Narayanasamy Microbial Plant Pathogens-Detection and Disease Diagnosis:

Bacterial and Phytoplasmal Pathogens, Vol.2
1. Auflage 2010
ISBN: 978-90-481-9769-9
Verlag: Springer Netherlands
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 256 Seiten

Microbial plant pathogens causing qualitative and quantitative losses in all corps are present not only in the infected plants, but also in the environmental comprising of soil, water and air. The vectors present in the environment spread the microbial pathogens to short and/or long distances. Detection of microbial pathogens rapidly and reliably by employing suitable sensitive applicable for different ecosystems. The pathogens have to be identified precisely and differentiated and quantified to plan appropriate short- and long-term strategies to contain the incidence and spread of diseases induced by them. This book aims to present all relevant and latest information on the detection techniques based on the biological, biochemical, immunological and nucleic acid characteristics of microbial pathogens presents in the host plants, as well as in the natural substrates that support the survival and perpetuation of the pathogens.

Autoren/Hrsg.

Narayanasamy, P.

Inhaltsverzeichnis

1;Preface;8
2;Acknowledgement;10
3;Contents;12
4;Table of Contents for Volumes 1 and 3;16
5;Chapter 1: Introduction;24
5.1;1.1 Microbial Plant Pathogens as a MajorLimiting Factor of Crop Production;24
5.2;1.2 Discovery of Bacteria as Plant Pathogens;25
5.3;1.3 Detection of Bacterial and Phytoplasmal Pathogens and Disease Diagnosis;25
5.4;References;27
6;Chapter 2: Detection of Bacterial and Phytoplasmal Pathogens;28
6.1;2.1 Detection of Bacterial Pathogens in Plant Organs;31
6.1.1;2.1.1 Biological Methods;31
6.1.1.1;2.1.1.1 Use of Media for Culturing Bacteria;35
6.1.1.2;2.1.1.2 Use of Diagnostic Hosts;37
6.1.1.3;2.1.1.3 Use of Bacteriophages (Phage Typing);37
6.1.2;2.1.2 Biochemical Methods;38
6.1.2.1;2.1.2.1 Properties of Bacteria in Culture;38
6.1.2.2;2.1.2.2 Metabolic Fingerprinting;39
6.1.2.3;2.1.2.3 Properties of Bacterial Cells;40
6.1.2.3.1;Direct Colony Thin Layer Chromatography;40
6.1.2.3.2;Polyacrylamide Gel Electrophoresis;41
6.1.2.3.3;Conductimetric Assay;43
6.1.2.3.4;Isozyme Analysis;43
6.1.2.3.5;Use of Fluorescent Markers/Bioluminescent Strains of Pathogens;44
6.1.3;2.1.3 Immunoassays;44
6.1.3.1;2.1.3.1 Agglutination Test;46
6.1.3.2;2.1.3.2 Gel Diffusion Test;47
6.1.3.3;2.1.3.3 Enzyme-Linked Immunosorbent Assay;47
6.1.3.4;2.1.3.4 Dot Immunobinding Assay;52
6.1.3.5;2.1.3.5 Immunofluorescence Test;52
6.1.3.6;2.1.3.6 Immunolabeling and Electron Microscopy;54
6.1.3.7;2.1.3.7 Immunomagnetic Fishing/Isolation of Bacterial Pathogens;55
6.1.3.8;2.1.3.8 Flow Cytometry;55
6.1.4;2.1.4 Nucleic Acid-Based Techniques;57
6.1.4.1;2.1.4.1 Nucleic Acid Hybridization Methods;57
6.1.4.2;2.1.4.2 Restriction Fragment Length Polymorphism;58
6.1.4.3;2.1.4.3 Polymerase Chain Reaction;59
6.1.4.3.1;Detection by Targeting Specific Gene Sequences;65
6.1.4.3.2;Detection by Targeting Non-nuclear Nucleic Acids;68
6.1.4.3.3;Detection by Using Variants of PCR;70
6.1.4.3.4;Integration of PCR with Other Detection Methods;76
6.1.4.4;2.1.4.4 Real-Time Polymerase Chain Reaction;81
6.1.4.5;2.1.4.5 Loop-Mediated Isothermal Amplification Technique;86
6.1.4.6;2.1.4.6 Isothermal and Chimeric Primer-Mediated Amplificationof Nucleic Acids (ICAN) Technique;87
6.1.4.7;2.1.4.7 DNA Array Technology;88
