GEOMICROBIOLOGY FIFTH EDITIONPDF电子书下载

Chapter 1 Introduction 1

References 3

Chapter 2 Earth as a Microbial Habitat 5

2.1 Geologically Important Features 5

2.2 Biosphere 10

2.3 Summary 11

References 11

Chapter 3 Origin of Life and Its Early History 15

3.1 Beginnings 15

3.1.1 Origin of Life on Earth: Panspermia 15

3.1.2 Origin of Life on Earth: de novo Appearance 16

3.1.3 Life from Abiotically Formed Organic Molecules in Aqueous Solution Organic Soup Theory 16

3.1.4 Surface Metabolism Theory 18

3.1.5 Origin of Life through Iron Monosulfide Bubbles in Hadean Ocean at the Interface of Sulfide-Bearing Hydrothermal Solution and Iron-Bearing Ocean Water 19

3.2 Evolution of Life through the Precambrian: Biological and Biochemical Benchmarks 20

3.2.1 Early Evolution According to Organic Soup Scenario 21

3.2.2 Early Evolution According to Surface Metabolist Scenario 27

3.3 Evidence 28

3.4 Summary 31

References 32

Chapter 4 Lithosphere as Microbial Habitat 37

4.1 Rock and Minerals 37

4.2 Mineral Soil 39

4.2.1 Origin of Mineral Soil 39

4.2.2 Some Structural Features of Mineral Soil 40

4.2.3 Effects of Plants and Animals on Soil Evolution 42

4.2.4 Effects of Microbes on Soil Evolution 42

4.2.5 Effects of Water on Soil Erosion 43

4.2.6 Water Distribution in Mineral Soil 43

4.2.7 Nutrient Availability in Mineral Soil 44

4.2.8 Some Major Soil Types 45

4.2.9 Types of Microbes and Their Distribution in Mineral Soil 47

4.3 Organic Soils 49

4.4 The Deep Subsurface 50

4.5 Summary 51

References 52

Chapter 5 The Hydrosphere as Microbial Habitat 57

5.1The Oceans 57

5.1.1 Physical Attributes 57

5.1.2 Ocean in Motion 59

5.1.3 Chemical and Physical Properties of Seawater 62

5.1.4 Microbial Distribution in Water Column and Sediments 68

5.1.5 Effects of Temperature, Hydrostatic Pressure, and Salinity on Microbial Distribution in Oceans 70

5.1.6 Dominant Phytoplankters and Zooplankters in Oceans 71

5.1.7 Plankters of Geomicrobial Interest 72

5.1.8 Bacterial Flora in Oceans 72

5.2Freshwater Lakes 73

5.2.1Some Physical and Chemical Features of Lakes 74

5.2.2Lake Bottoms 76

5.2.3Lake Fertility 77

5.2.4Lake Evolution 77

5.2.5Microbial Populations in Lakes 77

5.3Rivers 78

5.4Groundwaters 79

5.5Summary 82

References 83

Chapter 6 Geomicrobial Processes: Physiological and Biochemical Overview 89

6.1Types of Geornicrobial Agents 89

6.2Geomicrobially Important Physiological Groups of Prokaryotes 90

6.3Role of Microbes in Inorganic Conversions in Lithosphere and Hydrosphere 91

6.4Types of Microbial Activities Influencing Geological Processes 92

6.5Microbes as Catalysts of Geochernical Processes 93

6.5.1 Catabolic Reactions: Aerobic Respiration 94

6.5.2 Catabolic Reactions: Anaerobic Respiration 96

6.5.3 Catabolic Reactions: Respiration Involving Insoluble Inorganic Substrates as Electron Donors or Acceptors 98

6.5.4 Catabolic Reactions: Fermentation 100

6.5.5 How Energy Is Generated by Aerobic and Anaerobic Respirers and Fermenters During Catabolism 101

6.5.6 How Chemolithoautotrophic Bacteria Chemosynthetic Autotrophs Generate Reducing Power for Assimilating CO2 and Converting It into Organic Carbon 103

