Cambridge University Press
9780521846363 - Bacterial Physiology and Metabolism - by Byung Hong Kim and Geoffrey Michael Gadd
Index

Index

1/2O₂/H₂O 299, 303, 356

1,2-propanediol 64

1,3-diphosphoglycerate 63, 66, 99, 102, 488

1,3-diphosphoglycerate-polyphosphate phosphotransferase 488

1,3-propanediol 274, 275

¹⁴C-glucose 78

1-phosphofructokinase 206

2,3-diphosphoglycerate 63

2,3-butanediol 242, 243, 273, 274, 275

2-acetolactate 141, 261, 273

2-acetolactate synthase 273, 274

2-aminoadipate 220

2-aminoadipate pathway 141, 143

2-butanol 320

2H⁺ 302

2H⁺/H₂ 264

2-keto acid dehydrogenase complex 217

2-keto acids 215, 287

2-keto-3-deoxy-6 phosphogluconate (KDPG) 72

2-keto-3-deoxy-6-phosphogluconate aldolase 78, 236

2-keto-3-deoxygluconate 74

2-keto-3-methylvalerate 217

2-keto-6-aminocaproate 220

2-keto-6-phosphogluconate 74

2-ketoacid:ferredoxin oxidoreductase 287

2-ketobutyrate 141, 216, 217, 274, 282, 424

2-ketobutyrate dehydrogenase 85

2-ketobutyrate:ferredoxin oxidoreductase 282

2-ketogluconate 73, 74, 188

2-ketoglutarate 61, 87, 88, 91, 137, 140, 141, 146, 215, 217, 289, 313, 329, 378, 462, 464

2-ketoglutarate dehydrogenase 85, 87, 88, 91, 92, 275, 373, 378, 443

2-ketoglutarate synthase 87, 322

2-ketoglutarate/glutamine (2KG/Gln) ratio 440

2-ketoglutarate:ferredoxin oxidoreductase 87, 92, 313, 373

2-ketoisocaproate 217

2-ketoisovalerate 217

2-mercaptoethanesulfonic acid 225

2-methylnaphthalene 343

2-n-heptyl-4-hydroguinoline-N-oxide (HQNO) 110

2NO₃⁻ → N₂ 299

2-phosphoglycerate 63, 68, 236

2-propanol 320

3,6-dichloro-2-methoxybenzoate 227

30S small subunit 109, 177

3-aminobutyryl-CoA 284

3-chlorobenzoate 306

3-deoxy-D-arabinoheptulosonate (DAHP) synthase 460

3-hydroxyacyl-ACP 154

3-hydroxyacyl-ACP dehydratase 153, 154

3-hydroxyalkanoate 485

3-hydroxyaspartate pathway 212, 213, 217

3-hydroxybenzoate 227

3-hydroxybutyrate 485

3-hydroxybutyryl-ACP 153

3-hydroxydecanoyl-ACP dehydratase 153, 156

3-hydroxypimelyl-CoA 343

3-hydroxypropionaldehyde 262

3-hydroxypropionate 375

3-hydroxypropionate cycle 93, 354, 362, 363, 368, 375, 376, 377, 388, 402

3-hydroxypropionyl-CoA 375

3-keotacyl-ACP synthase 153

3-keto-5-aminohexanoate 284

3-ketoacyl-ACP reductase 153

3-ketoacyl-ACP reductase II 153

3-ketoacyl-ACP synthase I 156

3-ketoacyl-ACP synthase II 156

3-ketoacyl-ACP synthase III 153, 156

3-ketoacyl-ACP synthases 153, 154

3-ketoacyl-acyl-ACP synthase 451

3-phosphoglycerate 61, 63, 66, 69, 90, 140, 141, 145, 368, 372, 488

3-phosphoglycerate kinase 63, 370

4-aminobutyrate 188

4-chloromethane 308

4-hydroxybutyrate 188

5,6,7,8-tetrahydromethanopterin (H₄MPT) 322

5′-deoxyadenosylcobalamin 279

50S large subunit 177, 182

5-aminolevulinate 159, 161

5-hydroxybenzimidazolyl cobamide 325

5-methyl cytosine 173

5-phospho-D-ribosyl-1-pyrophosphate (PRPP) 143

6-methyl adenine 173

6-phosphogluconate 72, 74, 371

6-phosphogluconate dehydratase 72

6-phosphogluconate dehydrogenase 70, 71, 76, 78

6-phospho-β-glucosidase 426

7-mercaptoheptanoylthreonine phosphate (HS-CoB) 322, 325

A site 177

ABC pathway 43, 46, 47, 48, 98, 169, 207

Absidia cierulea 205

absorption spectra of photosynthetic organisms 393, 394

acetaldehyde 97, 214, 228, 255

acetaldehyde dehydrogenase 313

acetaldehyde/ethanol 97

acetate 74, 75, 77, 89, 97, 100, 104, 187, 189, 205, 209, 210, 225, 241, 242, 257, 259, 260, 261, 262, 263, 264, 265, 267, 268, 269, 271, 272, 275, 278, 279, 280, 282, 283, 284, 286, 287, 290, 305, 306, 308, 310, 313, 315, 317, 318, 320, 322, 326, 327, 328, 329, 330, 331, 333, 335, 337, 339, 340, 402, 403, 416, 432, 461, 462, 463, 489

acetate degradation to methane 327

acetate kinase 76, 260, 261, 262, 264, 275, 279, 282, 313, 326, 327, 330, 334

acetate oxidation 312, 318, 329

acetate:pyrophosphate kinase 313, 318, 489

acetate-consuming sulfidogens 339

acetic acid bacteria 104, 234, 241, 241–242

aceticlastic methanogens 320, 322, 326, 329, 333

Acetitomaculum ruminis 331

acetoacetate 214, 217, 225, 227, 269, 284, 441, 485

acetoacetyl-ACP 153

acetoacetyl-CoA 153, 217, 220, 264, 267, 485

acetoacetyl-CoA:acetate coenzyme A transferase 269

Acetobacter aceti 242, 243

Acetobacter spp. 241

Acetobacter xylinum 68, 89

Acetobacterium carbinolicum 331

Acetobacterium malicum 331

Acetobacterium wieringae 331

Acetobacterium woodii 129, 331, 334

Acetogenium kivui 331

acetoin 214, 241, 242, 260, 261

acetoin dehydrogenase complex 214

acetoin/2,3-butanediol 97

acetol (CH₃COCH₂OH) 64

acetone 214, 269, 271, 272

acetone/isopropanol 97

acetone-butanol-ethanol fermentation 269, 270

acetyl phosphate 99, 259, 289

acetylation 461, 462, 463

acetyl-CoA 60, 61, 69, 85, 86, 87, 89, 90, 99, 152, 153, 159, 187, 208, 209, 214, 217, 220, 228, 236, 237, 242, 256, 257, 259, 261, 263, 264, 267, 269, 273, 277, 278, 284, 289, 305, 313, 315, 319, 325, 326, 327, 329, 330, 331, 333, 340, 343, 374, 375, 377, 402, 461, 462, 463, 464, 485

acetyl-CoA carboxylase 153

acetyl-CoA pathway 86, 93, 313, 315, 316, 319, 329, 331, 332, 333, 354, 368, 372, 374, 377