6.1.4.8;2.1.4.8 Multilocus Sequence Typing System;89
6.2;2.2 Detection of Phytoplasmal Pathogens in Plant Organs;89
6.2.1;2.2.1 Histochemical Methods;92
6.2.2;2.2.2 Immunoassays;95
6.2.2.1;2.2.2.1 Rapid Slide Test;95
6.2.2.2;2.2.2.2 Enzyme-Linked Immunosorbent Assay;96
6.2.2.3;2.2.2.3 Immunofluorescence Technique;98
6.2.2.4;2.2.2.4 Immunosorbent Electron Microscopy and Gold-Labeled Antibody Decoration;98
6.2.3;2.2.3 Nucleic Acid-Based Techniques;100
6.2.3.1;2.2.3.1 Dot Blot Hybridization Assay;100
6.2.3.2;2.2.3.2 Restriction Fragment Length Polymorphism;103
6.2.3.3;2.2.3.3 Polymerase Chain Reaction-Based Assays;103
6.2.3.4;2.2.3.4 Real-Time Polymerase Chain Reaction;120
6.2.3.5;2.2.3.5 Heteroduplex Mobility Analysis;124
6.2.3.6;2.2.3.6 DNA Array Technology;125
6.3;2.3 Detection of Bacterial Pathogens in Seeds and Planting Materials;126
6.3.1;2.3.1 Detection of Bacterial Pathogens in Seeds;127
6.3.1.1;2.3.1.1 Biological Methods;127
6.3.1.2;2.3.1.2 Immunoassays;128
6.3.1.2.1;Agglutination-/Diffusion-Based Tests;128
6.3.1.2.2;Immunofluorescence Microscopy;128
6.3.1.2.3;Enzyme-Linked Immunosorbent Assay;129
6.3.1.3;2.3.1.3 Detection by Nucleic Acid-Based Assays;131
6.3.1.3.1;Nucleic Acid Hybridization Technique;132
6.3.1.3.2;Restriction Fragment Length Polymorphism Analysis;132
6.3.1.3.3;Polymerase Chain Reaction-Based Assays;132
6.3.1.3.4;Real-Time Polymerase Chain Reaction;135
6.3.2;2.3.2 Detection of Bacterial Pathogens in Propagative Planting Materials;137
6.3.2.1;2.3.2.1 Detection by Biological Methods;137
6.3.2.2;2.3.2.2 Detection by Immunoassays;137
6.3.2.2.1;Enzyme-Linked Immunosorbent Assay;137
6.3.2.2.2;Immunofluorescence Test;138
6.3.2.3;2.3.2.3 Detection by Nucleic Acid-Based Techniques;139
6.3.2.3.1; Nucleic Acid Hybridization Technique;139
6.3.2.3.2;Polymerase Chain Reaction-Based Assays;139
6.3.2.3.3;Real-Time Polymerase Chain Reaction;142
6.3.2.3.4;DNA Array Technology;144
6.3.2.3.5;Nucleic Acid Sequence-Based Amplification Assay;145
6.3.3;2.3.3 Detection of Bacterial Pathogens in Postharvest Produce;146
6.4;2.4 Detection of Phytoplasmal Pathogens in Planting Materials;148
6.5;Appendix 1: Media for Isolation of Bacterial Plant Pathogens;149
6.6;Appendix 2: Detection of Acidovorax avenae subsp. citrulli (Aac) by Pulsed-Field Gel Electrophoresis (PFGE) ;152
6.7;Appendix 3: Detection of Bacterial Pathogens by Slide Agglutination Test (Lyons and Taylor 1990);153
6.7.1;Preparation of Somatic Antigen;153
6.7.2;Production of Antiserum;153
6.7.3;Production of Staphylococcus aureus Reagent;153
6.7.4;Conjugation of Working Reagent;154
6.7.5;Slide Agglutination Test;154
6.8;Appendix 4: Detection of Xanthomonas campestris pv. vesicatoria by Enzyme-Linked Immunosorbent Assay (ELISA) Formats ;154
6.8.1;Preparation of Bacterial Cells (Antigen);154
6.8.2;Preparation of Plant Samples;155
6.8.3;ABC-Enzyme-Linked Immunosorbent Assay;155
6.9;Appendix 5: Detection of Erwinia chrysanthemi Using Fimbria-Specific Antibody in ELISA Technique (Singh et al. 2000);156
6.9.1;Production of Antiserum;156
6.9.2;Screening Hybridomas for Specific MAbs;156
6.9.3;Detection of Target Pathogen in Plant Tissues;156
6.10;Appendix 6: Detection of Erwinia chrysanthemi by Immunogold Labeling and Electron Microscopy Technique ;157
6.10.1;Immunogold Labeling;157
6.10.2;Electron Microscopy;157
6.11;Appendix 7: Detection of Clavibacter michiganensis subsp. michiganensis by Flow Cytometry (Chitaara et al. 2006);157
