GEOMICROBIOLOGY FIFTH EDITION2025|PDF|Epub|mobi|kindle电子书版本百度云盘下载

GEOMICROBIOLOGY FIFTH EDITIONPDF格式电子书版下载

注意：本站所有压缩包均有解压码： 点击下载压缩包解压工具

Chapter 1 Introduction1

References3

Chapter 2 Earth as a Microbial Habitat5

2.1 Geologically Important Features5

2.2 Biosphere10

2.3 Summary11

References11

Chapter 3 Origin of Life and Its Early History15

3.1 Beginnings15

3.1.1 Origin of Life on Earth: Panspermia15

3.1.2 Origin of Life on Earth: de novo Appearance16

3.1.3 Life from Abiotically Formed Organic Molecules in Aqueous Solution Organic Soup Theory16

3.1.4 Surface Metabolism Theory18

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 Water19

3.2 Evolution of Life through the Precambrian: Biological and Biochemical Benchmarks20

3.2.1 Early Evolution According to Organic Soup Scenario21

3.2.2 Early Evolution According to Surface Metabolist Scenario27

3.3 Evidence28

3.4 Summary31

References32

Chapter 4 Lithosphere as Microbial Habitat37

4.1 Rock and Minerals37

4.2 Mineral Soil39

4.2.1 Origin of Mineral Soil39

4.2.2 Some Structural Features of Mineral Soil40

4.2.3 Effects of Plants and Animals on Soil Evolution42

4.2.4 Effects of Microbes on Soil Evolution42

4.2.5 Effects of Water on Soil Erosion43

4.2.6 Water Distribution in Mineral Soil43

4.2.7 Nutrient Availability in Mineral Soil44

4.2.8 Some Major Soil Types45

4.2.9 Types of Microbes and Their Distribution in Mineral Soil47

4.3 Organic Soils49

4.4 The Deep Subsurface50

4.5 Summary51

References52

Chapter 5 The Hydrosphere as Microbial Habitat57

5.1The Oceans57

5.1.1 Physical Attributes57

5.1.2 Ocean in Motion59

5.1.3 Chemical and Physical Properties of Seawater62

5.1.4 Microbial Distribution in Water Column and Sediments68

5.1.5 Effects of Temperature, Hydrostatic Pressure, and Salinity on Microbial Distribution in Oceans70

5.1.6 Dominant Phytoplankters and Zooplankters in Oceans71

5.1.7 Plankters of Geomicrobial Interest72

5.1.8 Bacterial Flora in Oceans72

5.2Freshwater Lakes73

5.2.1Some Physical and Chemical Features of Lakes74

5.2.2Lake Bottoms76

5.2.3Lake Fertility77

5.2.4Lake Evolution77

5.2.5Microbial Populations in Lakes77

5.3Rivers78

5.4Groundwaters79

5.5Summary82

References83

Chapter 6 Geomicrobial Processes: Physiological and Biochemical Overview89

6.1Types of Geornicrobial Agents89

6.2Geomicrobially Important Physiological Groups of Prokaryotes90

6.3Role of Microbes in Inorganic Conversions in Lithosphere and Hydrosphere91

6.4Types of Microbial Activities Influencing Geological Processes92

6.5Microbes as Catalysts of Geochernical Processes93

6.5.1 Catabolic Reactions: Aerobic Respiration94

6.5.2 Catabolic Reactions: Anaerobic Respiration96

6.5.3 Catabolic Reactions: Respiration Involving Insoluble Inorganic Substrates as Electron Donors or Acceptors98

6.5.4 Catabolic Reactions: Fermentation100

6.5.5 How Energy Is Generated by Aerobic and Anaerobic Respirers and Fermenters During Catabolism101

6.5.6 How Chemolithoautotrophic Bacteria Chemosynthetic Autotrophs Generate Reducing Power for Assimilating CO2 and Converting It into Organic Carbon103