6.5.7 How Photosynthetic Microbes Generate Energy and Reducing Power 103

6.5.8 Anabolism: How Microbes Use Energy Trapped in High-Energy Bonds to Drive Energy-Consuming Reactions 105

6.5.9 Carbon Assimilation by Mixotrophs, Photoheterotrophs,and Heterotrophs 108

6.6Microbial Mineralization of Organic Matter 108

6.7Microbial Products of Metabolism That Can Cause Geomicrobial Transformations 110

6.8Physical Parameters That Influence Geomicrobial Activity 110

6.9Summary 112

References 113

Chapter 7 Nonmolecular Methods in Geomicrobiology 117

7.1 Introduction 117

7.2 Detection, Isolation, and Identification of Geomicrobially Active Organisms 118

7.2.1 In Situ Observation of Geomicrobial Agents 118

7.2.2 Identification by Application of Molecular Biological Techniques 120

7.3 Sampling 120

7.3.1 Terrestrial Surface/Subsurface Sampling 121

7.3.2 Aquatic Sampling 121

7.3.3 Sample Storage 122

7.3.4 Culture Isolation and Characterization of Active Agents from Environmental Samples 124

7.4 In Situ Study of Past Geomicrobial Activity 125

7.5 In Situ Study of Ongoing Geomicrobial Activity 126

7.6 Laboratory Reconstruction of Geomicrobial Processes in Nature 128

7.7 Quantitative Study of Growth on Surfaces 132

7.8 Test for Distinguishing between Enzymatic and Nonenzymatic Geomicrobial Activity 134

7.9 Study of Reaction Products of Geomicrobial Transformation 134

7.10 Summary 135

References 135

Chapter 8 Molecular Methods in Geomicrobiology 139

8.1Introduction 139

8.2Who Is There? Identification of Geomicrobial Organisms 139

8.2.1 Culture-Independent Methods 139

8.2.2 New Culturing Techniques 141

8.3What Are They Doing? Deducing Activities of Geomicrobial Organisms 141

8.3.1 Single-Cell Isotopic Techniques 142

8.3.2 Single-Cell Metabolite Techniques 144

8.3.3 Community Techniques Involving Isotopes 145

8.3.4 Community Techniques Involving Genomics 146

8.3.5 Probing for Expression of Metabolic Genes or Their Gene Products 147

8.4How Are They Doing It? Unraveling the Mechanisms of Geomicrobial Organisms 147

