Geomicrobiology, 4th ed.

2. The Earth as a Microbial Habitat 7 2.1 Geologically Important Features 7 2.2 The Biosphere 12 2.3 Summary 16 References 16 xvii Copyright © 2002 by Marcel Dekker, Inc. 3. The Origin of Life and Its Early History 21 3.1 The Beginnings 21 3.2 Evolution of Life Through the Precambrian: Biological and Biochemical Benchmarks 28 3.3 The Evidence 38 3.4 Summary 43 References 44 4. The Lithosphere as a Microbial Habitat 49 4.1 Rock and Minerals 49 4.2 Mineral Soil 51 4.3 Organic Soils 65 4.4 The Deep Subsurface 65 4.5 Summary 67 References 68 5. The Hydrosphere as a Microbial Habitat 73 5.1 The Oceans 73 5.2 Freshwater Lakes 95 5.3 Rivers 102 5.4 Groundwaters 103 5.5 Summary 108 References 109 6. Geomicrobial Processes: A Physiological and Biochemical Overview 117 6.1 Types of Geomicrobial Agents 117 6.2 Geomicrobially Important Physiological Groups of Prokaryotes 119 6.3 Role of Microbes in Inorganic Conversions in the Lithosphere and Hydrosphere 121 6.4 Types of Microbial Activities Influencing Geological Processes 122 6.5 Microbes as Catalysts of Geochemical Processes 123 6.6 Microbial Mineralization of Organic Matter 142 6.7 Microbial Products of Metabolism That Can Cause Geomicrobial Transformations 144 6.8 Physical Parameters That Influence Geomicrobial Activity 144 6.9 Summary 147 References 148 xviii Contents Copyright © 2002 by Marcel Dekker, Inc. 7. Methods in Geomicrobiology 153 7.1 Introduction 153 7.2 Detection and Isolation of Geomicrobially Active Organisms 155 7.3 In Situ Study of Past Geomicrobial Activity 164 7.4 In Situ Study of Ongoing Geomicrobial Activity 166 7.5 Laboratory Reconstruction of Geomicrobial Processes in Nature 168 7.6 Quantitative Study of Growth on Surfaces 172 7.7 Test for Distinguishing Between Enzymatic and Nonenzymatic Geomicrobial Activity 176 7.8 Study of Reaction Products of a Geomicrobial Transformation 176 7.9 Summary 177 References 177 8. Microbial Formation and Degradation of Carbonates 183 8.1 Distribution of Carbon in the Earth’s Crust 183 8.2 Biological Carbonate Deposition 184 8.3 Biodegradation of Carbonates 212 8.4 Biological Carbonate Formation and Degradation and the Carbon Cycle 218 8.5 Summary 220 References 221 9. Geomicrobial Interactions with Silicon 229 9.1 Distribution and Some Chemical Properties 229 9.2 Biologically Important Properties of Silicon and Its Compounds 231 9.3 Bioconcentration of Silicon 233 9.4 Biomobilization of Silicon and Other Constituents of Silicates (Bioweathering) 239 9.5 Role of Microbes in the Silicon Cycle 245 9.6 Summary 247 References 247 10. Geomicrobiology of Aluminum: Microbes and Bauxite 255 10.1 Introduction 255 10.2 Microbial Role in Bauxite Formation 256 10.3 Summary 263 References 264 Contents xix Copyright © 2002 by Marcel Dekker, Inc. 11. Geomicrobial Interactions with Phosphorus 267 11.1 Biological Importance of Phosphorus 267 11.2 Occurrence in the Earth’s Crust 268 11.3 Conversion of Organic into Inorganic Phosphorus and the Synthesis of Phosphate Esters 268 11.4 Assimilation of Phosphorus 270 11.5 Microbial Solubilization of Phosphate Minerals 271 11.6 Microbial Phosphate Immobilization 274 11.7 Microbial Reduction of Oxidized Forms of Phosphorus 278 11.8 Microbial Oxidation of Reduced Forms of Phosphorus 280 11.9 Microbial Role in the Phosphorus Cycle 281 11.10 Summary 283 References 283 12. Geomicrobially Important Interactions with Nitrogen 289 12.1 Nitrogen in the Biosphere 289 12.2 Microbial Interactions with Nitrogen 290 12.3 Microbial Role in the Nitrogen Cycle 297 12.4 Summary 298 References 299 13. Geomicrobial Interactions with Arsenic and Antimony 303 13.1 Introduction 303 13.2 Arsenic 303 13.3 Antimony 317 13.4 Summary 319 References 320 14. Geomicrobiology of Mercury 327 14.1 Introduction 327 14.2 