ABC permease 147
Acetate kinase 148
Acetivibrio FISH probe 60
Acetobacterium 388
Acetyl-CoA 11, 12, 14–16, 489
Acetyl-CoA synthase 16, 450
Acetyl-phosphate 11, 14
Acetylserine sulfhydrylase 160
Acid mine waters 412, 419, 421
Acid pH stress 145, 148, 156, 158
Acidic fens 41
Adenosine phosphosulphate 5, 7
Aerotaxis 172
Aggregation 171
Agmatinase 158
Alcaligenes eutrophus 246
Alcohol dehydrogenase 129, 219
Alkaline pH stress 145, 148, 159
Alkane utilization 281–3, 308
Alkene utilization 287
Alkyl hydroperoxide reductase 148
Alkylbenzene utilization 281
Allochromatium vinosum 101, 228
Alvinella pompejana symbiont 320
Aminobenzoate 490
Ammonification 242, 256
Anaerofilum FISH probe 60
Analysis of natural systems 89
Aniline 488, 489
Anoxic layers 168
Antibiotic inhibition 386
APS reductase 7, 92, 96, 97, 101, 128, 133, 148, 197, 227, 229
ApsA 97, 101
ArcAB regulon 204
Archaea 24, 39, 274
Archaea probe 42
Archaeoblobus lithotrophicus 316
Archaeoglobus 1, 22, 24, 39, 99, 101, 306, 309, 316, 321, 350
Archaeoglobus fulgidus 6, 16, 22, 102, 123, 124, 131, 201, 227, 228, 310, 316, 352, 440, 447, 450
Archaeoglobus probe 42
Archaeoglobus profundus 6, 22, 310, 316, 321
Archaeoglobus veneficus 316, 321, 348
Arginine decarboxylase 158
Aromatic hydrocarbons oxidized 289
Arsenate 14
Arsenate reductase 441, 447
Arsenate reduction 447, 448
Arsenic reduction 447
Arsenic transporter 441, 447
Arsenical sulphides 410, 416
Arsenite pump 441, 447
ATP sulphurylase 7, 96, 133
ATP synthase 10, 147, 148, 154, 215, 243
ATPase 10, 157–9, 441
a-type haem 192
Bacteria 39, 306, 364
Bacteria FISH probe 60
Bacteria probe 42
Bacterioferritin 187, 188, 202
Bacteroides fragilis 170
bc1 complex 193
bd- type oxygen reductase 187, 191, 192
Bdellovibrio bacteriovorus 132
Beggiatoa 171
Benzoyl CoA 490
Bilophila wadsworthia 23, 99
Biofilm 159, 169, 360–2, 367, 373, 391, 406, 417, 459, 463, 469, 472, 510
Biogeochemical cycling 405, 410
Bioinformatical studies 131, 186–8
Biophila wadsworthia FISH probe 60
Bioreactors 386, 387
Bioremediation 405, 408, 452, 490
Bisulphite disproportionation 5
Bisulphite reductase 7, 9, 41, 92, 96, 99, 101, 320
Bisulphite reduction 7
Bradyrhizobium japonicum 152
BTEX utilization 282
b-type haem 191, 192
Butyrate metabolism 514
Butytyl CoA dehydrogenase 514
C1-carrier 16
caa3 oxygen reductase 192
Caldivirga 39, 306
Caldivirga maquilingensis 103
Carbon mineralization 372
Carbon monoxide 15, 16
Carbon monoxide dehydrogenase 15, 16, 117, 124, 129, 219, 489
Carboxydothermus hydroformans 99
Catalase 169, 188, 196, 198, 200, 202, 470
Cathodic depolarising and corrosion 465–7
Caulobacter crescentus 152
cbb3 oxidases 191
Cellulomonas 446
Chaperones 152, 153
Chemoclines 168
Chloroflexi 349
Chondroitin sulphate 507, 508
Chromate detoxification 445
Chromate reduction 414, 438, 440
Chromate stress 145, 148, 195, 440
Chromate transport 440, 441
Chromosome size 124
Citric acid cycle 16
