Detection, Diagnosis and Management of Soil-borne Phytopathogens

Preface
Contents
Editors and Contributors
1: Soil-Borne Viruses: Outlook on Community and Recent Advances in Detection
1.1 Introduction
1.2 Transmission of Soil-Borne Viruses (SBVs)
1.2.1 Chytrid Fungi
1.2.1.1 Mechanism of Transmission.
1.2.2 Plasmodiophorids
1.2.2.1 Life Cycle
1.2.2.2 Plasmodiophorid-Vectored Viruses
1.3 Nematodes
1.3.1 Transmission of Viruses by Nematodes
1.3.1.1 Trichodorid-Transmitted Viruses
1.3.1.2 Longidorid-Transmitted Viruses
1.4 Detection of Soil-Borne Viruses (SBVs)
1.5 Management of SBVs
1.6 Conclusion
References
2: An In Silico Outlook for the Detection and Surveillance of Evolving and Persistent Plant Pathogens
2.1 Introduction
2.2 Agrigenomics
2.2.1 Polymerase Chain Reaction (PCR)
2.2.2 Next-Generation Sequencing-Based Methods
2.2.3 Second-Generation Technologies
2.2.4 Third-Generation Sequencing
2.3 Applications of Nanopore Sequencing for Plant Pathogen Detection
2.4 DNA Microarray for Detection of Plant Viruses
2.4.1 Methods for Detecting Plant Viruses
2.4.1.1 Array Fabrication on Solid Supports
2.4.1.2 Capture Probes
2.4.1.3 Array Spotting
2.4.1.4 Capture Probe Design
2.4.1.5 Target Preparation
2.4.1.6 Signal Amplification
2.4.1.7 Hybridization, Washing, and Scanning of Arrays
2.4.2 Novel Formats and Nonplanar Arrays
2.5 Precision Metabolism for Plant Pathogens
2.6 Artificial Intelligence-Based Methods for Plant Disease Detection
2.6.1 Supervised Learning
2.6.2 Unsupervised Learning
2.6.3 Semi-Supervised Learning
2.6.4 Reinforcement Learning
2.7 Conclusion
References
3: Emergent Tools and Techniques in Diagnosis of Soil-Borne Phytopathogens
3.1 Introduction
3.2 Advanced Techniques for Diagnosis of Soil-Borne Phytopathogens
3.2.1 Nucleic Acid-Based Diagnostic Techniques
3.2.1.1 Multiplex PCR
3.2.1.2 Real-Time PCR
3.2.1.3 Magnetic Capture Hybridization PCR
3.2.1.4 End-Point PCR
3.2.1.5 Nested PCR
3.2.1.6 BIO-PCR
3.3 DNA/RNA Probe-Based Assays-In Situ Hybridization
3.3.1 Fluorescent In Situ Hybridization
3.4 Next-Generation Sequencing
3.5 DNA Fingerprinting
3.5.1 PCR-Restriction Fragment Length Polymorphism (RFLP)
3.5.2 Random Amplified Polymorphic DNA (RAPD)
3.5.3 Amplified Fragment Length Polymorphism (AFLP)
3.5.4 Simple Sequence Repeats (SSR)
3.6 Protein-Based Approach
3.6.1 Elisa
3.6.2 Lateral Flow Devices
3.7 Multi-omics Approaches for Plant Disease Diagnosis
3.7.1 Genomic Approaches
3.7.2 Transcriptomics Approaches
3.7.3 Proteomic Approaches
3.7.4 Metabolomic Approaches
3.7.5 Metallomic Approaches
3.7.6 Databases and Software Tools for Multi-omics Study
3.8 Conclusion
3.9 Future Prospective
References
4: Diagnosis and Detection of Soil-Borne Fungal Phytopathogens in Major Crops
4.1 Introduction
4.2 Soil-Borne Plant Pathogens Produce a Variety of Symptoms
4.2.1 Rotten Roots
4.2.2 Rhizoctonia Root Rot Disease
4.2.3 Stem, Collar, and Head Rots
4.2.4 Wilts
4.2.5 Blights on Seedlings and Damping-Off Diseases
4.2.6 Pythium Damping-Off Disease
4.2.7 Damping-Off Phytophthora
4.2.8 Major Soil-Borne Disease Caused by Fungal Pathogens
4.3 Detection Methods of Soil-Borne Plant Pathogenic Fungal Species
4.3.1 Traditional Methods
4.3.2 Recent Detection Techniques for Soil-Borne Fungal Phytopathogens
4.3.2.1 PCR-Based Approaches
Conventional PCR
Real-Time PCR
End-Point PCR
Nested PCR
Multiplex PCR
4.3.2.2 Isothermal Amplification-Based Methods
Recombinase Polymerase Amplification (RPA)
Loop-Mediated Isothermal Amplification (LAMP)
