Plant Surface Microbiology (eBook)

Preface 5
Contents 7
Contributors 24
1 The State of the Art 31
2 Root Colonisation Following Seed Inoculation 42
1 Introduction 42
2 Bacterial Root Colonisation 42
3 Analysis of Tomato Root Tip Colonisation After Seed Inoculation Using a Gnotobiotic Assay 43
4 Genetic Tools for Studying Root Colonisation 47
5 Behaviour of Root-Colonising Pseudomonas Bacteria in a Gnotobiotic System 51
6 Influence of Abiotic and Biotic Factors 54
7 Conclusions 57
References and Selected Reading 57
3 Methanogenic Microbial Communities Associated with Aquatic Plants 63
1 Introduction 63
2 Role of Plants in Emission of CH4 to the Atmosphere 63
3 Role of Photosynthates and Plant Debris for CH4 Production 66
4 Methanogenic Microbial Communities on Plant Debris 68
5 Methanogenic Microbial Communities on Roots 70
6 Interaction of Methanogens and Methanotrophs 72
References and Selected Reading 73
4 Role of Functional Groups of Microorganisms on the Rhizosphere Microcosm Dynamics 79
1 Introduction 79
2 General Aspects of Functional Groups of Soil Microorganisms 80
3 Carbon Cycle Functional Groups 81
4 Functional Groups of Microrganisms of the Nitrogen Cycle 83
5 Functional Groups of Microrganisms of the Sulphur Cycle 85
6 Functional Groups of Microrganisms of the Phosphorus Cycle 87
7 Dynamics of the Rhizosphere Functional Groups of Microrganisms 88
8 Relationship Among r and k Strategist Functional Groups 89
9 Arbuscular Mycorrhizal Fungi Dynamics in the Rhizosphere 89
10 Dynamics Among the Functional Microrganism Groups of the Carbon, Nitrogen, Phosphorus and Sulphur Cycles 93
References and Selected Reading 96
5 Diversity and Functions of Soil Microflora in Development of Plants 98
1 Introduction 98
2 Functional Diversity of Soil Microflora 99
3 Role of Soil Microflora in Plant Development 103
4 Plant Growth Promoting Substances Produced by Soil Microbes 115
5 Conclusions 117
References and Selected Reading 118
6 Signalling in the Rhizobia–Legumes Symbiosis 126
1 Introduction 126
2 The Signals from the Host Plants 128
3 Signals from the Microsymbionts 134
4 Signal Perception and Molecular Biology of Nodule Initiation 138
References and Selected Reading 141
7 The Functional Groups of Micro-organisms Used as Bio- indicator on Soil Disturbance Caused by Biotech Products such as Bacillus thuringiensis and Bt Transgenic Plants 147
1 Introduction 147
2 General Aspects of Bacillus thuringiensis 148
3 Survival in the Soil 149
4 History of Bacillus thuringiensis-Transgenic Plants 150
5 Persistence of the Protein Crystal in the Soil 151
6 Effect of Bacillus thuringiensis and Its Bio-insecticide Protein on Functional Soil Microorganism Assemblage 152
References and Selected Reading 156
8 The Use of ACC Deaminase-Containing Plant Growth- Promoting Bacteria to Protect Plants Against the Deleterious Effects of Ethylene 159
1 Introduction 159
2 Ethylene 160
3 ACC Deaminase 161
4 Conclusions 166
References and Selected Reading 167
9 Interactions Between Epiphyllic Microorganisms and Leaf Cuticles 171
1 Introduction 171
2 Physical and Chemical Parameters of the Phyllosphere 173
3 Leaf Surface Colonisation and Species Composition 175
4 Alteration of Leaf Surface Wetting 176
5 Interaction of Bacteria with Isolated Plant Cuticles 178
6 Conclusions 179
References and Selected Reading 180
10 Developmental Interactions Between Clavicipitaleans and Their Host Plants 183
1 Introduction 183
2 Endophyte/Epibiont Niche 183
3 Coevolution of Clavicipitalean Fungi with Grass Hosts 184
4 The Jump from Insects to Plants 184
5 Developmental Differentiation of Endophytic and Epiphyllous Mycelium 186
6 Modifications of Plant Tissues for Nutrient Acquisition 191
7 Evolution of Asexual Derivatives of Epichloë 197
8 Conclusions 201
References and Selected Reading 201
11 Interactions of Microbes with Genetically Modified Plants 205
1 Introduction 205
2 Changes in Microbial Communities Induced by Genetically Modified Plants 207
3 Impact of Genetically Modified Plants on Symbiotic Interactions 210
4 Horizontal Gene Transfer 212
5 Conclusions 217
References and Selected Reading 218
12 Interaction Between Soil Bacteria and Ectomycorrhiza- Forming Fungi 223
1 Introduction 223
2 Bacteria 224
