Preface ....................................................... xix
Authors ....................................................... xxi
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
5.1 The 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
5.2 Freshwater Lakes .......................................... 73
5.2.1 Some Physical and Chemical Features of Lakes ....... 74
5.2.2 Lake Bottoms ....................................... 76
5.2.3 Lake Fertility ..................................... 77
5.2.4 Lake Evolution ..................................... 77
5.2.5 Microbial Populations in Lakes ..................... 77
5.3 Rivers .................................................... 78
5.4 Groundwaters .............................................. 79
5.5 Summary ................................................... 82
References ................................................ 83
Chapter 6 Geomicrobial Processes: Physiological and
Biochemical Overview ................................ 89
6.1 Types of Geomicrobial Agents .............................. 89
6.2 Geomicrobially Important Physiological Groups of
Prokaryotes ............................................... 90
6.3 Role of Microbes in Inorganic Conversions in Lithosphere
and Hydrosphere ........................................... 91
6.4 Types of Microbial Activities Influencing Geological
Processes ................................................. 92
6.5 Microbes as Catalysts of Geochemical 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
6.6 Microbial Mineralization of Organic Matter ............... 108
6.7 Microbial Products of Metabolism That Can Cause
Geomicrobial Transformations ............................. 110
6.8 Physical Parameters That Influence Geomicrobial
Activity ................................................. 110
6.9 Summary .................................................. 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
8.1 Introduction ............................................. 139
8.2 Who Is There? Identification of Geomicrobial Organisms ... 139
8.2.1 Culture-Independent Methods ....................... 139
8.2.2 New Culturing Techniques .......................... 141
8.3 What 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
8.4 How Are They Doing It? Unraveling the Mechanisms of
Geomicrobial Organisms ................................... 147
8.4.1 Genetic Approaches ................................ 148
8.4.2 Bioinformatic Approaches .......................... 151
8.4.3 Follow-Up Studies ................................. 151
8.5 Summary .................................................. 152
References ............................................... 152
Chapter 9 Microbial Formation and Degradation of
Carbonates ......................................... 157
9.1 Distribution of Carbon in Earth's 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
Silicates (Bioweathering) ................................ 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(III) 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 Earth's 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 Geomicrobiology 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 (Я-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 Geomicrobiology 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 Metallogenium ............................ 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 Iron(III) 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(III) 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(III) 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 Earth's 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(III) ..................... 422
18.1.5 Bioreduction of Chromium(VI) ...................... 422
18.1.6 In Situ Chromate Reducing Activity ................ 426
18.1.7 Applied Aspects of Chromium(VI) 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 Reduction 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(IV) ...................... 429
18.4.3 Microbial Reduction of U(IV) ...................... 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 Earth's 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 Sulfite 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 C02 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 Earth's 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 Earth's 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
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