Rolling Circle Amplification (RCA)
Nucleic Acid Sequence-Based Amplification (NASBA)
Helicase-Dependent Amplification (HDA)
4.3.2.3 Post Amplification Techniques
DNA Microarray
DNA Macroarray
4.3.2.4 DNA or RNA Probe-Based Assays
In Situ Hybridisation (ISH)
Fluorescence In Situ Hybridisation (FISH)
4.4 Use of Next-Generation Sequencing (NGS) in Plant Pathogen Detection
4.5 Conclusion and Future Challenges
References
5: Detection and Diagnosis of Important Soil-Borne Pathogens
5.1 Introduction
5.2 Major Plant Pathogens Causing Soil-Borne Diseases
5.3 Traditional Methods for Soil-Borne Pathogen Detection
5.4 Immunological/Serological Detection of Soil-Borne Pathogens
5.5 Enzyme-Linked Immunosorbent Assay (ELISA)
5.5.1 Direct ELISA
5.5.2 Indirect ELISA
5.5.3 Sandwich ELISA
5.5.4 Competitive ELISA
5.5.5 Phage Display
5.6 Lateral Flow Devices
5.7 Biochemical Methods for Soil-Borne Pathogen Detection
5.8 Molecular Methods for Soil-Borne Pathogen Detection
5.9 Nucleic Acid-Based Detection Techniques for Soil-Borne Pathogens
5.10 Polymerase Chain Reaction (PCR)
5.11 Random Amplified Polymorphic DNA (RAPD)
5.12 Restriction Fragment Length Polymorphism (RFLP)
5.13 Amplified Fragment Length Polymorphism (AFLP)
5.13.1 Simple Sequence Repeats (SSR)
5.13.2 Multiplex PCR
5.13.3 Real-time PCR
5.13.4 Colony PCR
5.13.5 Nested PCR
5.13.6 Bio PCR
5.14 DNA or RNA Probe-Based Assays
5.14.1 In Situ Hybridization
5.14.2 Fluorescent In Situ Hybridization
5.15 Isothermal Amplification Techniques
5.15.1 Loop-Mediated Isothermal Amplification (LAMP)
5.15.2 Rolling Circle Amplification
5.16 DNA-Based Point-of-Care Diagnostic Methods
5.17 Recent Advances in Soil-Borne Pathogen Detection
5.17.1 Ancillary Ways of Pathogen Detection
5.17.2 Gas Chromatography
5.18 On-Site Direct Diagnosis of Plant Diseases
5.18.1 Immunofluorescence (IF)
5.18.2 Flow Cytometry (FCM)
5.18.3 Next-Generation Sequencing
5.18.4 Disease Diagnostics Kits
5.19 ELISA (Enzyme-Linked Immunosorbent Assay) Kits
5.19.1 Direct Tissue Blotting
5.19.2 DNA/RNA Probes
5.19.3 Squash Blot Method
5.19.4 Use of Pocket Diagnostic Rapid Test Strips for Plant Diseases
5.19.5 PCRD-Nucleic Acid Detection
5.19.6 Diagnostic Kits´ Advantages
5.20 Conclusions
References
6: Genetic Enhancement of Biocontrol Agent as Effective Management of Soilborne Disease
6.1 Introduction
6.2 Biotechnological Strategies to Unravel/Decipher the Genetic Basis of Specific Mechanism of Action
6.2.1 Homology-Based Search
6.2.2 Forward Genetics Approach
6.2.3 Reverse Genetics Approach
6.2.4 Transcriptomics Study
6.2.5 Whole Genome Sequencing
6.2.6 Cloning and Characterization
6.3 Genetic Enhancements of Biocontrol Attributes/Mechanism/Activity
6.4 Improved Biocontrol Properties
6.4.1 Competition, Colonization and Growth Promotion
6.4.2 Antibiosis
6.4.3 Lysis (Mycoparasitism)
6.4.4 Induced Systemic Resistance (ISR)
6.5 Risk on Environmental Release
6.6 Conclusions
References
7: Red Root Rot Disease of Tropical Estate Forests: Pathogen Identification, Dispersal and Management
7.1 Background
7.2 Pathogen Identification
7.3 Dispersal
7.4 Management
7.4.1 Resistant Plants
7.4.2 Biocontrol Agents
7.4.3 Other Control Measures
7.5 Conclusion
References
8: Health Management of Rhizospheric Microbiome
8.1 Introduction
8.2 Rhizosphere Microbiome Composition and Their Roles
8.2.1 Composition of Rhizospheric Microbiome
8.2.2 Role of Rhizospheric Microbiome
8.3 Effect of the Rhizospheric Microbiome on Soil and Plant Health
8.3.1 Effect of the Rhizospheric Microbiome on Soil Health