3 Bacterial Community Structure 224
4 Association of Bacteria with Fungal/Ectomycorrhizal Structures 225
5 Bacteria Associated with Sporocarps and Ectomycorrhiza 226
6 Benefits from Bacteria/Ectomycorrhiza Interactions 227
7 Possible Mechanisms of Interaction 228
8 Biochemical Evidence for Interaction 229
9 Impacts of Environmental Pollution 232
10 Conclusions 232
References and Selected Reading 233
13 The Surface of Ectomycorrhizal Roots and the Interaction with Ectomycorrhizal Fungi 237
1 Introduction 237
2 Long and Short Roots of Ectomycorrhiza-Forming Plants 238
3 A Cuticle-Like Layer on the Surface of Short Roots 240
4 Involvement of the Cuticle-Like Layer in Mycorrhiza Formation 244
5 Involvement of the Cuticle-Like Layer in Hyphal Attachment 244
6 Digestion of the Suberin Layer and the Cell Wall of the Root Cap 246
7 Hartig Net Formation 247
8 Pectins in the Cortical Cell Walls of Nonmycorrhizal Long and Mycorrhizal Short Roots 248
9 Conclusions 249
References and Selected Reading 250
14 Cellular Ustilaginomycete – Plant Interactions 253
1 Introduction 253
2 The Term Smut Fungus 253
3 Life Cycle 254
4 Hosts 254
5 Cellular Interactions 255
6 Conclusions 261
References and Selected Reading 262
15 Interaction of Piriformospora indica with Diverse Microorganisms and Plants 263
1 Introduction 263
2 Interaction with Microorganisms 264
3 Interaction with Bryophyte 268
4 Interaction with Higher Plants 268
5 Cell Wall Degrading Enzymes 286
6 Conclusions 289
References and Selected Reading 290
16 Cellular Basidiomycete–Fungus Interactions 292
1 Introduction 292
2 Occurrence of Mycoparasites Within the Basidiomycota 292
3 Hosts 293
4 Cellular Interactions 293
5 Basidiomycetous Mycoparasitism, a Result of Convergent Evolution? 302
6 Conclusions 303
References and Selected Reading 303
17 Fungal Endophytes 305
1 Introduction 305
2 Definition of a Fungal Endophyte 305
3 Role of Endophytes 306
4 Modes of Endophytic Infection and Colonization 307
5 Isolation of Endophytes 308
6 Molecular Characterization of Endophytes 309
7 Are Endophytes Responsible for Host Exclusivity/ Recurrence in Saprobic Fungi? 310
8 Conclusions 311
References and Selected Reading 312
18 Mycorrhizal Development and Cytoskeleton 317
1 Introduction 317
2 Cytoskeletal Components 317
3 Organization of Cytoskeleton in Endomycorrhiza 322
4 Organization of Cytoskeleton in Ectomycorrhiza 324
5 Regulation of Actin Cytoskeleton Organization in Fungal Hyphae and Plant Cells 329
6 Actin Binding Proteins 331
7 Microtubule-Associated Proteins 332
8 Cell Cycle and Cytoskeleton in Mycorrhiza 337
9 Cytoskeletal Research Methods 339
References and Selected Reading 342
19 Functional Diversity of Arbuscular Mycorrhizal Fungi on Root Surfaces 354
1 Introduction 354
2 Mycorrhiza Formation and Ecological Specificity 355
3 Functioning of Arbuscular Mycorrhizas in Nutrient Exchange 357
4 Functional Diversity of Arbuscular Mycorrhizal Fungi in Root and Hyphal Interactions 361
5 Role of Arbuscular Mycorrhizal Fungi Associated with Roots in Soil Aggregation 363
6 Environmental Influence on Functional Diversity of Arbuscular Mycorrhizal Fungi 364
7 Role of Plant Mutants in Studying the Interactions Between Arbuscular Mycorrhizal Fungi and Roots 364
8 Conclusion and Future Research Needs 366
References and Selected Reading 366
20 Mycorrhizal Fungi and Plant Growth Promoting Rhizobacteria 373
1 Introduction 373
2 Main Types of Rhizosphere Microorganisms 374
3 Mycorrhizal Fungi 375
4 Plant Growth Promoting Rhizobacteria 376
5 Reasons for Studying Arbuscular Mycorrhizal Fungi and Plant Growth Promoting Rhizobacteria Interactions and Main Scenarios 378
6 Effect of Plant Growth Promoting Rhizobacteria on Mycorrhiza Formation 379
7 Effect of Mycorrhizas on the Establishment of Plant Growth Promoting Rhizobacteria in the Rhizosphere 379
8 Interactions Involved in Nutrient Cycling and Plant Growth Promotion 381
9 Interactions for the Biological Control of Root Pathogens 383
References and Selected Reading 384
21 Carbohydrates and Nitrogen: Nutrients and Signals in Ectomycorrhizas 394
1 Introduction 394
2 Trehalose Utilization by Ectomycorrhizal Fungi 395
3 Carbohydrate Uptake 395
4 Carbohydrate Metabolism 397
5 Carbohydrate Storage 397