acetyl-CoA synthesis 64, 236, 289, 326, 331, 367, 374

acetyl-CoA + CO₂/pyruvate 264

acetylene 131

acetylesterase 225

acetyl-phosphate 75, 76, 77, 187, 259, 260, 264, 282, 313

Achromatium spp. 359

acid mine drainage 367, 389

acid shock proteins 103

acid-alcohol fastness 19

Acidaminococcus fermentans 115, 283

Acidianus aceti 242

Acidianus ambivalens 375, 376

Acidianus brierleyi 359, 362, 363, 375, 376

Acidianus ruhlandii 364

Acidianus spp. 359

acidic hot spring 360

acidic pH 437

acidic proteases 206

Acidiphilium spp. 359, 389

Acidiphilum cryptum 307

Acidithiobacillus spp. 359

acid-labile sulfur 107

acidogenesis 269, 270, 271

acidophiles 103, 104, 360

acidophilic iron bacteria 363

acids 337

Acinetobacter calcoaceticus 209, 224, 486

Acinetobacter spp. 367, 486, 488

aconitase 87, 443

ACP 156

acrylate pathway 208, 211, 278, 280, 281, 282

acryloyl-CoA 375

acrylyl-CoA 280

Actinobacillus succinogenes 273

actinobacteria (actinomycetes) 185, 368, 435, 486, 489

Actinomyces israeli 188

actinomycin D 466

activation of the lac operon 415

activator proteins 413

activators 174, 410, 413, 420, 437, 464

active transport 16–17, 35, 37–38, 39, 61, 65, 66, 97, 98, 102, 206, 207

activities of TCA cycle enzymes in Escherichia coli 443

acyl carrier protein 209

acyl-ACP 152, 157, 486

acyl-ACP oxidase 155

acyl-CoA 208, 217, 269, 271, 287, 333

acyl-CoA dehydrogenase 106, 217

acyl-CoA synthetase 208

acylglyceride 152

acyl-phosphate 102, 271, 333

adaptive methylation 456, 457

adaptive mutations 457, 459

adenine 64, 101, 173, 221, 287, 467

adenine deaminase 221

adenine phosphoribosyltransferase 147

adenine-thymine 170

adenosine 98, 100

adenosine nucleotide 100, 101

adenosine triphosphate (ATP) 71, 98

adenosine-3′-phosphate-5′-phosphosulfate (PAPS) 139, 312

adenosine-5′-phosphosulfate (APS) 139, 312

adenosine-5′-phosphosulfate (APS) reductase 361

adenosylcobalamin 150

adenylate cyclase 414, 415, 418

adenylate energy charge (EC) 66, 85, 100, 101, 134, 135, 461, 464, 465, 482

adenylate kinase 99, 100

adenylates 100, 101

adenylic acid 149

adenylylation 138, 461, 462

adenylyltransferase 138, 461

adhesins 12, 18, 51

ADP 66, 90, 95, 98, 99, 100, 101, 102, 105, 135, 149, 462, 464, 488

ADP sulfurylase 361

ADP-dependent kinases 66

ADP-glucose 165, 166, 483

ADP-glucose pyrophosphorylase 165, 432, 483

ADP-ribose 135, 463

aerial mycelium 186, 453, 466

Aerobacter aerogenes 188, 203

Aerobacter cloacae 188

Aerobacter polymyxa 337

aerobes 9, 128, 132, 133, 150, 241, 253, 259, 299

aerobes and facultative anaerobes 129, 254

aerobic anoxygenic photosynthetic bacteria 401, 403

aerobic anoxygenic phototrophic bacteria 185, 386, 388, 389, 390, 394

aerobic chemolithotrophs 368

aerobic CO oxidizers 366

aerobic conditions 63, 85, 88, 92, 189, 216, 241, 242, 255, 260, 277, 281, 299, 303, 334, 341, 360, 367, 373, 386, 400, 401, 442, 444, 445

aerobic CO-utilizing carboxydobacteria 333

aerobic dark conditions 388

aerobic growth 443

aerobic metabolism 243, 290, 366

aerobic nitrate reduction 305

aerobic respiration 132, 299, 302, 303, 442, 451

aerobic-anaerobic interface 358

Aeromonas hydrophila 205, 307

aerotaxis 445

aerotolerant anaerobes 253, 254, 260

A-factor 466

Agrobacterium alvertimagni 367

Agrobacterium tumefaciens 51, 452

air 253

alanine 66, 140, 141, 178, 215, 217, 220, 282, 284, 286, 289, 416

alanine aminotransferase 289

Alcaligenes (Carbophilus) carboxidus 366, 367

Alcaligenes cycloclastes 300

Alcaligenes denitrificans 364, 365

Alcaligenes eutrophus 73, 109, 214, 364, 365, 378, 460, 485

Alcaligenes faecalis 300, 305

Alcaligenes latus 365

Alcaligenes ruhlandii 365

Alcaligenes spp. 299

alcohol dehydrogenase 75, 213, 225, 234, 242, 256, 269, 313

alcohol esters 157

alcohol residues 159

alcohols 157, 213, 225, 242, 310, 337

alcohol-specific phosphatidyltransferase 157

aldehyde 117, 269, 332, 333

aldehyde dehydrogenase 213, 225, 242, 256, 269

aldehyde oxidoreductase (AOR) 332

aldose-1-epimerase 434

algae 371, 386, 486

alginate 29, 490

aliphatic 320

aliphatic hydrocarbons 223, 225, 342, 343

alkaline conditions 257

alkaline phosphatase 7, 19, 441, 457, 459

alkaline protease 206

alkalophiles 103, 104, 105, 304

alkalophilic sulfur bacteria 360

alkanes 486, 487

alkylbenzene 306

alkylhydroperoxide reductase 446

allophycocyanin 392

allosteric enzyme 460

allosteric site 460

Alphaproteobacteria 159

alternative respiratory metabolism 303, 304

altrose-galactoside 459

amidophosphoribosyl transferase 459

amine group donor 163

amino acid activation 176

amino acid analogue 467

amino acid biosynthesis 137, 138, 140, 145, 419

amino acid decarboxylases 103

amino acid dehydratase 215

amino acid dehydrogenase 215

amino acid limitation 437

amino acid mixtures 281, 286

amino acid oxidase 215

amino acid production 467

amino acid sequences 175, 205, 439, 446

amino acid transporters 441

amino acid utilization 214–220

amino acid-limited conditions 437

amino acid-related genes 427

amino acids 9, 10, 16, 39, 63, 64, 87, 127, 140, 163, 167, 175, 176, 190, 206, 208, 212, 214, 215, 217, 220, 242, 259, 281, 286, 287, 357, 378, 419, 420, 421, 422, 424, 426, 439, 459, 467, 487

amino acids as electron donors and acceptors 286

amino group donor 138

amino sugars 63

aminoacyl residue 177

aminoacyl site (A site) 177

aminoacyl-tRNA 176, 177

aminoacyl-tRNA synthetase 176, 426

aminolevulinate synthase 159

amino-terminal transmembrane helix 456

aminotransferase 236

ammonia 127, 128, 129, 132, 134, 135, 137, 140, 304, 305, 312, 355, 356, 357, 358, 360, 365, 366, 435, 439, 440, 441, 461, 462, 463, 465, 487

ammonia assimilation 9, 137, 138, 441, 465

ammonia metabolism 135

ammonia monooxygenase (AMO) 356

ammonia oxidation 356, 357

ammonia switch 134

ammonia uptake 441

ammonia-limited conditions 440, 441, 462

ammonia-rich conditions 137, 138, 440, 441, 461, 462

amorphous cellulose 203

AMP 66, 69, 85, 88, 90, 98, 99, 100, 149, 313, 371, 459, 462, 464, 483, 488

AMP-3′-phosphate 140

amphibolic pathway 88, 91

Amycolatopis methanolica 234

amylase 13, 19, 202, 203, 466

amylopectin 202, 203

amylopullulanase 203

amylose 203

amytal 110

Anabaena azollae 129

Anabaena spp. 133

anabolism 67, 98, 100, 101, 126, 127, 277, 408, 464

Anaerobacter polyendosporus 184

anaerobes 9, 23, 24, 39, 40, 118, 139, 150, 219, 281, 286, 287, 304, 330, 335, 336, 337

anaerobes producing butyrate as fermentation product 263

anaerobes using oxidized metal ions as electron acceptors 307

anaerobic acidophile 256

anaerobic ammonia oxidation (ANAMMOX) 305

anaerobic archaeon 304

anaerobic chemolithotrophs 304, 333, 368, 374

anaerobic CO dehydrogenases 366

anaerobic CO₂ fixation 374

anaerobic conditions 61, 88, 92, 128, 156, 242, 252, 260, 274, 277, 281, 298, 299, 303, 304, 305, 310, 334, 337, 340, 341, 343, 358, 360, 363, 366, 401, 442, 444, 445

anaerobic degradation 342, 343

anaerobic denitrifier 362

anaerobic digester 305

anaerobic ecosystems 298, 306, 309, 320

anaerobic enzymes 277, 303, 434, 442

anaerobic fermentation 252–290

anaerobic fermentative bacteria 41, 87, 213, 268

anaerobic growth 443

anaerobic H₂-oxidizers 365

anaerobic metabolism 88

anaerobic methanogenic archaea 150

anaerobic nitrification 358

anaerobic photosynthetic bacteria 387

anaerobic photosynthetic conditions 387

anaerobic purple photosynthetic bacteria 371

anaerobic respiration 38, 63, 108, 115, 252, 277, 288, 290, 298, 298–344, 341, 445

