Dion Molecular Mechanisms of Plant and Microbe Coexistence

1. Auflage 2008
ISBN: 978-3-540-75575-3
Verlag: Springer-Verlag
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 491 Seiten

Molecular Mechanisms of Plant and Microbe Coexistence presents studies on the complex and manifold interactions of plants and microbes at the population, genomics and proteomics level. The role of soil microbial diversity in enhancing plant health and plant microbe beneficial symbioses is discussed. Microbial communities are shown in the light of evolution. Main topics include genome coexistence and the functional genomics and proteomics of plant-associated microbes, which could form the basis for new environmentally benign strategies to combat infectious plant diseases and regulate plant growth. Further chapters focus on the role of signaling during the different stages of plant microbe coexistence, in symbiotic or pathogenic relationships, in quorum sensing and plant viral infections. Methods for studying the interactions in the root zone complement the book, which will certainly be of relevance in the practical application to agriculture, food security and for maintaining the balance of our ecosystems.

Autoren/Hrsg.

Dion, Patrice

Inhaltsverzeichnis

1;Foreword;7
2;Preface;9
3;Contents;13
4;Contributors;15
5;Coexistence Between Populations;20
5.1;Plant Associated Soil Micro-organisms;21
5.1.1;1.1 Micro-organisms of the Rhizosphere 1.1.1 The Rhizosphere;21
5.1.2;1.1.2 Fungi: Symbionts, Saprotrophs, Pathogens;22
5.1.3;1.1.3 Plant Beneficial Bacteria;24
5.1.4;1.1.4 Protozoa;28
5.1.5;1.2 Organismic Interactions 1.2.1 Microbe- Microbe Interactions;29
5.1.6;1.2.2 Plant Microbe Interactions;34
5.1.7;1.2.3 Tri-Partite Interaction: Mycorrhizas and Helper Bacteria;42
5.1.8;1.2.4 Role of Micro-organisms in Weathering;46
5.1.9;1.3 Chemical Ecology of the Rhizosphere 1.3.1 Endophytic Organisms as Sources of Bioactive Secondary Metabolites;46
5.1.10;1.3.2 The Roles of Streptomycetes in Plant Pathogenesis and Symbiosis;48
5.1.11;1.4 Concluding Remarks and Future Prospects;51
5.1.12;References;54
5.2;Role of Microbial Diversity for Soil, Health and Plant Nutrition;70
5.2.1;2.1 Introduction;70
5.2.2;2.2 Soil Microbial Diversity;71
5.2.3;2.3 Evolution of Farming;72
5.2.4;2.3.1 Present and the Future Scenario;73
5.2.5;2.4 Carbon Flow into Agro- and Natural Ecosystems;74
5.2.6;2.4.1 Increase of Greenhouse Gases and Climatic Change;75
5.2.7;2.4.2 Increasing Carbon Sequestration in Soils;77
5.2.8;2.5 Nitrogen Fixation Through Soil Microbes;78
5.2.9;2.6 Effect of GE Crops on Microbial Diversity;80
5.2.10;2.6.1 GE Crops Exuding Specific Molecules into Rhizosphere and Possibilities of Enhancing Microbial Cooperation;82
5.2.11;2.7 Genetically Engineered Bio-control Agents;83
5.2.12;2.8 Conclusions and Outlook for the Future;85
5.2.13;References;86
5.3;Reconstructing Soil Biology;92
5.3.1;3.1 Introduction;92
5.3.2;3.2 Postulated Origin of Land Colonization in Sulfide- rich Springs;94
5.3.3;3.3 The Advent of the Cyanobacteria;95