6.5.7 How Photosynthetic Microbes Generate Energy and Reducing Power103

6.5.8 Anabolism: How Microbes Use Energy Trapped in High-Energy Bonds to Drive Energy-Consuming Reactions105

6.5.9 Carbon Assimilation by Mixotrophs, Photoheterotrophs,and Heterotrophs108

6.6Microbial Mineralization of Organic Matter108

6.7Microbial Products of Metabolism That Can Cause Geomicrobial Transformations110

6.8Physical Parameters That Influence Geomicrobial Activity110

6.9Summary112

References113

Chapter 7 Nonmolecular Methods in Geomicrobiology117

7.1 Introduction117

7.2 Detection, Isolation, and Identification of Geomicrobially Active Organisms118

7.2.1 In Situ Observation of Geomicrobial Agents118

7.2.2 Identification by Application of Molecular Biological Techniques120

7.3 Sampling120

7.3.1 Terrestrial Surface/Subsurface Sampling121

7.3.2 Aquatic Sampling121

7.3.3 Sample Storage122

7.3.4 Culture Isolation and Characterization of Active Agents from Environmental Samples124

7.4 In Situ Study of Past Geomicrobial Activity125

7.5 In Situ Study of Ongoing Geomicrobial Activity126

7.6 Laboratory Reconstruction of Geomicrobial Processes in Nature128

7.7 Quantitative Study of Growth on Surfaces132

7.8 Test for Distinguishing between Enzymatic and Nonenzymatic Geomicrobial Activity134

7.9 Study of Reaction Products of Geomicrobial Transformation134

7.10 Summary135

References135

Chapter 8 Molecular Methods in Geomicrobiology139

8.1Introduction139

8.2Who Is There? Identification of Geomicrobial Organisms139

8.2.1 Culture-Independent Methods139

8.2.2 New Culturing Techniques141

8.3What Are They Doing? Deducing Activities of Geomicrobial Organisms141

8.3.1 Single-Cell Isotopic Techniques142

8.3.2 Single-Cell Metabolite Techniques144

8.3.3 Community Techniques Involving Isotopes145

8.3.4 Community Techniques Involving Genomics146

8.3.5 Probing for Expression of Metabolic Genes or Their Gene Products147

8.4How Are They Doing It? Unraveling the Mechanisms of Geomicrobial Organisms147

8.4.1Genetic Approaches148

8.4.2Bioinformatic Approaches151

8.4.3Follow-Up Studies151

8.5Summary152

References152

Chapter 9 Microbial Formation and Degradation of Carbonates157

9.1 Distribution of Carbon in Earths Crust157

9.2 Biological Carbonate Deposition157

9.2.1 Historical Perspective of Study of Carbonate Deposition158

9.2.2 Basis for Microbial Carbonate Deposition161

9.2.3 Conditions for Extracellular Microbial Carbonate Precipitation164

9.2.4 Carbonate Deposition by Cyanobacteria167

9.2.5 Possible Model for Oolite Formation168

9.2.6 Structural or Intracellular Carbonate Deposition by Microbes168

9.2.7 Models for Skeletal Carbonate Formation171

9.2.8 Microbial Formation of Carbonates Other Than Those of Calcium173

9.2.8.1 Sodium Carbonate173

9.2.8.2 Manganous Carbonate174

9.2.8.3 Ferrous Carbonate176

9.2.8.4 Strontium Carbonate177

9.2.8.5 Magnesium Carbonate177

9.3 Biodegradation of Carbonates178

9.3.1 Biodegradation of Limestone178

