Soilborne Microbial Plant Pathogens and Disease Management, Volume One

Contents Preface.......................................................................................................................................................................................... xi Acknowledgment........................................................................................................................................................................xiii Author.......................................................................................................................................................................................... xv Chapter 1 Introduction.............................................................................................................................................................. 1 1.1 Economic Importance and Distribution of Diseases Caused by Soilborne Microbial Plant Pathogens........ 1 1.2 Concepts and Implications of Infection by Soilborne Microbial Plant Pathogens........................................ 1 1.3 Nature of Soilborne Microbial Plant Pathogens Causing Crop Diseases...................................................... 3 1.3.1 Pathogen Biology............................................................................................................................. 3 1.3.2 Ecological and Epidemiological Perspectives.................................................................................. 3 1.4 Principles of Management of Crop Diseases Caused by Soilborne Microbial Pathogens............................ 3 1.4.1 Prevention of Pathogen Introduction and Inoculum Production...................................................... 3 1.4.2 Inhibition of Pathogen Development................................................................................................ 4 1.5 Development of Integrated Disease Management Systems........................................................................... 4 References................................................................................................................................................................ 4 Chapter 2 Detection and Identification of Soilborne Fungal Plant Pathogens.......................................................................... 7 2.1 Detection of Fungal Pathogens In Soil Environments................................................................................... 7 2.1.1 Isolation-Based Methods.................................................................................................................. 7 2.1.1.1 Baiting Assays.................................................................................................................. 8 2.1.1.2 Direct Plating of Soil Samples........................................................................................ 11 2.1.1.3 Plating of Water Samples................................................................................................ 12 2.1.2 Physical and Chemical Methods.................................................................................................... 13 2.1.3 Immunoassays................................................................................................................................ 16 2.1.3.1 Enzyme-Linked Immunosorbent Assay.......................................................................... 17 2.1.3.2 Dipstick Immunoassay.................................................................................................... 20 2.1.3.3 Lateral Flow Devices...................................................................................................... 21 2.1.3.4 Dot Immunobinding Assay............................................................................................. 21 2.1.3.5 Tissue Blot Immunoassay............................................................................................... 22 2.1.3.6 Western Blot Analysis..................................................................................................... 22 2.1.3.7 Immunofluorescence Assay............................................................................................ 22 2.1.3.8 Immunosorbent Electron Microscopy............................................................................ 22 2.1.4 Nucleic Acid-Based Techniques..................................................................................................... 22 2.1.4.1 Fluorescence Microscopy............................................................................................... 23 2.1.4.2 Hybridization Methods................................................................................................... 23 2.1.4.3 Polymerase Chain Reaction-Based Assays..................................................................... 24 2.2 Assessment of Variability in Soilborne Fungal Pathogens.......................................................................... 59 2.2.1 Variability in Biological Characteristics........................................................................................ 59 2.2.2 Variability in Vegetative Compatibility.......................................................................................... 60 2.2.3 Variability in Genomic Characteristics.......................................................................................... 62 2.2.3.1 Nucleic Acid Hybridization Techniques......................................................................... 63 2.2.3.2 Polymerase Chain Reaction-Based Methods.................................................................. 63 References.............................................................................................................................................................. 75 Chapter 3 Biology of Soilborne Fungal Plant Pathogens........................................................................................................ 89 3.1 Biological Characteristics of Fungal Pathogens.......................................................................................... 89 3.1.1 Disease Incidence and Distribution................................................................................................ 89 3.1.2 Disease Cycles of Fungal Pathogens.............................................................................................. 91 3.1.2.1 Production of Pathogen Propagules................................................................................ 91 3.1.2.2 Survival and Dispersal of Fungal Pathogens.................................................................. 96 3.1.2.3 Transmission of Soilborne Fungal Pathogens through Vectors.................................... 100 3.1.2.4 Host Range of Fungal Pathogens.................................................................................. 101 3.1.2.5 Disease Complexes of Soilborne Fungal Pathogens and Nematodes........................... 103 3.2 Genetic Characteristics of Fungal Pathogens............................................................................................ 104 3.2.1 Pathogenicity of Fungal Pathogens.............................................................................................. 104 3.2.2 Production of Toxic Metabolites and Enzymes by Fungal Pathogens......................................... 108 3.3 Process of Infection of Fungal Pathogens..................................................................................................112 3.3.1 Germination of Spores..................................................................................................................112 3.3.2 Penetration and Colonization of Host Tissues.............................................................................. 115 3.3.3 In Planta Expression of Fungal Pathogen Genes.......................................................................... 129 3.3.4 Molecular Basis of Interactions between Host Plants and Fungal Pathogens.............................. 135 3.3.5 Influence of Environment on Disease Development.................................................................... 142 References.............................................................................................................................................................143 Chapter 4 Detection and Identification of Soilborne Bacterial Plant Pathogens.................................................................. 155 4.1 Detection of Bacterial Pathogens.............................................................................................................. 156 4.1.1 Isolation-Dependent Methods...................................................................................................... 156 4.1.1.1 Use of Indicator Plants.................................................................................................. 156 4.1.1.2 Use of Selective Media................................................................................................. 156 4.1.1.3 Use of Bacteriophages.................................................................................................. 158 4.1.1.4 Biochemical and Physical Methods.............................................................................. 158 4.1.2 Isolation-Independent Methods.................................................................................................... 159 4.1.2.1 Immunoassays............................................................................................................... 159 4.1.2.2 Nucleic Acid-Based Techniques................................................................................... 163 4.2 Variability in Bacterial Pathogens..............................................................................................................178 4.2.1 Variability in Cultural Characteristics...........................................................................................178 4.2.2 Variability in Pathogenicity...........................................................................................................178 4.2.3 Variability in Biochemical Properties.......................................................................................... 