Clostridium FISH probe 60
CO cycling 215
Cobalamin 450
Cobalt sorbents 394
COD/sulphate ratio 387
Coenzyme B 9, 279
Coenzyme M 277, 278
Cold stress 145, 148
Colonizing the gut wall 505
Community analysis 96
Community structure 360–2
Consortium 274, 490, 493
CooMKLXUHF complex 11, 14, 128
Copper inhibition 386
Copper sulphide 419
Corrosion 307, 360, 459, 460, 463, 469, 472
Corrosion models 465
Corrosion of alloys
Corrosion of cables 460
Corrosion rates 461
Corrosion reaction 461
Corrosive phosphorus 475
Cr(III) precipitates 445
Crenarchaeote 39
Crohn's disease 513
Cryptanaerobacter FISH probe 60
c-type haem 191, 233, 440
Cu(II) toxicity 131
Cysteine desulfurase 441, 448
Cysteine synthase 441
Cytochrome – decahaem 224
Cytochrome – octahaem 224
Cytochrome bd 170
Cytochrome bd oxygen reductase 188
Cytochrome bd quinol:oxygen oxidoreductase, 192
Cytochrome c 8, 9, 14, 128, 148, 155, 170, 192, 195, 203, 218, 219, 222, 227, 232, 448, 468
Cytochrome c oxidase 187
Cytochrome c3 222–4, 232, 414, 415, 425, 437, 439, 446, 448, 486
Cytochrome c553 192, 193, 222, 224
Cytochrome c554 224
Cytochrome c7 425, 437, 439
Cytochrome in outer membrane 468
Denaturing gradient gel electrophoresis (DGGE) 41
Desulfacinum 24, 309, 318
Desulfacinum hydrothermale 310, 320
Desulfacinum infernum 313, 320
Desulfacium subterraneum 310
Desulfarculus 24
Desulfarculus baarsii FISH probe 60
Desulfatibacillum 24
Desulfatibacillum aliphaticivorans 284, 287
Desulfatibacillum alkenivorans 284, 287
Desulfitobacterium 99
Desulfitobacterium hafniense 470
Desulfoacinum infernum 313
Desulfoacinum subterraneum 313
Desulfoarculus baarsii 97
Desulfobacca 24
Desulfobacca acetoxidans probe 42
Desulfobacter 1, 24, 168, 185, 320, 345, 450, 470, 504, 505
Desulfobacter anilini 489
Desulfobacter FISH probe 60
Desulfobacter postagatei 16, 117
Desulfobacter probe 42
Desulfobacter vibroformis 310
Desulfobacterace 24, 364
Desulfobacteraceae FISH probe 60
Desulfobacteraceae probe 42
Desulfobacterales probe 42
Desulfobacteriaceae 22, 41, 97, 117, 124, 134
Desulfobacterium 1, 24, 185, 309, 320, 362, 450, 470
Desulfobacterium anilini 97, 99, 348, 489
Desulfobacterium autotrophicum 117, 124, 131, 320
Desulfobacterium autotrophicum FISH probe 60
Desulfobacterium autotrophicum probe 42
Desulfobacterium catecholicum 242
Desulfobacterium catecholicum FISH probe 60
Desulfobacterium cetonicum 283, 310, 313
Desulfobacterium indolicum 487
Desulfobacterium niacini FISH probe 60
Desulfobacterium niacini probe 42
Desulfobacterium phenolicum 282
Desulfobacterium vacuolatum FISH probe 60
Desulfobacterium vacuolatum probe 42
Desulfobacula 24
Desulfobacula FISH probe 60
Desulfobacula phenolica 282
Desulfobacula toluolica 283, 284
Desulfobibrionaceae 23
Desulfobotulus 24
Desulfobotulus sapovorans FISH probe 60
Desulfobulbaceae 24, 97, 124
Desulfobulbaceae FISH probe 60
Desulfobulbaceae probe 42
Desulfobulbus 1, 24, 41, 168, 274, 309, 362, 364, 450, 504, 505
