Ehrlich H.L. Geomicrobiology (Boca Raton; London, 2009). - ОГЛАВЛЕНИЕ / CONTENTS
Навигация

Архив выставки новых поступлений | Отечественные поступления | Иностранные поступления | Сиглы
ОбложкаEhrlich H.L. Geomicrobiology / H.L.Ehrlich, D.K.Newman. - 5th ed. - Boca Raton; London: CRC Press, 2009. - xxi, 606 p.: ill., maps. - Incl. bibl. ref. - Ind.: p.589-606. - ISBN 978-0-8493-7906-2
 

Место хранения: 041 | Институт почвоведения и агрохимии CO РАН | Новосибирск

Оглавление / Contents
 
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


Архив выставки новых поступлений | Отечественные поступления | Иностранные поступления | Сиглы
 

[О библиотеке | Академгородок | Новости | Выставки | Ресурсы | Библиография | Партнеры | ИнфоЛоция | Поиск]
  Пожелания и письма: branch@gpntbsib.ru
© 1997-2024 Отделение ГПНТБ СО РАН (Новосибирск)
Статистика доступов: архив | текущая статистика
 

Документ изменен: Wed Feb 27 14:24:10 2019. Размер: 44,140 bytes.
Посещение N 1537 c 30.10.2012