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Introduction to Geomicrobiology

De
440 pages
Introduction to Geomicrobiology is a timely and comprehensive overview of how microbial life has affected Earth’s environment through time. It shows how the ubiquity of microorganisms, their high chemical reactivity, and their metabolic diversity make them a significant factor controlling the chemical composition of our planet.


The following topics are covered:


  • how microorganisms are classified, the physical constraints governing their growth, molecular approaches to studying microbial diversity, and life in extreme environments
  • bioenergetics, microbial metabolic capabilities, and major biogeochemical pathways
  • chemical reactivity of the cell surface, metal sorption, and the microbial role in contaminant mobility and bioremediation/biorecovery
  • microbiological mineral formation and fossilization
  • the function of microorganisms in mineral dissolution and oxidation, and the industrial and environmental ramifications of these processes
  • elemental cycling in biofilms, formation of microbialites, and sediment diagenesis
  • the events that led to the emergence of life, evolution of metabolic processes, and the diversification of the biosphere.

Artwork from the book is available to instructors at www.blackwellpublishing.com/konhauser.

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1
2
Preface, ix
Contents
Microbial properties and diversity, 1 1.1 Classification of life, 1 1.2 Physical properties of microorganisms, 5 1.2.1 Prokaryotes, 5 1.2.2 Eukaryotes, 8 1.3 Requirements for growth, 10 1.3.1 Physical requirements, 10 1.3.2 Chemical requirements, 11 1.3.3 Growth rates, 17 1.4 Microbial diversity, 18 1.5 Life in extreme environments, 22 1.5.1 Hydrothermal systems, 23 1.5.2 Polar environments, 26 1.5.3 Acid environments, 28 1.5.4 Hypersaline and alkaline environments, 29 Deep-subsurface environments, 30 1.5.6 Life on other planets, 32 1.5.7 Panspermia, 34 1.6 Summary, 35
1.5.5
Microbial metabolism, 36 2.1 Bioenergetics, 36 2.1.1 Enzymes, 36 2.1.2 Oxidation-reduction, 37 2.1.3 ATP generation, 42 2.1.4 Chemiosmosis, 43 2.2 Photosynthesis, 47 2.2.1 Pigments, 47 2.2.2 The light reactions – anoxygenic photosynthesis, 49
2.3
2.4
2.5
2.6
2.2.3 Classification of anoxygenic photosynthetic bacteria, 51 2.2.4 The light reactions – oxygenic photosynthesis, 54 2.2.5 The dark reactions, 56 2.2.6 Nitrogen fixation, 57 Catabolic processes, 58 2.3.1 Glycolysis and fermentation, 59 2.3.2 Respiration, 61 Chemoheterotrophic pathways, 65 2.4.1 Aerobic respiration, 65 2.4.2 Dissimilatory nitrate reduction, 66 2.4.3 Dissimilatory manganese reduction, 67 2.4.4 Dissimilatory iron reduction, 69 2.4.5 Trace metal and metalloid reductions, 72 2.4.6 Dissimilatory sulfate reduction, 74 2.4.7 Methanogenesis and homoacetogenesis, 77 Chemolithoautotrophic pathways, 79 2.5.1 Hydrogen oxidizers, 79 2.5.2 Homoacetogens and methanogens, 81 2.5.3 Methylotrophs, 82 2.5.4 Sulfur oxidizers, 84 2.5.5 Iron oxidizers, 86 2.5.6 Manganese oxidizers, 89 2.5.7 Nitrogen oxidizers, 91 Summary, 92
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3
CONTENTS