Desulfobulbus FISH probe 60
Desulfobulbus mediterraneus 348
Desulfobulbus probe 366
Desulfobulbus propionicus 12, 16, 242, 243, 363
Desulfobulbus rhabdoformis 310, 313
Desulfocapsa 24
Desulfocapsa thiozymogenes FISH probe 60
Desulfocella 24
Desulfocella FISH probe 60
Desulfococcus 24, 40, 41, 90, 91, 134, 168, 185, 274, 450, 470
Desulfococcus FISH probe 60
Desulfococcus multivorans FISH probe 60, 489
Desulfococcus probe 42
Desulfofaba 24
Desulfofaba FISH probe 60
Desulfofaba gelida FISH probe 60
Desulfofaba probe 42
Desulfoferrodoxin 199
Desulfofrigus 24, 40, 345
Desulfofrigus FISH probe 60
Desulfofrigus probe 42
Desulfofustis 24
Desulfofustis FISH probe 60
Desulfohalobiaceae 24, 320
Desulfohalobiaceae FISH probe 60
Desulfohalobium 24
Desulfomic cavernae 346
Desulfomic macestense 346
Desulfomicrobiaceae 24
Desulfomicrobioaceae FISH probe 60
Desulfomicrobium (strain Ben-RB) 448
Desulfomicrobium 24, 314, 345, 362, 416, 439
Desulfomicrobium aspheronum 310
Desulfomicrobium baculatum 437
Desulfomicrobium probe 42
Desulfomonas hansenii FISH probe 60
Desulfomonas pigra 504
Desulfomonile 24, 41, 95
Desulfomonile FISH probe 60
Desulfomonile probe 42
Desulfomonile tiedjei 97
Desulfomonile tiedjei FISH probe 60
Desulfomusa 24
Desulfomusa FISH probe 60
Desulfonatronovibrio 24
Desulfonatronovibrio hydrogenovorans 320
Desulfonatronum 24
Desulfonatronum lacustre 348
Desulfonatronumaceae 24
Desulfonauticus 24, 318
Desulfonauticus submarinus 310, 320
Desulfonema 90, 168, 172, 345, 362–4, 366
Desulfonema FISH probe 60
Desulfonema magnum 348
Desulfonema probe 42
Desulforegula 24
Desulforegula FISH probe 60, 362
Desulforhabdus 24
Desulforhabdus amnigena 320
Desulforhopalus 24
Desulforhopalus FISH probe 60
Desulforhopalus singoporenssi 242
Desulfosarcina 24, 40, 41, 90, 134, 274, 345
Desulfosarcina cetonica 282, 284
Desulfosarcina FISH probe 60
Desulfosarcina probe 42
Desulfosarcina variabilis FISH probe 60
Desulfospira 24
Desulfospira FISH probe 60
Desulfosporomuse 39
Desulfosporosinus 24, 39, 306, 314, 345, 351
Desulfosporosinus 446, 447
Desulfosporosinus probe 42
Desulfotalea 24, 345
Desulfotalea FISH probe 60
Desulfotalea psychrophila 6, 123, 124, 127, 131, 203, 215, 222, 225, 226, 440, 447, 450
Desulfothermus 24
Desulfotignum 24
Desulfotignum FISH probe 60
Desulfotomaculum (strain B 10) 350
Desulfotomaculum (strain B2T) 346
Desulfotomaculum 1, 22, 24, 39, 101, 168, 306, 314, 345, 350, 351, 504, 505
Desulfotomaculum FISH probe 60
Desulfotomaculum halophilum 310, 314, 315
Desulfotomaculum kuznetsovii 310, 314, 346
Desulfotomaculum nigrificans 310, 314
Desulfotomaculum norvegicum 224, 437, 439
Desulfotomaculum orientis 489
Desulfotomaculum probe 42
Desulfotomaculum reducens MI-1 103
Desulfotomaculum thermobenzoicum 242
Desulfotomaculum thermocisternum 310, 314, 315
Desulfotomaculum thermosapovorans 348
Desulfovibrio (strain B) 484
Desulfovibrio (strain Ben-RA) 448
