Microbiology of Extreme Soils (eBook)

Foreword 6
Preface 7
Contents 10
Contributors 12
Principles of Extreme Soil Microbiology 17
The Microbiological Promises of Extreme Soils 18
1.1 Introduction 18
1.2 Extreme Soils and Microbial Community Structure and Evolution 19
1.3 Extreme Soils and Microbial Physiology 20
1.4 Microbial Functions in Extreme Soils 21
1.5 Practical Value of Extreme Soils 21
1.6 Extreme Soils and the Boundaries of Life 22
1.7 Extreme Soils and Our Past 24
1.8 Extreme Soils and Our Future 25
References 26
Microbial Diversity, Life Strategies, and Adaptation to Life in Extreme Soils 29
2.1 Introduction: What Is an Extreme Environment? 29
2.2 Physicochemical Factors Limiting to Life 32
2.3 Soil as Habitat for Micro-Organisms 40
2.4 Extreme Soils 42
2.5 Microbial Diversity and Community Structure in Extreme Soils 46
2.6 Conclusions: The Significance of Studying Extremophiles in Soil 51
References 52
Extreme Views on Prokaryote Evolution 58
3.1 Introduction 58
3.2 Scope and Limitations of This Review 59
3.3 Selection as It Occurs in the Laboratory and in the Real World 60
3.4 Bacteria in Soils, a Substrate for Evolutionary Change 61
3.5 The Context of Extreme Soils 69
3.6 The Extreme Soil Adaptive Landscapes 71
3.7 Conclusions 76
References 76
Biodiversity: Extracting Lessons from Extreme Soils 84
4.1 Introduction 84
4.2 Lesson One: Biodiversity in Soils Is Hidden 86
4.3 Lesson Two: Soil Species Have More Than One Survival Strategy 87
4.4 Lesson Three: Extreme Soils Are Ecosystems 88
4.5 Lesson Four: Soils Are Major Drivers of Biodiversity 90
4.6 Lesson Five: Global Changes Are Rapidly Changing Soils 92
4.7 Conclusions 93
References 94
Natural Extreme Soils 98
Halophilic and Halotolerant Micro-Organisms from Soils 99
5.1 Introduction 99
5.2 Microbial Diversity 100
5.3 Halophilic Micro-Organisms from Soils 103
5.4 Biotechnological Applications 113
5.5 Conclusions 117
References 118
Atacama Desert Soil Microbiology 128
6.1 Introduction 128
6.2 Atacama Soil Organics 130
6.3 Isolation and Detection of Heterotrophic Bacteria 133
6.4 Cyanobacteria-Dominated Microbial Consortia 135
6.5 Patchiness of Transition from High- to Low-Density Populations 139
6.6 Relevance to Exobiology 139
6.7 Conclusions: NASA-Supported Research in the Atacama Desert 140
References 141
Microbial Communities and Processes in Arctic Permafrost Environments 144
7.1 Introduction 144
7.2 The Permafrost Environment 146
7.3 The Permafrost Microbiota 150
7.4 Role and Significance of the Microbiota 157
7.5 Conclusions: Future Directions for Research 160
References 161
Aerobic, Endospore-Forming Bacteria from Antarctic Geothermal Soils 166
8.1 Introduction: Taxonomy of Bacillus Species and Related Genera 166
8.2 Habitats of Thermophiles 169
8.3 Antarctic Geothermal Soils 170
8.4 Endospore Formers from Antarctic Geothermal Soils 175
8.5 Adaptations for Growth at High Temperatures 179
8.6 Nutrition and Growth Conditions of Thermophiles 181
8.7 Conclusions 182
References 182
Peatland Microbiology 187
9.1 Introduction 187
9.2 General Description of Peatlands 187
9.3 Cycles in Peatlands 192
9.4 Diversity of Organisms Colonizing Peatlands 194
9.5 Conclusions 209
References 209
Subsurface Geomicrobiology of the Iberian Pyritic Belt 214
10.1 Introduction 214
10.2 The Río Tinto Ecosystem 215
10.3 Geomicrobiology of the Iron Cycle in the Río Tinto Ecosystem 216
10.4 Subsurface Geomicrobiology of the Iberian Pyritic Belt 219
10.5 Conclusions 229
References 230
The Potential for Extant Life in the Soils of Mars 233
11.1 Introduction 233
11.2 Mars as a Microbial Habitat 235
11.3 Searching for Microbes in the Soils of Mars 239
11.4 Detection of Life in Martian Soils 243
11.5 Conclusions 245
References 247
Anthropogenic Extreme Soils 252
Bacteriology of Extremely Cold Soils Exposed to Hydrocarbon Pollution 253
12.1 Introduction 253
12.2 An Overview of the Bacteriology of Pristine Antarctic Soils 255
12.3 Hydrocarbons in Polar Soils 258
12.4 Bacteriology of Hydrocarbon-Contaminated Polar Soils 262
12.5 Bioremediation in Extremely Cold Soils 267
12.6 Major Challenges for the Near Future 272
12.7 Conclusions 273
References 274
Microbiology of Oil-Contaminated Desert Soils and Coastal Areas in the Arabian Gulf Region 281
13.1 Introduction 281
13.2 The Gulf Oil Spill 282
13.3 Composition of Crude Oil 283
13.4 General Description of Oil-Utilizing Micro-Organisms 283
13.5 Oil-Utilizing Micro-Organisms in the Arabian Gulf Desert Soils 285
13.6 Micro-Organisms in the Gulf Coastal Areas 286
13.7 Extremophilic Oil-Utilizing Micro-Organisms 288
13.8 Microbial Consortia and Associations 289
13.9 Responses of Micro-Organisms to Environmental Variables 290
13.10 Bioremediation Strategies 295
13.11 Conclusions 298
References 299
Microbial Communities in Fire-Affected Soils 305
14.1 Introduction 305
14.2 The Effects of Surface Fires on Microbial Environments 307
14.3 The Effects of Underground Fires on Microbial Environments 310
14.4 Microbial Communities in Fire-Affected Soils 314
14.5 Conclusions 317
References 319
Endophytes and Rhizosphere Bacteria of Plants Growing in Heavy Metal- Containing Soils 323
15.1 Introduction: Heavy Metal Contamination of Soils 323
15.2 Heavy Metal Tolerance and Hyperaccumulation in Plants 323
15.3 Rhizosphere Bacteria and Endophytes 325
15.4 Diversity of Bacterial Communities Associated with Heavy Metal- Tolerant Plants 327
15.5 The Influence of Associated Micro-Organisms on Plant Heavy Metal Tolerance and Uptake 330
15.6 Potential Applications of Improved Plant– Microbe Interactions 331
15.7 Conclusions 332
References 333
Interactions of Fungi and Radionuclides in Soil 339
16.1 Introduction 339
16.2 Fungi as Regulators of Radionuclide Movement 340
16.3 Effects of Radionuclides on Fungi 346
16.4 Conclusions and Perspectives 355
References 356
Index 362