Cell surface reactivity and metal sorption, 93 3.1 The cell envelope, 93 3.1.1 Bacterial cell walls, 93 3.1.2 Bacterial surface layers, 97 3.1.3 Archaeal cell walls, 100 3.1.4 Eukaryotic cell walls, 100 3.2 Microbial surface charge, 101 3.2.1 Acid–base chemistry of microbial surfaces, 101 3.2.2 Electrophoretic mobility, 104 3.2.3 Chemical equilibrium models, 105 3.3 Passive metal adsorption, 108 3.3.1 Metal adsorption to bacteria, 108 3.3.2 Metal adsorption to eukaryotes, 111 3.3.3 Metal cation partitioning, 112 3.3.4 Competition with anions, 114 3.4 Active metal adsorption, 114 3.4.1 Surface stability requirements, 115 3.4.2 Metal binding to microbial exudates, 116 3.5 Bacterial metal sorption models, 119 3.5.1Kdcoefficients, 119 3.5.2 Freundlich isotherms, 120 3.5.3 Langmuir isotherms, 121 3.5.4 Surface complexation models (SCM), 122 3.5.5 Does a generalized sorption model exist?, 124 3.6 The microbial role in contaminant mobility, 126 3.6.1 Microbial sorption to solid surfaces, 127 3.6.2 Microbial transport through porous media, 131 3.7 Industrial applications based on microbial surface reactivity, 133 3.7.1 Bioremediation, 133 3.7.2 Biorecovery, 136 3.8 Summary, 138
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5
4.1 4.2 4.3
Biomineralization, 139 Biologically induced mineralization, 139 4.1.1 Mineral nucleation and growth, 139 4.1.2 Iron hydroxides, 143 4.1.3 Magnetite, 149 4.1.4 Manganese oxides, 150 4.1.5 Clays, 153 4.1.6 Amorphous silica, 156 4.1.7 Carbonates, 160 4.1.8 Phosphates, 166 4.1.9 Sulfates, 169 4.1.10 Sulfide minerals, 171 Biologically controlled mineralization, 174 4.2.1 Magnetite, 174 4.2.2 Greigite, 178 4.2.3 Amorphous silica, 179 4.2.4 Calcite, 183 Fossilization, 185 4.3.1 Silicification, 186 4.3.2 Other authigenic minerals, 189 Summary, 191
4.4
Microbial weathering, 192 5.1 Mineral dissolution, 192 5.1.1 Reactivity at mineral surfaces, 192 5.1.2 Microbial colonization and organic reactions, 195 5.1.3 Silicate weathering, 200 5.1.4 Carbonate weathering, 205 5.1.5 Soil formation, 206 5.1.6 Weathering and global climate, 209 5.2 Sulfide oxidation, 211 5.2.1 Pyrite oxidation mechanisms, 211 5.2.2 Biological role in pyrite oxidation, 215 5.2.3 Bioleaching, 223 5.2.4 Biooxidation of refractory gold, 229
6
5.3
5.4
Microbial corrosion, 230 5.3.1 Chemolithoautotrophs, 231 5.3.2 Chemoheterotrophs, 232 5.3.3 Fungi, 234 Summary, 234
CONTENTS
Microbial zonation, 235 6.1 Microbial mats, 235 6.1.1 Mat development, 236 6.1.2 Photosynthetic mats, 240 6.1.3 Chemolithoautotrophic mats, 246 6.1.4 Biosedimentary structures, 249 6.2 Marine sediments, 259 6.2.1 Organic sedimentation, 260 6.2.2 An overview of sediment diagenesis, 262 6.2.3 Oxic sediments, 265 6.2.4 Suboxic sediments, 266 6.2.5 Anoxic sediments, 272 6.2.6 Preservation of organic carbon into the sedimentary record, 280 6.2.7 Diagenetic mineralization, 283 6.2.8 Sediment hydrogen concentrations, 287 6.2.9 Problems with the biogeochemical zone scheme, 288 6.3 Summary, 292
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Early microbial life, 293 7.1 The prebiotic Earth, 293 7.1.1 The Hadean environment, 294 7.1.2 Origins of life, 296 7.1.3 Mineral templates, 301 7.2 The first cellular life forms, 305 7.2.1 The chemolithoautotrophs, 305 7.2.2 Deepest-branchingBacteria andArchaea, 309 7.2.3 The fermenters and initial respirers, 311 7.3 Evolution of photosynthesis, 312 7.3.1 Early phototrophs, 312 7.3.2 Photosynthetic expansion, 319 7.3.3 The cyanobacteria, 323 7.4 Metabolic diversification, 327 7.4.1 Obligately anaerobic respirers, 327 7.4.2 Continental platforms as habitats, 331 7.4.3 Aerobic respiratory pathways, 334 7.5 Earth’s oxygenation, 340 7.5.1 The changing Proterozoic environment, 340 7.5.2 Eukaryote evolution, 345 Summary, 349
7.6
References, 350 Index, 406