Desulfovibrio 24, 40, 41, 91, 96, 168, 185, 306, 309, 314, 318, 345, 364, 388, 414, 439, 450, 470
Desulfovibrio acrylicus FISH probe 60
Desulfovibrio aestuarii FISH probe 60
Desulfovibrio africanus 223
Desulfovibrio alaskensis 123, 216, 310, 313, 475
Desulfovibrio bastinii 310, 313
Desulfovibrio capillatus 310, 313
Desulfovibrio desulfuricans (strain ATCC 27774) 202, 223, 227, 228, 242, 244, 248, 250, 251
Desulfovibrio desulfuricans (strain CSN) 243
Desulfovibrio desulfuricans (strain Dv01) 185, 243
Desulfovibrio desulfuricans (strain Essex 6) 243
Desulfovibrio desulfuricans (strain G-20) 102, 123, 124, 131, 188, 215, 224, 225, 437, 440, 446, 447, 450
Desulfovibrio desulfuricans 6, 21, 170, 198, 200, 242, 313, 415, 446, 449, 489, 510, 511
Desulfovibrio fairfieldensis 510
Desulfovibrio fairfieldensis FISH probe 60
Desulfovibrio fructosovorans 12, 216, 437
Desulfovibrio furfuralis 242
Desulfovibrio gabonensis 310, 313
Desulfovibrio geothermicum 346
Desulfovibrio gigas 170, 192, 194, 198, 216, 223, 437, 439, 489
Desulfovibrio gracilis 310, 313
Desulfovibrio halophilus probe 42
Desulfovibrio hydrothermalis 310, 318
Desulfovibrio indonesiensis 346, 468, 474, 475
Desulfovibrio infernum 310
Desulfovibrio latus 320
Desulfovibrio longreachii 313
Desulfovibrio longus 310, 313
Desulfovibrio magneticus 132
Desulfovibrio multispirans 242
Desulfovibrio oxamicus 242
Desulfovibrio oxyclinae probe 42, 185, 313
Desulfovibrio piger 504, 511
Desulfovibrio profundus 242, 310, 318, 346, 350, 351
Desulfovibrio putealis 351, 352
Desulfovibrio salexigens 170
Desulfovibrio simplex 242
Desulfovibrio termitidis 170, 242
Desulfovibrio thermophilus 315
Desulfovibrio vietnamensis 310, 313
Desulfovibrio vulgaris (strain DP4) 103
Desulfovibrio vulgaris 5, 6, 8–12, 15, 102, 123, 124, 131, 141, 170, 172, 186, 188, 200, 215, 223, 224, 257, 320, 414, 415, 425, 437, 439, 445, 446, 450, 466, 484
Desulfovibrio vulgaris Myazaki 192, 198, 437
Desulfovibrio zoesterae 318
Desulfovibrioaceae 22
Desulfovibrionaceae 24, 41, 93, 117, 124
Desulfovibrionaceae FISH probe 60
Desulfovibrionaceae probe 42
Desulfovibrionales probe 42
Desulfovirga 24
Desulfurellales probe 42
Desulfuromonadaceae 23
Desulfuromonales FISH probe 60
Desulfuromonales probe 42
Desulfuromonas 345
Desulfuromonas acetoxidans 425, 437, 439
DhcARnfCDGEAB 224, 226
Diffusion chamber 172
Dimethyl mercury 450
Dimethyl sulfoxide reductase 155
Dimethyl sulfoxide reduction 1
Dissimilatory sulphate reduction 6, 12, 15
Diurnal changes 168, 172, 185
DMSO reductase 244, 246
dsrAB/DsrAB 99, 101, 154, 228, 232
DsrMKJOP complex 128, 154, 227, 228, 233, 466
d-type haem 191
EchABCDEF complex 11, 14, 127
Electron transfer and corrosion 464, 471
Electron transport 9
Energy coupling/energetics 5, 266, 267, 270, 279
Engineered systems 90
Environmental diversity 96
Environmental genomics 102
Environmental technology 383, 384
ERGO 121
Ethylbenzene utilized 290, 292
Eubacterium FISH probe 60