5.3.4;3.4 Biogeochemical Cycling Based on Microbial Phototrophic Inputs;97
5.3.5;3.5 Factors Involved in the Establishment of Mutualistic Symbioses;98
5.3.6;3.6 The Symbiotic Continuum;100
5.3.7;3.7 Microsymbiotic and Macrosymbiotic Factors Shaping Interactions;102
5.3.8;3.8 The Evolution of Symbionts and Hypersymbionts;103
5.3.9;3.9 Evolution and the Persistence of Environments;105
5.3.10;3.10 The Heterotrophization of Soil Microbial Life;106
5.3.11;3.11 Conclusions;106
5.3.12;References;108
5.4;Rhizosphere Colonization: Molecular Determinants from Plant- Microbe Coexistence Perspective;115
5.4.1;4.1 Introduction;115
5.4.2;4.2 Genetic Regulation of Plant–Microbe Association;116
5.4.3;4.3 Genomics and Proteomics of Plant–Microbe Coexistence;120
5.4.4;4.4 Strategies to Enhance Plant–Microbe Coexistence;130
5.4.5;4.5 Concluding Remarks and Future Prospects;132
5.4.6;References;133
5.5;Belowground Mycorrhizal Endosymbiosis and Aboveground Insects: Can Multilevel Interactions be Exploited for a Sustainable Control of Pests?;140
5.5.1;5.1 Introduction;140
5.5.2;5.2 The Effect of Aboveground Herbivory on AM Symbiosis;143
5.5.3;5.3 The Effect of AM Symbiosis on Plant Direct Defences Against Herbivore Insects;145
5.5.4;5.4 The Effect of AM Symbiosis on Plant Indirect Defences Against Herbivore Insects;148
5.5.5;5.5 Signal-Transduction Pathways Involved in Plant Response to AM and to Herbivore Insects;150
5.5.6;5.6 New Tools in the Study of Multitrophic Interactions;153
5.5.7;5.7 Towards a Multilevel Approach of Pest Control in Agriculture;156
5.5.8;5.8 Synthesis and Future Directions;158
5.5.9;References;161
6;Coexistence Between Genomes;168
6.1;Evolutionary Genomics: Linking Macromolecular Structure, Genomes and Biological Networks;169
6.1.1;6.1 Introduction;169
6.1.2;6.2 Evolutionary Genomics, Networks and Systems 6.2.1 The Genomic Revolution;171
6.1.3;6.2.2 Phylogenomics;172
6.1.4;6.2.3 Network Biology: Understanding the Wiring Diagram of Life;172
6.1.5;6.2.4 Molecular Mechanics and Evolution;174
6.1.6;6.3 Defining an Evolutionary Genomic Framework;175
6.1.7;6.4 Exploring the Evolution of Modern RNA 6.4.1 Diversity of Non- protein Coding RNA;176
6.1.8;6.4.2 Phylogenetic Analysis of RNA Structure;178
6.1.9;6.5 Exploring the Evolution of the Protein World 6.5.1 The Hierarchical Nature of Protein Structure;182
6.1.10;6.5.2 An Evolutionarily Structured Universe of Protein Architecture;183
6.1.11;6.5.3 Evolutionary Patterns and Transformation Pathways;183
6.1.12;6.5.4 Sharing Patterns of Fold Architecture in Life;186
6.1.13;6.6 Exploring the Evolution of Networks;186
6.1.14;6.7 Evolutionary Genomics and Organismal Coexistence;188
6.1.15;References;191
6.2;Evolutionary Genomics of the Nitrogen-Fixing Symbiotic Bacteria;196
6.2.1;7.1 Introduction;196
6.2.2;7.2 Origin, Taxonomy and Phylogeny;198
6.2.3;7.3 Genome Structure;199
6.2.4;7.4 Symbiotic Genome Compartments;201
6.2.5;7.5 Horizontal Gene Transfer and Mobile Elements;203
6.2.6;7.6 Genetic and Metabolic Redundancy;204