6.11.1;Labeling of Target Bacterial Cells;157
6.11.2;Flow cytometric Analysis;158
6.12;Appendix 8: Detection of Erwinia amylovora by Polymerase Chain Reaction (PCR) (Stöger et al. 2006);158
6.12.1;Extraction of DNA;158
6.12.2;Polymerase Chain Reaction;159
6.13;Appendix 9: Detection of Xanthomonas campestris pv. vesicatoria (Xcv) by PCR Assay (Park et al. 2009);159
6.13.1;PCR Amplification;159
6.13.2;Dot Blot Analysis;159
6.14;Appendix 10: Detection of Xanthomonas axonopodis pv. citri (Xac) by Immuno-Capture (IC) and Nested (N)-PCR Assay ;160
6.14.1;Magnetic Immunocapture of Target Pathogen Cells;160
6.14.2;PCR Reactions;160
6.15;Appendix 11: Detection of Xylella fastidiosa (Xf) in Xylem Exudates of Grapevine By IC-PCR Technique (Guo and Lu 2004;161
6.15.1;Extraction of Xylem Exudates;161
6.15.2;Preparation of Xf Suspension by Immunocapture Procedure;161
6.15.3;PCR Amplification;161
6.16;Appendix 12: Detection of Xanthomonas axonopodis pv. citri by Real Time PCR Assay (Mavrodieva et al. 2004);162
6.16.1;Sample Preparation Using the IT 1-2-3 RAPID DNA Purification Kit;162
6.16.2;Real-Time PCR Assay;162
6.17;Appendix 13: Detection of Phytoplasmal Pathogens by Histological Techniques (Galvis et al. 2007);163
6.17.1;DAPI Fluorescence Test;163
6.17.2;Transmission Electron Microscopy (TEM);163
6.18;Appendix 14: Detection of Spiroplasma Infecting Carrot by Nested PCR Assay (Green et al. 1999; Lee et al. 2006);163
6.18.1;Extraction of Pathogen DNA;163
6.18.2;Nested PCR and RFLP Analysis for Phytoplasmas;164
6.18.3;Nested PCR and RFLP Analysis for Spiroplasmas;165
6.19;Appendix 15: Detection of Phytoplasmas by Oligonucleotide Microarray-Based Assay (Nicolaisen and Bertaccini 2007);165
6.19.1;PCR Amplification;165
6.19.2;Labeling of Hybridization Probes;165
6.19.3;Printing and Post-processing of Oligonucleotide Arrays;165
6.19.4;Microarray Hybridization;166
6.19.5;Microarray Scanning;166
6.20;Appendix 16: Detection of Clavibacter michiganensis subsp. michiganensis (Cmm) by Immunomagnetic Separation (IMS) – PlatingTechnique;166
6.20.1;Coating Magnetic Beads;166
6.20.2;Standardization of IMS Technique;167
6.20.3;Isolation of Target Pathogen from Naturally Infected Seeds by IMS;167
6.21;Appendix 17: Detection of Xanthomonas campestris pv. carotae by PCR Assay (Meng et al. 2004);167
6.21.1;Preparation of Seed-wash;167
6.21.2;DNA Extraction from Seed-Wash;168
6.22;Appendix 18: Detection of Acidovorax avenae subsp. citrulli by Immuno-capture PCR Assay (Xiao et al. 2007);168
6.22.1;Selection of Antibodies and Primers;168
6.22.2;Detection by Standard PCR Assay;168
6.22.3;Detection by Immuno-capture (IC)-PCR Assay;168
6.23;Appendix 19: Detection of Burkholderia glumae in Rice Seeds by Real-time PCR Assay (Sayler et al. 2006);169
6.23.1;Preparation of Seed-wash;169
6.23.2;Real-time PCR Assay;169
6.24;References;169
7;Chapter 3: Detection of Bacterial and Phytoplasmal Pathogens in the Environment;193
7.1;3.1 Detection of Bacterial Pathogens in the Environment;194
7.1.1;3.1.1 Detection of Bacterial Pathogens in Soil;194
7.1.1.1;3.1.1.1 Biological Methods;194
7.1.1.2;3.1.1.2 Immunoassays;195
7.1.1.2.1;Immunofluorescence Tests;195
7.1.1.2.2;Enzyme-Linked Immunosorbent Assay;196
7.1.1.3;3.1.1.3 Nucleic Acid-Based Techniques;196
7.1.1.3.1;Polymerase Chain Reaction-Based Assays;196
7.1.2;3.1.2 Detection of Bacterial Pathogens in Water;200
7.1.2.1;3.1.2.1 Biological Methods;201
7.1.2.2;3.1.2.2 Immunoassays;202