anaerobic ribonucleotide reductase 150

anaerobic route 451

Anaerobiospirillum succiniciproducens 273

ANAMMOX bacteria 358

anaplerotic sequence 88, 89, 416

Ancalomicrobium spp. 187

animal guts 482

anions 38

anoxygenic cyclic electron transport 398

anoxygenic photosynthesis 386

anoxygenic phototrophic bacteria 187

antenna molecules 386, 394, 395, 396, 397, 398, 401, 431, 487

antenna pigment 389

antenna proteins 430, 431

anthranilate 143, 220

antibiotic resistance 228

antibiotics 13, 29, 35, 46, 466

anticodon 176

antiholin-like protein A 493

antimycin A 110

antiport 38

antisense RNA 428, 435

antiterminator 420, 421, 422, 425, 426, 427

anti-σ factor 410, 411, 448, 449, 456

AOR 332, 333

apo-aconitase 429

apoprotein 279

apoptosis 492

APS 139, 312, 313

APS kinase 139

APS reductase 313

aquaporin 22, 26

Aquaspirillum autotrophicum 365

Aquaspirillum spp. 359

Aquifex spp. 359

ara regulon 413

arabinose 207, 411, 413

arabinose catabolism 437

arc system 443, 444, 445, 454

archaea 13, 14, 23, 24–26, 28, 46, 60, 65, 92, 98, 113, 127, 128, 129, 157, 159, 203, 206, 287, 302, 304, 310, 312, 315, 320, 329, 358, 359, 360, 362, 363, 371, 373, 422, 433, 439, 441, 485, 493

archaeal cell wall 20–21

archaeal coenzymes 226, 322

archaeal cytoplasmic membrane phospholipids 159

archaeal membrane 152

Archaeoglobus fulgidus 255, 311, 315, 323, 371

Archaeoglobus spp. 71, 288

arginine 41, 64, 134, 135, 141, 188, 219, 220, 286, 441, 487

arginine biosynthesis 141

arginine degradation 219

arginine deiminase 286

arginine fermentation by anaerobic bacteria 286

arginine phosphate 99

arginine/ornithine antiport 41

aromatic acids 342

aromatic aldehydes 333

aromatic amino acid synthesis 460

aromatic amino acids 63, 70, 141, 286, 320

aromatic compounds 306, 308, 330, 343, 411

aromatic compounds metabolised through catechol 229

aromatic compounds metabolized through benzoyl-CoA under anaerobic conditions 343

aromatic compounds metabolized through protocatechuate 228

aromatic hydrocarbons 220, 225, 227, 228, 231, 342, 343

arrangement of electron carriers in H⁺-translocating membrane 111

arsenate 308, 335, 360

arsenate reductase 309

arsenic 1, 306

arsenite 367

Arthrobacter globiformis 484

Arthrobacter paraffineus 224

Arthrobacter simplex 224

Arthrobacter spp. 72, 73, 232, 365, 452

artificial electron carrier 97

As(III) 364, 367

As(V) 309, 367

As(VI) 306, 367

As(VI) →As(0) 299

ascorbic acid 242

asparagine 140, 141, 217

asparagine degradation 441

asparagine synthetase 140

aspartase 216

aspartate 140, 141, 142, 149, 216, 217, 284, 423, 459

aspartate decarboxylase 284

aspartate kinase 100, 423

aspartate kinase isoenzyme 424, 459

aspartate residue 428, 441, 445, 454, 455

aspartate series amino acids 423

aspartate transcarbamoylase 149

aspartyl-phosphate residue 457

Aspergillus nidulans 208

assembly of cellular structure 181–182, 183

assembly of polymers into cellular structure 126

assimilation of acetate 243

assimilation of inorganic nitrogen 127–138

assimilatory metal reduction 306, 309

assimilatory nitrate reductase 136, 302

assimilatory nitrate reduction 70, 136, 137, 139

assimilatory nitrite reductase 302

assimilatory sulfate reduction 139, 312

asymmetric cell division 184, 186

ATP 1, 9, 26, 60, 63, 64, 66, 69, 71, 72, 74, 76, 77, 85, 86, 87, 88, 90, 91, 95, 98, 99, 100, 101, 102, 103, 105, 106, 110, 112, 113, 114, 115, 116, 128, 130, 132, 133, 135, 137, 139, 140, 143, 148, 149, 159, 164, 174, 176, 178, 182, 187, 188, 205, 206, 241, 252, 253, 255, 256, 257, 259, 260, 261, 262, 264, 267, 271, 273, 275, 278, 279, 280, 281, 282, 284, 286, 287, 289, 298, 303, 305, 312, 313, 317, 318, 327, 328, 333, 334, 339, 340, 343, 354, 370, 375, 377, 378, 386, 394, 402, 414, 417, 428, 442, 463, 488, 489

ATP generation 336

ATP hydrolysis 38, 39, 49, 95, 98, 99, 101, 130

ATP requirement for growth and Y_ATP 192

ATP requirement for polymer synthesis by Escherichia coli 191

ATP sulfurylase 139, 313, 318

ATP synthase (ATPase) 26, 45, 101, 105, 110, 112–113

ATP synthase (ATPase) inhibitors 110, 327

ATP synthesis 87, 99, 101, 102, 105, 110, 111, 112, 113, 114, 116, 149, 233, 271, 279, 283, 287, 298, 313, 318, 327, 328, 330, 334, 339, 340, 461

ATP synthesis and production of pyruvate 63

ATP synthesis coupled to the oxidation of Fe²⁺ in Acidithiobacillus ferrooxidans 363

ATP synthesis in denitrification 302

ATP yield 188, 189

ATP:citrate lyase 87, 313, 373

ATP-binding cassette 453

ATP-binding cassette (ABC) pathway 38, 46, 165, 170

ATP-binding cassette (ABC) transporters 39

ATP-binding motif 39, 49

ATP-citrate lyase 92

ATP-dependent acetyl-CoA carboxylase 375

ATP-dependent protease 411

ATP-dependent transport 38–39

ATP-polyphosphate phosphotransferase (polyphosphate kinase) 488

atrazine 306

attachment 186

attenuation 419, 420, 421, 422, 423, 424, 426

Au(0) 306

Au(III) 306

AUG (TAC on DNA) 176

Aureobasidium pullulans 203

autogenous regulation 428–430, 466

autoinducer synthase 452

autoinducers 117, 452, 453, 466

autokinase domain 455

autolysin sensor kinase (LytS) 493

autolysis 492

autophosphorylation 457

autotransporter 52

autotransporter and proteins requiring single accessory factors 47, 51

autotrophic methanogens 331

autotrophic methylotrophs 230, 232, 234, 235

autotrophs 8

auxotrophic mutants 467

azide 110

Azoarcus tolulyticus 341, 343

azoferredoxin 130, 131, 134, 135, 136

azoferredoxin-ribose-ADP 135

Azolla spp. 129

Azospirillum lipoferum 129, 365

Azotobacter beijerinckii 485

Azotobacter chroococcum 73, 133, 135

Azotobacter paspali 129

Azotobacter spp. 72, 490

Azotobacter vinelandii 24, 89, 109, 129, 133

B₁₂ box 428

Bacillus amyloliquefaciens 203

Bacillus anthracis 89

Bacillus arsenicoselenatis 307, 308

Bacillus azotoformans 300

Bacillus brevis 466

Bacillus cereus 203, 452

Bacillus circulans 205

Bacillus fastidiosus 202

Bacillus firmus 104

Bacillus flavum 468

Bacillus licheniformis 206, 300

Bacillus lithotrophicum 312

Bacillus megaterium 206

Bacillus mycoides 452

Bacillus oxalophilus 212

Bacillus polymyxa 129, 205, 242, 273

Bacillus schlegelii 365

Bacillus selenitireducens 307

Bacillus spp. 29, 202, 203, 214, 232, 241, 242, 261, 302, 359, 368, 417, 490

Bacillus stearothermophilus 13, 202

Bacillus subtilis 67, 73, 79, 88, 156, 174, 184, 185, 206, 216, 219, 242, 274, 305, 372, 409, 410, 413, 417, 418, 419, 424, 426, 428, 439, 441, 446, 451, 455, 465, 466

