Plant, Soil and Microbes in Tropical Ecosystems

Foreword
Preface
Contents
About the Editors
Chapter 1: Plant-Rhizobacteria Interactions to Induce Biotic and Abiotic Stress Tolerance in Plants
	1.1 Introduction
	1.2 Rhizobacteria as Beneficial Agents
	1.3 Plant-Rhizobacteria Interactions and Abiotic Stress Tolerance
	1.4 Plant-Rhizobacteria Interaction and Biotic Stress Tolerance
		1.4.1 Mechanisms of Rhizobacteria-Mediated Phytopathogen Tolerance in Plants
	1.5 Conclusion
	References
Chapter 2: Rhizospheric and Endophytic Microorganisms and Their Role in Alleviation of Salinity Stress in Plants
	2.1 Rhizosphere as a Site of Plant-Microbial Interaction
	2.2 Endophytes in Plant-Microbe Interaction
		2.2.1 Fungal Endophytes
		2.2.2 Bacterial Endophytes
	2.3 Salinity Stress in Plants
	2.4 Mechanisms of Rhizospheric and Endophytic Bacteria for Salinity Stress Alleviation
		2.4.1 ACC Deaminase Production
		2.4.2 Maintaining Ion Homeostasis and Detoxification
		2.4.3 Detoxification of Reactive Oxygen Species (ROS)
		2.4.4 Improvement in Nutrient Acquisition
		2.4.5 Maintaining Osmotic Balance
	2.5 Approaches for Stress Mitigation Using Rhizospheric and Endophytic Bacteria
	2.6 Conclusion and Future Prospects
	References
Chapter 3: Rhizospheric Diversity of Cyanobacteria and Their Significance in Tropical Ecosystem
	3.1 Introduction
	3.2 Rhizospheric Diversity of Cyanobacteria in Tropical Ecosystem
	3.3 Significance of Cyanobacteria in Tropical Ecosystem
		3.3.1 Phytohormone Production
		3.3.2 Cyanobacteria as a Biofertilizer
		3.3.3 Advantages of BGA Biofertilizers
	3.4 Plant Protection Against Diseases and Pest
	References
Chapter 4: Cyanobacteria in Rhizosphere: Dynamics, Diversity, and Symbiosis
	4.1 Introduction
	4.2 Rhizospheric Diversity of Cyanobacteria
	4.3 Biofertilizer
		4.3.1 Free-Living Cyanobacteria
		4.3.2 Symbiotic System: Cyanobacteria-Azolla
	4.4 Cyanobacterium Role in Bioremediation
		4.4.1 Reclamation of Usar Land
		4.4.2 Cyanobacterial Bioremediation
	4.5 The Role of Cyanobacteria as Plant Growth Promoter
	4.6 Plant Growth Promotion Through Direct Transfer of Fixed Carbon
	4.7 Cyanobacterium Role as Biocontrol Agent
	4.8 Cyanobacterium Role in Reduction of Methane Gas
	4.9 Conclusion
	References
Chapter 5: Effects of Herbicides on Soil Enzymes and Their Regulatory Factors in Agroecosystem: A Review
	5.1 Introduction
	5.2 Overall Production and Consumption of Herbicides
	5.3 Classification of Herbicides
		5.3.1 Based on Mode of Application
		5.3.2 Based on Formulation
		5.3.3 Based on Translocation
		5.3.4 Based on Application Time
		5.3.5 Based on Mode of Action
	5.4 Fate of Herbicides After Application in the Soil
	5.5 Soil Enzymes
		5.5.1 An Indicator of Soil Health
		5.5.2 Sources and Status of Enzymes in the Soil
		5.5.3 Indispensable Soil Enzymes
			5.5.3.1 Oxidoreductase
			5.5.3.2 Hydrolases
	5.6 Soil Enzyme and Herbicide Interaction
		5.6.1 Dehydrogenase
		5.6.2 Urease
		5.6.3 Phosphatase
		5.6.4 β-glucosidase
		5.6.5 Catalase
		5.6.6 Arylsulfatase
	5.7 Factors Affecting Soil Enzyme-Herbicide Interactions
		5.7.1 Temperature
		5.7.2 Soil Moisture
		5.7.3 Soil Organic Matter
		5.7.4 Soil pH
		5.7.5 Soil Texture, Type, and Depth Profile
		5.7.6 Heavy Metal Amendment