9.3.2 Cyanobacteria, Algae, and Fungi That Bore into Limestone180

9.4 Biological Carbonate Formation and Degradation and the Carbon Cycle183

9.5 Summary184

References184

Chapter 10 Geomicrobial Interactions with Silicon191

10.1 Distribution and Some Chemical Properties191

10.2 Biologically Important Properties of Silicon and Its Compounds192

10.3 Bioconcentration of Silicon193

10.3.1 Bacteria193

10.3.2 Fungi195

10.3.3 Diatoms195

10.4 Biomobilization of Silicon and Other Constituents of SilicatesBioweathering198

10.4.1 Solubilization by Ligands198

10.4.2 Solubilization by Acids200

10.4.3 Solubilization by Alkali201

10.4.4 Solubilization by Extracellular Polysaccharide202

10.4.5 Depolymerization of Polysilicates202

10.5 Role of Microbes in the Silica Cycle202

10.6 Summary203

References204

Chapter 11 Geomicrobiology of Aluminum: Microbes and Bauxite209

11.1 Introduction209

11.2 Microbial Role in Bauxite Formation210

11.2.1 Nature of Bauxite210

11.2.2 Biological Role in Weathering of the Parent Rock Material210

11.2.3 Weathering Phase211

11.2.4 Bauxite Maturation Phase211

11.2.5 Bacterial Reduction of Fe in Bauxites from Different Locations214

11.2.6 Other Observations of Bacterial Interaction with Bauxite214

11.3 Summary215

References215

Chapter 12 Geomicrobial Interactions with Phosphorus219

12.1 Biological Importance of Phosphorus219

12.2 Occurrence in Earths Crust219

12.3 Conversion of Organic into Inorganic Phosphorus and Synthesis of Phosphate Esters220

12.4 Assimilation of Phosphorus221

12.5 Microbial Solubilization of Phosphate Minerals222

12.6 Microbial Phosphate Immobilization223

12.6.1 Phosphorite Deposition223

12.6.1.1 Authigenic Formations224

12.6.1.2 Diagenetic Formation226

12.6.2 Occurrences of Phosphorite Deposits226

12.6.3 Deposition of Other Phosphate Minerals226

12.7 Microbial Reduction of Oxidized Forms of Phosphorus227

12.8 Microbial Oxidation of Reduced Forms of Phosphorus228

12.9 Microbial Role in the Phosphorus Cycle229

12.10 Summary229

References229

Chapter 13 Geomicrobially Important Interactions with Nitrogen233

13.1 Nitrogen in Biosphere233

13.2 Microbial Interactions with Nitrogen233

13.2.1 Ammonification233

13.2.2 Nitrification235

13.2.3 Ammonia Oxidation235

13.2.4 Nitrite Oxidation236

13.2.5 Heterotrophic Nitrification236

13.2.6 Anaerobic Ammonia Oxidation Anammox236

13.2.7 Denitrification237

13.2.8 Nitrogen Fixation238

13.3 Microbial Role in the Nitrogen Cycle239

13.4 Summary240

References240

Chapter 14 Geomicrobial Interactions with Arsenic and Antimony243

14.1 Introduction243

14.2 Arsenic243

14.2.1 Distribution243

14.2.2 Some Chemical Characteristics243

14.2.3 Toxicity244

14.2.4 Microbial Oxidation of Reduced Forms of Arsenic245

14.2.4.1 Aerobic Oxidation of Dissolved Arsenic245

14.2.4.2 Anaerobic Oxidation of Dissolved Arsenic247

14.2.5 Interaction with Arsenic-Containing Minerals247

14.2.6 Microbial Reduction of Oxidized Arsenic Species250