Euryarchaeota 1, 124
Evolution 22, 96, 132, 292
Extracellular substances 472
Fatty acid oxidation 308, 389, 390, 409, 504, 506, 514
Fe(II) transporter 148
Fe(III) reduction 1, 19, 351
Fecal sulphate reduction 509
Fe-hydrogenase 8, 188, 195, 437, 439, 447, 467, 468
Fermentation 20, 23, 307, 506, 508
Ferredoxin 11, 14, 227, 247, 439, 485
Ferredoxin-thioredoxin reductase 441
Ferritin 188, 202
Fibrobacter 88
Fingerprint 40, 41, 58, 102, 123
Firmicutes 24, 39, 99
Firmicutes FISH probe 60
Firmicutes probe 42
FISH technique 60, 361
Flavodoxin 148
Flavoproteins 194
Flavorubredoxin 194
Florescence in situ hybridization (FISH) 91
FNR regulon 204
Formate cycling 15, 222, 231
Formate dehydrogenase 12, 15, 128, 155, 215, 218, 219, 222, 224, 227, 231, 246
Fumarate reduction 1
Fumarate:quinone oxidoreductase 192
Fur regulon 161, 200
GAP4 STADEN package 120
Gas hydrate formations 333, 335
GenDB 121
Gene organization 129
Gene targeted primers 42
Genes 96
Genome 9, 12, 15, 103, 117, 118, 123, 186, 187, 195, 215
Genome annotation 120
Genome sequencing 118
Geobacter 131, 446
Geobacter metallireducens 132
Geobacter sulfurreducens 128, 132
Global regulators 145, 160, 162, 186
Glutaredoxin 187, 188
Glycine betaine 146
Glycolate oxidase 148, 230
Glycolysis 194
Glycoprotease 153
Glycoproteins 507
Goethite 473
Greigite 407
Growth in the gut 506
Haem a 192
Haem b 219, 222, 228
Haem c 253
Haem-copper oxygen reductase 188, 192, 193
Heam d 191
Heam o 192
Heat shock response 131, 145, 148, 153, 162
Hemerythrin 199
Hg(II) toxicity 131
Hmc complex 9, 128, 223, 225–8, 232
hmc genes 9, 148
Hme complex 9, 227
Hme genes 9
Horizontal gene transfer 103, 133
HrcA 152
Human colon 504
Human disease 510
Hydrocarbon oxidation 266, 267, 270, 279, 280, 284
Hydrogen cycling 14, 20, 215, 216, 222
Hydrogen evolution 462, 509
Hydrogen peroxide 196
Hydrogen peroxide reductase 197–9
Hydrogenase 8, 10–12, 14, 41, 127, 128, 170, 190, 195, 215, 216, 218, 219, 222, 223, 227, 231, 440, 445, 465–7, 475, 485
Hydroperoxidase I 188, 198
Hydrothermal vents 241, 310, 316
Hydroxyl radicals 269
Hydroxylamine 256
HynBAC3 224
HysBA 226
Inflammatory bowel disease 511
Influent dilution 386
Inhibition of SRB 386
Interspecies hydrogen transfer 17, 20, 274, 282, 451
Intestinal SRB 511
Intraspecies formate transfer 16
Intraspecies hydrogen transfer 12, 14, 15, 20, 21
Iron oxidation
fixed-bed reactor 411
Iron storage enzymes 202
Iron sulphide 407, 421
Iron sulphide and corrosion 469
Isoprenoid biosynthesis 133
Isothermal microcalorimetry 440
Isotope array approach 96
Isotope ratios for carbon 272, 282
Isotopes of sulphur 22
KEGG database 121
Lactate dehydrogenase 14, 148, 170, 230
Lactate metabolism 508
Lactate oxidation 11, 12
Lactate permease 148, 230
Lawsoni intracellularis 23
Lawsonia intracellularis FISH probe 60
Lead precipitation 424
Low temperature stress 144
Mackinawite 407
MAGPIE 121
Malonomonas rubra 23, 170