		5.7.7 Cultivation System
		5.7.8 Fertilizer and Pesticide Treatment
	5.8 Conclusions
	References
Chapter 6: Diversity of Pathogenic Fungi in Agricultural Crops
	6.1 Introduction
	6.2 Concepts of Plant Disease
	6.3 Diversity Based on Lifestyle
		6.3.1 Biotrophs
		6.3.2 Necrotrophs
		6.3.3 Hemibiotrophs
	6.4 Historically Known Major Fungal Diseases
		6.4.1 Phytophthora Infestans
		6.4.2 Hemileia vastatrix
		6.4.3 Helminthosporium oryzae
	6.5 Global Perspectives of Major Fungal Diseases
		6.5.1 Diversity of Fungal Diseases of Rice
		6.5.2 Diversity of Fungal Diseases of Maize
		6.5.3 Diversity of Fungal Diseases of Vegetables
	6.6 Top Ten Fungal Diseases
	6.7 Diversity of Major Disease-Causing Fungal Genera
		6.7.1 Colletotrichum
		6.7.2 Diaporthe
		6.7.3 Sclerotium rolfsii
	6.8 Diversity of Emerging Fungal Pathogens in Agro-Ecosystem
	6.9 Perspectives and Future Outlook
	References
Chapter 7: Application of Soil Microorganisms for Agricultural and Environmental Sustainability: A Review
	7.1 Introduction
	7.2 Microbial Functions in the Soil
	7.3 Applications of Soil Microbes
		7.3.1 Application of Soil Microbes in Agriculture
			7.3.1.1 Soil Microbes as Biofertilizers
			7.3.1.2 Soil Microbes as Biocontrol Agents
			7.3.1.3 Soil Microbes in Saline Agricultural Soils
		7.3.2 Applications of Microbes in Industries
			7.3.2.1 Enzyme Production
			7.3.2.2 Triacylglycerol Production
			7.3.2.3 Biosurfactants
			7.3.2.4 Food Industry
		7.3.3 Pharmaceutical Applications
		7.3.4 Environmental Applications
			7.3.4.1 Bioremediation
			7.3.4.2 Phytoremediation
		7.3.5 Applications of Soil Microbes as Genetically Modified Microorganisms
	7.4 Advances in Soil Microbial Ecology
		7.4.1 DNA Extraction, PCR, Cloning, and Sequencing Techniques
		7.4.2 Fungal PCR Primers
		7.4.3 Metagenomics, Metaproteomics, and Metatranscriptomics
		7.4.4 Community Profiling Techniques
			7.4.4.1 DGGE and TGGE
			7.4.4.2 T-RFLP Analysis of 16SrDNA for Characterization of Microbial Communities
			7.4.4.3 SSCP Analysis for Microbial Characterization
			7.4.4.4 ARDRA and ARISA
		7.4.5 Microarray Technology
	7.5 Future Prospects of Soil Microbial Ecology
	7.6 Conclusion
	References
Chapter 8: Biotic Constraints to Wheat Production in Tropics: Microbial Control Strategies and Mechanism
	8.1 Introduction
	8.2 Wheat Production: Acreage and Yield
		8.2.1 Global Scenario
		8.2.2 Indian Scenario
	8.3 Biotic Constraints for Wheat Production
		8.3.1 Fungal Diseases
			8.3.1.1 Wheat Rust
			8.3.1.2 Powdery Mildew
			8.3.1.3 Karnal Bunt
			8.3.1.4 Fusarium Head Blight
			8.3.1.5 Blotch
			8.3.1.6 Leaf Blight
			8.3.1.7 Wheat Blast
		8.3.2 Bacterial Diseases
	8.4 Biological Control
		8.4.1 Type of Interactions Contributing to Biological Control
			8.4.1.1 Cell Wall-Degrading Enzymes (CWDEs) and Parasitism
			8.4.1.2 Antibiosis
			8.4.1.3 Competition for Nutrients and Space
			8.4.1.4 Induced Resistance in the Host Plants
	8.5 BCAs: Methods of Delivery
	8.6 Commercial BCAs for Wheat Diseases
	8.7 Biological Control Research in India: Past to Present
		8.7.1 Commonwealth Institute of Biological Control (CIBC)
		8.7.2 All India Coordinated Research Project on Biological Control of Crop Pests and Weeds (AICRP-BCandW)
		8.7.3 The Society for Biocontrol Advancement (SBA)
