Biocommunication in Soil Microorganisms (eBook)

Preface 6
Why Biocommunication of Soil Microorganisms? 6
On the Interorganismic Level (Between Same and Related Organisms) 8
On the Intraorganismic Level 9
In Vitro Analyses Lack Context-Dependent Behaviors of Real Life Habitats 11
Biocommunication of Soil Microorganisms 11
Contributions to the biocommunication of soil microorganisms 12
References 13
Contents 14
Contributors 18
Chapter 1: Introduction: Key Levels of Biocommunication of Bacteria 22
1.1 Introduction: Communicative Competences of Bacteria 22
1.2 Semiochemical Vocabulary and Communicative Goals of Bacteria 24
1.3 Transorganismic Communication of Soil Bacteria 25
1.4 Interorganismic Communication 26
1.4.1 Interpretation and Coordination 27
1.5 Intraorganismic Communication 30
1.5.1 Intracellular Communication 32
1.5.2 Bacterial Evolution and the Agents of Natural Genome Editing 33
1.5.3 Lytic vs. Persistent Viral Life Strategies 33
1.5.4 Bacteria as Global Habitat for Viruses 35
1.6 The Origins of Bacterial Group Identity 37
1.6.1 Obligate Viral Settlers of Bacteria 37
1.6.2 The Role of Persistent Viruses in Gene Word Order of Bacteria 39
1.6.3 Infection-Driven Group Identity and Group Immunity 40
1.7 Transfer of Viral Competences as Modular Tools 41
1.7.1 Molecular Identity Markers 41
1.7.2 Persistent Phages Determine Bacterial Identity 41
1.7.3 Addiction Modules Function as Counterbalanced Viral Competences 43
1.7.4 The Persistent Viral Lifestyle of Plasmids and the Role of tRNAs 44
1.8 Swarming Group Behavior and Group Identity 45
1.9 Genetic Content Operators and Viral Gene Factories 47
1.10 Conclusion 48
References 48
Part I: Intracellular Biocommunication 56
Chapter 2: Communication Among Phages, Bacteria, and Soil Environments 57
2.1 Introduction 57
2.2 General Concepts 58
2.2.1 Microbe-Containing Environments 58
2.2.2 Communication and Microorganisms 61
2.2.3 Bacteriophages, Bacteria, and Environments 62
2.3 Pathways of Communication in Soil 64
2.3.1 Bacteria-to-Phage Communication 65
2.3.1.1 Bacterial Impact on Phage Phenotype 65
Destructive Infection: Antagonism, Deception, and Primitive Immunity 65
Reductive Infection: Sleeping with the Enemy 66
2.3.1.2 Bacterial Impact on Phage Genotype (Evolution) 66
2.3.1.3 Bacterial Impact on Phage Location 67
2.3.2 Phage-to-Bacteria Communication 68
2.3.2.1 The Many Costs of Phage 68
2.3.2.2 Phage Infection as Symbiosis 68
2.3.2.3 Phage-Mediated Horizontal Gene Transfer (Transduction) 70
2.3.2.4 Kill the Winner 70
2.3.3 Phage-to-Bacteria-to-Environment Communication 73
2.3.3.1 Lysis-Mediated Phage-Environment Communication 73
2.3.3.2 Prophage-Mediated Environmental Modification 74
2.3.4 Phage-to-Environment Communication 75
2.3.5 Environment-to-Phage and/or to-Bacteria Communication 75
2.3.6 Environment-to-Phage Communication 77
2.3.6.1 Predation of Phages 77
2.3.6.2 Phage Movement 77
2.3.6.3 Phage Survival 78
2.4 Conclusion 79
References 79
Chapter 3: Soil Bacteria and Bacteriophages 86
3.1 Soil Bacteria Types, Characteristics, Prevalence, Genetic Diversity, and Source 86
3.1.1 Soil (General) 86
3.1.1.1 Soil Bacteria Characteristics, Prevalence, Genetic Diversity, and Source 86
3.1.2 Soil Bacteria (Pathogens, Phytopathogens) and Nonpathogenic 94