6.2.7;7.7 An Ancestral Chromosome?;205
6.2.8;7.8 Conclusions;207
6.2.9;References;207
6.3;Genetic and Epigenetic Nature of Transgenerational Changes in Pathogen Exposed Plants;212
6.3.1;8.1 Introduction;212
6.3.2;8.2 Genome Stability is Regulated via Multiple Pathways;213
6.3.3;8.3 The Homologous Recombination as a Mechanism Supporting Rearrangements;213
6.3.4;8.4 Regulation of Gene Expression via Chromatin Modifications;214
6.3.5;8.5 Exposure to Stress Influences Methylation Status and HRF;215
6.3.6;8.6 Systemic Signaling in Plants;216
6.3.7;8.7 Systemic Recombination Signal Is One of the Mechanisms of Stress Response;216
6.3.8;8.8 Can Pathogen Induce Genome Rearrangements?;216
6.3.9;8.9 Compatible Viral Infection Leads to the Production of SRS and Global Increase in HRF;217
6.3.10;8.10 SRS Results in Heritable Changes in HRF and Methylation Pattern;217
6.3.11;8.11 Viral Infection Leads to Global Genome Hypermethylation in the Progeny of Infected Plants;219
6.3.12;8.12 Viral Infection Results in Loci-Specific Methylation Changes;219
6.3.13;8.13 Viral Infection Results in the Destabilization of R- Gene Loci in the Progeny of Infected Plants;220
6.3.14;8.14 Stability of the Actin, RENT and 5.8 S Loci is not Changed;221
6.3.15;8.15 Conclusion;223
6.3.16;References;224
6.4;Recent Advances in Functional Genomics and Proteomics of Plant Associated Microbes;228
6.4.1;9.1 Introduction;228
6.4.2;9.2 Plant and Genetic Diversity in the Rhizosphere Soil;230
6.4.3;9.3 Gene Expression in the Rhizosphere Soil 9.3.1 Reporter Gene;231
6.4.4;9.3.2 Extraction and Characterization of mRNA;233
6.4.5;9.3.3 Linking Enzyme Activity to Gene Expression;235
6.4.6;9.3.4 Proteomic Approach;237
6.4.7;9.4 Linking Gene Expression to Functions: The Use of Stable Isotope Probes ( SIP);239
6.4.8;9.5 Other Techniques Used to Link Activity to Phylogenetic Information;241
6.4.9;9.6 The Metagenome;242
6.4.10;9.7 Microarray;243
6.4.11;9.8 Conclusions;245
6.4.12;References;248
6.5;Molecular Mechanisms of Biocontrol by Trichoderma spp.;255
6.5.1;10.1 Introduction;255
6.5.2;10.2 Mechanisms of Biocontrol: An Overview;257
6.5.3;10.3 Role of Hydrolytic Enzymes;259
6.5.4;10.4 Antibiosis;260
6.5.5;10.5 Induced Resistance;262
6.5.6;10.6 Signal Transduction and Biocontrol;263
6.5.7;10.7 The Genomics and Proteomics;264
6.5.8;10.8 The Transgenic Approach;266
6.5.9;10.9 Conclusion;268
6.5.10;References;270
7;Coexistence Between Molecules;275
7.1;Quorum Sensing in Bacteria-Plant Interactions;276
7.1.1;11.1 Introduction;276
7.1.2;11.2 The Paradigm of AHL Quorum Sensing: The lux System;277
7.1.3;11.3 Molecular Mechanisms of AHL Production and Detection 11.3.1 AHL Production;283
7.1.4;11.3.2 AHL Detection;284
7.1.5;11.4 The Complexity of QS: QS Networks, Interspecies Crosstalk, Quorum Quenching, QS Mimics and Host Responses 11.4.1 QS Networks;286
7.1.6;11.4.2 Interspecies Crosstalk;289
7.1.7;11.4.3 Quorum Quenching, QS Mimics and Host Response;291
7.1.8;11.5 Conclusions;293
7.1.9;References;293
7.2;Signals in the Underground: Microbial Signaling and Plant Productivity;301
