Introduction to GeomicrobiologyIntroduction 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:
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From inside the book
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Page 3
... species are passed onto another, leading to the acquisition of physiological properties or meta- bolic traits that are not concordant with their 16S rRNA phylogenies (Doolittle, 1999). An example we are all familiar with from the news ...
... species are passed onto another, leading to the acquisition of physiological properties or meta- bolic traits that are not concordant with their 16S rRNA phylogenies (Doolittle, 1999). An example we are all familiar with from the news ...
Page 10
... species is subject to a number of variables that affect their rates of growth. We can divide these requirements into two categories, physical and chemical. Phys- ical aspects include temperature, pH, and osmotic pressure, while the ...
... species is subject to a number of variables that affect their rates of growth. We can divide these requirements into two categories, physical and chemical. Phys- ical aspects include temperature, pH, and osmotic pressure, while the ...
Page 11
... species that have a definite geometrical arrangement around the central carbon atom. The resultant molecules form what are known as functional groups, each of which possesses characteristic chemical and physical properties that can be ...
... species that have a definite geometrical arrangement around the central carbon atom. The resultant molecules form what are known as functional groups, each of which possesses characteristic chemical and physical properties that can be ...
Page 18
... species also decrease their requirements for limiting metals by altering metabolic pathways or by changing the type of metal-containing enzyme in key pathways. For instance, under iron-limiting conditions, many marine species are able ...
... species also decrease their requirements for limiting metals by altering metabolic pathways or by changing the type of metal-containing enzyme in key pathways. For instance, under iron-limiting conditions, many marine species are able ...
Page 19
... species, and in any given part of the mat there exists a highly organized community where nutrients and metabolites are continuously recycled between cells in close proximity. One of the primary goals of microbial eco- logists has been ...
... species, and in any given part of the mat there exists a highly organized community where nutrients and metabolites are continuously recycled between cells in close proximity. One of the primary goals of microbial eco- logists has been ...
Contents
412 Iron hydroxides | 143 |
413 Magnetite | 149 |
414 Manganese oxides | 150 |
415 Clays | 153 |
416 Amorphous silica | 156 |
417 Carbonates | 160 |
418 Phosphates | 166 |
419 Sulfates | 169 |
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30 | |
32 | |
34 | |
35 | |
36 | |
37 | |
213 ATP generation | 42 |
214 Chemiosmosis | 43 |
22 Photosynthesis | 47 |
222 The light reactions anoxygenic photosynthesis | 49 |
223 Classification of anoxygenic photosynthetic bacteria | 51 |
224 The light reactions oxygenic photosynthesis | 54 |
225 The dark reactions | 56 |
226 Nitrogen fixation | 57 |
23 Catabolic processes | 58 |
231 Glycolysis and fermentation | 59 |
232 Respiration | 61 |
24 Chemoheterotrophic pathways | 65 |
242 Dissimilatory nitrate reduction | 66 |
243 Dissimilatory manganese reduction | 67 |
244 Dissimilatory iron reduction | 69 |
245 Trace metal and metalloid reductions | 72 |
246 Dissimilatory sulfate reduction | 74 |
247 Methanogenesis and homoacetogenesis | 77 |
25 Chemolithoautotrophic pathways | 79 |
252 Homoacetogens and methanogens | 81 |
253 Methylotrophs | 82 |
254 Sulfur oxidizers | 84 |
255 Iron oxidizers | 86 |
256 Manganese oxidizers | 89 |
257 Nitrogen oxidizers | 91 |
3 Cell surface reactivity and metal sorption | 93 |
312 Bacterial surface layers | 97 |
313 Archaeal cell walls | 100 |
