of Endophytes in Plant Growth Promotion
	11.5	 Mechanisms of Plant Growth Promotion
		11.5.1	 Direct Mechanisms
			11.5.1.1	 Phytohormone Production
			11.5.1.2	 Nutrient Acquisition
				Nitrogen
				Phosphorous
				Iron
		11.5.2	 Indirect Mechanisms of Plant Growth Promotion
			11.5.2.1	 Competition for Colonization Sites
			11.5.2.2	 Volatile Organic Compounds and Antagonizing Agents
			11.5.2.3	 Quorum Quenching
			11.5.2.4	 Siderophores Production
			11.5.2.5	 Lytic Enzyme Production
			11.5.2.6	 Induced Systemic Resistance
				Detoxification and Degradation of Virulence Factors
				Insect and Pest Tolerance
				Cold and Drought Stress Tolerance
				Metal Stress Tolerance
	11.6	 Bioactive Compounds from Endophytes
	11.7	 Conclusions and Future Perspectives
	References
12: Mycorrhiza: A Sustainable Option for Better Crop Production
	12.1	 Introduction
	12.2	 Role and Limitations of Inorganic Chemicals in Environmental Sustainability
	12.3	 Types and Functions of AM Fungal Biodiversity in Rhizospheric Soil
	12.4	 Types of Mycorrhiza and its Role in Functional Diversity
		12.4.1	 Endomycorrhizas
		12.4.2	 Arbuscular Mycorrhizal Fungi
		12.4.3	 Ectomycorrhiza
		12.4.4	 Ericoid Mycorrhiza
	12.5	 Effect of Organic and Inorganic Fertilizer and its Role in AM Diversity
	12.6	 AMF in Sustainable Crop Production
	12.7	 Diversity of AMF for Sustainable Agriculture: Methods and Constrain
	12.8	 Methods of Isolation and Propagation of Mycorrhizal Species
	12.9	 Monosporal Culture of AMF: Source of Pure Mycorrhizal Species
	12.10	 Root Organ Culture of AMF: Benefit in Biofertilizers Production
	12.11	 Mass Propagation of Mycorrhizal Spores: Application as Biofertilizers
		12.11.1 Substrate-Based Production System
		12.11.2 Substrate-Free Production System
		12.11.3 In Vitro Production System
	12.12	 Quality Production of AMF Fungi: Limitation and Prospects
	12.13	 Growth and Propagation of Arbuscular Mycorrhizal Fungi
		12.13.1 Trap Culture
	12.14	 Conclusion and Future Prospects
	References
13: Phyllospheric Microbes: Diversity, Functions, Interaction, and Applications in Agriculture
	13.1	 Introduction
	13.2	 Phyllospheric Subdivision and Dominant Microbes
	13.3	 Diversity of Phyllospheric Microbiome
	13.4	 Structure and Function of Phyllosphere-Associated Microbiome
		13.4.1	 Structure of Phyllospheric Microbes
		13.4.2	 Functions of Phyllospheric Microbes
			13.4.2.1	 Recycling
			13.4.2.2	 Biocontrol Agents
			13.4.2.3	 Growth Promoters
			13.4.2.4	 Stress Tolerance
			13.4.2.5	 Pathogenic Phyllospheric Microbes
	13.5	 Factors Effecting Structure and Function of Phytomicrobiome
	13.6	 Phyllospheric Interaction and Ecosystem Dynamic
		13.6.1	 Microbes Interaction
		13.6.2	 Chemical Exchange
		13.6.3	 Climate Interaction
		13.6.4	 Environment Interaction
	13.7	 Phyllospheric Microbes and Food Safety
	13.8	 Applications of Phyllospheric Microbiota in Agriculture
	13.9	 Future Prospective
	References
14: Mitigation Strategies for Abiotic Stress Tolerance in Plants Through Stress-Tolerant Plant Growth-Promoting Microbes
	14.1	 Introduction
	14.2	 Microbial Diversity of Microbes of Plants Growing Under Extreme Environments
		14.2.1	 Saline Environments