		8.7.4 Project Directorate of Biological Control (PDBC)
	8.8 Future Outlook
	References
Chapter 9: Phytohormones as Fundamental Regulators of Plant-Microbe Associations Under Stress Conditions
	9.1 Introduction
	9.2 Roles of Various Phytohormones in Plant Tolerance of Stresses
		9.2.1 Cytokinins
		9.2.2 Auxins
		9.2.3 Abscisic Acid
		9.2.4 Gibberellic Acid
	9.3 Plant-Associated Microbes
		9.3.1 Plant Growth-Promoting Bacteria
			9.3.1.1 Phytohormones Produced by Plant Growth-Promoting Rhizobacteria
			9.3.1.2 Enhancement of Plant Development by Plant Growth-Promoting Rhizobacteria Under Stress Conditions
		9.3.2 Arbuscular Mycorrhizal Fungi Associated with Plants
			9.3.2.1 Phytohormones Produced by Arbuscular Mycorrhizal Fungi
			9.3.2.2 Enhancement of Plant Development by Arbuscular Mycorrhizal Fungi Under Stress Conditions
		9.3.3 Ectomycorrhizal Fungi Associated with Plants
			9.3.3.1 Phytohormones Produced by Ectomycorrhizal Fungi
			9.3.3.2 Enhancement of Plant Development by Ectomycorrhizal Fungi Under Stress Conditions
	9.4 Conclusion
	References
Chapter 10: Use of PGPR to Optimize Soil and Crop Productivity Under Abiotic Stress
	10.1 Introduction
	10.2 PGPR Mechanisms in Relation to Crop Productivity Under Abiotic Stresses
		10.2.1 PGPRs Under Drought Stress
		10.2.2 PGPRs Under Salinity Stress
		10.2.3 PGPRs Under Thermic Stress
	10.3 PGPRs in Soil Productivity Under Abiotic Stresses
	10.4 PGPRs as a Remedial Agent Against Abiotic Stresses
	10.5 Conclusion and Future Implication
	References
Chapter 11: Framework for Studying Rhizospheric Microflora Under the Effect of Improved Crop Variety
	11.1 Introduction
	11.2 Formulation of Hypothesis
	11.3 Source of Stress to Rhizosphere Soil Microflora
	11.4 Experimental Design
	11.5 Evaluation of Result
	11.6 Conclusion
	References
Chapter 12: Role of Rhizospheric Bacteria in Disease Suppression During Seedling Formation in Millet
	12.1 Introduction
	12.2 Millets Crop
	12.3 Millets Seedling Disease
	12.4 Role of Rhizospheric Bacteria in Disease Suppression
	12.5 Mechanism of Disease Suppression
	12.6 Lytic Enzymes
	12.7 Antibiotics
	12.8 Volatile Organic Compounds (VOCs)
	12.9 Siderophore
	12.10 Lipopeptides
	12.11 Induced Systemic Resistance
	12.12 Conclusion
	References
Chapter 13: Metagenomics of Plant Rhizosphere and Endophytic Association: Concepts and Applications
	13.1 Introduction
	13.2 Study of Microbial Community in Plant Rhizosphere and Endophytic Association
		13.2.1 Sampling, DNA Extraction, and Sequencing
		13.2.2 Methods of Metagenomics Analysis
			13.2.2.1 Amplicon-Based Metagenomics (16S/18S/ITS)
			13.2.2.2 Shotgun Metagenomics
			13.2.2.3 Metatranscriptomics and Metaproteomics
	13.3 Future Perspective and Applications
	References
Chapter 14: Methods of Assessments of Microbial Diversity and Their Functional Role in Soil Fertility and Crop Productivity
	14.1 Introduction
	14.2 Approaches for Soil Microbial Community Assessment
		14.2.1 Overview of Microbial Diversity Methods
		14.2.2 Quantitative Real-Time PCR
		14.2.3 Isolation, Library Preparation, and Sequencing
		14.2.4 Brief Summary of Sequencing by Reversible Termination
		14.2.5 Third-Generation Sequencing Technology
	14.3 NGS Reads Processing
