Molecular Mechanisms of Plant and Microbe Coexistence (eBook)

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