7.2.1;12.1 Introduction;301
7.2.2;12.2 Peace Talks in the Underground: Plant Microbe Signaling in Rhizobium- Legume Symbiosis;302
7.2.3;12.2.1 The Legume Signals: Biosynthesis and Function of the Nodulation Gene Inducers;302
7.2.4;12.2.2 The Bacterial Signals: Biosynthesis of Nod Factors;305
7.2.5;12.3 PGPR Signals that Promote Plant Growth and Development;308
7.2.6;12.3.1 Biofertilization: Living Fertilizers in the Rhizosphere;308
7.2.7;12.3.2 Biocontrol: Warfare in the Underground – Signaling in Hostile Associations;310
7.2.8;12.3.3 Biocontrol: Alliances in the Underground – Microbial Signals Enhancing Resistance of Plants to Phytopathogens;314
7.2.9;12.3.4 Phytostimulation: Constructive Communication – Microbial Production of Plant Growth Promoting Compounds;315
7.2.10;12.3.5 Volatile Signals from PGPR: A Scent of Victory – Role in Plant Growth Promotion and Systemic Resistance;316
7.2.11;12.4 Conclusions and Future Prospects;317
7.2.12;References;319
7.3;Protein-Protein Interactions in Plant Virus Movement and Pathogenicity;329
7.3.1;13.1 Introduction;329
7.3.2;13.2 Cell-to-Cell Movement of Plant Viruses;330
7.3.3;13.3 The Role of the Cytoskeleton;332
7.3.4;13.4 Involvement of the Endomembrane System in Virus Movement;334
7.3.5;13.5 Modification of and Passage Through Plasmodesmata;336
7.3.6;13.6 Movement and Pathogenicity;337
7.3.7;13.7 Antiviral Defence by RNA Silencing;337
7.3.8;13.8 Plant Proteins Interacting with Viral Silencing Suppressors;339
7.3.9;13.9 Conclusion;342
7.3.10;References;343
7.4;Effects of Root Exudates in Microbial Diversity and Activity in Rhizosphere Soils;349
7.4.1;14.1 Introduction;349
7.4.2;14.2 Rhizodeposition: Classification, Quantification and Effects on Biotic Processes of the Rhizosphere Soil;350
7.4.3;14.3 Methodology for Collecting Root Exudates and Studying the Rhizosphere Effect;351
7.4.4;14.4 Effects of Root Exudates on Microbial Activity of Rhizosphere Soils;353
7.4.5;14.4.1 Competition Between Plants and Microorganisms for Soil Nutrients;353
7.4.6;14.4.2 Soil Respiration;355
7.4.7;14.4.3 Nutrient Dynamics and Functional Aspects of Rhizosphere Soil;356
7.4.8;14.4.4 Enzyme Activity in the Rhizosphere Soil;358
7.4.9;14.5 Microbial Diversity in the Rhizosphere;362
7.4.10;14.6 Effect of Transgenic Plants on Microbial Diversity in the Rhizosphere Soil;365
7.4.11;14.7 Conclusions;367
7.4.12;References;368
8;Methods to Study Plant and Microbe Coexistence;376
8.1;Siderotyping, a Straightforward Tool to Identify Soil and Plant- Related Pseudomonads;377
8.1.1;15.1 Introduction;377
8.1.2;15.2 Soil- and Plant-related Pseudomonads: A World within the Microbial World;378
8.1.3;15.3 Conventional Tools for Pseudomonad Characterization and Identification 15.3.1 Phenotypic Tools;379
8.1.4;15.3.2 Genotypic Tools;381
8.1.5;15.4 Siderotyping, or How to Identify Pseudomonads Through a Unique Phenotypic Character;382
8.1.6;15.5 An Application Within Plant-Pathogen Pseudomonads: Correlation Between Siderotyping and Numerical Taxonomy;386