		14.3.1 Generated Read Quality Filtration
		14.3.2 De Novo Assembly of Sequenced Reads Microbial Communities
		14.3.3 Analysis of Microbial Diversity
		14.3.4 Classification of Microbial Diversity with Bioinformatic Tools
			14.3.4.1 MG-RAST
			14.3.4.2 MEGAN
			14.3.4.3 QIIME
			14.3.4.4 MGnify
		14.3.5 Analysis of Microbial Community Metabolic Potential
	14.4 Application of NGS Technology to Assess Microbial Diversity with Soil Fertility
		14.4.1 Microbial Community Diversity and Composition
		14.4.2 Application of High-Throughput Sequencing on Soil Fertility
		14.4.3 Role of High-Throughput Sequencing on Microbial Diversity and Crop Productivity
	14.5 Conclusion
	References
Chapter 15: Development of Biofertilizers and Microbial Consortium an Approach to Sustainable Agriculture Practices
	15.1 Introduction
	15.2 Biofertilizers
		15.2.1 Role of Biofertilizers in Agriculture
		15.2.2 Types of Microbial Fertilizers
			15.2.2.1 Nitrogen Biofertilizers
				Symbiotic Nitrogen Fixer
				Free-Living Non-photosynthetic Nitrogen Fixer
				Free-Living Photosynthetic Nitrogen Fixer
				Associative Nitrogen Fixer
			15.2.2.2 Phosphorus Biofertilizers
			15.2.2.3 Plant Growth-Promoting Biofertilizers (PGPB)
			15.2.2.4 Potassium Biofertilizers
		15.2.3 Biofertilizer Production
		15.2.4 Quality of Biofertilizer
		15.2.5 Application of Biofertilizers
	15.3 Introduction of Microbial Consortia
		15.3.1 Microbial Consortium as Biofertilizers
		15.3.2 Interaction Between Microbes and Plants
		15.3.3 Interaction Among the Bacterial Groups
		15.3.4 Interaction Between Bacteria and Fungi
		15.3.5 Merits and Demerits of Microbial Consortium
			15.3.5.1 Merits
			15.3.5.2 Demerits
		15.3.6 Construction of Artificial Microbial Consortium at Industrial Level and Their Interaction
		15.3.7 Microbial Consortium in Stress Environment
	15.4 Impact on Soil Microorganism
	15.5 Regulatory Issues of Biofertilizers
	15.6 Regulatory Issues of Microbial Consortium
	15.7 Global Biofertilizer Market
	15.8 Global Efforts on Sustainable Agropractices
	15.9 Prospects and Challenges of Biofertilizer Application
	15.10 Conclusions
	References
Chapter 16: Biofertilizers as Microbial Consortium for Sustainability in Agriculture
	16.1 Introduction
	16.2 Development of Multifunctional MC
	16.3 Impact of MC as Biofertilizer in Different Environmental Conditions
	16.4 Microbiome Engineering of Biofertilizers
	16.5 The Standard Norms for Biofertilizers Based on MC
	16.6 Ordinance and Commercialization of MC as Biofertilizer
	16.7 Conclusion and Future Prospects
	References
Chapter 17: Biofertilizers and Biopesticides: A Whole New Dimension for Ameliorating Soil Fertility and Organic Agriculture Pr...
	17.1 Introduction
	17.2 Need of Bio-Based Fertilizer and Pesticides
	17.3 Biofertilizer: A Boon for Sustainable Agriculture Practice
	17.4 Types of Biofertilizers
		17.4.1 Nitrogen-Fixing Biofertilizers
		17.4.2 Phosphate Solubilizing Biofertilizers
		17.4.3 Potassium-Solubilizing Biofertilizers
		17.4.4 Zinc-Solubilizing Biofertilizers
		17.4.5 Mycorrhiza Biofertilizers
	17.5 Biopesticides
	17.6 Categories of Biopesticides
		17.6.1 Microbial Pesticides
		17.6.2 Plant-Incorporated Protectants (PIPs)
		17.6.3 Biochemical Pesticides
	17.7 Conclusion
	References
Index