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