Rhizosphere Microbes: Biotic Stress Management

Preface
Contents
Editors and Contributors
Chapter 1: Detection and Identification of Soil-Borne Pathogens: Classical to Recent Updates
	1.1 Introduction
	1.2 Classification of Soil-Borne Pathogens
	1.3 Significance of Soil-Borne Diseases
	1.4 Soil-Borne Pathogens Vs. Foliar Pathogens
	1.5 Groups of Soil-Borne Pathogens
	1.6 Detection Methods for Major Soil-Borne Pathogens
	1.7 Detection of Soil-Borne Pathogens
		1.7.1 Traditional Methods
			1.7.1.1 Direct Quantification
			1.7.1.2 Enumeration of Pathogens
				1.7.1.2.1 Enumeration of Bacteria
					Direct or Microscopic Visualization of Bacteria
					Culture or Cultivation-Based Enumeration of Bacteria
					Most Probable Number Technique (MPN)
					Plate Count Technique
				1.7.1.2.2 Enumeration of Fungal Pathogens
			1.7.1.3 Use of Selective Media
			1.7.1.4 Indicator Plants
			1.7.1.5 Baiting or Trapping Techniques
			1.7.1.6 Bioassay Tests
		1.7.2 Biochemical Methods for Bacteria
			1.7.2.1 Basic Biochemical Tests
			1.7.2.2 Biolog
			1.7.2.3 Fatty Acid Methyl Ester (FAME) Analysis
		1.7.3 Bacteriophage Typing
		1.7.4 Immunological Methods
			1.7.4.1 ELISA
			1.7.4.2 Lateral Flow Immunoassays
			1.7.4.3 Immunofluorescence Assay
			1.7.4.4 Western Blot
		1.7.5 Molecular Methods
			1.7.5.1 Fluorescent Microscopy
			1.7.5.2 DNA/RNA Sequencing
			1.7.5.3 DNA Fingerprinting
			1.7.5.4 Polymerase Chain Reaction (PCR)-Based Detection
			1.7.5.5 Isothermal Amplification Techniques
		1.7.6 Recent Techniques
			1.7.6.1 Real-Time PCR
			1.7.6.2 DNA Microarrays (Gene Chip Technology)
			1.7.6.3 Metagenomics
			1.7.6.4 Whole-Genome Sequencing
			1.7.6.5 Electronic Nose System
			1.7.6.6 Loop-Mediated Isothermal Amplification (LAMP)
	1.8 Conclusion
	References
Chapter 2: Microarray-Based Detection and Identification of Bacterial and Viral Plant Pathogens
	2.1 Introduction
	2.2 Influence of Plant Disease on Global Agriculture
	2.3 Plant-Pathogen Interaction and Defense Mechanism
	2.4 Microarray-Based Study of Plant Defense Mechanism
		2.4.1 Principle of Microarray
		2.4.2 Construction of Microarray
		2.4.3 Types of Microarrays
	2.5 Databases and Tools for Studying Plant-Pathogen Interaction
		2.5.1 Bacterial and Viral Pathogen Identification by Bioinformatics Tools
	2.6 Conclusion
	References
Chapter 3: Application of Molecular Ecology Approaches in Sustainable Agriculture for a Better Understanding of Plant-Microbio...