3.1.2.1 Human Pathogens 94
3.1.2.2 Phytopathogens 95
3.1.2.3 Nonpathogenic Bacteria 96
3.1.3 Bacteriophages (Abbr. Phages) (Systematics, Life Cycle, and Genetics) 97
3.1.3.1 Phages Systematic 97
3.1.3.2 Phages Life Cycles 101
3.1.3.3 Phages Genetic 103
3.1.4 Interaction Between Phages and Soil-Bacteria 104
3.1.5 Mutual Effect of Microbial Activity in Soil and Effect on Bacteriophages 107
3.1.6 Genetic Transfer Involving Bacteriophages and Bacteria in Soil Environment 112
3.1.7 Bacteriophage Transport in the Subsurface and Soil Bacteria 114
3.1.8 Discussion, Remarks and Thoughts 118
References 121
Chapter 4: Soil Phage Ecology: Abundance, Distribution, and Interactions with Bacterial Hosts 132
4.1 Introduction 132
4.2 Measuring Viral Abundance in Soils 133
4.2.1 Targeted Assays 133
4.2.2 Total Direct Counts of Viruses in Soil 134
4.3 Trends in Soil Viral Abundance and Distribution 135
4.4 The Virus-to-Bacterium Ratio 138
4.5 Viral Diversity in Soil Ecosystems 140
4.5.1 Marker Genes 140
4.5.2 Pulsed-Field Gel Electrophoresis 141
4.5.3 Randomly Amplified Polymorphic DNA-PCR 141
4.5.4 Transmission Electron Microscopy 142
4.5.5 Metagenomic Analysis of Soil Viral Assemblages 143
4.6 The Importance of Lysogeny in Soil Environments 144
4.7 Viral Impacts in Soil Ecosystems 145
4.7.1 Bacterial Mortality, Clonal Diversity, and Community Succession 145
4.7.2 Phage Conversion, Host Fitness, and Horizontal Gene Transfer 147
4.8 Conclusion 148
References 149
Chapter 5: Identification and Analysis of Prophages and Phage Remnants in Soil Bacteria 156
5.1 Introduction 156
5.1.1 Overview of Soil Microbes 156
5.1.2 Horizontal Gene Transfer in Bacteria 157
5.1.3 Significance of Prophages 158
5.1.4 Prophages and Associated Fitness Islands 159
5.2 Soil Prophage Genomics 160
5.2.1 Prophage Existence in Soil Bacteria 160
5.2.1.1 Prophages Detected by Protein Similarity Approach 160
5.2.1.2 Prophages Detected by DRAD 165
5.2.1.3 Prophages Reported by Other Methods Compared with PSA and DRAD 170
5.2.2 Impact of Prophages in Soil Bacteria 172
5.2.2.1 Organization of Prophages in Selected Soil Bacteria 172
5.2.2.2 Prophage Encoded Gene Clusters in Soil Bacteria 173
5.3 Summary and Conclusions 175
References 176
Chapter 6: Back to the Soil: Retroviruses and Transposons 180
6.1 Soil Bacteria and Associated Retroelements 180
6.1.1 Insertion Sequences 181
6.1.2 Beneficial Effects of Horizontal Transfer of Genes 182
6.1.3 Abundance of Transposons in Soil Bacteria 183
6.2 Origin of Transposons 185
6.2.1 Single Stranded RNA to Double-Stranded Nucleic Acid 185
6.2.2 Pretransposons and Archea 186
6.2.3 Birth of Intracellular or Molecular Immunity 187
6.2.4 Self vs. Nonself and REs 188
6.3 Endogenous Retroviruses from Soil to Mammals: Protective Lessons 189
6.4 Innate Immunity and Development of Immunity Based on Pattern Recognition 191
6.5 Evolution of Antitransposon Resistance in Bacteria to Large Mammals 192
6.6 The Big Bang of Immunity 197
6.6.1 Adaptive Immunity and TEs 197
6.6.2 Generation of Deversity and Somatic Recombination 198
6.6.3 RAG1/RAG2 Dilemma 199
6.6.4 Classical Immunity Barrowed Its Model from Molecular Immunity 200
6.7 Summary and Conclusion 201
Appendix 202
References 203