Marine arctic sediment 41
Marine sediments 343, 345, 350
Marine subsurface 344, 348
Mats 168, 171–3, 185, 241
Membrane fluidity 145
Membrane hybridization 59
Membrane reactor 396
Menaquinone 10, 12
Mercaptopyruvate sulphur transferase 514
Mercuric lyase 450
Mercuric reductase 441, 450
Mercuric transport 441
Mercury reduction 450
Mercury resistance 441, 449, 450
Metabolic island 99
Metal hydroxides 412
Metal precipitation 393, 412
Metal recovery 393, 408
Metal reductases 445
Metal reduction 332, 414, 437, 451
Metal removal 416, 417
Metal sorption 393
Metal sulphides 405–8, 419
Metalloid reduction 414
Metalloid sulphides 409, 411
Methane 2, 307, 335
Methane monooxygenase 269
Methane oxidation 269, 330, 335
Methane presence 272
Methanobacterium foricicum 249
Methanogenesis in gut 505
Methanogens 88, 90, 225, 227, 274, 385, 387, 389, 410, 484
Methanosaeta 372
Methanosarcina acetivorans 132
Methanosarcina thermophila 132
Methionine sulfoxide reductase 153, 188
Methyl mercury 450, 451
Methylmalonyl-CoA pathway 16, 129
Methylnaphthalene utilized 290, 292
Methyltetrahydrofolate 450
Microarry 93, 95, 103, 121, 131, 142, 154, 159, 187
Microautoradiography 361
Microbial communities 361, 451, 459
Microbial Community Analysis (MiCA) 58
Microelectrodes 361, 369, 391
Migration 172
Mn(IV) reduction 1, 19, 340, 351
Mn-containing catalase 471
MnS 407
Mo(V) species 248, 249
Modeling 332
Molybdate inhibition 372, 386, 451
Molybdate transport 157
Mössbauer data 251, 254
Mucin 508
Myxococcales probe 42
NAD(P)H hydrogen peroxide oxidoreductase 201
NAD(P)H peroxidase 188, 197
NAD(P)H superoxide oxidoreductase 201
NADH dehydrogenase 128, 231
NADH oxidase 169, 170
NADH:rubredoxin oxidoreductase 170
NADH:quinone oxidoreductase 128, 193
NADP-reducing hydrogenase 216
Nanometer metal precipitates 445
Nanowires 275
nap genes 246
Naphthalene oxidization 277, 282
Neelaredoxin 199
NhcB 228
Nickel sorbents 394
NiFe-hydrogenase 8, 96, 195, 216, 222, 224, 437, 439, 468
NiFeSe-hydrogenase 195, 224, 437
Nigerythrin 188, 200
Nitrate as electron acceptor 1, 18, 171, 233, 242, 257, 308, 332, 351, 373, 423
Nitrate reductase 154, 244, 248, 249, 441
Nitrate stress 145, 148, 155, 243, 371
Nitric oxide 194, 256
Nitric oxide reductase 194
Nitrite inhibition 131, 233, 243
Nitrite reductase 154, 224, 233, 242, 244, 250, 251, 253, 257, 486
Nitrite stress 145, 148, 152, 157
Nitroaniline 484
Nitroaromatics 484, 486
Nitrobenzene 484
Nitrogenase 175, 226, 266
Nitrospira 39
Nitrospira FISH probe 60
Nitrospiraceae FISH probe 60
NrfA 255
Numbers of SRB in stools 504
Oceanic crust 342
Off-gas treatment 384
OhcABC 226
Oil fields 241, 243, 309, 310
Oil reservoirs 281, 307, 308, 320
Olavius algarvensis symbiont FISH probe 60
Olavius crassitunicatus symbiont FISH probe 60
Organomercury lyase 450
Organosulphonate reduction 99, 102
Osmotic stress 145, 146, 148
o-type haem 192
Oxic/anoxic interface 17, 18, 168, 169, 363, 408, 471, 476