8.4.1Genetic Approaches 148

8.4.2Bioinformatic Approaches 151

8.4.3Follow-Up Studies 151

8.5Summary 152

References 152

Chapter 9 Microbial Formation and Degradation of Carbonates 157

9.1 Distribution of Carbon in Earths Crust 157

9.2 Biological Carbonate Deposition 157

9.2.1 Historical Perspective of Study of Carbonate Deposition 158

9.2.2 Basis for Microbial Carbonate Deposition 161

9.2.3 Conditions for Extracellular Microbial Carbonate Precipitation 164

9.2.4 Carbonate Deposition by Cyanobacteria 167

9.2.5 Possible Model for Oolite Formation 168

9.2.6 Structural or Intracellular Carbonate Deposition by Microbes 168

9.2.7 Models for Skeletal Carbonate Formation 171

9.2.8 Microbial Formation of Carbonates Other Than Those of Calcium 173

9.2.8.1 Sodium Carbonate 173

9.2.8.2 Manganous Carbonate 174

9.2.8.3 Ferrous Carbonate 176

9.2.8.4 Strontium Carbonate 177

9.2.8.5 Magnesium Carbonate 177

9.3 Biodegradation of Carbonates 178

9.3.1 Biodegradation of Limestone 178

9.3.2 Cyanobacteria, Algae, and Fungi That Bore into Limestone 180

9.4 Biological Carbonate Formation and Degradation and the Carbon Cycle 183

9.5 Summary 184

References 184

Chapter 10 Geomicrobial Interactions with Silicon 191

10.1 Distribution and Some Chemical Properties 191

10.2 Biologically Important Properties of Silicon and Its Compounds 192

10.3 Bioconcentration of Silicon 193

10.3.1 Bacteria 193

10.3.2 Fungi 195

10.3.3 Diatoms 195

10.4 Biomobilization of Silicon and Other Constituents of SilicatesBioweathering 198

10.4.1 Solubilization by Ligands 198

10.4.2 Solubilization by Acids 200

10.4.3 Solubilization by Alkali 201

10.4.4 Solubilization by Extracellular Polysaccharide 202

10.4.5 Depolymerization of Polysilicates 202

10.5 Role of Microbes in the Silica Cycle 202

10.6 Summary 203

References 204

Chapter 11 Geomicrobiology of Aluminum: Microbes and Bauxite 209

11.1 Introduction 209

11.2 Microbial Role in Bauxite Formation 210

11.2.1 Nature of Bauxite 210

11.2.2 Biological Role in Weathering of the Parent Rock Material 210

11.2.3 Weathering Phase 211

11.2.4 Bauxite Maturation Phase 211

11.2.5 Bacterial Reduction of Fe in Bauxites from Different Locations 214

11.2.6 Other Observations of Bacterial Interaction with Bauxite 214

11.3 Summary 215

References 215

Chapter 12 Geomicrobial Interactions with Phosphorus 219

12.1 Biological Importance of Phosphorus 219

12.2 Occurrence in Earths Crust 219

12.3 Conversion of Organic into Inorganic Phosphorus and Synthesis of Phosphate Esters 220

12.4 Assimilation of Phosphorus 221

12.5 Microbial Solubilization of Phosphate Minerals 222

12.6 Microbial Phosphate Immobilization 223

12.6.1 Phosphorite Deposition 223

12.6.1.1 Authigenic Formations 224

12.6.1.2 Diagenetic Formation 226

12.6.2 Occurrences of Phosphorite Deposits 226

12.6.3 Deposition of Other Phosphate Minerals 226

12.7 Microbial Reduction of Oxidized Forms of Phosphorus 227

12.8 Microbial Oxidation of Reduced Forms of Phosphorus 228

12.9 Microbial Role in the Phosphorus Cycle 229

12.10 Summary 229

References 229

Chapter 13 Geomicrobially Important Interactions with Nitrogen 233

13.1 Nitrogen in Biosphere 233

13.2 Microbial Interactions with Nitrogen 233

13.2.1 Ammonification 233

13.2.2 Nitrification 235

13.2.3 Ammonia Oxidation 235

13.2.4 Nitrite Oxidation 236

13.2.5 Heterotrophic Nitrification 236

