Soilborne Microbial Plant Pathogens and Disease Management, Volume One

Preface

1 Introduction

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 Index