Bacillus thuringiensis 452

bacitracin 167

bacterial cytokine 492

bacterial electron transport system 105

bacterial leaching 360

bacterial molecular chaperones and their equivalent in eukaryotes 448

bacterial mRNA 420

bacterial strains producing amino acids 468

bacterial survival 109

bacteriochlorophyll (BCHL) 161, 389, 390, 393, 394, 395

bacteriochlorophyll a (BCHL a) 388, 389, 395, 398, 399, 401

bacteriochlorophyll g 388

bacteriocins 29, 466

bacteriophage 435

bacteriophage T4 410

bacteriopheophytin 389, 392, 394, 395, 400

bacteriorhodopsin 404, 405

Bacterium dechromaticans 307

Bacteroides fragilis 23, 279

Bacteroides gingivalis 23

Bacteroides melaninogenicus 23, 284

Bacteroides spp. 24

bacteroids 133, 490, 492

baeocytes 186

balanced growth 182

Balnearium lithotrophicum 312, 366

basal body 10, 11, 181, 455

basal structure 181

base pairing 171, 173, 174

base-pairing sRNAs of known function in Escherichia coli 434

baseplate 396

Bdellovibrio bacterivorus 23

Bdellovibrio spp. 186

Beggiatioa spp. 305, 359, 360

Beijerinkia indica 129

benzene 227, 306, 308, 335, 341, 343

benzene rings 141, 227

benzoate 308, 335, 339, 342, 343

benzoyl-CoA 343

benzoyl-CoA reductase 343

benzyl viologen 97

betaine 286

betaine/n,n-dimethyl glycine antiporter 41

Bifidobacterium bifidum 75, 77, 188, 258, 259

Bifidobacterium spp. 257, 258

bifidum pathway 77

bifidus bacteria 75, 77

bifunctional enzyme 375, 377

bilin 392

binary fission 183, 183–184, 186, 389

binding proteins 39

biochemistry of denitrification 299

biochemistry of N₂ fixation 129

biochemistry of sulfidogenesis 312

biochemistry of sulfur compound oxidation 360

biocontrol agents 205

biodegradable plastic 485

bioenergetics of N₂ fixation 132

biofilm formation 451

biofilms 12, 13, 432, 492

biological energy 93, 98, 116, 117

Biolphila wadsworthia 336

bioluminescence 116, 117

biopolar division 184

bioremediation 309, 344

biosynthesis 66, 69, 70, 85, 87, 88, 90, 91, 92, 93, 98, 100, 116, 117, 126–181, 182, 208, 210, 212, 234, 242, 257, 259, 267, 315, 319, 325, 331, 333, 355, 356, 366, 377, 396, 408, 426, 442

biosynthesis in LAB 259

biosynthesis in methanogens 328

biosynthesis of aromatic amino acids 147

biosynthesis of glutamate, glutamine, proline and arginine 146

biosynthesis of isoleucine, valine and leucine 144

biosynthesis of polysaccharides 61

biosynthesis of threonine, methionine and lysine 142

biosynthetic precursors 88

biotin 10, 89, 278, 279

biotin carboxylase 153

biotin carboyl carrier protein (BCCP) 153

biotin-limited conditions 467

blue-green algae 387

Bradyrhizobium spp. 389

branched acyl-ACP 154

branched fatty acids 154

branched fermentative pathway 187, 253, 257, 263, 271

branched pathway 253

branching 389

Brevibacterium flavum 117, 243, 468

Brevibacterium lactofermentum 468

Brevibacterium spp. 467

Brocadia anammoxidans 305

Brucella abortus 71

b-type cytochromes 300, 301, 302

budding 184, 187, 389

butanediol 214, 241, 242

butanediol fermentation 273, 274

butanol 213, 269, 271, 272, 466

butanol fermentation by Clostridium acetobutylicum 269

butanol-producing clostridia 269

butter and wine maturation 262

butyrate 187, 189, 263, 264, 265, 267, 268, 269, 271, 272, 283, 284, 286, 330, 331, 337, 339, 340, 402, 463

butyrate and acetone-butanol-ethanol fermentations 263–272

butyrate fermentation 263, 265, 283

butyrate metabolism by purple bacteria 403

butyrate oxidation by Syntrophomonas wolfei with Methanospirillum hungatei 338

butyrate/acetate ratio 264

butyrate-acetate fermentation of glucose 265

butyrate-producing saccharolytic clostridia 269

Butyribacterium methylotrophicum 263, 331

Butyrivibrio fibrisolvens 254, 263

Butyrivibrio spp. 23, 263

butyryl-ACP 153

butyryl-CoA 189, 269, 271

butyryl-phosphate 189, 265

C₁ carriers 157, 225, 235, 315, 322, 329, 374

C₁ compounds 229, 230, 232, 235, 241, 323

C₂ compounds 210

cadaverine 103

calcium 8, 29

Calvin cycle 92, 230, 232, 235, 241, 354, 356, 359, 362, 363, 366, 367, 368, 370, 371, 373, 377, 387, 401, 402, 404

Caminibacter spp. 304, 312, 365

cAMP 414, 415

cAMP-CRP (cAMP receptor protein) complex 414, 415, 417, 432, 436, 437

cAMP-CRP independent catabolite repression in Escherichia coli 416

Campylobacter jejuni 451

Candida lipolytica 224

Candida spp. 240

Candidatus Brocadia anammoxidans 28

caproate 267

capsular polysaccharide 46, 161

capsules and slime layers 12, 181, 182, 435

carbamate kinase 286

carbamoyl phosphate 99, 148, 286

carbamoyl phosphate synthetase 148

carbohydrate reserve materials: glycogen and trehalose 483–484

carbohydrates 60, 89, 104, 242, 299, 306, 411, 483, 485

carbon 1, 7, 8, 306, 432, 441, 465, 487

carbon assimilation by methylotrophs 235–241

carbon catabolite repression (CCR) 414, 415, 417

carbon catabolite repression in Bacillus subtilis 418

carbon catabolite repression in Gram-positive bacteria with a low G + C content 417

carbon cycle 309

carbon dioxide (CO₂) 29, 70, 75, 78, 79, 80, 85, 86, 87, 91, 92, 97, 189, 212, 230, 234, 235, 236, 241, 242, 257, 265, 268, 271, 272, 273, 277, 278, 282, 287, 298, 305, 308, 315, 319, 320, 322, 324, 325, 327, 328, 330, 333, 334, 337, 340, 356, 359, 362, 363, 366, 368, 370, 371, 372, 373, 374, 375, 387, 401, 402, 403, 487

carbon disulfide (CS₂) 362

carbon fixation 445

carbon metabolism 313

carbon metabolism in colourless sulfur bacteria 362

carbon metabolism in cyanobacteria 404

carbon metabolism in homoacetogens 330

carbon metabolism in photoorganotrophs 402

carbon metabolism in phototrophs 401–403

carbon metabolism in syntrophic bacteria 339

carbon monoxide (CO) 9, 97, 232, 304, 320, 330, 333, 354, 366, 367, 374

carbon monoxide dehydrogenase (CODH) 312, 315, 316, 322, 325, 327, 329, 330, 331, 333, 366, 367, 374