		14.2.2	 Arid and Semi-Arid Environments
		14.2.3	 Acidic Environments
		14.2.4	 Alkaline Environments
		14.2.5	 Hot Environments
		14.2.6	 Cold Environments
	14.3	 Mitigation Strategies for Abiotic Stress Tolerance in Plants
		14.3.1	 Phytohormones Production
		14.3.2	 Nitrogen Fixation
			14.3.2.1	 Mineral Solubilization
			14.3.2.2	 ACC Deaminase Production
			14.3.2.3	 Exopolysaccharides Matrix
			14.3.2.4	 Siderophores Production and Biocontrol
	14.4	 Conclusion and Future Prospects
	References
15: Plant- and Microbes-Mediated Secondary Metabolites: Remunerative Venture for Discovery and Development
	15.1	 Introduction
	15.2	 Medicinal or Therapeutic Plants
		15.2.1	 The Other Sources of Medicinal Natural Substances
		15.2.2	 Plants Metabolites
	15.3	 Natural Substances
		15.3.1	 Natural Substances from Fungi
		15.3.2	 Plants as Ordinary Substances
		15.3.3	 Marine Environment and Products
		15.3.4	 Algae and its Products
		15.3.5	 Porifera and Products Derived
		15.3.6	 Marine Sources of Natural Substances
	15.4	 Drug Innovation: Natural Substance
		15.4.1	 Dereplication
			15.4.1.1	 Methods of Dereplication
		15.4.2	 Searching of Database
	15.5	 Hyphenated Instrumentation “Classical Versus Hyphenated (on-line) Approaches”
	15.6	 Conclusion and Prospects
	References
16: Potential Strategies for Control of Agricultural Occupational Health Hazards
	16.1	 Introduction
	16.2	 Chemical Hazards of Toxic Compounds
		16.2.1	 Persistent Organic Pollutants (POPs)
	16.3	 Chemical Hazards Due to Pesticides Usage
	16.4	 Use of Xenoestrogens in Day-to-Day Life and Health Hazards
	16.5	 Protection from Pesticides
	16.6	 Communication of Risks and Potential Hazards
	16.7	 Respiratory Hazards and Protection
	16.8	 Skin Disorders and Infections
	16.9	 Musculoskeletal Injuries
	16.10	 Ergonomic Protections
	16.11	 Heat-Related Stress and Prevention
	16.12	 Conclusion
	References
17: Insecticides Derived from Natural Products: Diversity and Potential Applications
	17.1	 Introduction
	17.2	 Botanicals for Pest Management
	17.3	 Phytochemicals with Insecticidal Properties
	17.4	 Plant Proteins with Anti-Nutritional Effects on Insects
	17.5	 Microbial Insecticides
		17.5.1	 Entomopathogenic Bacteria
		17.5.2	 Entomopathogenic Actinomycetes
		17.5.3	 Entomopathogenic Fungi
		17.5.4	 Entomopathogenic Virus
		17.5.5	 Entomopathogenic Protozoa
		17.5.6	 Entomopathogenic Nematode
	17.6	 Semiochemicals
	17.7	 Attract and Reward Strategy
	17.8	 Push–Pull Strategy
	17.9	 Miscellaneous Compounds of Natural Origin
	17.10	 Conclusion and Future Perspective
	References
18: Bacillus thuringiensis as Potential Biocontrol Agent for Sustainable Agriculture
	18.1	 Introduction
	18.2	 Background
	18.3	 Developments of Bt Research
	18.4	 Prevalence and Genetic Diversity of Bt
		18.4.1	 The Bt Genome
			18.4.1.1	 The cry Genes
			18.4.1.2	 Genetic Diversity in Bt
		18.4.2	 Insecticidal Proteins of Bt
			18.4.2.1	 Classification of Bt Insecticidal Crystal Proteins
			18.4.2.2	 Crystal Morphology and Solubility
			18.4.2.3	 Structural Features of Crystal Proteins
			18.4.2.4	 Mode of Action (MOA)
		18.4.3	 Other Insecticidal Constituents of Bt
	18.5	 Bt as a Biocontrol Agent
		18.5.1	 Bt Formulations