13.2.6 Anaerobic Ammonia Oxidation Anammox 236

13.2.7 Denitrification 237

13.2.8 Nitrogen Fixation 238

13.3 Microbial Role in the Nitrogen Cycle 239

13.4 Summary 240

References 240

Chapter 14 Geomicrobial Interactions with Arsenic and Antimony 243

14.1 Introduction 243

14.2 Arsenic 243

14.2.1 Distribution 243

14.2.2 Some Chemical Characteristics 243

14.2.3 Toxicity 244

14.2.4 Microbial Oxidation of Reduced Forms of Arsenic 245

14.2.4.1 Aerobic Oxidation of Dissolved Arsenic 245

14.2.4.2 Anaerobic Oxidation of Dissolved Arsenic 247

14.2.5 Interaction with Arsenic-Containing Minerals 247

14.2.6 Microbial Reduction of Oxidized Arsenic Species 250

14.2.7 Arsenic Respiration 251

14.2.8 Direct Observations of Arsenite Oxidation and Arsenate Reduction In Situ 254

14.3 Antimony 256

14.3.1 Antimony Distribution in Earth's Crust 256

14.3.2 Microbial Oxidation of Antimony Compounds 256

14.3.3 Microbial Reduction of Oxidized Antimony Minerals 257

14.4 Summary 257

References 258

Chapter 15 Geornicrobiology of Mercury 265

15.1 Introduction 265

15.2 Distribution of Mercury in Earth's Crust 265

15.3 Anthropogenic Mercury 266

15.4 Mercury in Environment 266

15.5 Specific Microbial Interactions with Mercury 267

15.5.1 Nonenzymatic Methylation of Mercury by Microbes 267

15.5.2 Enzymatic Methylation of Mercury by Microbes 268

15.5.3 Microbial Diphenylmercury Formation 269

15.5.4 Microbial Reduction of Mercuric Ion 269

15.5.5 Formation of Meta-Cinnabar (?-HgS)from Hg(Ⅱ)by Cyanobacteria 270

15.5.6 Microbial Decomposition of Organomercurials 270

15.5.7 Oxidation of Metallic Mercury 270

15.6 Genetic Control of Mercury Transformations 271

15.7 Environmental Significance of Microbial Mercury Transformations 272

15.8 Mercury Cycle 272

15.9 Summary 273

References 274

Chapter 16 Geornicrobiology of Iron 279

16.1 Iron Distribution in Earth's Crust 279

16.2 Geochemically Important Properties 279

16.3 Biological Importance of Iron 280

16.3.1 Function of Iron in Cells 280

16.3.2 Iron Assimilation by Microbes 280

16.4 Iron as Energy Source for Bacteria 282

16.4.1 Acidophiles 282

16.4.2 Domain Bacteria: Mesophiles 282

16.4.2.1 Acidithiobacillus (Formerly Thiobacillus)ferrooxidans 282

16.4.2.2 Thiobacillus prosperus 294

16.4.2.3 Leptospirillum ferrooxidans 294

16.4.2.4 Metallogeuium 295

16.4.2.5 Ferromicrobium acidophilum 295

16.4.2.6 Strain CCH7 295

16.4.3 Domain Bacteria: Thermophiles 295

16.4.3.1 Sulfobacillus thermosulfidooxidans 295

16.4.3.2 Sulfobacillus acidophilus 296

16.4.3.3 Acidimicrobium ferrooxidans 296

16.4.4 Domain Archaea: Mesophiles 296

16.4.4.1 Ferroplasma acidiphilum 296

16.4.4.2 Ferroplasma acidarmanus 296

16.4.5 Domain Archaea: Thermophiles 296

16.4.5.1 Acidianus brierleyi 296

16.4.5.2 Sulfolobus acidocaldarius 298

16.4.6 Domain Bacteria: Neutrophilic Iron Oxidizers 298

16.4.6.1 Unicellular Bacteria 298

16.4.7 Appendaged Bacteria 298

16.4.7.1 Gallionella ferruginea 298

16.4.7.2 Sheathed, Encapsulated, and Wall-Less Iron Bacteria 301

16.5 Anaerobic Oxidation of Ferrous Iron 302

16.5.1 Phototrophic Oxidation 302

16.5.2 Chemotrophic Oxidation 303

16.6 IronIII as Terminal Electron Acceptor in Bacterial Respiration 304

16.6.1 Bacterial Ferric Iron Reduction Accompanying Fermentation 304

16.6.2 Ferric Iron Respiration: Early History 306