Oxoglutarate synthase 489
Oxygen and corrosion
Oxygen detoxification 169
Oxygen gradients 171
Oxygen reduction 1, 170, 187, 188, 191, 194–7
Oxygen stress 131, 145, 148, 186, 194–6, 198
Oxygen tolerance 169, 172, 173, 185, 187, 196
Oxygen toxicity 169
Oxygenases 266
Oxygen-sulphide gradients 173
OxyR 204
PAPS reductase 148
Paracoccus pantotrophus 244, 246, 249
Pb(II) immobilization 424, 446
PEDANT 121
Pelobacter 23
Pelobacter carbinolicus 132, 348
Pelotomaculum 99, 101
Pelotomaculum FISH probe 60
Pelotomaculum probe 42
Pelotomaculum thermopropionicum FISH probe 60
Peptococcaceae FISH probe 60
Periplasm 15
Peroxidase 197, 199, 201, 202
Peroxiredoxin 198
PerR regulon 161, 200
pH homeostasis 158
Phosphate acetyltransferase 148, 230
PHRED program 120
Phylochip 93, 96
Phylogenic Assignment Tool (PAT) 58
Phylogenic diversity 21
Plasmids 124, 198, 440
Pollution control 383
Polyamine biosynthesis 159
Polyglucose reserves 194
Probe characterization 88
Probe labeling 59
Probes for 16S rRNA 364, 391
Propionate oxidation 16
Propionly-CoA 16
Proteases 152, 153
Proteobacteria FISH probe 60
Proteobacteria probe 42
Proteomic analysis 121, 190, 446
Proteomics 131, 186, 187, 467
Protohaem IX farnesyl transferase 192
Proton stoichiometries 10
Proton translocation 10
Protonophores 15
Pyrite 407
Pyrobaculum 101
Pyrobaculum islandicum 22
Pyrococcus 317
Pyrophosphatase 7, 148, 229
Pyruvate synthase 489
Pyruvate:ferredoxin oxidoreductase 11, 14, 148, 230
Pyruvate-formate lyase 15, 230
Qmo complex 9, 128, 225, 227, 233, 466
Quinol oxidase 191
Quinol:cytochrome c oxidoreductase 193
Reactive oxygen species 186, 187, 196, 197, 202
Redox cycling 19
Redox potentials 3, 13
Reverse sample genome probing (RSGP) 92
Rhodanese 514
Rhodobacter sphaeroides 244, 246
Ribonucleotide reductase 173
Rice roots 41
RnfCDGEAB 226
rRNA sequencing 40
Rubredoxin 195, 199, 201
Rubredoxin:oxygen oxidoreductase 169, 188, 194, 199
Rubrerythrin 148, 186, 188, 198, 199
Ruminococcus FISH probe 60
Saccharopine dehydrogenase 158
Saline subsurface environment 346
Salt stress 146
Salt stress response 131
Salt tolerance 350
Sapropels 340
Selenate reduction 415, 448
Selenide,water dikinase 441
Selenium removal 414
Selenocysteine synthetase 448
Selenophosphate synthase 448
Sensing system for nitrate 247
Seryl-tRNA selenium transferase 441
Shewanella oneidensis 425
Sigma factors 147, 153
Sodium/proton transporter 157, 159, 160
Soil treatment 384
Solid waste treatment 384
Spatial distribution 368
Spermidine decarboxylase 158
Sporobacter FISH probe 60
Sporotomaculum 99
Sporotomaculum FISH probe 60
Sporotomaculum probe 42
Stress response 145, 160
Structure of ccNir 251
Structure of nitrate reductase 245
Subsurface metabolism 351
Succinate:quinone oxidoreductase 192
Succinyl-CoA 11
Sulfide concentration 386
Sulfospirillum deleyianum 251, 253
Sulphate activation 6, 7, 167, 215
Sulphate adenylyltransferase 147, 148
Sulphate in the gut 506