7.1.2.3;3.1.2.3 Nucleic Acid-Based Methods;202
7.1.3;3.1.3 Detection of Bacterial Pathogens in Air;204
7.1.4;3.1.4 Detection of Bacterial Pathogens in Alternative Host Plants;205
7.1.5;3.1.5 Detection of Bacterial Pathogens in Vector Insects;206
7.1.5.1;3.1.5.1 Biological Methods;206
7.1.5.2;3.1.5.2 Immunoassays;207
7.1.5.3;3.1.5.3 Nucleic Acid-Based Techniques;207
7.1.5.3.1;Nucleic Acid Hybridization Techniques;207
7.1.5.3.2;Polymerase Chain Reaction;208
7.2;3.2 Detection of Phytoplasmal Pathogens in the Environment;211
7.2.1;3.2.1 Detection of Phytoplasmal Pathogens in Alternative Host Plants;211
7.2.1.1;3.2.1.1 Nucleic Acid-Based Techniques;211
7.2.2;3.2.2 Detection of Phytoplasmal Pathogens in Insect Vectors;212
7.2.2.1;3.2.2.1 Immunoassays;213
7.2.2.2;3.2.2.2 Nucleic Acid-Based Assays;213
7.2.2.2.1;Nucleic Acid Hybridization Technique;213
7.3;Appendix 1: Detection of Ralstonia solanacearum Race 1 Strains in Soils by BIO-PCR Assay (Lin et al. 2009);217
7.3.1;Bacterial Enrichment Using MSM-1 Broth;217
7.4;Appendix 2: Detection of Xylella fastidiosa (Xf) in Vector Insects by PCR Assay (Krell et al. 2007);218
7.4.1;Extraction of DNA;218
7.5;References;218
8;Chapter 4: Assessment of Variability in Bacterial and Phytoplasmal Pathogens;222
8.1;4.1 Assessment of Variability in Bacterial Pathogens;223
8.1.1;4.1.1 Assessment of Variations in Pathogenicity;223
8.1.2;4.1.2 Assessment of Variations in Phage Sensitivity;223
8.1.3;4.1.3 Assessment of Variations in Cultural Characteristics;224
8.1.4;4.1.4 Assessment of Variations in Biochemical Characteristics;225
8.1.4.1;4.1.4.1 Fatty Acid Analysis;225
8.1.4.2;4.1.4.2 Polyacrylamide Gel Electrophoretic Analysis;225
8.1.5;4.1.5 Assessment of Variations in Immunological Characteristics;227
8.1.6;4.1.6 Assessment of Variations in Nucleic Acid Characteristics;228
8.1.6.1;4.1.6.1 Restriction Fragment Length Polymorphism Method;228
8.1.6.2;4.1.6.2 Polymerase Chain Reaction-Based Techniques;229
8.1.6.3;4.1.6.3 Random Amplified Polymorphic DNA Technique;234
8.1.6.4;4.1.6.4 Amplified Fragment Length Polymorphism Technique;236
8.1.6.5;4.1.6.5 DNA Microarray Technology;237
8.1.7;4.1.7 Assessment of Variability in Resistance to Chemicals;238
8.2;4.2 Assessment of Variability in Phytoplasmal Pathogens;239
8.2.1;4.2.1 Assessment of Variability in Immunological Characteristics;240
8.2.2;4.2.2 Assessment of Variability in Genomic Characteristics;240
8.2.2.1;4.2.2.1 Polymerase Chain Reaction-Dependent Techniques;241
8.2.2.2;4.2.2.2 Subtractive Suppression Hybridization;244
8.2.2.3;4.2.2.3 Single-Strand Conformation Polymorphism Analysis;245
8.2.2.4;4.2.2.4 Heteroduplex Mobility Assay;246
8.3;Appendix 1: Differentiation of Strains of Clavibacter michiganensis subsp. michiganensis (Cmm) by Macrorestriction PulsedField Gel Electrophoresis (PFGE) Technique;247
8.4;References;248
9;Chapter 5: Diagnosis of Bacterial Diseases of Plants;254
9.1;5.1 Choice of Diagnostic Tests for Bacterial Diseases;255
9.1.1;5.1.1 Conventional Techniques;255
9.1.2;5.1.2 Biochemical Tests;256
9.1.3;5.1.3 Immunoassays;258
9.1.4;5.1.4 Nucleic Acid-Based Techniques;259
9.2;5.2 Choice of Diagnostic Tests for Phytoplasmal Diseases;261
9.2.1;5.2.1 Biological Methods;261
9.2.2;5.2.2 Nucleic Acid-Based Techniques;261
9.3;5.3 Agencies Involved in Disease Diagnosis;262
9.3.1;5.3.1 Disease Diagnostic Centers;263
9.3.2;5.3.2 Plant Quarantines;264
9.4;References;266
10;Index;268