14.2.7 Arsenic Respiration251

14.2.8 Direct Observations of Arsenite Oxidation and Arsenate Reduction In Situ254

14.3 Antimony256

14.3.1 Antimony Distribution in Earth's Crust256

14.3.2 Microbial Oxidation of Antimony Compounds256

14.3.3 Microbial Reduction of Oxidized Antimony Minerals257

14.4 Summary257

References258

Chapter 15 Geornicrobiology of Mercury265

15.1 Introduction265

15.2 Distribution of Mercury in Earth's Crust265

15.3 Anthropogenic Mercury266

15.4 Mercury in Environment266

15.5 Specific Microbial Interactions with Mercury267

15.5.1 Nonenzymatic Methylation of Mercury by Microbes267

15.5.2 Enzymatic Methylation of Mercury by Microbes268

15.5.3 Microbial Diphenylmercury Formation269

15.5.4 Microbial Reduction of Mercuric Ion269

15.5.5 Formation of Meta-Cinnabar (?-HgS)from Hg(Ⅱ)by Cyanobacteria270

15.5.6 Microbial Decomposition of Organomercurials270

15.5.7 Oxidation of Metallic Mercury270

15.6 Genetic Control of Mercury Transformations271

15.7 Environmental Significance of Microbial Mercury Transformations272

15.8 Mercury Cycle272

15.9 Summary273

References274

Chapter 16 Geornicrobiology of Iron279

16.1 Iron Distribution in Earth's Crust279

16.2 Geochemically Important Properties279

16.3 Biological Importance of Iron280

16.3.1 Function of Iron in Cells280

16.3.2 Iron Assimilation by Microbes280

16.4 Iron as Energy Source for Bacteria282

16.4.1 Acidophiles282

16.4.2 Domain Bacteria: Mesophiles282

16.4.2.1 Acidithiobacillus (Formerly Thiobacillus)ferrooxidans282

16.4.2.2 Thiobacillus prosperus294

16.4.2.3 Leptospirillum ferrooxidans294

16.4.2.4 Metallogeuium295

16.4.2.5 Ferromicrobium acidophilum295

16.4.2.6 Strain CCH7295

16.4.3 Domain Bacteria: Thermophiles295

16.4.3.1 Sulfobacillus thermosulfidooxidans295

16.4.3.2 Sulfobacillus acidophilus296

16.4.3.3 Acidimicrobium ferrooxidans296

16.4.4 Domain Archaea: Mesophiles296

16.4.4.1 Ferroplasma acidiphilum296

16.4.4.2 Ferroplasma acidarmanus296

16.4.5 Domain Archaea: Thermophiles296

16.4.5.1 Acidianus brierleyi296

16.4.5.2 Sulfolobus acidocaldarius298

16.4.6 Domain Bacteria: Neutrophilic Iron Oxidizers298

16.4.6.1 Unicellular Bacteria298

16.4.7 Appendaged Bacteria298

16.4.7.1 Gallionella ferruginea298

16.4.7.2 Sheathed, Encapsulated, and Wall-Less Iron Bacteria301

16.5 Anaerobic Oxidation of Ferrous Iron302

16.5.1 Phototrophic Oxidation302

16.5.2 Chemotrophic Oxidation303

16.6 IronIII as Terminal Electron Acceptor in Bacterial Respiration304

16.6.1 Bacterial Ferric Iron Reduction Accompanying Fermentation304

16.6.2 Ferric Iron Respiration: Early History306

16.6.3 Metabolic Evidence for Enzymatic Ferric Iron Reduction308

16.6.4 Ferric Iron Respiration: Current Status309

16.6.5 Electron Transfer from Cell Surface of a Dissimilatory Fe Reducer to Ferric Oxide Surface313

16.6.6 Bioenergetics of Dissimilatory Iron Reduction314

16.6.7 Ferric Iron Reduction as Electron Sink314

16.6.8 Reduction of Ferric Iron by Fungi315