	3.1 Introduction
	3.2 Understanding Molecular Ecology Using Molecular Approaches to Determine the Plant-Microbiome Interactions
		3.2.1 Metagenomics
		3.2.2 Metabolomics
		3.2.3 Transcriptomics
		3.2.4 Proteomics
		3.2.5 CRISPR
	3.3 Application of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era
		3.3.1 Case Studies
	3.4 Composition and Driving Factors of the Plant-Microbiome (PM) Interactions
		3.4.1 Plant-Driven Forces
			3.4.1.1 Plant Species
			3.4.1.2 Plant Age
			3.4.1.3 Plant Health Status
			3.4.1.4 Microbial-Driven Forces
		3.4.2 Soil Effect
		3.4.3 Salicylic Acid (SA)
			3.4.3.1 Phenylalanine Ammonia-Lyase (PAL) Pathway
			3.4.3.2 Isochorismate (IC) Pathway
	3.5 Rhizosphere Engineering
	3.6 Frontiers in Multiomics for Plant Disease Ecology
	3.7 Multiomics in Suppressive Soils for Plant Disease Management
	3.8 Conclusion
	References
Chapter 4: Detection and Diagnosis of Important Soil-Borne Diseases: An Overview
	4.1 Introduction
	4.2 Important Soil-Borne Phytopathogens
	4.3 Detection and Diagnosis
		4.3.1 Identification Through Visual Symptoms
		4.3.2 Identification Through Cultural Characteristics
		4.3.3 Identification Through Microscopic Observations
		4.3.4 Identification Through Serological Reactions
		4.3.5 Identification Through Molecular Methods
		4.3.6 Identification Through Analysis of Edaphic and Plant Factors
		4.3.7 Identification Through Environmental Factors and Prediction Model
	4.4 Future Aspects and Conclusion
	References
Chapter 5: Omics Approaches to Revisit Rhizobacterial Biome
	5.1 Introduction
	5.2 Computational Strategies behind ``Omics´´ Approaches
		5.2.1 Genomics, Proteomics, and Metabolomics
		5.2.2 Metagenomics
			5.2.2.1 Metagenomics Analysis Methods
				5.2.2.1.1 Sequence Similarity-Based Methods
				5.2.2.1.2 Sequence Composition-Based Methods
				5.2.2.1.3 Hybrid Methods
				5.2.2.1.4 Marker-Based Methods
				5.2.2.1.5 Commonly Used Sequence Search Algorithms
			5.2.2.2 Bioinformatics Analysis of Metagenomics Data
			5.2.2.3 Metagenomics Workflow
	5.3 Plant Growth-Promoting Rhizobacteria (PGPR)
	5.4 Pangenome
		5.4.1 Types of Pangenome
		5.4.2 Pangenome Formats
		5.4.3 Levels of Pangenomes
	5.5 RhizoDB (http://xbase.warwick.ac.uk/rhizodb/)
	5.6 Genome-Wide Association Studies (GWAS) for Understanding Plant-Microbe Interactions
	5.7 Conclusion, Future Prospects, and Challenges
	References
Chapter 6: ``The Key Influencers´´ of Rhizosphere Microbial Population Dynamics
	6.1 Introduction
	6.2 Role of Edaphic Factors
	6.3 Effects of Agricultural Management Practices
	6.4 Role of the Host Plant in Rhizosphere Microbial Population Structure Composition and Function
	6.5 Role of Root Exudates
	6.6 Conclusion
	References
Chapter 7: Engineering the Plant Microbiome for Biotic Stress Tolerance: Biotechnological Advances
	7.1 Introduction
	7.2 Rhizosphere Engineering for Stress Management
		7.2.1 Natural Processes
			7.2.1.1 Soil Suppressiveness
				7.2.1.1.1 Allelopathy
				7.2.1.1.2 Niche Competition and Microbiostasis
				7.2.1.1.3 Antibiosis
				7.2.1.1.4 Induced Systemic Resistance
			7.2.1.2 Crop Rotation
		7.2.2 Genetic Modification
			7.2.2.1 Designer Microorganism Approach
				7.2.2.1.1 Designing a Microorganism for Biosynthesis of Desirable Molecules
				7.2.2.1.2 Regulation of Gene Expression
				7.2.2.1.3 Designer Microorganisms: A Success Story
		7.2.3 Designer Plant Approach
		7.2.4 Designer Rhizomicrobiome Approach
			7.2.4.1 Rhizosphere Vis-à-Vis Designer Rhizosphere