16.6.3 Metabolic Evidence for Enzymatic Ferric Iron Reduction 308

16.6.4 Ferric Iron Respiration: Current Status 309

16.6.5 Electron Transfer from Cell Surface of a Dissimilatory Fe Reducer to Ferric Oxide Surface 313

16.6.6 Bioenergetics of Dissimilatory Iron Reduction 314

16.6.7 Ferric Iron Reduction as Electron Sink 314

16.6.8 Reduction of Ferric Iron by Fungi 315

16.6.9 Types of Ferric Compounds Attacked by Dissimilatory Iron Reduction 315

16.7 Nonenzymatic Oxidation of Ferrous Iron and Reduction of Ferric Iron by Microbes 316

16.7.1 Nonenzymatic Oxidation 316

16.7.2 Nonenzymatic Reduction 317

16.8 Microbial Precipitation of Iron 318

16.8.1 Enzymatic Processes 318

16.8.2 Nonenzymatic Processes 319

16.8.3 Bioaccumulation of Iron 320

16.9 Concept of Iron Bacteria 320

16.10 Sedimentary Iron Deposits of Putative Biogenic Origin 322

16.11 Microbial Mobilization of Iron from Minerals in Ore, Soil,and Sediments 325

16.12 Microbes and Iron Cycle 326

16.13 Summary 327

References 329

Chapter 17 Geomicrobiology of Manganese 347

17.1 Occurrence of Manganese in Earths Crust 347

17.2 Geochemically Important Properties of Manganese 347

17.3 Biological Importance of Manganese 348

17.4 Manganese-Oxidizing and Manganese-Reducing Bacteria and Fungi 348

17.4.1 Manganese-Oxidizing Bacteria and Fungi 348

17.4.2 Manganese-Reducing Bacteria and Fungi 351

17.5 Biooxidation of Manganese 352

17.5.1 Enzymatic Manganese Oxidation 352

17.5.2 Group I Manganese Oxidizers 354

17.5.2.1 Subgroup Ia 354

17.5.2.2 Subgroup Ib 357

17.5.2.3 Subgroup Ic 357

17.5.2.4 Subgroup Id 358

17.5.2.5 Uncertain Subgroup Affiliations 359

17.5.3 Group Ⅱ Manganese Oxidizers 359

17.5.4 Group Ⅲ Manganese Oxidizers 362

17.5.5 Nonenzymatic Manganese Oxidation 362

17.6 Bioreduction of Manganese 363

17.6.1 Organisms Capable of Reducing Manganese Oxides Only Anaerobically 364

17.6.2 Reduction of Manganese Oxides by Organisms Capable of Reducing Manganese Oxides Aerobically and Anaerobically 365

17.6.3 Bacterial Reduction of Manganese(Ⅲ) 370

17.6.4 Nonenzymatic Reduction of Manganese Oxides 371

17.7 Bioaccumulation of Manganese 372

17.8 Microbial Manganese Deposition in Soil and on Rocks 375

17.8.1 Soil 375

17.8.2 Rocks 377

17.8.3 Ores 378

17.9 Microbial Manganese Deposition in Freshwater Environments 379

17.9.1 Bacterial Manganese Oxidation in Springs 379

17.9.2 Bacterial Manganese Oxidation in Lakes 379

17.9.3 Bacterial Manganese Oxidation in Water Distribution Systems 383

17.10 Microbial Manganese Deposition in Marine Environments 384

17.10.1 Microbial Manganese Oxidations in Bays, Estuaries,Inlets, the Black Sea, etc 385

17.10.2 Manganese Oxidation in Mixed Layer of Ocean 386

17.10.3 Manganese Oxidation on Ocean Floor 387

17.10.4 Manganese Oxidation around Hydrothermal Vents 392

17.10.5 Bacterial Manganese Precipitation in Seawater Column 396

17.11 Microbial Mobilization of Manganese in Soils and Ores 397

17.11.1 Soils 397

17.11.2 Ores 398

17.12 Microbial Mobilization of Manganese in Freshwater Environments 399

17.13 Microbial Mobilization of Manganese in Marine Environments 400

17.14 Microbial Manganese Reduction and Mineralization of Organic Matter 401

17.15 Microbial Role in Manganese Cycle in Nature 402

17.16 Summary 405

References 406

Chapter 18 Geomicrobial Interactions with Chromium, Molybdenum, Vanadium,Uranium, Polonium, and Plutonium 421