16.6.9 Types of Ferric Compounds Attacked by Dissimilatory Iron Reduction315

16.7 Nonenzymatic Oxidation of Ferrous Iron and Reduction of Ferric Iron by Microbes316

16.7.1 Nonenzymatic Oxidation316

16.7.2 Nonenzymatic Reduction317

16.8 Microbial Precipitation of Iron318

16.8.1 Enzymatic Processes318

16.8.2 Nonenzymatic Processes319

16.8.3 Bioaccumulation of Iron320

16.9 Concept of Iron Bacteria320

16.10 Sedimentary Iron Deposits of Putative Biogenic Origin322

16.11 Microbial Mobilization of Iron from Minerals in Ore, Soil,and Sediments325

16.12 Microbes and Iron Cycle326

16.13 Summary327

References329

Chapter 17 Geomicrobiology of Manganese347

17.1 Occurrence of Manganese in Earths Crust347

17.2 Geochemically Important Properties of Manganese347

17.3 Biological Importance of Manganese348

17.4 Manganese-Oxidizing and Manganese-Reducing Bacteria and Fungi348

17.4.1 Manganese-Oxidizing Bacteria and Fungi348

17.4.2 Manganese-Reducing Bacteria and Fungi351

17.5 Biooxidation of Manganese352

17.5.1 Enzymatic Manganese Oxidation352

17.5.2 Group I Manganese Oxidizers354

17.5.2.1 Subgroup Ia354

17.5.2.2 Subgroup Ib357

17.5.2.3 Subgroup Ic357

17.5.2.4 Subgroup Id358

17.5.2.5 Uncertain Subgroup Affiliations359

17.5.3 Group Ⅱ Manganese Oxidizers359

17.5.4 Group Ⅲ Manganese Oxidizers362

17.5.5 Nonenzymatic Manganese Oxidation362

17.6 Bioreduction of Manganese363

17.6.1 Organisms Capable of Reducing Manganese Oxides Only Anaerobically364

17.6.2 Reduction of Manganese Oxides by Organisms Capable of Reducing Manganese Oxides Aerobically and Anaerobically365

17.6.3 Bacterial Reduction of Manganese(Ⅲ)370

17.6.4 Nonenzymatic Reduction of Manganese Oxides371

17.7 Bioaccumulation of Manganese372

17.8 Microbial Manganese Deposition in Soil and on Rocks375

17.8.1 Soil375

17.8.2 Rocks377

17.8.3 Ores378

17.9 Microbial Manganese Deposition in Freshwater Environments379

17.9.1 Bacterial Manganese Oxidation in Springs379

17.9.2 Bacterial Manganese Oxidation in Lakes379

17.9.3 Bacterial Manganese Oxidation in Water Distribution Systems383

17.10 Microbial Manganese Deposition in Marine Environments384

17.10.1 Microbial Manganese Oxidations in Bays, Estuaries,Inlets, the Black Sea, etc385

17.10.2 Manganese Oxidation in Mixed Layer of Ocean386

17.10.3 Manganese Oxidation on Ocean Floor387

17.10.4 Manganese Oxidation around Hydrothermal Vents392

17.10.5 Bacterial Manganese Precipitation in Seawater Column396

17.11 Microbial Mobilization of Manganese in Soils and Ores397

17.11.1 Soils397

17.11.2 Ores398

17.12 Microbial Mobilization of Manganese in Freshwater Environments399

17.13 Microbial Mobilization of Manganese in Marine Environments400

17.14 Microbial Manganese Reduction and Mineralization of Organic Matter401

17.15 Microbial Role in Manganese Cycle in Nature402

17.16 Summary405

References406

Chapter 18 Geomicrobial Interactions with Chromium, Molybdenum, Vanadium,Uranium, Polonium, and Plutonium421