32 Microbial surface charge | 101 |
322 Electrophoretic mobility | 104 |
323 Chemical equilibrium models | 105 |
33 Passive metal adsorption | 108 |
332 Metal adsorption to eukaryotes | 111 |
333 Metal cation partitioning | 112 |
334 Competition with anions | 114 |
341 Surface stability requirements | 115 |
342 Metal binding to microbial exudates | 116 |
35 Bacterial metal sorption models | 119 |
352 Freundlich isotherms | 120 |
353 Langmuir isotherms | 121 |
354 Surface complexation | 122 |
355 Does a generalized sorption model exist? | 124 |
36 The microbial role in contaminant mobility | 126 |
361 Microbial sorption to solid surfaces | 127 |
362 Microbial transport through porous media | 131 |
37 Industrial applications based on microbial surface reactivity | 133 |
372 Biorecovery | 136 |
38 Summary | 138 |
4 Biomineralization | 139 |
4110 Sulfide minerals | 171 |
42 Biologically controlled mineralization | 174 |
422 Greigite | 178 |
423 Amorphous silica | 179 |
424 Calcite | 183 |
43 Fossilization | 185 |
431 Silicification | 186 |
432 Other authigenic minerals | 189 |
44 Summary | 191 |
5 Microbial weathering | 192 |
512 Microbial colonization and organic reactions | 195 |
513 Silicate weathering | 200 |
514 Carbonate weathering | 205 |
515 Soil formation | 206 |
516 W eathering and global climate | 209 |
52 Sulfide oxidation | 211 |
522 Biological role in pyrite oxidation | 215 |
523 Bioleaching | 223 |
524 Biooxidation of refractory gold | 229 |
53 Microbial corrosion | 230 |
531 Chemolithoautotrophs | 231 |
532 Chemoheterotrophs | 232 |
533 Fungi | 234 |
6 Microbial zonation | 235 |
611 Mat development | 236 |
612 Photosynthetic mats | 240 |
613 Chemolithoautotrophic mats | 246 |
614 Biosedimentary structures | 249 |
62 Marine sediments | 259 |
621 Organic sedimentation | 260 |
622 An overview of sediment diagenesis | 262 |
623 Oxic sediments | 265 |
624 Suboxic sediments | 266 |
625 Anoxic sediments | 272 |
626 Preservation of organic carbon Preservation of organic carbon | 280 |
627 Diagenetic mineralization | 283 |
628 Sediment hydrogen concentrations | 287 |
629 Problems with the biogeochemical zone scheme | 288 |
63 Summary | 292 |
7 Early microbial life | 293 |
711 The Hadean environment | 294 |
712 Origins of life | 296 |
713 Mineral templates | 301 |
72 The first cellular life forms | 305 |
722 Deepestbranching Bacteria and Archaea | 309 |
723 The fermenters and initial respirers | 311 |
73 Evolution of photosynthesis | 312 |
732 Photosynthetic expansion | 319 |
733 The cyanobacteria | 323 |
74 Metabolic diversification | 327 |
742 Continental platforms as habitats | 331 |
743 Aerobic respiratory pathways | 334 |
75 Earths oxygenation | 340 |
752 Eukaryote evolution | 345 |
76 Summary | 349 |
References | 350 |
Index | 406 |
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Common terms and phrases
acid activity adsorbed adsorption aerobic respiration algae amino amorphous anaerobic anionic anoxic Archaea Archean atmosphere bacterium Beggiatoa biofilms biological biomass Ca2+ calcite calcium carboxyl cell surface cell wall chemical chemoheterotrophs chemolithoautotrophs complex concentrations cyanobacteria cycle cytochrome cytoplasm degradation deposits diffusion dissolution dissolved Earth’s electron acceptor environment enzymes Fe(III Fe2+ Fe3+ ferric hydroxide ferrooxidans filamentous formation functional groups growth H+ H+ HCO3 heterotrophic hydrogen hydrothermal inorganic ions iron isotopic layers ligands Lovley magnetite metabolic metal cations methane methanogens micro microorganisms mineral surface Mn2+ MnO2 molecules nitrate nucleation nutrients ocean organic carbon organic compounds organic matter oxic oxidation oxygen pathway phase phosphate photosynthesis plasma membrane pore waters potential precipitation production proteins protons purple bacteria pyrite rates reaction reactive redox rock seafloor sedimentary siderophores silica solution sorption species stromatolites substrate sulfate reduction sulfate-reducing bacteria sulfide temperatures tion water column zone