Preface	9
	1 Microbial properties and diversity	11
	1.1 Classification of life	11
	1.2 Physical properties of microorganisms	15
	1.2.1 Prokaryotes	15
	1.2.2 Eukaryotes	18
	1.3 Requirements for growth	20
	1.3.1 Physical requirements	20
	1.3.2 Chemical requirements	21
	1.3.3 Growth rates	27
	1.4 Microbial diversity	28
	1.5 Life in extreme environments	32
	1.5.1 Hydrothermal systems	33
	1.5.2 Polar environments viable population is available to seed the global	36
	1.5.3 Acid environments	38
	1.5.4 Hypersaline and alkaline environments	39
	1.5.5 Deep-subsurface environments	40
	1.5.6 Life on other planets	42
	1.5.7 Panspermia	44
	1.6 Summary	45
	2 Microbial metabolism	46
	2.1 Bioenergetics	46
	2.1.1 Enzymes	46
	2.1.2 Oxidation-reduction	47
	2.1.3 ATP generation	52
	2.1.4 Chemiosmosis	53
	2.2 Photosynthesis	57
	2.2.1 Pigments	57
	2.2.2 The light reactions – anoxygenic photosynthesis	59
	2.2.3 Classification of anoxygenic photosynthetic bacteria	61
	2.2.4 The light reactions – oxygenic photosynthesis	64
	2.2.5 The dark reactions	66
	2.2.6 Nitrogen fixation	67
	2.3 Catabolic processes	68
	2.3.1 Glycolysis and fermentation	69
	2.3.2 Respiration	71
	2.4 Chemoheterotrophic pathways	75
	2.4.1 Aerobic respiration	75
	2.4.2 Dissimilatory nitrate reduction	76
	2.4.3 Dissimilatory manganese reduction	77
	2.4.4 Dissimilatory iron reduction	79
	2.4.5 Trace metal and metalloid reductions	82
	2.4.6 Dissimilatory sulfate reduction	84
	2.4.7 Methanogenesis and homoacetogenesis	87
	2.5 Chemolithoautotrophic pathways	89
	2.5.1 Hydrogen oxidizers	89
	2.5.2 Homoacetogens and methanogens	91
	2.5.3 Methylotrophs	92
	2.5.4 Sulfur oxidizers	94
	2.5.5 Iron oxidizers	96
	2.5.6 Manganese oxidizers	99
	2.5.7 Nitrogen oxidizers	101
	3 Cell surface reactivity and metal sorption	103
	3.1 The cell envelope	103
	3.1.1 Bacterial cell walls	103
	3.1.2 Bacterial surface layers	107
	3.1.3 Archaeal cell walls	110
	3.1.4 Eukaryotic cell walls	110
	3.2 Microbial surface charge	111
	3.2.1 Acid–base chemistry of microbial surfaces	111
	3.2.2 Electrophoretic mobility	114
	3.2.3 Chemical equilibrium models	115
	3.3 Passive metal adsorption	118
	3.3.1 Metal adsorption to bacteria	118
	3.3.2 Metal adsorption to eukaryotes	121
	3.3.3 Metal cation partitioning	122
	3.3.4 Competition with anions	124
	3.4 Active metal adsorption	124
	3.4.1 Surface stability requirements	125
	3.4.2 Metal binding to microbial exudates	126
	3.5 Bacterial metal sorption models	129
	3.5.1 Kd coefficients	129
	3.5.2 Freundlich isotherms	130
	3.5.3 Langmuir isotherms	131
	3.5.4 Surface complexation	132
	3.5.5 Does a generalized sorption model exist?	134
	3.6 The microbial role in contaminant mobility	136
	3.6.1 Microbial sorption to solid surfaces	137
	3.6.2 Microbial transport through porous media	141
	3.7 Industrial applications based on microbial surface reactivity	143
	3.7.1 Bioremediation	143
	3.7.2 Biorecovery	146
	3.8 Summary	148
	4 Biomineralization	149
	4.1 Biologically induced mineralization	149
	4.1.1 Mineral nucleation and growth	149
	4.1.2 Iron hydroxides	153
	4.1.3 Magnetite	159
	4.1.4 Manganese oxides	160
	4.1.5 Clays	163
	4.1.6 Amorphous silica	166
	4.1.7 Carbonates	170
	4.1.8 Phosphates	176
	4.1.9 Sulfates	179
	4.1.10 Sulfide minerals	181
	4.2 Biologically controlled mineralization	184
	4.2.1 Magnetite	184
	4.2.2 Greigite	188
	4.2.3 Amorphous silica	189
	4.2.4 Calcite	193
	4.3 Fossilization	195
	4.3.1 Silicification	196
	4.3.2 Other authigenic minerals	199
	4.4 Summary	201
	5 Microbial weathering	202
	5.1 Mineral dissolution	202
	5.1.1 Reactivity at mineral surfaces	202
	5.1.2 Microbial colonization and organic reactions	205
	5.1.3 Silicate weathering	210
	5.1.4 Carbonate weathering	215
	5.1.5 Soil formation	216
	5.1.6 W eathering and global climate	219
	5.2 Sulfide oxidation	221
	5.2.1 Pyrite oxidation mechanisms	221
	5.2.2 Biological role in pyrite oxidation	225
	5.2.3 Bioleaching	233
	5.2.4 Biooxidation of refractory gold	239
	5.3 Microbial corrosion	240
	5.3.1 Chemolithoautotrophs	241
	5.3.2 Chemoheterotrophs	242
	5.3.3 Fungi	244
	5.4 Summary	244
	6 Microbial zonation	245
	6.1 Microbial mats	245
	6.1.1 Mat development	246
	6.1.2 Photosynthetic mats	250
	6.1.3 Chemolithoautotrophic mats	256
	6.1.4 Biosedimentary structures	259
	6.2 Marine sediments	269
	6.2.1 Organic sedimentation	270
	6.2.2 An overview of sediment diagenesis	272
	6.2.3 Oxic sediments	275
	6.2.4 Suboxic sediments	276
	6.2.5 Anoxic sediments	282
	6.2.6 Preservation of organic carbon Preservation of organic carbon	290
	6.2.7 Diagenetic mineralization	293
	6.2.8 Sediment hydrogen concentrations	297
	6.2.9 Problems with the biogeochemical zone scheme	298
	6.3 Summary	302
	7 Early microbial life	303
	7.1 The prebiotic Earth	303
	7.1.1 The Hadean environment	304
	7.1.2 Origins of life	306
	7.1.3 Mineral templates	311
	7.2 The first cellular life forms	315
	7.2.1 The chemolithoautotrophs	315
	7.2.2 Deepest-branching Bacteria and Archaea	319
	7.2.3 The fermenters and initial respirers	321
	7.3 Evolution of photosynthesis	322
	7.3.1 Early phototrophs	322
	7.3.2 Photosynthetic expansion	329
	7.3.3 The cyanobacteria	333
	7.4 Metabolic diversification	337
	7.4.1 Obligately anaerobic respirers	337
	7.4.2 Continental platforms as habitats	341
	7.4.3 Aerobic respiratory pathways	344
	7.5 Earth’s oxygenation	350
	7.5.1 The changing Proterozoic environment	350
	7.5.2 Eukaryote evolution	355
	7.6 Summary	359
	References	360
	Index	416