		7.2.5 Exogenous Amendments
			7.2.5.1 Beneficial Microorganisms
			7.2.5.2 Chemical Nutrients
			7.2.5.3 Compost
	7.3 Conclusion and Future Prospects
	References
Chapter 8: Potential of Bacterial Endophytes in Biological Control of Soil-Borne Phytopathogens
	8.1 Introduction
	8.2 Isolation and Characterization of Bacterial Endophytes from Different Crops
	8.3 Plant Colonization Ability of Bacterial Endophytes
	8.4 Important Soil-Borne Phytopathogens
		8.4.1 Wilt (Fusarium oxysporum)
		8.4.2 Collar Rot (Sclerotium rolfsii)
		8.4.3 Root Rot (Rhizoctonia solani)
		8.4.4 Stem Rot (Sclerotinia sclerotiorum)
	8.5 Biological Control of Soil-Borne Phytopathogens by Bacterial Endophytes in Different Crops
	8.6 Mechanism of Biological Control of Soil-Borne Phytopathogens by Bacterial Endophytes
		8.6.1 Antimicrobial Metabolites
		8.6.2 Induced Systemic Resistance
		8.6.3 HCN and Siderophore Production
	8.7 Conclusion and Way Forward
	References
Chapter 9: Endophytes: Rendering Systemic Resistance to Plants
	9.1 Introduction
	9.2 Brief Overview of Fungal and Bacterial Endophytes
	9.3 Plant Endophyte Interaction
	9.4 Role of Endophytes in Contributing Systemic Resistance to Plants Diseases and Mode of Action
		9.4.1 Different Modes of Action of Endophytes in Combating Plant Pathogens
			9.4.1.1 Competitive Root Colonization
			9.4.1.2 Hyperparasitism
			9.4.1.3 Competition for Ferric Iron Ions
			9.4.1.4 Competition for Nutrients and Niches (CNN)
			9.4.1.5 Antibiosis and Antibiotics Suppressing Pathogens
			9.4.1.6 Production of Defense-Related Enzymes
			9.4.1.7 Production of Pathogenesis-Related Proteins
			9.4.1.8 Induced Systemic Resistance
	9.5 Applications of Endophytes
		9.5.1 Application of Endophytes in Plant Growth Promotion
		9.5.2 Application of Endophytes in Disease Management
	9.6 Bioformulation of Endophytic Microorganisms
	9.7 Future Prospects
	References
Chapter 10: Arbuscular Mycorrhizal Fungi (AMF) as Potential Biocontrol Agents
	10.1 Introduction
	10.2 History, Classification and Taxonomy
	10.3 Distribution and Ecology
	10.4 Defence Mechanism of AMF
		10.4.1 Enhancement of Nutrient Uptake
		10.4.2 Damage Compensation
		10.4.3 Interaction with Microbial Communities Present in Mycorrhizosphere
		10.4.4 Competition for Colonization
		10.4.5 Physiological and Histological Changes
		10.4.6 Competition for Photosynthates
		10.4.7 Changes in Root Exudates
		10.4.8 Activation of Plant Defence Mechanisms
		10.4.9 Mycorrhizal Networks
		10.4.10 Enhancement in Pollution Tolerance
		10.4.11 Molecular Mechanism of Interaction Between AMF Plant and Pathogen
		10.4.12 Potential Application of AMF as a Biocontrol Agent
			10.4.12.1 Nematode
			10.4.12.2 Fungus
			10.4.12.3 Bacteria
			10.4.12.4 Virus
		10.4.13 Pest Control
	10.5 Future Prospects and Conclusion
	References
Chapter 11: Rhizosphere Microbes and Wheat Health Management
	11.1 Introduction
	11.2 Effects of Organic Manuring on Rhizosphere Microflora
	11.3 Plant Root Exudates and Rhizomicrobiome Interactions
	11.4 Rhizomicrobiome and Wheat Health Dynamics
		11.4.1 Rhizosphere Microflora as Potential Biological Control Agents
		11.4.2 Rhizosphere Microflora Is Used to Dissolve Several Plant Nutrients
		11.4.3 Rhizosphere Microflora as Plant Pathogens
	11.5 Assertive Role of Beneficial Rhizosphere Microflora
	11.6 Conclusion
	References
Chapter 12: Exploring the Potential of Secondary Metabolites from Indigenous Trichoderma spp. for Their Plant Growth Promotion...