8.3.2 Abiotic Stress Management
8.3.3 Biotic Stress Management
8.4 Interaction Between Plant and Rhizospheric Microbiome
8.4.1 Impact of Plant and Microbiome Interaction on Plant Health, Growth, and Disease
8.4.2 Rhizosphere Microorganisms and Acquisition of Plant Nutrient
8.4.3 Metabolomics: The Plant-Rhizomicrobes Interactions
8.5 Strategies for Health Management of Rhizospheric Microbiome
8.5.1 Cultural Practices for Health Management of Rhizospheric Microbiome
8.5.2 Microbial Inoculation in Soil
8.5.3 Recruitment of Beneficial Organisms
8.5.4 Genetic Manipulation of Plants
8.6 Conclusion
8.7 Future Prospects
References
9: Detection and Management of Basal Stem Rot of Oil Palm: Classical to Modern Approaches
9.1 Introduction
9.2 Basal Stem Rot of Oil Palm: Phytopathological Aspects
9.2.1 Geographical Distribution and Economic Loss
9.2.2 Causal Organism
9.2.3 Host Range
9.2.4 Morphology
9.2.5 Taxonomy
9.2.6 Symptoms
9.2.7 Epidemiology and Favourable Conditions
9.2.8 Survival and Spread
9.2.9 Artificial Inoculation Methods
9.3 Basal Stem Rot of Oil Palm: Detection and Diagnostic Tools
9.3.1 Manual Methods/Field Based
9.3.1.1 Based on Visual Symptoms
9.3.2 Lab-Based Methods
9.3.2.1 Cultural Methods
9.3.3 Biochemical Methods
9.3.3.1 Ethylenediaminetetraacetic acid (EDTA)
9.3.3.2 Isozyme Analysis
9.3.3.3 Ergosterol Analysis
9.3.3.4 Altered Proteins
9.3.3.5 Metabolic Profiling
9.3.4 Molecular Methods
9.3.4.1 Nucleic Acid-Based Detection
9.3.4.2 Protein-Based Detection Methods
9.3.5 Remote-Based Methods
9.3.5.1 VOC Profiling
9.3.5.2 Tomography
9.3.5.3 Microfocus X-Ray Fluorescence (μXRF)
9.3.5.4 Electrical Resistance
9.3.5.5 Hyperspectral Imaging
9.3.5.6 Multispectral Imaging
9.3.5.7 Terrestrial Laser Scanning
9.3.5.8 RGB Cameras
9.4 Basal Stem Rot of Oil Palm: Integrated Disease Management Strategies
9.4.1 Cultural Practices
9.4.1.1 Preventing the Entry of Pathogens
9.4.1.2 Clean Clearing/Sanitation
9.4.1.3 Windrows
9.4.1.4 Soil Modification Practices
9.4.1.5 Surgery
9.4.1.6 Isolation Trenches
9.4.1.7 Fallowing
9.4.1.8 Planting Legume Cover Crops (LCC)
9.4.2 Nutritional Management
9.4.2.1 Major Nutrients
9.4.2.2 Micronutrients
9.4.2.3 Beneficial Elements
9.4.2.4 Soil Amendments
9.4.3 Management of Ganoderma Using Chemical Fungicides
9.4.3.1 Delivery Systems
9.4.3.2 Chitosan-Based Nano Fungicides
9.4.4 Biological Control of Ganoderma in Oil Palm
9.4.4.1 Fungal and Bacterial Antagonists
9.4.4.2 Fungal and Bacterial Endophytes
9.4.4.3 Arbuscular Mycorrhizal Fungi (AMF)
9.4.4.4 Delivery Mechanism
9.4.4.5 Challenges in Field Level Testing of Biocontrol Agents
9.4.4.6 The Concept of Biocontrol Consortium
9.5 Breeding for Genetic Resistance
9.5.1 Genetic Engineering
9.5.2 Application of Omic Technologies
9.5.2.1 Transcriptomics
9.5.2.2 Proteomics
9.5.2.3 Metabolomics
9.6 Conclusion
References
10: Talaromyces flavus: An Important Rhizospheric Inhabitant
10.1 Introduction
10.2 Classification
10.3 Secondary Metabolites
10.4 Enzymes
10.5 Talaromyces flavus in Biological Pest Control
10.6 Conclusion
References
11: Harnessing Beneficial Rhizospheric Microorganisms for Biotic Stress Management in Medicinal and Aromatic Plants
11.1 Introduction
11.2 Mechanisms Employed by Rhizospheric Microorganisms
11.2.1 Soil Nutrient Solubilization
11.2.2 Competition for Available Resources
11.2.3 Rhizosphere Colonization
11.2.4 Iron Chelating Siderophores
11.2.5 Antibiosis
11.2.6 Lytic Enzymes Secretion
11.2.7 Phytohormones Production