Chapter 7: Ubiquitous Bacteriophage Hosts in Rice Paddy Soil 207
7.1 Introduction 207
7.2 Abundance and Morphology of Viruses in the Floodwater 208
7.3 Abundance of Bacteriophages of Common Heterotrophic Bacteria in the Floodwater 210
7.4 Morphology and Host Range of Sphingomonas/Novosphingobium Phages 212
7.5 Frequency of Phage-Infected Bacterial Cells in the Floodwater 215
7.6 Comparison of Lysogeny Between Copiotrophic and Oligotrophic Bacteria 217
7.7 Characteristics and Diversity of Phages in Rice Field Soils - Estimation by g23 Gene Sequences of T4-Type Phages 221
7.8 Changes in Major Capsid Genes (g23) of T4-Type Bacteriophages with Soil Depth 225
7.9 Conclusions 228
References 229
Chapter 8: Phage Biopesticides and Soil Bacteria: Multilayered and Complex Interactions 232
8.1 Phages as Biopesticides 232
8.1.1 Aerial Application of Phage Biopesticides and Impact on Soil Ecology 233
8.2 Phage Biopesticides in Greenhouse Soils: Control of Pectobacterium carotovorum 234
8.3 Phages and Rhizobacteria 235
8.3.1 Effect of Soil on Phages 236
8.3.2 Phages in the Rhizosphere 237
8.3.3 Effect of Phages on Root Nodulation 238
8.3.4 Effect of Phages on Yield and Disease Control 238
8.4 Lysogeny and Soil-Phage Interaction 239
8.4.1 Lysogeny as a Bacteriophage Survival Mechanism 239
8.4.2 Phage Gene Transfer in Soil 240
8.5 Detection of Phages in Soil Systems 241
8.5.1 Isolation of Phage Particles 242
8.5.1.1 Enrichment Methods 242
8.5.1.2 Elution Methods 243
8.5.2 Direct Detection by Microscopy 244
8.5.3 Direct Detection of Biopesticides by Molecular Methods 244
8.6 Summary 246
References 247
Chapter 9: Interactions Between Bacteriophage DinoHI and a Network of Integrated Elements Which Control Virulence in Dichelobacter nodosus, the Causative Agent of Ovine Footrot 253
9.1 Introduction 253
9.2 Transmission of Ovine Footrot 253
9.2.1 Virulence of D. nodosus 254
9.3 Mobile Genetic Elements in the D. nodosus Genome 254
9.3.1 The intA Element 255
9.3.2 The intB Element 255
9.3.3 The intC Element 256
9.3.4 The intD Element 257
9.3.5 The Virulence-Related Locus, vrl 257
9.3.6 The Bacteriophage DinoHI 258
9.3.7 Element X 258
9.4 A Model for the Control of Virulence by Integrated Genetic Elements 258
9.4.1 CsrA 258
9.4.2 PnpA 260
9.4.3 10Sa RNA 260
9.4.4 Model for Virulence 260
9.5 Different Forms of the intA Element 261
9.6 Interactions Between the Integrated Genetic Elements 262
9.6.1 vapGH and Bacteriophage Immunity 262
9.6.2 A Repressor Gene Common to Bacteriophage DinoHI and the intB Element 264
9.6.3 Interactions Between the vrl, DinoHI and the intA Element 265
9.6.4 Mobilisation of the intA Element by the intD Mobilisation Cassette 265
9.6.5 Common Repeated Sequences on the intA and intD Elements 266
9.6.6 Relationships Between the intC and intD Elements 266
9.7 Evolutionary Significance 266
9.8 Conclusions 267
References 267
Chapter 10: Gene Network Holography of the Soil Bacterium Bacillus subtilis 270
10.1 Introduction 270
10.2 Functional Holography Analysis of Gene Expression 272
10.2.1 Holographic Presentation of the Genes 272
10.2.2 Internal Structure of Gene Operons 273
10.3 Minimal Spanning Tree Analysis 276
10.4 Time Progression of the Sporulation and Competence Networks 278