carbon monoxide dehydrogenase pathway 93, 315, 329, 331, 374

carbon monoxide oxidation: carboxydobacteria 366–367

carbon rearrangement 236

carbon skeleton supply in sulfidogens 318

carbon skeletons for biosynthesis 61, 141, 319, 461

carbon starvation pathway 437

Carbon Storage Regulator A 67

carbonate 148

carbonyl sulfide (COS) 362

carbonylcyanide m-chlorophenylhydrazone (CCCP) 327

carbonylcyanide p-trifluromethoxy-phenylhydrazone (FCCP) 327

carboxydobacteria 304, 366, 367

carboxylation 342

carboxyltransferase 153

carboxypeptidation 167

carboxysomes 29, 372

cardiolipin 157

carotenoids 159, 388, 389, 390, 392, 393, 394, 395, 401

carotenoids in cyanobacteria and photosynthetic bacteria 392

carrier proteins 35, 37, 38, 39

catabolic genes 413

catabolism 98, 100, 101, 127, 128, 408, 411, 464

catabolism and anabolism 128

catabolite control protein A 67, 414, 417

catabolite repression 413–419

catabolite repressor/activator (Cra) protein 414, 415, 416

catabolite responsive element 417

catalase 241, 254, 255, 260, 446

catechol 227, 229

catecholamide 43

cations 36, 38

Caulobacter cereus 490

Caulobacter crescentus 187

Caulobacter crescentus 174, 183, 187

CcpA-dependent catabolite repression 418

cdNiR 302

CDP 488

CDP-diacylglycerol 157

CDP-glyceride 167

CDP-glycerol 164

CDP-ribitol 164

cell cycle 173

cell division 183, 184

cell division inhibitor A 183

cell division topological specificity factor E 183

cell envelope 434

cell mass 187

cell number 187

cell surface 181, 429

cell surface pH 493

cell surface proteins 47

cell surface structure 14, 104

cell wall 12, 13, 17–19, 43, 161, 165, 167, 169, 181, 435

cell wall proteins in Gram-positive bacteria 169, 170

cell-cell communication 452

cell-cycle transcriptional regulator 183

cell-division apparatus

cell-division cycle 183

cell-free extract 78

cellobiase 203, 205, 206, 207

cellobiose phosphorylase 205

cellulases 203

cellulolytic bacteria 29

cellulolytic clostridia 269

Cellulomonas flavigena 73, 204, 206

Cellulomonas spp. 72

cellulose 202, 203, 205, 257, 340, 411

cellulose degradation 203, 205

cellulose-degrading enzymes 204

cellulosome complex 29, 203

central glycolytic gene regulator protein 67, 419

central metabolism 60, 217, 464

central metabolism and PHB synthesis in Azotobacter beijerinckii 486

Cephalosporium roseum 224

CFA synthase 156

CH₂Cl₂ 330

CH₃ donor 157

CH₃Cl →CH₄ + HCl 299

CH₃-H₄F 315

CH₃-H₄MPT 327

changes in free energy in methanogenesis 328

channel-forming protein 49

chaperone/usher pathway 46, 47, 48, 169

chaperones 178, 446

chaperonins 178, 446

chelating agents 16, 29

chemical energy 93, 116, 117

chemical modifications 178, 460, 463, 464

chemical N₂ fixation process 129

chemiosmotic theory 105

chemoheterotrophs 126

chemolithotrophic acidophilic archaea 375, 376

chemolithotrophic anaerobes 315

chemolithotrophic growth 334

chemolithotrophic homoacetogenesis 334

chemolithotrophic metabolism 192, 354

chemolithotrophic methanogens 320

chemolithotrophic sulfidogens 315

chemolithotrophic sulfur bacteria 358

chemolithotrophs 9, 91, 92, 93, 108, 110, 189, 304, 306, 310, 354, 354–378

chemolithotrophs using other electron donors 367–368

chemolithotrophs: what makes them unable to use organics 377–378

chemoorganotrophs 9, 403

chemostat 192

chemotaxis 455, 455–457, 463

chemotaxis regulon 455

chemotrophs 9, 116, 117

chitin 204, 205

chitin deacetylase 205

chitinase 205

chitosan 205

CHL a 393

Chlamydia spp. 19–20, 435

chlorate 336

chloride 7, 8, 37, 403, 404

chlorinated hydrocarbons 306

Chlorobium tepidum 395

Chloroflexaceae 388

Chloroflexus aurantiacus 375, 376, 402

Chloroflexus spp. 388

chlorophyll 87, 159, 161, 386, 389, 390, 392, 398, 399

chlorophyll a 390, 394, 398

chloroplasts 113, 177, 394

chlorosome 395, 396, 398

chromate 306, 307, 309

Chromatiaceae 387

Chromatium vinosum 129

chromium 1

Chromobacterium violaceum 205

chromosomal DNA 171

chromosome 26, 28, 171, 173, 183, 184, 410, 413, 436

chromosome partition protein 183

chromosome segregation 171, 173, 174

chromosome translocation 184

Chrysiogenes arsenatis 308, 309

cis-3,4-enoyl-ACP 154

cis-vaccenic (cis-11-octadecenoic) acid 156, 451

citramalate 375

citrate 29, 66, 87, 188, 260, 261, 273, 275, 277, 313, 416, 462

citrate conversion to acetate by Pediococcus halophilus 261

citrate fermentation 116

citrate fermentation by enteric bacteria 276

citrate fermentation by facultative anaerobes 275

citrate lyase 260, 275, 462, 463, 464

citrate metabolism 463

citrate synthase 88, 91, 92, 313, 329, 373, 443, 462, 463, 485

citrate synthesis 87, 313

citrate transporter 277

citrate/lactate exchange 261

citric acid cycle 86

Citrobacter diversus 305

citrulline 41, 286

Cladosporium resinae 224

classification of methylotrophs 232

clostridia 256, 263

clostridial butyrate fermentation 485

clostridial fermentation 253, 263

clostridial ferredoxin 107

Clostridium aceticum 73, 74, 330, 331

Clostridium acetobutylicum 118, 269, 271, 272, 337, 435, 466

Clostridium acidiurici 287

Clostridium aminobutyricum 188

Clostridium beijerinckii 269

Clostridium botulinum 286

Clostridium butyricum 24, 186, 187, 254, 255, 263, 264, 265, 267, 268, 269, 271

Clostridium butyricum as a probiotic 268

Clostridium cellulolyticum 269, 417

Clostridium cellulovorans 204, 269

Clostridium cylindrosporum 287

Clostridium fervidum 113

Clostridium formicoaceticum 115, 330, 331, 332

Clostridium glycolicum 188, 287

Clostridium josui 269

Clostridium kluyveri 188, 263, 267, 268

Clostridium litoralis 282

Clostridium methoxybenzovorans 331

Clostridium novyi 284

Clostridium oroticum 254, 287

Clostridium pasteurianum 129, 188, 254, 263

Clostridium perfringens 219, 271, 304

Clostridium propionicum 278, 280, 281, 282

Clostridium purinolyticum 287

Clostridium saccharobutylicum 269

Clostridium saccharoperbutylacetonicum 269

Clostridium scatologenes 331

Clostridium sphenoides 269

Clostridium sticklandii 254, 282, 284, 286

Clostridium subterminale 284

Clostridium symbiosum 115

Clostridium tetanomorphum 188, 283

Clostridium thermoaceticum 188, 305, 331, 332

Clostridium thermoautotrophicum 331

Clostridium thermocellum 204, 257, 269

Clostridium thermosaccharolyticum 64

Clostridium tyrobutyricum 265

Clostridium ultunense 333, 338, 340

Clostridium spp. 23, 24, 29, 202, 263, 281, 287, 417, 490

CMP 157

CO oxidation 331, 367, 374

[CO] 327, 330, 331, 334

[CO]-bound CODH 374

CO₂ → CH₄ 299

CO₂ fixation 93, 354, 368, 374, 375, 376, 377, 401

CO₂ fixation in H₂-oxidizers 366

CO₂ fixation pathways in chemolithotrophs 368–377

CO₂ fixation through the 3-hydroxypropionate cycle 375, 376

CO₂ fixation through the Calvin cycle 369

CO₂ fixation through the reductive TCA cycle 373

CO₂ reduction 374

CO₂/CO 334, 367

CO₂/formate 97

CO₂-fixing organisms 371

CO₂-limited conditions 372

coal 140

cobalamin (vitamin B₁₂) 325, 428

cobalt (III) 307

CoB-SH 325

CO-containing resources 330

co-culture 337, 339, 340

coding region 176

codon base pairing 176

coenzyme A 85, 208, 209, 271

coenzyme A recovery mechanism 271

coenzyme A transferase 485

coenzyme B₁₂ 279, 283, 374

coenzyme F₄₂₀ 322, 323, 329

coenzyme F₄₃₀ 161, 322, 325

coenzyme M 10, 72, 157, 225, 322, 323, 324, 325

coenzyme Q 87, 106, 107, 108, 111, 112, 242, 299, 303, 334, 354, 364, 367, 443

coenzyme tetrahydrofolate 158

coenzymes 115, 139, 140, 153, 234, 322, 360

coenzymes in methanogens 322

cofactors 27, 45, 46, 72, 150, 178, 274, 279, 334, 368

cold induced proteins (CIP) 448, 449, 450

cold shock (CS) box 449

cold shock protein A 449

cold shock proteins (CSP) 432, 434, 449, 450, 491

cold shock response (CSR) 448–451

cold-shock conditions 156

Colletrotrichum linemuthanum 205

colonies 492

colourless sulfur bacteria 358

Comamonas (Zavarginia) compransoris 367

Comamonas testosterone 453

compatible solutes 29, 484

complementary base pairing 171

complete oxidizers 311, 312, 318

complex fermentations 272

complex I 106, 110, 111, 112

complex II 106

complex III 106, 112

complex IV 106, 110, 112

complex media 10, 189, 466

complexation 178

complexes 310

composition and structure of prokaryotic cells 7–30

compounds reduced by the nitrogenase complex 132

CoM-SH 325

CoM-S-S-CoB heterodisulfide 325

conjugation 51, 452

constitutive enzymes 411, 413

contaminated soil 309, 310

control of central metabolic pathways in bacteria 465

conversion of acetate to central metabolic intermediates 209

conversion of citrate to acetoin by lactic-acid bacteria 262

conversion of pentoses to HMP intermediates 208

conversion of propionyl-CoA to succinyl-CoA through the methylmalonyl-CoA pathway 211