11.2.8 Detoxification of Virulence Factors
11.3 Functions of Soil Microorganisms in Rhizospheric Microbial Community Shifting
11.4 Induced Resistance
11.5 Soil Microbial Mixture Against Biotic Stress
11.6 Correlation Between Soil Microorganisms and Enhancement of Plant Secondary Metabolites
11.7 Problem Associated with the Application of Rhizospheric Microorganisms
11.8 Conclusion and Future Perspectives
References
12: Nematophagous Fungi: Biology, Ecology and Potential Application
12.1 Introduction
12.2 Historical Background
12.3 Occurrence and Distribution
12.4 Classification
12.5 Ecology
12.6 Plant-Parasitic Nematodes have an Impact on Agriculture
12.7 Types of Nematophagous Fungi
12.8 Mechanism and Mode of Action of Nematophagous Fungi to Control Plant-Parasitic Nematode
12.8.1 Chemotaxis and Adhesion (Host Recognition, Host Specificity, and Infection)
12.8.2 Differentiation and Signaling
12.8.3 Nematodes Cuticle and Eggshell Penetration by NPF
12.9 Potential Application
12.10 Future Prospects
12.11 Conclusion
References
13: Rhizosphere Microbiome: Interactions with Plant and Influence in Triggering Plant Disease Resistance
13.1 Introduction
13.2 Microbial Diversity in the Rhizosphere
13.3 Factors Affecting the Occurrence and Diversity of Rhizosphere Microbiome
13.3.1 Biotic Factors
13.3.1.1 Host Plant Factors
Plant Genotype Affecting Rhizosphere Microbiome
Root Exudates Produced by Host Plant for Recruiting Microbial Diversity
Plant Metabolites and Their Role Played in Rhizosphere Microbiome
13.3.1.2 Microbial Factors
13.3.2 Abiotic Factors
13.3.2.1 Structure and Soil Type
13.3.2.2 Soil pH
13.3.2.3 Soil Nutrients
13.3.2.4 Effects of UV Radiation, CO2, and Temperature
13.4 Plant-Microbe Interactions in the Rhizosphere
13.4.1 Beneficial Interactions
13.4.1.1 Symbiotic and Nonsymbiotic Interactions
Arbuscular Mycorrhizal Fungi (AMF)
Rhizobium Bacteria
Plant Growth-Promoting Rhizobacteria (PGPR) and Plant Growth-Promoting Fungi (PGPF)
13.4.2 Pathogenic or Detrimental Interactions
13.5 Mechanisms of Rhizosphere Microbiomes in Inducing Plant Disease Resistance
13.5.1 Arbuscular Mycorrhizal Fungi (AMF)
13.5.1.1 Enhanced Nutrient Uptake and Morphological Alteration in the Root System
13.5.1.2 Competition
13.5.1.3 Alteration in Chemical Constituents of Plant Tissues
Mycorrhizal-Induced Resistance
13.5.2 Rhizobium Bacteria
13.5.2.1 Mycoparasitism
13.5.2.2 Antibiotic Production
13.5.2.3 Siderophore Production
13.5.2.4 Hydrolytic Enzyme Production
13.5.2.5 Induced Systemic Resistance (ISR)
13.5.3 Plant Growth-Promoting Rhizobacteria (PGPR) and Plant Growth-Promoting Fungi (PGPF)
13.5.3.1 Competition
13.5.3.2 Mycoparasitism
13.5.3.3 Antibiosis
13.5.3.4 Lytic Enzyme Production
13.5.3.5 Siderophore Production
13.5.3.6 Induced Systemic Resistance
13.6 Mechanisms of Rhizosphere Microbiomes in Enhancement of Plant Growth
13.6.1 Rhizosphere Microorganisms Promote Uptake of Mineral Nutrients
13.6.2 Secondary Metabolites and Phytohormone Production
13.7 Rhizosphere Microorganisms Enhanced Abiotic Stresses Tolerance
13.8 Tools/Techniques Employed to Understand the Plant-Microbe Interactions
13.8.1 Omics Technologies
13.8.2 Sequencing Technique
13.8.3 Chromatography, Mass Spectrometry, Nuclear Magnetic Resonance
13.8.4 Phospholipid Fatty Acid (PLFA) Analysis
13.8.5 Microscopy
13.8.6 qPCR
13.9 Future Prospects
13.10 Conclusion
References
14: Rhizospheric Functional Attributes of Paenibacillus polymyxa in Disease and Nutrient Management for Sustainable Crop Produ...
