Verfügbarkeit: Geomicrobiology

Geomicrobiology:

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Bibliographische Detailangaben
1. Verfasser:	Ehrlich, Henry Lutz 1925- (VerfasserIn)
Format:	Buch
Sprache:	English
Veröffentlicht:	Boca Raton [u.a.] Taylor & Francis 2009
Ausgabe:	5. ed.
Schlagworte:	Geomicrobiology Geomikrobiologie
Online-Zugang:	Inhaltsverzeichnis
Beschreibung:	Includes bibliographical references and index
Beschreibung:	XXI, 606 S. Ill., graph. Darst.
ISBN:	9780849379062

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245	1	0	\|a Geomicrobiology \|c Henry Lutz Ehrlich ; Dianne K. Newman
250			\|a 5. ed.
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Datensatz im Suchindex

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adam_text	Contents Preface .............................................................................................................................................xix Authors ............................................................................................................................................xxi Chapter 1 Introduction ..................................................................................................................1 References ....................................................................................................................3 Chapter 2 Earth as aMicrobial 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 Lithosphère 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 VII viii Contents 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 Lithosphère 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 CO, 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 Contents IX 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 Isotopie 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 x Contents 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 Contents xi 11.2.5 Bacterial Reduction of FeCIII) 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 x¡¡ Contents 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 (ß-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 Contents xiii 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 xiv Contents 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 la ......................................................................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 HI 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 Contents xv 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 СгіготішпЩІ) .......................................................422 18.1.5 Bioreduction of ChromiumCVI) .......................................................422 18.1.6 In Situ Chromate Reducing Activity ...............................................426 18.1.7 Applied Aspects of ChromiumCVI) Reduction ...............................427 18.2 Microbial Interaction with Molybdenum ......................................................427 18.2.1 Occurrence and Properties of Molybdenum ...................................427 18.2.2 Microbial Oxidation and Reduction ................................................427 18.3 Microbial Interaction with Vanadium ...........................................................428 18.3.1 Bacterial Oxidation of Vanadium ....................................................428 18.4 Microbial Interaction with Uranium .............................................................429 18.4.1 Occurrence and Properties of Uranium ...........................................429 18.4.2 Microbial Oxidation of U(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 xvi Contents 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 CO;, 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 LakeSenoye ...................................................................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 Contents xvii 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 xviii Contents 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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spelling	Ehrlich, Henry Lutz 1925- Verfasser (DE-588)137523815 aut Geomicrobiology Henry Lutz Ehrlich ; Dianne K. Newman 5. ed. Boca Raton [u.a.] Taylor & Francis 2009 XXI, 606 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index Geomicrobiology Geomikrobiologie (DE-588)4156734-1 gnd rswk-swf Geomikrobiologie (DE-588)4156734-1 s DE-604 Newman, Dianne K. Sonstige oth Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017121152&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis
spellingShingle	Ehrlich, Henry Lutz 1925- Geomicrobiology Geomicrobiology Geomikrobiologie (DE-588)4156734-1 gnd
subject_GND	(DE-588)4156734-1
title	Geomicrobiology
title_auth	Geomicrobiology
title_exact_search	Geomicrobiology
title_full	Geomicrobiology Henry Lutz Ehrlich ; Dianne K. Newman
title_fullStr	Geomicrobiology Henry Lutz Ehrlich ; Dianne K. Newman
title_full_unstemmed	Geomicrobiology Henry Lutz Ehrlich ; Dianne K. Newman
title_short	Geomicrobiology
title_sort	geomicrobiology
topic	Geomicrobiology Geomikrobiologie (DE-588)4156734-1 gnd
topic_facet	Geomicrobiology Geomikrobiologie
url	http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017121152&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
work_keys_str_mv	AT ehrlichhenrylutz geomicrobiology AT newmandiannek geomicrobiology

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