10.4.1 Time Progress of Sporulation Initiation Gene Network 279
10.4.2 Time Progress of Competence Gene Network Response 282
10.5 Time Progress of Cannibalism Gene Network 285
10.6 Discussion 291
References 293
Chapter 11: Population and Comparative Genomics Inform Our Understanding of Bacterial Species Diversity in the Soil 297
11.1 Introduction 297
11.2 Species Classification by 16s rRNA Comparison 298
11.3 Whole Genome Comparisons Aid Species Classification 299
11.4 Analyses by Genome-Tree Building 300
11.5 The Core Genome Hypothesis 301
11.6 Conclusion 303
References 304
Part II: Intercellular and Trans-Kingdom Biocommunication 307
Chapter 12: Plasmids of the Rhizobiaceae and Their Role in Interbacterial and Transkingdom Interactions 308
12.1 Introduction 308
12.2 Pathogenic Members of the Rhizobiaceae: Agrobacteria 309
12.2.1 Agrobacterium and Plant Hypertrophies 309
12.2.2 Ti and Ri Plasmids 312
12.2.3 Interbacterial and Host-Bacterial Signaling 316
12.2.4 Agrobacterial Genomes 320
12.3 Symbiotic Members of the Rhizobiaceae: Rhizobia 322
12.3.1 Rhizobia, Legumes, and Nitrogen Fixation 322
12.3.2 Nodules and the Nodulation Process 324
12.3.3 Rhizobial Genomes 326
12.3.4 Horizontal Transfer and Quorum Sensing 331
12.3.5 Genome Plasticity in Alpha-Rhizobia 334
12.4 Conclusions 335
References 338
Chapter 13: Quorum Sensing and Quorum Quenching in Soil Ecosystems 351
13.1 Introduction 352
13.1.1 Quorum Sensing 352
13.1.1.1 A Brief History 352
13.1.1.2 Multiple Systems, Multiple Signals 353
13.1.2 Quorum Quenching 357
13.2 Biological Significance of QQ 358
13.2.1 Known Organisms and Activities Involved in AHL Signal Degradation 358
13.2.1.1 Oxidase and Reductase 359
13.2.1.2 Amidohydrolases 361
13.2.1.3 Lactonases 362
13.2.2 The Biology of QS Signal Degradation 362
13.2.2.1 The Agrobacterium Paradigm 363
13.2.2.2 QS and QQ Among Natural Microbial Communities in Soils 365
AHL-Based QS and QQ in the Soil Environment 365
Degradation of Non-AHL, QS Signals 366
13.3 Applied Outcomes: Ecological Engineering of QQ-Bacteria in the Rhizosphere 367
13.4 QS: A Broad Communication System 368
13.4.1 QS Regulation Is Not Restricted to Bacteria 368
13.4.2 Beyond Sensing a Quorum 368
13.4.3 QS Signals May Be Involved in Interkingdom Communications 369
13.5 Concluding Remarks 370
References 371
Chapter 14: Integration of Cell-to-Cell Signals in Soil Bacterial Communities 380
14.1 Introduction 380
14.2 Examples of QS in Soil Bacterial Communities 381
14.2.1 The Role of Sinorhizobium meliloti Quorum Sensing in the Interaction with Its Plant Hosts 383
14.2.1.1 Signal Exchange Leading to the Establishment of the S. meliloti-Medicago Symbiosis 383
14.2.1.2 QS Signal Generation During S. meliloti-Medicago Interactions 384
14.2.1.3 Responses of S. meliloti to AHL QS Signals 385
14.2.1.4 Plant Hosts Detect Rhizobial AHLs and Manipulate Bacterial Signaling 386
14.2.1.5 S. meliloti Responds to Non-AHL QS Signals from Other Microbes 387
14.2.2 QS in Pseudomonas aeruginosa, a Model Environmental Bacterium and Opportunistic Pathogen 388
14.2.3 Integration of QS into Global Regulatory Networks 391
14.3 GacS/GacA Is a Two-Component System Controlling Environmental Adaptation, Biofilm Formation, and Motility in gamma-Proteobacteria 391