6 Carbohydrates as Signal, Regulating Fungal Gene Expression in Ectomycorrhizas 398
7 Nitrogen 401
8 Utilization of Inorganic Nitrogen 402
9 Utilization of Organic Nitrogen 403
10 Proteolytic Activities of Ectomycorrhizal Fungi 403
11 Uptake of Amino Acids 404
12 Regulation of Fungal Nitrogen Export in Mycorrhizas by the Nitrogen- Status of Hyphae 404
13 Carbohydrate and Nitrogen-Dependent Regulation of Fungal Gene Expression 406
14 Conclusions 406
References and Selected Reading 407
22 Nitrogen Transport and Metabolism in Mycorrhizal Fungi and Mycorrhizas 413
1 Introduction 413
2 Nitrate and Nitrite Transport 415
3 Ammonium Transport 418
4 Amino Acid Transport 423
5 Reduction of Nitrate to Nitrite and Ammonium 425
6 Assimilation ofAmmonium 429
7 Amino Acid Metabolism 437
8 Conclusion and Future Prospects 439
References and Selected Reading 441
23 Visualisation of Rhizosphere Interactions of Pseudomonas and Bacillus Biocontrol Strains 450
1 Introduction 450
2 Tomato Foot and Root Rot and the Need for Biological Control 450
3 Selection of Antagonistic Strains 451
4 In Vivo Biocontrol Assays 453
5 Microscope Analysis of Infection and Biocontrol 456
6 Conclusions 462
References and Selected Reading 462
24 Microbial Community Analysis in the Rhizosphere by in Situ and ex Situ Application of Molecular Probing, Biomarker and Cultivation Techniques 468
1 Introduction 468
2 In Situ Studies of Microbial Communities Using Specific Fluorescence Labeling and Confocal Laser Scanning Microscopy 470
3 Ex Situ Studies of Microbial Communities After Separation of Rhizosphere Compartments 476
4 Conclusions 482
References and Selected Reading 483
25 Methods for Analysing the Interactions Between Epiphyllic Microorganisms and Leaf Cuticles 489
1 Introduction 489
2 Physical Characterisation of Cuticle Surfaces by Contact Angle Measurements 489
3 Chemical Characterisation of Cuticle Surfaces 491
4 A New in Vitro System for the Study of Interactions Between Microbes and Cuticles 493
5 Conclusions 504
References and Selected Reading 504
26 Quantifying the Impact of ACC Deaminase- Containing Bacteria on Plants 506
1 Introduction 506
2 Selection of Bacterial Strains that Contain ACC Deaminase 506
3 Culture Conditions for the Induction of Bacterial ACC Deaminase Activity 508
4 Gnotobiotic Root Elongation Assay 509
5 Measurement of ACC Deaminase Activity 510
6 Measurement of ACC in Plant Roots, Seed Tissues and Seed Exudates 512
References and Selected Reading 518
27 Applications of Quantitative Microscopy in Studies of Plant Surface Microbiology 520
1 Introduction 520
2 Quantitation of Symbiotic Interactions Between Rhizobium and Legumes by Visual Counting Techniques 521
3 Quantitation of Symbiotic Interactions Between Rhizobium and Legumes by Image Analysis 543
4 A Working Model for Very Early Stages of Root Hair Infection by Rhizobia 546
5 Improvements in Specimen Preparation and Imaging Optics for Plant Rhizoplane Microbiology 546
6 CMEIAS: A New Generation of Image Analysis Software for in Situ Studies of Microbial Ecology 548
7 Conclusions 561
References and Selected Reading 561
28 Analysis of Microbial Population Genetics 568
1 Introduction 568
2 Materials for RAPD, AFLP and ITS 569
3 RAPD 570
3 AFLP 573
6 ITS-RFLP analysis 576
7 Statistical analysis 578
8 Concluding Remarks 580
References and Selected Reading 581
29 Functional Genomic Approaches for Studies of Mycorrhizal Symbiosis 583
1 Introduction 583
2 Material and Methods 584
3 RNA Quantification 586
4 Conversion Protocol 593
5 Troubleshooting 594
6 Sequencing Strategies 594
7 Macroarrays 598
8 Generation of Radiolabeled Probes 601
9 Hybridization of Macroarrays to Radiolabeled Probes 602
10 Data Analysis 602
11 Example of Laccaria bicolor Macroarrays 604
12 Conclusions 606
References and Selected Reading 607
30 Axenic Culture of Symbiotic Fungus Piriformospora indica 609
1 Introduction 609
2 Morphology 609
3 Taxonomy of the Fungus 611
4 Chlamydospore Formation and Germination 613
5 Cultivation 613
6 Carbon and Energy Sources 616
7 Biomass on Individual Amino Acids 620
8 Growth on Complex Media 620
9 Phosphatic Nutrients 621
10 Composition of Media 622
11 Conclusions 628
References and Selected Reading 628
Subject Index 630