	12.1 Introduction
	12.2 Diversity of Different Trichoderma Isolates
	12.3 Metabolites Present in Trichoderma spp. Are Associated with Crop Plants
		12.3.1 Anthraquinones
		12.3.2 Daucanes
		12.3.3 Simple Pyrones
		12.3.4 Koninginins
		12.3.5 Trichodermides
		12.3.6 Viridans
		12.3.7 Viridiofungins
	12.4 Nitrogen Heterocyclic Compounds
		12.4.1 Derivatives of Trichodenones and Cyclopentenone
		12.4.2 Harzialactones and Derivatives
		12.4.3 Trichothecenes
		12.4.4 Isocyano Metabolites
		12.4.5 Setin-like Metabolites
		12.4.6 Bisorbicillinoids
		12.4.7 Diketopiperazines
		12.4.8 Ergosterol Derivatives
		12.4.9 Peptabiols
		12.4.10 Cyclonerodiol Derivatives
		12.4.11 Statins
	12.5 Secondary Metabolites Present in Trichoderma Isolates Associated with Pulse Rhizosphere
		12.5.1 Lytic Enzyme
		12.5.2 Proteases
		12.5.3 B1,3-Glucanases
		12.5.4 Chitinase
	12.6 Future Line of Research
	12.7 Conclusion
	References
Chapter 13: Uncultivable Soil Microbes Contributing to Sustainable Agriculture
	13.1 Introduction
	13.2 Microbes Isolated Through Culture-Dependent Approach
	13.3 Microbes Not Isolated But Identified Through Culture-Independent Approach
	13.4 Microbe Sequence Information Through Culture-Independent Approach
	13.5 Methods to Identify Uncultivable Soil Microbes (Metagenomic Approach)
		13.5.1 Characterization of Soil Bacterial Communities by DGGE and Clone Library Preparation
		13.5.2 Characterization of Soil Fungal Communities by DGGE and Clone Library Preparation
	13.6 Uncultivable Microbes Making Agriculture Sustainable
	13.7 Conclusion
	References
Chapter 14: Rhizosphere Microbiome: Significance in Sustainable Crop Protection
	14.1 Introduction
		14.1.1 Focus on `Microbiome to Medicine´ for Sustainable Crop Protection
		14.1.2 Rhizosphere and Its Relevance in Plant Disease Management (PDM)
	14.2 Rhizosphere Microbiome Composition
		14.2.1 Rice
		14.2.2 Wheat
		14.2.3 Maize
		14.2.4 Pea
		14.2.5 Citrus
		14.2.6 Grape
		14.2.7 Glacier Buttercup
		14.2.8 Others
	14.3 Rhizosphere: The Destination in Search of Beneficial Microbes
		14.3.1 Disease-Suppressive Soils
		14.3.2 Biocontrol Agents (BCAs)
		14.3.3 Plant Growth-Promoting Rhizobacteria (PGPR)
		14.3.4 Mycorrhiza: An Important Member of Rhizosphere
		14.3.5 Host Plant Resistance Modulators
		14.3.6 Source of Antibiotics
	14.4 Strategies of Crop Protection Derived from Rhizosphere Microbiome
		14.4.1 Bio-priming for Stress Resistance
		14.4.2 Biological Control
		14.4.3 Volatile Organic Compounds (VOCs) as Bio-fumigants
		14.4.4 Horizontal Gene Transfer (HGT)
		14.4.5 Transgenics
	References
Chapter 15: Bacterial Inoculants for Control of Fungal Diseases in Solanum lycopersicum L. (Tomatoes): A Comprehensive Overview
	15.1 Introduction
	15.2 Prevalence of Seed-Borne Mycoflora: A Historical Perspective
	15.3 Management of Fungal Diseases in Tomatoes
		15.3.1 Use of Chemical Fungicides (Chemical Method)
		15.3.2 Biological Management
	15.4 Plant Growth-Promoting Rhizobacteria: Tapping for BCA
	15.5 Mechanisms Involved in Disease Suppression (Indirect Mechanisms)
		15.5.1 Production of Antibiotics
		15.5.2 Competition
		15.5.3 Induced Systemic Resistance (ISR)
		15.5.4 Production of Cellulolytic/Cell Wall-Degrading Enzymes
		15.5.5 Production of Hydrogen Cyanide (HCN)
		15.5.6 Production of Siderophore
	15.6 Future Perspective
	15.7 Conclusions
	References
Chapter 16: Prior Weakening as a Tool to Control Soilborne Plant Pathogens and Associated Disease Pressure
	16.1 Introduction
		16.1.1 Management Strategies
		16.1.2 Prior Weakening
	16.2 Direct Field Exposure to Sublethal Heating (SLH)
		16.2.1 M. phaseolina
		16.2.2 Fusarium oxysporum f. sp. cumini
	16.3 Indirect Exposures by Simulation
		16.3.1 Fusarium oxysporum f. sp. niveum
		16.3.2 Fusarium oxysporum f. sp. ciceri
		16.3.3 F. o. f. sp. basilici and Sclerotium rolfsii
		16.3.4 Verticillium dahliae
		16.3.5 Sclerotium rolfsii
		16.3.6 Meloidogyne incognita, S. rolfsii and Pythium ultimum
		16.3.7 Ralstonia solanacearum
		16.3.8 Clostridium perfringens
	16.4 Mechanism Involved
		16.4.1 Direct Heat
		16.4.2 Heat Shock Proteins (HSPs)
		16.4.3 Melanin Synthesis
		16.4.4 Leakage of Organic Substances
		16.4.5 Crack Formation
		16.4.6 Delayed Germination and Mortality
		16.4.7 Nutrient Leakage
		16.4.8 Microbial Antagonism
	16.5 Conclusion and Future Perspective
	References