14.3.1 Discovery of GacA and GacS in gamma-Proteobacteria 391
14.3.2 GacS-GacA Signal Transduction 393
14.3.2.1 Structure/Function Analysis of GacS Orthologs 393
14.3.2.2 Sensor Kinases RetS and LadS Modulate Function of GacS 395
14.3.3 Structure/Function Analysis of GacA Orthologs 396
14.3.4 GacA Regulons in Soil gamma-Proteobacteria 399
14.3.4.1 Evolutionarily Conserved Targets of the GacS/GacA Orthologs: The csr RNA 399
14.3.4.2 Orthologs of gacS/gacA Are Central to Biofilm Formation in gamma-Proteobacteria 401
14.4 The Elusive GacS Signal 401
14.4.1 Evidence for the Self-Produced GacS Signal 402
14.4.2 Evidence for the Eukaryotic Contribution to the GacS/GacA-Mediated Signaling 402
14.5 Conclusions and Future Directions 403
References 404
Chapter 15: Beneficial Rhizobacteria Induce Plant Growth: Mapping Signaling Networks in Arabidopsis 413
15.1 Agricultural Impact of Plant Growth-Promoting Rhizobacteria 413
15.2 Low-Molecular Weight Bacterial Signals 414
15.3 Probing Bacterial-Mediated Plant Growth Signaling Pathways 414
15.3.1 Bacterial Regulation of Auxin Synthesis, Transport, and Distribution in Planta 415
15.3.2 Transcriptional Regulation of Cell Wall Rigidity by GB03 416
15.3.3 GB03 Volatile Organic Compounds Elevate Plant Energy Acquisition 417
15.3.4 GB03 Regulates Iron Assimilation Independent of Metal Chelation 418
15.4 GB03 Volatile Organic Compounds Augment Arabidopsis Reproductive Success 419
15.5 Induced Growth Promotion Beyond the Model Plant 419
References 420
Chapter 16: Signal and Nutrient Exchange in the Interactions Between Soil Algae and Bacteria 423
16.1 Introduction 423
16.2 Phylogenetic Diversity of Algal-Associated Prokaryotic Microbiota 424
16.3 Nutrient and Signal Exchange in Algal-Bacterial Interactions 426
16.3.1 Carbon and Nitrogen Exchange in the Phycosphere 426
16.3.2 Bacterially Produced Plant Hormones Stimulate Algal Growth 428
16.3.3 Bidirectional Vitamin Exchange and Vitamin-Mediated Signaling in Algal-Bacterial Interactions 428
16.3.4 The Role of Algal Signals in Modulating Bacterial Quorum Sensing 430
16.4 Conclusions and Future Directions 433
References 433
Chapter 17: Communication Among Soil Bacteria and Fungi 437
17.1 Introduction 437
17.2 Antagonistic Interactions 438
17.2.1 Alteration of Abiotic Environmental Factors 438
17.2.2 Antibiotic Production 438
17.2.3 Trehalose 439
17.2.4 Excretion of Extracellular Enzymes 440
17.3 Symbiotic Interactions 441
17.3.1 Mycorrhization Helper Bacteria 441
17.3.2 Endosymbionts 442
17.4 Concluding Remarks 443
References 444
Chapter 18: Microbe-Microbe, Microbe-Plant Biocommunication 448
18.1 Introduction 448
18.2 Rhizosphere and Biocommunication 451
18.2.1 What Is Rhizosphere/Mycorhizosphere? 451
18.2.2 Rhizoplane Organisms 452
18.2.3 Root Exudates 454
18.3 Rhizobia-Legumes Symbiosis 456
18.4 QS in Rhizobium 456
18.5 QS in Pseudomonas aeruginosa 456
18.6 QS in Azotobacter 457
18.7 QS in Agrobacterium tumefaciens 457
18.8 Microbe-Plant Communication 460
18.9 QS and Mycorrhizal Fungi or Beneficial Endophytes: Tripartite Associations Between Plants, Fungi, and Bacteria 463
18.10 Parallel Communication of Plant Roots with Bacteria and Fungi 466
18.11 Conclusion 467
18.12 Future Perspectives 468
References 469
Index 474