18.1 Microbial Interaction with Chromium 421

18.1.1 Occurrence of Chromium 421

18.1.2 Chemically and Biologically Important Properties 421

18.1.3 Mobilization of Chromium with Microbially Generated Lixiviants 422

18.1.4 Biooxidation of Chromium 422

18.1.5 Bioreduction of Chromium 422

18.1.6 In Situ Chromate Reducing Activity 426

18.1.7 Applied Aspects of Chromium Reduction 427

18.2 Microbial Interaction with Molybdenum 427

18.2.1 Occurrence and Properties of Molybdenum 427

18.2.2 Microbial Oxidation and Reduction 427

18.3 Microbial Interaction with Vanadium 428

18.3.1 Bacterial Oxidation of Vanadium 428

18.4 Microbial Interaction with Uranium 429

18.4.1 Occurrence and Properties of Uranium 429

18.4.2 Microbial Oxidation of U 429

18.4.3 Microbial Reduction of U 430

18.4.4 Bioremediation of Uranium Pollution 431

18.5 Bacterial Interaction with Polonium 432

18.6 Bacterial Interaction with Plutonium 432

18.7 Summary 432

References 433

Chapter 19 Geomicrobiology of Sulfur 439

19.1 Occurrence of Sulfur in Earths Crust 439

19.2 Geochemically Important Properties of Sulfur 439

19.3 Biological Importance of Sulfur 440

19.4 Mineralization of Organic Sulfur Compounds 440

19.5 Sulfur Assimilation 441

19.6 Geomicrobially Important Types of Bacteria That React with Sulfur and Sulfur Compounds 442

19.6.1 Oxidizers of Reduced Sulfur 442

19.6.2 Reducers of Oxidized Forms of Sulfur 446

19.6.2.1 Sulfate Reduction 446

19.6.2.2 Sulfate Reduction 448

19.6.2.3 Reduction of Elemental Sulfur 448

19.7 Physiology and Biochemistry of Microbial Oxidation of Reduced Forms of Sulfur 449

19.7.1 Sulfide 449

19.7.1.1 Aerobic Attack 449

19.7.1.2 Anaerobic Attack 450

19.7.1.3 Oxidation of Sulfide by Heterotrophs and Mixotrophs 451

19.7.2 Elemental Sulfur 451

19.7.2.1 Aerobic Attack 451

19.7.2.2 Anaerobic Oxidation of Elemental Sulfur 451

19.7.2.3 Disproportionation of Sulfur 451

19.7.3 Sulfite Oxidation 452

19.7.3.1 Oxidation by Aerobes 452

19.7.3.2 Oxidation by Anaerobes 453

19.7.4 Thiosulfate Oxidation 453

19.7.4.1 Disproportionation of Thiosulfate 455

19.7.5 Tetrathionate Oxidation 456

19.7.6 Common Mechanism for Oxidizing Reduced Inorganic Sulfur Compounds in Domain Bacteria 456

19.8 Autotrophic and Mixotrophic Growth on Reduced Forms of Sulfur 456

19.8.1 Energy Coupling in Bacterial Sulfur Oxidation 456

19.8.2 Reduced Forms of Sulfur as Sources of Reducing Power for CO2 Fixation by Autotrophs 457

19.8.2.1 Chemosynthetic Autotrophs 457

19.8.2.2 Photosynthetic Autotrophs 457

19.8.3 CO2 Fixation by Autotrophs 457

19.8.3.1 Chemosynthetic Autotrophs 457

19.8.3.2 Photosynthetic Autotrophs 458

19.8.4 Mixotrophy 458

19.8.4.1 Free-Living Bacteria 458

19.8.5 Unusual Consortia 458

19.9 Anaerobic Respiration Using Oxidized Forms of Sulfur as Terminal Electron Acceptors 459

19.9.1 Reduction of Fully or Partially Oxidized Sulfur 459

19.9.2 Biochemistry of Dissimilatory Sulfate Reduction 459

19.9.3 Sulfur Isotope Fractionation 461

19.9.4 Reduction of Elemental Sulfur 462

19.9.5 Reduction of Thiosulfate 463

19.9.6 Terminal Electron Acceptors Other Than Sulfate, Sulfite,Thiosulfate, or Sulfur 463

19.9.7 Oxygen Tolerance of Sulfate-Reducers 464

19.10 Autotrophy, Mixotrophy, and Heterotrophy among Sulfate-Reducing Bacteria 464

19.10.1 Autotrophy 464

19.10.2 Mixotrophy 465

19.10.3 Heterotrophy 465

19.11 Biodeposition of Native Sulfur 466

19.11.1 Types of Deposits 466

19.11.2 Examples of Syngenetic Sulfur Deposition 466

19.11.2.1 Cyrenaican Lakes, Libya, North Africa 466

19.11.2.2 Lake Senoye 469

19.11.2.3 Lake Eyre 469

19.11.2.4 Solar Lake 470

19.11.2.5 Thermal Lakes and Springs 470

19.11.3 Examples of Epigenetic Sulfur Deposits 472

19.11.3.1 Sicilian Sulfur Deposits 472

19.11.3.2 Salt Domes 472

19.11.3.3 Gaurdak Sulfur Deposit 474

19.11.3.4 Shor-Su Sulfur Deposit 474

19.11.3.5 Kara Kum Sulfur Deposit 475

19.12 Microbial Role in Sulfur Cycle 475

19.13 Summary 476

References 477

Chapter 20 Biogenesis and Biodegradation of Sulfide Minerals at Earths Surface 491