coordinate induction 411

coordinate induction and sequential induction of multiple enzymes by a single inducer 411

copiotrophic environments 482

copper 1, 9, 360, 368

copper protein (CuNiR) 302

copper-containing blue protein 363

copper-containing small protein 302

core polysaccharide 164, 165, 169

core polysaccharide-lipid A 165

co-repressor 420

corrinoids 161, 334, 335, 374

corrosion 310

Corynebacterium glutamicum 224, 243, 468, 492

Corynebacterium spp. 467, 486

coryneform bacteria 72, 141, 243, 467

Cr(VI) → Cr(III) 299

creatine phosphate 99

Crenarchaeota 24

crotonate 188, 339

crotonate fermentation 338

crotonyl-ACP 153

crotonyl-CoA 271, 339

crotonyl-CoA/butyryl-CoA 97

CRP or catabolite activator protein (CAP) 414, 415

CRP-cAMP complex 435

CRP-dependent catabolite repression 418

CrsA (carbon storage regulator) protein 432

crystalline cellulose 203

CS box 451

CSP 449

Csr system 432

CsrA (Carbon Storage Regulator) protein 90, 431

CsrA protein 432

CsrA/CsrB system 432

CTP 149, 157, 164, 174

CtrA (cell cycle transcriptional regulator) 187

c-type cytochromes 302, 308, 336, 361

cumulative inhibition 460

cyanide (CN⁻) 110

cyanobacteria 27, 91, 92, 129, 133, 185, 186, 187, 371, 386, 387, 389, 390, 392, 393, 394, 395, 398, 399, 401, 402, 403, 435, 487, 490

cyanophycin 487

cyanophycin synthesis 487

cyclic 2,3-diphosphoglycerate (cDPG) 68, 69

cyclic AMP (cAMP) 414

cyclic dienoyl-CoA 343

cyclic electron transport 398, 399, 400, 401

cycling of elements 1, 344

cycling of metals 306

cyclopentanes 26

cyclopropane 156

cyclopropane fatty acid (CFA) 154, 156

cyclopropane fatty acid synthase 156

cycloproprane ring 24

Cylindrocarpon tonkinense 304

cysteine 63, 64, 107, 139, 140, 141, 181, 216, 217

cysteine residues 445

cysteine sulfinate desulfinase 449

cysteine synthesis 139

cystidine trinucleotide 149

cysts 24, 29, 233, 489, 490

cytochrome a 97, 107

cytochrome a₁ 357

cytochrome a₃ 107

cytochrome aa₃ 109

cytochrome b 97, 107, 111, 112, 115, 284, 327, 333, 336

cytochrome b₅₅₈ 106

cytochrome b₅₆₂ 107

cytochrome bf complex 398

cytochrome c 74, 97, 106, 107, 111, 112, 299, 302, 303, 313, 336, 354, 357, 361

cytochrome c oxidase 106, 357

cytochrome c₂ 400

cytochrome c₃ 97, 317

cytochrome c₅₅₂ 356

cytochrome c₅₅₄ 356

cytochrome c_m552 356

cytochrome d 109, 133, 302, 443

cytochrome f 97

cytochrome o 109, 133

cytochrome oxidase 106, 107, 112, 113, 356, 363, 443

cytochromes 8, 17, 87, 106, 107, 108, 110, 111, 159, 161, 253, 257, 279, 301, 308, 309, 334, 354, 378

Cytophaga spp. 490

cytoplasm 21, 27–29, 43, 47, 102, 103, 104, 107, 164, 165, 167, 169, 181, 302, 317, 355, 394, 428, 445

cytoplasmic chaperones 50

cytoplasmic cleavage 183

cytoplasmic enzyme 302, 361

cytoplasmic F₄₂₀-reducing hydrogenase 325

cytoplasmic flagellar proteins 181

cytoplasmic membrane 10, 13, 18, 19, 21–27, 39, 43, 46, 47, 49, 50, 51, 60, 73, 97, 102, 105, 112, 113, 157, 165, 167, 169, 170, 171, 181, 220, 224, 268, 363, 364, 394, 395, 399, 401, 430, 451, 453, 486, 488, 489

cytoplasmic membrane (CM) assembly 170

cytoplasmic membrane enzyme 414

cytoplasmic membrane proteins 44, 170, 300, 448

cytoplasmic membrane ring 181

cytoplasmic regulator protein 453, 454, 455

cytoplasmic signalling components 456

cytosine 173

cytosol 27, 29

D-alanine 17

D-alanyl-D-alanine 163

D-amino acid oxidase 215

D-amino acids 215

dark conditions 402, 403

dark reactions 396

DCCD 113, 327

DCPIP 97

DCPIP: 2,6-dichlorophenolindophenol 97

D-cycloserine 20

de novo biosynthesis of purine nucleotides 149, 152

de novo biosynthesis of pyridine nucleotides 150

de novo pathway 148

deacetylation 463

deadenylylation 462

deamination of cysteine and methionine 216

deamination products of amino acids 217

debranching enzyme 203, 483, 484

decarboxylation 97, 115, 287

Dechloromonas agitata 336

Dechloromonas spp. 336, 342, 366

Dechlorosoma suillum 336, 364

decrystallizing enzyme 205

Deferribacter thermophilus 307

degradation 344

degradation of amino acids with a side chain 218

degradation of aromatic amino acids 227

degradation of nucleic acid bases 220

degradation of organic compounds 298

degradation of purine bases 222

degradation of pyrimidine bases 223

degradation of xenobiotics under fermentative conditions 289

degradative plasmids 228

Dehalobacter restrictus 335, 336

Dehalococcoides ethenogenes 335, 336

dehalogenating conditions 336

dehalogenating enzymes 335, 336

dehalogenating facultative anaerobe 336

dehalogenating organisms 336

dehalogenation 336

dehalorespiration 334–336

dehalorespiratory bacteria 335

Dehalospirillum multivorans 45, 335, 336

dehydratase 212, 216

dehydration reaction 153

dehydrogenase complex 217

dehydrogenases 105, 108, 110, 216

dehydrogenation 215, 342

Deinococcus radiodurans 309

Deinococcus spp. 435

Deltaproteobacteria 186

denitrification 117, 128, 299, 299–306, 303, 304, 305, 341, 342, 362, 444, 445, 454