180 4.2.4 Variability in Physical Properties................................................................................................. 180 4.2.5 Variability in Immunological Properties...................................................................................... 180 4.2.6 Variability in Genomic Nucleic Acid Characteristics.................................................................. 181 References............................................................................................................................................................ 187 Chapter 5 Biology of Soilborne Bacterial Plant Pathogens.................................................................................................. 195 5.1 Disease Cycles of Bacterial Plant Pathogens............................................................................................ 195 5.1.1 Ralstonia solanacearum............................................................................................................... 195 5.1.1.1 Disease Incidence and Distribution.............................................................................. 195 5.1.1.2 Host Range and Sources of Infection........................................................................... 196 5.1.1.3 Modes of Dispersal of Bacterial Pathogens.................................................................. 197 5.1.1.4 Survival of the Pathogen............................................................................................... 198 5.1.1.5 Process of Infection of Susceptible Plants.................................................................... 199 5.1.2 Pectobacterium spp. and Dickeya spp.......................................................................................... 208 5.1.2.1 Disease Incidence and Distribution.............................................................................. 208 5.1.2.2 Host Range and Sources of Infection........................................................................... 208 5.1.2.3 Modes of Dispersal of Pathogens................................................................................. 209 5.1.2.4 Process of Infection of Susceptible Plants.................................................................... 210 5.1.3 Streptomyces spp.......................................................................................................................... 213 5.1.3.1 Disease Incidence and Distribution.............................................................................. 213 5.1.3.2 Pathogenicity and Host Range...................................................................................... 213 5.1.4 Agrobacterium spp........................................................................................................................216 5.1.4.1 Disease Incidence and Distribution...............................................................................216 5.1.4.2 Process of Infection...................................................................................................... 217 5.1.5 Xanthomonas spp......................................................................................................................... 221 5.1.5.1 Disease Incidence and Distribution.............................................................................. 221 5.1.5.2 Process of Infection...................................................................................................... 222 5.1.6 Clavibacter michiganensis........................................................................................................... 224 References............................................................................................................................................................ 225 Chapter 6 Detection and Biology of Soilborne Viral Plant Pathogens................................................................................. 233 6.1 Detection of Soilborne Viruses.................................................................................................................. 234 6.1.1 Detection of Viruses with Abiotic Transmission.......................................................................... 234 6.1.1.1 Biological Methods....................................................................................................... 234 6.1.1.2 Immunoassays............................................................................................................... 234 6.1.1.3 Polymerase Chain Reaction-Based Assays................................................................... 235 6.1.2 Detection of Viruses with Biotic Transmission............................................................................ 236 6.1.2.1 Viruses Transmitted by Fungal Vectors........................................................................ 236 6.1.2.2 Detection of Viruses Transmitted by Nnematodes........................................................ 243 6.2 Biology of Soilborne Viruses..................................................................................................................... 247 6.2.1 Viruses with Abiotic Transmission............................................................................................... 248 6.2.2 Viruses with Biotic Transmission................................................................................................. 249 6.2.2.1 Viruses Transmitted by Fungal Vectors........................................................................ 249 6.2.2.2 Viruses Transmitted by Nematode Vectors................................................................... 252 6.2.3 Process of Infection...................................................................................................................... 254 6.2.4 Mechanisms of Transmission of Viruses by Vectors.................................................................... 255 6.2.5 Movement of Viruses.................................................................................................................... 258 6.2.5.1 Movement of Viruses with Abiotic Transmission......................................................... 258 6.2.5.2 Movement of Viruses Transmitted by Fungal Vectors.................................................. 259 6.2.5.3 Movement of Viruses Transmitted by Nematode Vectors............................................. 261 6.2.6 Role of RNA Silencing in Virus Disease Development............................................................... 262 References............................................................................................................................................................ 265 Chapter 7 Ecology and Epidemiology of Soilborne Microbial Plant Pathogens.................................................................. 273 7.1 Nature and Functions of Soils................................................................................................................... 273 7.1.1 Interactions of Microorganisms with Components of Soils......................................................... 273 7.1.1.1 Interactions among Microorganisms............................................................................ 273 7.1.2 Pathogen Suppression in Soils..................................................................................................... 274 7.2 Influence of Agricultural Practices On Soil Microorganisms.................................................................... 277 7.2.1 Cropping Systems........................................................................................................................ 277 7.2.2 Tillage........................................................................................................................................... 278 7.2.3 Application of Nutrients............................................................................................................... 278 7.2.4 Irrigation Practices....................................................................................................................... 278 7.3 Epidemiology of Soilborne Crop Diseases................................................................................................ 280 7.3.1 Components of Epidemics of Soilborne Diseases........................................................................ 281 7.3.1.1 Dynamics of Fungal Pathogen-Host Plant Interactions................................................ 281 7.3.1.2 Dynamics of Host-Bacterial Pathogen Interactions...................................................... 296 7.3.1.3 Dynamics of Host-Viral Pathogen Interactions............................................................ 301 7.4 Forecasting Systems For Diseases Caused by Soilborne Microbial Pathogens........................................ 304 7.4.1 Pathogen-Based Forecasting........................................................................................................ 305 7.4.2 Pathogen Distribution-Based Forecasting.................................................................................... 306 7.4.3 Environment-Based Forecasting.................................................................................................. 306 7.4.4 Management-Based Forecasting.................................................................................................. 308 References............................................................................................................................................................ 308 Index...........................................................................................................................................................................................315