		18.5.2	 Expression of cry Genes in Other Microorganisms
		18.5.3	 Expression of cry Genes from Bt in Plants through a Transgenic Approach
	18.6	 Development of Insect Resistance to Bt
		18.6.1	 Mechanism of Insect Resistance to Bt
		18.6.2	 Strategies for Management of Bt-Resistant Insect
		18.6.3	 Enhancing Toxicity of Cry Proteins
			18.6.3.1	 Potentiation of Cry Toxin Activity by Additional Proteins
			18.6.3.2	 Modifications in the Cry Toxin Gene
	18.7	 Conclusion and Future Prospectus
	References
19: Entomopathogenic Microbes for Sustainable Crop Protection: Future Perspectives
	19.1	 Introduction
	19.2	 Entomopathogenic Bacteria
		19.2.1	 Classification of Entomopathogenic Bacteria
			19.2.1.1	 Spore-Forming Bacteria
			19.2.1.2	 Non-spore-Forming Entomopathogenic Bacteria
		19.2.2	 Mode of Action of Entomopathogenic Bacteria
			19.2.2.1	 Crystal Proteins or Cry Toxins
			19.2.2.2	 Cytotoxic Proteins or Cyt Toxins
			19.2.2.3	 Vegetative Insecticidal Protein or Vip Proteins
			19.2.2.4	 Binary Toxins or Bin Toxins
	19.3	 Entomopathogenic Fungi
		19.3.1	 Mode of Action of Entomopathogenic Fungi
	19.4	 Entomopathogenic Nematodes
		19.4.1	 Mode of Action of Entomopathogenic Nematodes
	19.5	 Entomopathogenic Viruses
		19.5.1	 Classification of Entomopathogenic Viruses
			19.5.1.1	 Baculovirus (Nucleopolyhedrovirus [NPV]/Granulovirus [GV])
			19.5.1.2	 Entomopoxvirus
			19.5.1.3	 Cypovirus (Cytoplasmic Polyhedrosis Virus)
			19.5.1.4	 Polydnavirus
			19.5.1.5	 Ascovirus
	19.6	 Safety and Ecotoxicology
	19.7	 Future Prospects
	References
20: Soil Microbes as Biopesticides: Agricultural Applications and Future Prospects
	20.1	 Introduction
	20.2	 Need of Biopesticides
	20.3	 Biopesticides
		20.3.1	 Microbial Pesticides
			20.3.1.1	 Bacteria
			20.3.1.2	 Fungi
			20.3.1.3	 Nematodes
			20.3.1.4	 Viruses
			20.3.1.5	 Protozoa
	20.4	 Potential Applications of Soil Microbes as Biopesticides
		20.4.1	 Bacteria as Biopesticides
		20.4.2	 Fungi as Biopesticide
		20.4.3	 Nematodes as Biopesticide
		20.4.4	 Virus as Biopesticide
		20.4.5	 Protozoa as Biopesticides
	20.5	 Conclusion and Future Prospects
	References
21: Biofertilizers for Agricultural Sustainability: Current Status and Future Challenges
	21.1	 Introduction
	21.2	 Biofertilizers and its Types
		21.2.1	 Bacterial Biofertilizers
			21.2.1.1	 Nitrogen-Fixing Bacteria
				Rhizobium
				Azospirillum
				Azotobacter
			21.2.1.2	 Phosphorus-Solubilizing Microbes
			21.2.1.3	 Phytohormones-Producing Microbes
			21.2.1.4	 Mineral-Solubilizing Microbes
		21.2.2	 Fungal Biofertilizers
			21.2.2.1	 Arbuscular Mycorrhizal Fungi
			21.2.2.2	 Other Fungi
		21.2.3	 Algal Biofertilizers
			21.2.3.1	 Blue-Green Algae
			21.2.3.2	 Cyanobacteria
	21.3	 Production of Biofertilizers
	21.4	 Methods Used for the Application of Biofertilizers
	21.5	 Precautions for Biofertilizers Applications
	21.6	 Advantages of Biofertilizers
	21.7	 Commercial Production and Release of Biofertilizers
	21.8	 Biotechnological Role of Biofertilizers
	21.9	 Challenges of Biofertilizers
	21.10	 Conclusion and Future Prospects
	References
22: Current Trends in Microbial Biotechnology for Agricultural Sustainability: Conclusion and Future Challenges
	References