18.1 Microbial Interaction with Chromium421

18.1.1 Occurrence of Chromium421

18.1.2 Chemically and Biologically Important Properties421

18.1.3 Mobilization of Chromium with Microbially Generated Lixiviants422

18.1.4 Biooxidation of Chromium422

18.1.5 Bioreduction of Chromium422

18.1.6 In Situ Chromate Reducing Activity426

18.1.7 Applied Aspects of Chromium Reduction427

18.2 Microbial Interaction with Molybdenum427

18.2.1 Occurrence and Properties of Molybdenum427

18.2.2 Microbial Oxidation and Reduction427

18.3 Microbial Interaction with Vanadium428

18.3.1 Bacterial Oxidation of Vanadium428

18.4 Microbial Interaction with Uranium429

18.4.1 Occurrence and Properties of Uranium429

18.4.2 Microbial Oxidation of U429

18.4.3 Microbial Reduction of U430

18.4.4 Bioremediation of Uranium Pollution431

18.5 Bacterial Interaction with Polonium432

18.6 Bacterial Interaction with Plutonium432

18.7 Summary432

References433

Chapter 19 Geomicrobiology of Sulfur439

19.1 Occurrence of Sulfur in Earths Crust439

19.2 Geochemically Important Properties of Sulfur439

19.3 Biological Importance of Sulfur440

19.4 Mineralization of Organic Sulfur Compounds440

19.5 Sulfur Assimilation441

19.6 Geomicrobially Important Types of Bacteria That React with Sulfur and Sulfur Compounds442

19.6.1 Oxidizers of Reduced Sulfur442

19.6.2 Reducers of Oxidized Forms of Sulfur446

19.6.2.1 Sulfate Reduction446

19.6.2.2 Sulfate Reduction448

19.6.2.3 Reduction of Elemental Sulfur448

19.7 Physiology and Biochemistry of Microbial Oxidation of Reduced Forms of Sulfur449

19.7.1 Sulfide449

19.7.1.1 Aerobic Attack449

19.7.1.2 Anaerobic Attack450

19.7.1.3 Oxidation of Sulfide by Heterotrophs and Mixotrophs451

19.7.2 Elemental Sulfur451

19.7.2.1 Aerobic Attack451

19.7.2.2 Anaerobic Oxidation of Elemental Sulfur451

19.7.2.3 Disproportionation of Sulfur451

19.7.3 Sulfite Oxidation452

19.7.3.1 Oxidation by Aerobes452

19.7.3.2 Oxidation by Anaerobes453

19.7.4 Thiosulfate Oxidation453

19.7.4.1 Disproportionation of Thiosulfate455

19.7.5 Tetrathionate Oxidation456

19.7.6 Common Mechanism for Oxidizing Reduced Inorganic Sulfur Compounds in Domain Bacteria456

19.8 Autotrophic and Mixotrophic Growth on Reduced Forms of Sulfur456

19.8.1 Energy Coupling in Bacterial Sulfur Oxidation456

19.8.2 Reduced Forms of Sulfur as Sources of Reducing Power for CO2 Fixation by Autotrophs457

19.8.2.1 Chemosynthetic Autotrophs457

19.8.2.2 Photosynthetic Autotrophs457

19.8.3 CO2 Fixation by Autotrophs457

19.8.3.1 Chemosynthetic Autotrophs457

19.8.3.2 Photosynthetic Autotrophs458

19.8.4 Mixotrophy458

19.8.4.1 Free-Living Bacteria458

19.8.5 Unusual Consortia458

19.9 Anaerobic Respiration Using Oxidized Forms of Sulfur as Terminal Electron Acceptors459

19.9.1 Reduction of Fully or Partially Oxidized Sulfur459

19.9.2 Biochemistry of Dissimilatory Sulfate Reduction459

19.9.3 Sulfur Isotope Fractionation461

19.9.4 Reduction of Elemental Sulfur462

19.9.5 Reduction of Thiosulfate463

19.9.6 Terminal Electron Acceptors Other Than Sulfate, Sulfite,Thiosulfate, or Sulfur463

19.9.7 Oxygen Tolerance of Sulfate-Reducers464

19.10 Autotrophy, Mixotrophy, and Heterotrophy among Sulfate-Reducing Bacteria464

19.10.1 Autotrophy464

19.10.2 Mixotrophy465

19.10.3 Heterotrophy465

19.11 Biodeposition of Native Sulfur466

19.11.1 Types of Deposits466

19.11.2 Examples of Syngenetic Sulfur Deposition466

19.11.2.1 Cyrenaican Lakes, Libya, North Africa466

19.11.2.2 Lake Senoye469

19.11.2.3 Lake Eyre469

19.11.2.4 Solar Lake470

19.11.2.5 Thermal Lakes and Springs470

19.11.3 Examples of Epigenetic Sulfur Deposits472

19.11.3.1 Sicilian Sulfur Deposits472

19.11.3.2 Salt Domes472

19.11.3.3 Gaurdak Sulfur Deposit474

19.11.3.4 Shor-Su Sulfur Deposit474

19.11.3.5 Kara Kum Sulfur Deposit475

19.12 Microbial Role in Sulfur Cycle475

19.13 Summary476

References477

Chapter 20 Biogenesis and Biodegradation of Sulfide Minerals at Earths Surface491

