Table of Contents
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