denitrifiers 9, 298, 299, 303, 310, 343

denitrifiers other than facultatively anaerobic chemoorganotrophs 304

denitrifying bacteria 137, 189, 300, 342

denitrifying conditions 302, 306, 342

Denitrobacterium detoxificans 336

Denitrovibrio acetiphilus 305

deoxyhexoses 13

deoxynucleoside triphosphate 149, 171

deoxynucleotide 149, 171

deoxyribonucleic acid (DNA) replication 170–174

deoxyribonucleoside monophosphate 220

deoxyribonucleotides 150, 190

deoxyribose 220

deoxythymidine phosphate (dTMP) 150

deoxyuridine diphosphate (dUDP) 150

Derxia gummosa 129, 133, 365

desiccation 12, 29, 490

desulfhydrase 216

Desulfitobacterium chlorrespirans 335

Desulfitobacterium dehalogenans 335

Desulfitobacterium frappieri 335

Desulfitobacterium hafniense 335

Desulfitobacterium spp. 335, 336

Desulfoarculus spp. 311

Desulfobacca acetoxidans 311

Desulfobacter centonicum 341

Desulfobacter hydrogenophilus 319

Desulfobacter postgatei 319

Desulfobacter spp. 311, 313, 315, 316

Desulfobacterium spp. 311

Desulfobacula toluolica 341

Desulfobotulus spp. 311

Desulfobulbus spp. 311, 315

Desulfobulus propionicus 339

Desulfococcus spp. 311

Desulfomicrobium spp. 311

Desulfomonas spp. 311

Desulfomonile limimaris 335

Desulfomonile tiedjei 335, 336

Desulfomonile spp. 335

Desulfonema limicola 319

Desulfonema spp. 311

Desulfosarcina variabilis 319

Desulfosarcina spp. 311

Desulfotomaculum acetoxidans 311, 318, 319

Desulfotomaculum auripigmentum 307

Desulfotomaculum nigrificans 311

Desulfotomaculum orientis 319

Desulfotomaculum ruminis 129

Desulfotomaculum spp. 23, 313, 318, 489

Desulfovibrio baarsii 311

Desulfovibrio dechloracetivorans 335

Desulfovibrio desulfuricans 118, 307, 336

Desulfovibrio gigas 115, 137, 254, 255, 305, 311

Desulfovibrio halophilus 484

Desulfovibrio vulgaris 45, 129, 255

Desulfovibrio spp. 24, 255, 306, 311, 314, 317

Desulfovirga adipica 311

Desulfurella spp. 312, 313, 315

Desulfurimonas acetoxidans 307

Desulfurobacterium crinifex 304, 312, 365

Desulfurococcus amylolyticus 65

Desulfurococcus spp. 312

Desulfuromonas acetoxidans 307, 308, 318, 319

Desulfuromonas chloroethenica 335

Desulfuromonas spp. 312, 313, 315

Desulfuromusa spp. 312

detoxification 309

dextrin 202

D-glutamate 17, 163

diacetyl 261

diacylglycerol 18, 486

diacylglycerol acyltransferase (DGAT) 486

diaminopimelate 17, 141

diaminopimelate pathway 141

diauxic growth 413, 414

dicarboxylic acid cycle 210, 212

dicarboxylic acid cycle–glycerate pathway 217, 223

dicarboxylic acids 212, 287

diffusion 35, 37

diglycerol tetraesters 23

dihydrodipicolinate synthase 459

dihydrolipoate 85

dihydrolipoate acetyltransferase 85

dihydrolipoate dehydrogenase 85

dihydroxyacetone 240

dihydroxyacetone pathway 240

dihydroxyacetone phosphate 63, 64, 156, 236, 240, 370, 464

dihydroxyacetone synthase 240

dimethyl sulfide (DMS) 303

dimethyl sulfoxide (DMSO) 303, 444

dimethyl sulfoxide reductase 45

dinitrogenase 130, 131

dinitrogenase reductase 130, 131, 134

diol dehydrogenase 214

dioxygenases 225, 227, 228

dipeptide binding protein 434

diphytanol 26

disaccharide phosphorylases 205

disaccharides 205, 207, 484

‘disporic’ phenotype 184

disproportionation 340

dissimilation of methane by methanotrophs 233

dissimilatory metal reduction 306, 309

dissimilatory nitrate reductase 302

dissimilatory nitrate reduction 136, 137, 139, 301, 305

dissimilatory nitrite reductase 302

disulfide 20, 313

disulfide bonds 181, 445

divalent attenuation 423, 424

divalent metal ions 16, 29

diversity of electron transport chains 108

division septum 184

DNA 27, 28, 103, 126, 127, 170, 171, 172, 173, 174, 175, 182, 183, 184, 191, 192, 206, 220, 408, 410, 411, 421, 429, 430, 448

DNA binding protein (DBP) 171

DNA double helix 171

DNA G + C content 359

DNA homology 359

DNA ligase 173

DNA methyltransferase 173

DNA modification reaction 173

DNA polymerase 149, 171, 172, 173

DNA replication 26, 170, 171, 172, 173

DNA synthesis 150, 172

DNA template 409

DNA topoisomerase 171

DNA translocase 184

DNA-binding protein 183, 411, 434

DNA-dependent RNA polymerase 174

DNase 206

double stranded helix 170

D-ribose high-affinity transport system 434

D-ribose-5-phosphate 143

dry weight of a single cell 127

D-sorbitol 242

d-type cytochromes 302

dual control 420

dual function enzymes 331, 367, 374

dual mechanism 422

dual repression–attenuation mechanism 423

Ectothiorhodospiraceae 387, 388

ED – FDA variant 236

ED – TA variant 236

EDTA 16, 29, 38

effector(s) 413, 427, 444

effluents 309

electricity 117

electricity generation 308

electrochemical gradient 37, 38, 39, 105

electrogenic transport 38

electron acceptors 9, 63, 66, 71, 75, 88, 93, 97, 105, 108, 115, 117, 139, 221, 253, 255, 257, 259, 260, 262, 264, 271, 272, 277, 278, 281, 286, 287, 288, 289, 298, 299, 300, 303, 304, 305, 306, 308, 309, 310, 312, 313, 317, 320, 322, 333, 335, 336, 337, 339, 340, 341, 343, 358, 360, 362, 363, 364, 365, 366, 367, 394, 444

electron acceptors used in anaerobic metabolism 252–253, 336

electron balance 272

electron carriers 86, 88, 97, 105, 107, 108, 110, 111, 117, 128, 132, 216, 241, 252, 253, 312, 313, 322, 326, 333, 367, 377, 392, 394, 398

electron donors 93, 105, 108, 115, 117, 130, 150, 220, 252, 263, 279, 282, 286, 287, 300, 304, 306, 308, 309, 310, 312, 313, 318, 320, 321, 326, 333, 335, 336, 340, 342, 354, 359, 360, 362, 363, 364, 366, 367, 377, 386, 387, 394, 398, 400, 402, 403

electron metabolism in complete oxidizing sulfidogens 319

electron sink 305, 308, 335, 485

electron transfer reactions 108, 300, 312, 357, 394, 398

electron transport 19, 27, 85, 86, 105, 107, 109, 111, 113, 170, 309, 310, 336, 416, 443, 445, 485

electron transport and ATP yield in sulfidogens 317

electron transport chain 74, 75, 87, 88, 105, 108, 109, 139, 189, 242, 252, 361, 363, 364, 366, 395

electron transport chains in Paracoccus denitrificans 300

electron transport inhibitors 110

electron transport phosphorylation (ETP) 104, 105–16, 252, 260, 287, 298, 302, 317, 327, 334, 357

electron transport system in nitrite oxidation by Nitrobacter winogradskyi 358

electron transport systems 109, 110, 233, 299

electroneutral transport 38

electrons 111

element cycling under anaerobic conditions 340–344

elemental composition 7–9

elemental sulfur (S⁰) 358, 366

elements 7, 8, 126

elongation factors 178

elongation process 176, 178

Embden–Meyerhof–Parnas (EMP) pathway 60, 61, 61–67, 64, 65, 66, 67, 68, 69, 71, 72, 73, 74, 75, 77, 78, 79, 98, 99, 141, 156, 255, 257, 270, 272, 273, 330, 370, 377, 402, 460, 463, 489

EMP–FDA variant 236

EMP–TA variant 236, 241

EMP pathway intermediates 207

emulsion 224

endergonic reactions 337

endogenous metabolism 482, 483

endogenous respiration 466

endoglucanase 202

endonuclease 174

endonuclease IV 446

endonuclease RNase E 430, 431

endospore formers 492

endospores 184, 185

endo-β-glucanases 203

energy conservation 109, 110, 116, 336

energy conservation in dehalorespiration 336

energy conservation in homoacetogens 334

energy conservation in methanogenesis 327

energy efficiency 377

energy efficiency in C1 metabolism 241

energy expenditure for biosynthesis 182

energy expenditure for maintenance 183

energy expenditure in CO₂ fixation 377

energy sources for survival under starvation conditions 483

energy status 66, 69, 88, 99, 189

energy transduction in prokaryotes 37, 93, 93–98, 116, 182

energy, environment and microbial survival 69, 482–493

energy-rich conditions 482

enhancer-binding protein 441

enolpyruvate 163

enoyl-ACP reductase 153, 154

enteric bacteria 61, 73, 91, 220, 242, 256, 261, 263, 277, 330, 333, 416, 424, 429, 439, 441, 444