14.1 Introduction
14.2 Ecology and Distribution
14.3 Biocontrol of Fungal and Bacterial Diseases
14.4 Mechanism for Biocontrol of Fungal and Bacterial Plant Pathogens
14.5 Nutrient Supplementation and Plant Growth Promotion
14.6 Conclusion and Way Forward
References
15: Biochar-Mediated Suppression of Soil-Borne Pathogens in Agronomically Important Crops: An Outlook
15.1 Introduction
15.2 Background on Plant Diseases
15.3 Biochar Production and Characterization
15.4 Effects of Biochar on Physical Characteristics of Soil
15.5 Effects of Biochar on Chemical Characteristics of Soil
15.6 Effects of Biochar on Microbial Characteristics of Soil
15.7 Biochar for the Management of Plant Diseases
15.8 Possible Mechanism for the Control of Plant Disease by Biochar
15.9 Future Perspective
15.10 Conclusion
References
16: Harnessing Rhizosphere Microbiomes in Crop Productivity
16.1 Introduction
16.2 Diversity of Microbes in Plant Rhizosphere
16.3 Factors Affecting Plant Microbiota
16.4 Relationship Among the Microbial Communities in Rhizosphere
16.5 Bacteria in Plant Nutrients
16.6 Role of PGPR on Plants Productivity
16.7 Mycorrhizal Fungi and Plant Productivity
16.8 Archean Microbiota in Crop Productivity: A New Area of Research
16.9 Conclusion
References
17: Microbial Management of Fusarium Wilt in Banana: A Comprehensive Overview
17.1 Introduction
17.2 Symptoms
17.3 Epidemiology
17.4 Distribution in India
17.5 Disease Cycle
17.6 Mechanism of Biocontrol
17.6.1 Endophytic Bacteria
17.6.2 Bacillus spp.
17.6.3 Pseudomonas spp.
17.6.4 Trichoderma spp.
17.6.5 Arbuscular Mycorrhizal Fungi
17.7 Conclusions and Future Perspectives
References
18: Soil Health Management and Microorganisms: Recent Development
18.1 Introduction
18.2 Biological Indicators and Standard Analytical Procedures Used to Determine Soil Health
18.3 Role of Soil Physical and Chemical Indicators for Microbial Sustainability
18.4 The Effect of Soil Water Infiltration Rate on Microorganisms
18.4.1 Water Infiltration in the Soil
18.4.2 Effect of Water Infiltration Rate on Microbes
18.4.3 Effect of Bulk Density on Soil Microbes
18.5 Effect of Bulk Density on Bacterial Population
18.5.1 Bacteria
18.5.2 Enzymatic Activity
18.5.3 Soil pH
18.5.4 Bacteria
18.5.5 Electrical Conductivity (EC)
18.5.6 Effect of Ion-Exchange Capacity on Soil Microbes
18.6 Aggregate Stability and Soil Slaking
18.6.1 Bacteria
18.6.2 Fungi
18.7 Molecular Techniques to Measure Soil Health: Microbial Biomass
18.7.1 Fluorescence Microscopy
18.7.2 DNA Measurement
18.7.3 Fluorescence In Situ Hybridization
18.7.4 RNA Measurement
18.7.5 Stable Isotope Probing
18.8 Molecular Techniques to Measure Soil Health: Genetic and Functional Biodiversity
18.9 Denaturing Gradient Gel Electrophoresis
18.10 Temperature Gradient Gel Electrophoresis
18.11 Terminal Restriction Fragment Length Polymorphism (TRFLP)
18.12 BIOLOG
18.13 Microbial Resilience
18.14 Omics and Soil Microbial Diversity
18.14.1 Soil Nucleic Acid High-Throughput Sequencing Technologies
18.14.2 Soil Metaproteomics
18.14.3 Soil Metabolomics
18.15 Targeted and Untargeted Approaches to Soil Microbial Diversity Management
18.16 Targeted Approach
18.16.1 Zero Tillage/Conservation Tillage
18.16.2 Biofertilizer Application
18.17 Untargeted Approach
18.17.1 Organic Farming and Conservation Agriculture
18.17.2 Organic Fertilizers/Manures
18.17.3 Crop Rotation
18.17.4 Cover Cropping/Permanent Soil Cover
18.18 Future Prospects
18.19 Conclusion
References