Table Of ContentSoilborne Microbial Plant Pathogens and
Disease Management, Volume One
Nature and Biology
Soilborne Microbial Plant Pathogens and
Disease Management, Volume One
Nature and Biology
Prof. P. Narayanasamy
CRC Press
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Contents
Dedicated
To
the memory of my parents
for their
Love and affection
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
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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
Contents ix
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