8.1.7;15.6 Conclusions;387
8.1.8;References;388
8.2;Molecular Strategies for Identifying Determinants of Oomycete Pathogenicity;391
8.2.1;16.1 Introduction;391
8.2.2;16.1.1 Diseases Caused by Oomycetes;392
8.2.3;16.1.2 Taxonomy;393
8.2.4;16.2 Life Cycles;393
8.2.5;16.2.1 Pathogenic Lifestyles;394
8.2.6;16.2.2 Importance of Spores;395
8.2.7;16.3 Tools for Molecular Analyses;397
8.2.8;16.3.1 DNA-Mediated Transformation;398
8.2.9;16.3.2 Heterologous Systems for Functional Studies;399
8.2.10;16.3.3 Genomics Data;400
8.2.11;16.3.4 Classical Genetics;402
8.2.12;16.4 Molecular Insights into Pathogenicity;403
8.2.13;16.4.1 Developmental Biology of Spores;403
8.2.14;16.4.2 Genes Expressed in Colonized Plants;406
8.2.15;16.4.3 Cell Wall Degrading Enzymes (CWDEs);406
8.2.16;16.4.4 Effectors: Avirulence Factors, Elicitors, and Others;407
8.2.17;16.5 Conclusion;411
8.2.18;References;412
8.3;Molecular Methods for Studying Microbial Ecology in the Soil and Rhizosphere;419
8.3.1;17.1 Introduction;419
8.3.2;17.2 Analyzing Nucleic Acids;421
8.3.3;17.2.1 Extracting DNA and RNA;422
8.3.4;Soil Sample;422
8.3.5;17.2.2 Re-Association Kinetics;424
8.3.6;17.2.3 Cloning, Sequencing and Metagenomics;425
8.3.7;17.2.4 Sequence Databases;428
8.3.8;17.3 Phospholipid Fatty Acids (PLFA);428
8.3.9;17.4 Whole Soil Molecular Approaches 17.4.1 Stable Isotope Probing;429
8.3.10;17.4.2 Fluorescence In Situ Hybridization (FISH);430
8.3.11;17.4.3 Green Fluorescent Protein (GFP) and Other Marker Gene Technologies;432
8.3.12;17.4.4 Microarrays;433
8.3.13;17.5 PCR-based Methods;433
8.3.14;17.5.1 DNA Fingerprinting;434
8.3.15;17.5.2 Quantitative and Real-Time PCR;437
8.3.16;17.5.3 Statistical Methods;438
8.3.17;17.6 Conclusions;439
8.3.18;References;439
8.4;Morphotyping and Molecular Methods to Characterize Ectomycorrhizal Roots and Hyphae in Soil;445
8.4.1;18.1 Introduction;445
8.4.2;18.2 Background 18.2.1 Taxa Forming ECM;446
8.4.3;18.2.2 Description of ECM Structures in Roots and in Soils;446
8.4.4;18.3 Study Design;453
8.4.5;18.4 Morphotyping of ECM Roots 18.4.1 Introduction;453
8.4.6;18.4.2 Extraction of Roots from Soils and Sample Storage;454
8.4.7;Procedure;454
8.4.8;Procedure;455
8.4.9;Other Considerations;456
8.4.10;18.5 Molecular Identification of ECM Roots and Hyphae in Soil 18.5.1 Introduction;456
8.4.11;18.5.2 Guidelines for Sampling Design and Collection of Samples;456
8.4.12;18.5.3 DNA Extraction;457
8.4.13;Procedure;457
8.4.14;Other Considerations;458
8.4.15;Procedure;459
8.4.16;Other Considerations;460
8.4.17;18.5.4 Polymerase Chain Reaction (PCR);460
8.4.18;Procedure;463
8.4.19;Procedure;465
8.4.20;Other Considerations;465
8.4.21;18.5.5 PCR-Based Techniques;466
8.4.22;Procedure;467
8.4.23;Other Considerations;467
8.4.24;Procedure;468
8.4.25;Other Considerations;469
8.4.26;Procedure;470
8.4.27;Other Considerations;471
8.4.28;Procedure;472
8.4.29;Other Considerations;473
8.4.30;Procedure (Using ABI Prism 7700 Equipment; Applied Biosystems);475
8.4.31;Other Considerations;476
8.4.32;References;477
9;Index;483