Detection, Diagnosis and Management of Soil-borne Phytopathogens

Description

This edited book provides an overview of omics technologies and methods for integration across multiple omics layers used in the plant disease diagnosis and developing management strategies. The book concentrates on the prevalence of soil-borne disease management in various important crops with use of different strategies, including host resistance and biological control etc. The special focus is on the resolving practical problems encountered after the resistance development in the pathogens against several chemical pesticides. Further, special attention is given to the emergence of new diseases or the re-emergence of old ones on several crops, and on the results and problems encountered by using microbial inoculants, biofumigation and other non-chemical control methods. This book has 18 contributory chapters from the eminent experts in the field of plant pathology, microbiology and biotechnology working on different aspects of soil-borne diseases of important agricultural crops. This edited volume is of interest and useful to researchers in plant pathology, agriculture sciences, plant genomics ecology, policy makers, also it is a valuable source of reference to the relevant researchers and students globally. 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