Sulphate permease 148
Sulphate reduction 41, 96, 168, 215, 218, 229, 330, 332, 335, 340, 343, 360, 385, 389
Sulphate reduction in gut 505
Sulphate supply 335
Sulphate transport 10
Sulphate:methane interface 337
Sulphide effects gut mucosa 512
Sulphide oxidation 243, 273, 308, 332, 333, 337, 360, 371
Sulphide production in gut 508
Sulphidogenesis 19
Sulphidogenic reactors 388
Sulphidogenic vs methanogenis 386
Sulphite oxidase 514
Sulphite reductase 9, 22, 101, 128, 133, 148, 154, 227–9, 233, 243
Sulphur cycle 241, 374, 375, 383, 384
Sulphur oxidation 363
Sulphur reduction 1, 317
Superoxide 196
Superoxide dismutase 169, 188, 196, 199, 201, 446, 470
Superoxide reductase 186, 198
Synechococcus 249
Syntrophic interaction 275
Syntrophobacter 95
Syntrophobacteraceae 41, 97
Syntrophobacteraceae FISH probe 60
Syntrophobacteraceae probe 42
Syntrophobacterales probe 42
Syntrophus FISH probe 60
Taxonomic differences 24
Tc(VII) reduction 446
Technecium precipitation 409, 413, 415
Terminal restriction fragment length polymorphism (T-RFLP) 58
Tetrahydrofolate 16
Tetrahydromethanopterin 16
Thermoacetogenium 314
Thermoacetogenium phaeum 129
Thermocladium 39
Thermococcus 317
Thermodesulfatator 306, 318, 321
Thermodesulfatator indicus 310, 321
Thermodesulfobacterium 24, 39, 97, 99, 306, 309, 315, 318
Thermodesulfobacterium commune 103, 132, 310, 315
Thermodesulfobacterium hydrogenophilum 310, 315, 321
Thermodesulfobacterium probe 42
Thermodesulfobacterium thermophilum 310, 315
Thermodesulfobiaceae 1
Thermodesulfobium 23, 24, 309
Thermodesulfobium narugense 39, 242
Thermodesulforhabdus 24, 309, 314
Thermodesulforhabdus norvegicum 310, 313, 320
Thermodesulfotomaculum orientis 6
Thermodesulfovibrio 1, 23, 24, 39, 97, 306, 309, 350
Thermodesulfovibrio FISH probe 60
Thermodesulfovibrio islandicus 99, 242
Thermodesulfovibrio yellowstonii 103, 132
Thermodesulfovibrionaceae 24
Thermodynamics 2
Thermoproteales 39
Thio peroxidase 197, 198, 202
Thiobacillus denitrificans 97, 396
Thiobacillus ferroxidans 396
Thiobacillus thioparus 396
Thiol-peroxidase 187, 188
Thioploca 171
Thioredoxin 188, 441
Thioredoxin disulphide reductase 441
Thioredoxin reductase 153, 188, 441, 448
Thiosulphate reductase 8, 425
Thiothrix 363
Thiovirga sulfuroxydans 363
Thiovulvum 171
Tiosphaera pantotropha 246
TmcCBA 226, 232
Toluene oxidation 283, 290
TpI-c3 complex 8, 222
TpII-c3 complex 9, 128
Transcriptomic analysis 121
Transcriptomics 102, 187
Transporters 157
Transposase 124, 127, 155, 157
TRF-CUT 58
tRFLP fragment sorter 58
Trinitrotoluene 483, 493
Trophic interactions 17
Tryptophanase 160
Twin Arginine Translocator system 246
U(VI) reduction 415, 446
Ubiquinone pool 248
Uranium reduction 413, 415, 446
Vectoral distributions 366
Veillonella 446
Vibrio alginolyticus 128
Wastewater treatment 384
Wautersia eutropha 246
Wetland systems 419
Wolinella succinogenes 251, 253
Xylene utilized 290
YACOP 121
Znic sulphide 419