20.1 Introduction491

20.2 Natural Origin of Metal Sulfides491

20.2.1 Hydrothermal Origin Abiotic491

20.2.2 Sedimentary Metal Sulfides of Biogenic Origin493

20.3 Principles of Metal Sulfide Formation494

20.4 Laboratory Evidence in Support of Biogenesis of Metal Sulfides495

20.4.1 Batch Cultures495

20.4.2 Column Experiment: Model for Biogenesis of Sedimentary Metal Sulfides497

20.5 Biooxidation of Metal Sulfides498

20.5.1 Organisms Involved in Biooxidation of Metal Sulfides498

20.5.2 Direct Oxidation499

20.5.3 Indirect Oxidation503

20.5.4 Pyrite Oxidation504

20.6 Bioleaching of Metal Sulfide and Uraninite Ores507

20.6.1 Metal Sulfide Ores507

20.6.2 Uraninite Leaching511

20.6.3 Mobilization of Uranium in Granitic Rocks by Heterotrophs512

20.6.4 Study of Bioleaching Kinetics513

20.6.5 Industrial versus Natural Bioleaching513

20.7 Bioextraction of Metal Sulfide Ores by Complexation513

20.8 Formation of Acid Coal Mine Drainage514

20.8.1 New Discoveries Relating to Acid Mine Drainage515

20.9 Summary517

References518

Chapter 21 Geomicrobiology of Selenium and Tellurium527

21.1 Occurrence in Earths Crust527

21.2 Biological Importance527

21.3 Toxicity of Selenium and Tellurium528

21.4 Biooxidation of Reduced Forms of Selenium528

21.5 Bioreduction of Oxidized Selenium Compounds528

21.5.1 Other Products of Selenate and Selenite Reduction530

21.5.2 Selenium Reduction in the Environment531

21.6 Selenium Cycle532

21.7 Biooxidation of Reduced Forms of Tellurium532

21.8 Bioreduction of Oxidized Forms of Tellurium533

21.9 Summary533

References534

Chapter 22 Geomicrobiology of Fossil Fuels537

22.1 Introduction537

22.2 Natural Abundance of Fossil Fuels537

22.3 Methane537

22.3.1 Methanogens539

22.3.2 Methanogenesis and Carbon Assimilation by Methanogens541

22.3.2.1 Methanogenesis541

22.3.3 Bioenergetics of Methanogenesis544

22.3.4 Carbon Fixation by Methanogens544

22.3.5 Microbial Methane Oxidation545

22.3.5.1 Aerobic Methanotrophy545

22.3.5.2 Anaerobic Methanotrophy547

22.3.6 Biochemistry of Methane Oxidation in Aerobic Methanotrophs548

22.3.7 Carbon Assimilation by Aerobic Methanotrophs549

22.3.8 Position of Methane in Carbon Cycle550

22.4 Peat550

22.4.1 Nature of Peat550

22.4.2 Roles of Microbes in Peat Formation552

22.5 Coal552

22.5.1 Nature of Coal552

22.5.2 Role of Microbes in Coal Formation553

22.5.3 Coal as Microbial Substrate554

22.5.4 Microbial Desulfurization of Coal555

22.6 Petroleum556

22.6.1 Nature of Petroleum556

22.6.2 Role of Microbes in Petroleum Formation556

22.6.3 Role of Microbes in Petroleum Migration in Reservoir Rock557

22.6.4 Microbes in Secondary and Tertiary Oil Recovery558

22.6.5 Removal of Organic Sulfur from Petroleum559

22.6.6 Microbes in Petroleum Degradation559

22.6.7 Current State of Knowledge of Aerobic and Anaerobic Petroleum Degradation by Microbes560

22.6.8 Use of Microbes in Prospecting for Petroleum563

22.6.9 Microbes and Shale Oil563

22.7 Summary564

References565

Glossary577

Index589