Distribution of Mercury in the Earth’s Crust 328 14.3 Anthropogenic Mercury 328 14.4 Mercury in the Environment 329 14.5 Specific Microbial Interactions with Mercury 330 14.6 Genetic Control of Mercury Transformations 335 14.7 Environmental Significance of Microbial Mercury Transformations 336 14.8 A Mercury Cycle 337 14.9 Summary 338 References 339 xx Contents Copyright © 2002 by Marcel Dekker, Inc. 15. Geomicrobiology of Iron 345 15.1 Iron Distribution in the Earth’s Crust 345 15.2 Geochemically Important Properties 345 15.3 Biological Importance of Iron 347 15.4 Iron as Energy Source for Bacteria 349 15.5 Anaerobic Oxidation of Ferrous Iron 376 15.6 Iron(III) as Terminal Electron Acceptor in Bacterial Respiration 377 15.7 Nonenzymatic Oxidation of Ferrous Iron and Reduction of Ferric Iron by Microbes 393 15.8 Microbial Precipitation of Iron 395 15.9 The Concept of Iron Bacteria 397 15.10 Sedimentary Iron Deposits of Putative Biogenic Origin 398 15.11 Microbial Mobilization of Iron from Minerals in Ore, Soil, and Sediments 403 15.12 Microbes and the Iron Cycle 404 15.13 Summary 406 References 408 16. Geomicrobiology of Manganese 429 16.1 Occurrence of Manganese in the Earth’s Crust 429 16.2 Geochemically Important Properties of Manganese 430 16.3 Biological Importance of Manganese 431 16.4 Manganese-Oxidizing and -Reducing Bacteria and Fungi 431 16.5 Bio-oxidation of Manganese 435 16.6 Bioreduction of Manganese 447 16.7 Bioaccumulation of Manganese 459 16.8 Microbial Manganese Deposition in Soil and on Rocks 463 16.9 Microbial Manganese Deposition in Freshwater Environments 468 16.10 Microbial Manganese Deposition in Marine Environments 477 16.11 Microbial Mobilization of Manganese in Soils and Ores 496 16.12 Microbial Mobilization of Manganese in Freshwater Environments 499 16.13 Microbial Mobilization of Manganese in Marine Environments 500 16.14 Microbial Manganese Reduction and Mineralization of Organic Matter 503 16.15 Microbial Role in the Manganese Cycle in Nature 503 16.16 Summary 507 References 508 Contents xxi Copyright © 2002 by Marcel Dekker, Inc. 17. Geomicrobial Interactions with Chromium, Molybdenum, Vanadium, Uranium, and Polonium 529 17.1 Microbial Interactions with Chromium 529 17.2 Microbial Interaction with Molybdenum 536 17.3 Microbial Interaction with Vanadium 537 17.4 Microbial Interaction with Uranium 539 17.5 Bacterial Interaction with Polonium 541 17.6 Summary 541 References 542 18. Geomicrobiology of Sulfur 549 18.1 Occurrence of Sulfur in the Earth’s Crust 549 18.2 Geochemically Important Properties of Sulfur 550 18.3 Biological Importance of Sulfur 551 18.4 Mineralization of Organic Sulfur Compounds 551 18.5 Sulfur Assimilation 552 18.6 Geomicrobially Important Types of Bacteria That React with Sulfur and Sulfur Compounds 553 18.7 Physiology and Biochemistry of Microbial Oxidation of Reduced Forms of Sulfur 562 18.8 Autotrophic and Mixotrophic Growth on Reduced Forms of Sulfur 573 18.9 Anaerobic Respiration Using Oxidized Forms of Sulfur as Electron Acceptors 577 18.10 Autotrophy, Mixotrophy, and Heterotrophy Among Sulfate-Reducing Bacteria 585 18.11 Biodeposition of Native Sulfur 587 18.12 Microbial Role in the Sulfur Cycle 601 18.13 Summary 602 References 603 19. Biogenesis and Biodegradation of Sulfide Minerals at the Earth’s Surface 621 19.1 Introduction 621 19.2 Natural Origins of Metal Sulfides 622 19.3 Principles of Metal Sulfide Formation 626 19.4 Laboratory Evidence in Support of Biogenesis of Metal Sulfides 627 19.5 Bio-oxidation of Metal Sulfides 630 19.6 Bioleaching of Metal Sulfide and Uraninite Ores 642 xxii Contents Copyright © 2002 by Marcel Dekker, Inc. 19.7 Bioextraction of Metal Sulfide Ores by Complexation 651 19.8 Formation of Acid Coal Mine Drainage 652 19.9 Summary 657 References