20.1 Introduction 491

20.2 Natural Origin of Metal Sulfides 491

20.2.1 Hydrothermal Origin Abiotic 491

20.2.2 Sedimentary Metal Sulfides of Biogenic Origin 493

20.3 Principles of Metal Sulfide Formation 494

20.4 Laboratory Evidence in Support of Biogenesis of Metal Sulfides 495

20.4.1 Batch Cultures 495

20.4.2 Column Experiment: Model for Biogenesis of Sedimentary Metal Sulfides 497

20.5 Biooxidation of Metal Sulfides 498

20.5.1 Organisms Involved in Biooxidation of Metal Sulfides 498

20.5.2 Direct Oxidation 499

20.5.3 Indirect Oxidation 503

20.5.4 Pyrite Oxidation 504

20.6 Bioleaching of Metal Sulfide and Uraninite Ores 507

20.6.1 Metal Sulfide Ores 507

20.6.2 Uraninite Leaching 511

20.6.3 Mobilization of Uranium in Granitic Rocks by Heterotrophs 512

20.6.4 Study of Bioleaching Kinetics 513

20.6.5 Industrial versus Natural Bioleaching 513

20.7 Bioextraction of Metal Sulfide Ores by Complexation 513

20.8 Formation of Acid Coal Mine Drainage 514

20.8.1 New Discoveries Relating to Acid Mine Drainage 515

20.9 Summary 517

References 518

Chapter 21 Geomicrobiology of Selenium and Tellurium 527

21.1 Occurrence in Earths Crust 527

21.2 Biological Importance 527

21.3 Toxicity of Selenium and Tellurium 528

21.4 Biooxidation of Reduced Forms of Selenium 528

21.5 Bioreduction of Oxidized Selenium Compounds 528

21.5.1 Other Products of Selenate and Selenite Reduction 530

21.5.2 Selenium Reduction in the Environment 531

21.6 Selenium Cycle 532

21.7 Biooxidation of Reduced Forms of Tellurium 532

21.8 Bioreduction of Oxidized Forms of Tellurium 533

21.9 Summary 533

References 534

Chapter 22 Geomicrobiology of Fossil Fuels 537

22.1 Introduction 537

22.2 Natural Abundance of Fossil Fuels 537

22.3 Methane 537

22.3.1 Methanogens 539

22.3.2 Methanogenesis and Carbon Assimilation by Methanogens 541

22.3.2.1 Methanogenesis 541

22.3.3 Bioenergetics of Methanogenesis 544

22.3.4 Carbon Fixation by Methanogens 544

22.3.5 Microbial Methane Oxidation 545

22.3.5.1 Aerobic Methanotrophy 545

22.3.5.2 Anaerobic Methanotrophy 547

22.3.6 Biochemistry of Methane Oxidation in Aerobic Methanotrophs 548

22.3.7 Carbon Assimilation by Aerobic Methanotrophs 549

22.3.8 Position of Methane in Carbon Cycle 550

22.4 Peat 550

22.4.1 Nature of Peat 550

22.4.2 Roles of Microbes in Peat Formation 552

22.5 Coal 552

22.5.1 Nature of Coal 552

22.5.2 Role of Microbes in Coal Formation 553

22.5.3 Coal as Microbial Substrate 554

22.5.4 Microbial Desulfurization of Coal 555

22.6 Petroleum 556

22.6.1 Nature of Petroleum 556

22.6.2 Role of Microbes in Petroleum Formation 556

22.6.3 Role of Microbes in Petroleum Migration in Reservoir Rock 557

22.6.4 Microbes in Secondary and Tertiary Oil Recovery 558

22.6.5 Removal of Organic Sulfur from Petroleum 559

22.6.6 Microbes in Petroleum Degradation 559

22.6.7 Current State of Knowledge of Aerobic and Anaerobic Petroleum Degradation by Microbes 560

22.6.8 Use of Microbes in Prospecting for Petroleum 563

22.6.9 Microbes and Shale Oil 563

22.7 Summary 564

References 565

Glossary 577

Index 589