دانلود کتاب Rhizosphere Microbes: Biotic Stress Management

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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