Enterobacter aerogenes 274

Enterobacter agglomerans 205, 335, 336

Enterobacter cloacae 307

Enterobacter spp. 272, 273, 277

enterobactin 43

Enterococcus (Streptococcus) faecalis 254, 258, 259, 260

Enterococcus hirae 113

Enterococcus spp. 257, 258, 259, 417

Entner–Doudoroff (ED) pathway 60, 63, 68, 71, 72, 72–74, 78, 79, 98, 255, 378, 402, 485

environmental factors 24, 182, 434

EnvZ/OmpR two-component system regulating the expression of outer membrane proteins OmpC and OmpF 454

enzyme activity 145, 409, 463, 464, 488

enzyme activity modulation through chemical modification 463

enzyme activity modulation through structural changes 408, 460–464

enzyme induction 412

enzyme synthesis 408, 409

enzyme-bound [CO] 315, 325, 327, 329

enzymes 19, 26, 27, 29, 254, 255, 256, 277, 299, 300, 302, 303, 308, 324, 326, 332, 343, 360, 370, 401, 408, 411, 416, 419, 426, 428, 444, 483, 485

enzymes of the ED pathway 72

epimerase 70, 75, 259

Epulopiscium fishelsoni 27, 185

equilibrium constant 94

ergosterol 156

Erwinia amylovora 256

Erwinia carotovora 205, 431, 432

Erwinia chrysanthemi 17

Erwinia spp. 273, 274, 277

erythro-3-hydroxyaspartate 212

erythro-3-hydroxyaspartate dehydratase 212

erythro-3-methylmalyl-CoA 375, 377

Erythrobacter spp. 368, 389

Erythromicrobium hydrolyticum 389

Erythromicrobium ramosum 389

Erythromicrobium spp. 389

Erythromonas spp. 389

Erythromonas ursincola 389

erythrose-4-phosphate 60, 61, 69, 70, 77, 140, 141

Escherichia coli 2, 10, 15, 17, 19, 26, 38, 45, 46, 52, 60, 64, 67, 69, 72, 73, 74, 78, 88, 89, 90, 91, 92, 104, 111, 112, 126, 128, 137, 140, 150, 156, 170, 172, 187, 188, 192, 208, 210, 212, 216, 219, 254, 272, 273, 276, 277, 372, 409, 410, 411, 413, 414, 416, 419, 420, 424, 426, 428, 429, 430, 431, 432, 433, 434, 435, 437, 439, 440, 442, 444, 445, 446, 448, 451, 453, 454, 455, 457, 460, 461, 483, 488

Escherichia coli host factor 435

essential elements 483

esterase 214

ethane 335, 336

ethanol 68, 74, 75, 76, 213, 241, 242, 243, 252, 255, 256, 257, 259, 267, 268, 269, 271, 272, 273, 274, 290, 310, 313, 315, 319, 320, 337, 340, 416, 437, 448, 492

ethanol + acetate 188

ethanol fermentation 255–257

ethanol fermentation by Saccharomyces cerevisiae and Zymomonas mobilis 256

ether linkage 152

ethylbenzene 308, 342, 343

ethylene 131

ethyleneglycol 188

Eubacterium acidaminophilum 282

Eubacterium limosum 41, 254, 263, 331

Eubacterium spp. 263

eukaryotes 159, 165, 230, 240, 256, 322, 485, 486, 488, 492

eukaryotic electron transport chain 106

eukaryotic ribosome 177

Euryarchaeota 24

eutrophication 299

evolution (or production) hydrogenases 364

excitation of antenna molecules and resonance transfer 397

exciton 397, 398, 399

exergonic 337

exine 29, 30, 490

exoenzyme regulatory protein 432

exoglucanase 203

exonuclease activity 173

exo-β-glucanases 203, 204

exponential growth 182, 409, 410, 431, 432

export of cell surface structural components 43

exporter apparatus 181

expression of the flagella regulon 456

external pH 114, 274

extracellular enzymes 43, 202, 205, 206

extracellular oxidation of glucose by Gram-negative bacteria 72

extracellular proteins 178

extracellular signalling cascade 186

extracytoplasmic function σ-factor 409, 448, 490

F layer 186

F₁F₀-ATPase 113

F₄₂₀ 71, 72, 322, 323, 325, 326, 327, 367

F₄₂₀-dependent glucose-6-phosphate dehydrogenase 71, 323

F₄₃₀ 335

facilitated diffusion 37

facultative anaerobes 88, 216, 253, 256, 257, 273, 274, 275, 277, 284, 299, 303, 304, 305, 360, 442

facultative anaerobic enteric bacteria 242, 259, 278

facultative anaerobic Gram-negative bacteria 152

facultative chemolithotrophic Gram-negative bacterium 360

facultative chemolithotrophs 310, 358, 362, 363, 364, 366, 370, 371, 377, 378

facultative syntrophic association between Ruminococcus albus and methanogens 340

facultative syntrophy 340

FAD (flavin adenine dinucleotide) 86, 87, 105, 106, 107, 220

FAD/FADH₂ 97

FADH₂ 260

Faraday constant 96, 102

fatty acid biosynthesis 152, 153, 154, 156

fatty acid composition of a membrane 156

fatty acid desaturase 155, 156

fatty acid metabolism 444

fatty acid utilization 208

fatty acids 15, 23, 104, 117, 152, 192, 206, 208, 213, 214, 225, 268, 310, 340, 451, 490

Fd(oxidized)/Fd(reduced) 264, 333

FDA variant 236

FDH I 277

Fe(II) 7, 41, 304, 310, 354, 360, 362, 363, 364

Fe(II) oxidation 362–364

Fe(III) 7, 41, 43, 298, 306, 307, 308, 309, 310, 336, 360, 361, 362

Fe(III) and Mn(IV) reduction 306

Fe(III) reductase 17, 308

Fe(III) reduction 310, 341

Fe(III) uptake 41–43

Fe(III)/Fe(II) 363

Fe(III)-reducing bacteria 17, 306, 308, 309

Fe(III)-reducing conditions 308

Fe³⁺ → Fe²⁺ 299

Fe³⁺/Fe²⁺ 97

feedback inhibition 64, 67, 145, 149, 459, 460

feedback inhibition and feedforward activation 459–460

feedback inhibition of enzyme activities in the synthesis of aspartate family amino acids 460, 462

feedback regulation 446

feedforward activation 67, 460

fermentation 63, 93, 102, 114, 189, 252, 253, 259, 298, 310, 341, 467

fermentation and anaerobic respiration 252

fermentation balance 255–267, 271

fermentation balance in Clostridium butyricum 265

fermentation of amino acids and nucleic acid bases 281–287

fermentation of dicarboxylic acids 287

fermentation of individual amino acids 281

fermentation of lactate 116

fermentation of purine and pyrimidine bases 287

fermentation of purine bases by Clostridium purinolyticum 288

fermentation products 40, 214, 257, 268, 272, 337

fermentative amino acid production 467

fermentative anaerobic bacteria 92

fermentative bacteria 91, 115, 252, 298, 309, 436

fermentative conditions 91, 189, 275, 277

fermentative degradation of formiminoglycine 289

fermentative metabolism 310, 364

fermentative nitrate reduction 305

fermentative production of antibiotics 467

fermentative propionate-producers 305

fermentative sulfidogenesis 310

fermentative sulfur reduction 288

ferredoxin 66, 97, 130, 132, 221, 263, 264, 267, 270, 282, 289, 312, 313, 315, 318, 327, 330, 333, 334, 343, 367, 398

ferredoxin oxidoreductase 289

ferredoxin reductase 446

ferredoxin(oxidized)/ferredoxin(reduced) ratio 264

ferredoxin:methanophenazine oxidoreductase 327

ferrichrome 43

Ferroglobus placidus 304, 307, 363, 366

Ferroplasma spp. 362

Ferroplasma acidarmanus 307

[Fe–S] clusters 45, 107, 300

[Fe–S] molbydoprotein 357

[Fe–S] proteins 8, 45, 106, 107, 111, 112, 130, 139, 253, 264, 300, 309, 394

filament 10, 11, 181, 455

filament cap protein 11

filamentous anoxygenic phototrophic bacteria 387, 388, 394, 395, 400, 402, 403

filamentous sulfur bacteria 305, 360

fimbriae 10, 12

firmicutes 184, 185, 187, 330

flagella 10, 12, 49, 181, 410, 455, 457

flagella and pili 10–12

flagellar filament formation in Gram-negative bacteria 181

flagellar motor 181

flagellar regulon 455

flagellar rotation 456, 457, 458

flagellin 11, 47, 50, 411

flagellin export mechanism 411

flagellum 10, 11, 181

flavin 215, 278

flavin adenine dinucleotide (FAD) 85, 252, 308

Flavobacterium autothermophilum 365

flavodoxin 130, 132

flavoproteins 107, 253

Flectobacillus major 23

flippase 170

fluid mosaic model 22, 23

FMN (flavin mononucleotide) 106, 107, 111

FMN/FMNH₂ 97

FMNH₂ 106, 111, 117

FMNH₂ oxidation 117

fnr (fumarate and nitrate reductase) mutant 444

FNR protein 88, 92, 277, 303, 444

fnr system 444

folate 10, 159

folded proteins 44, 178

foodstuffs 482

foreign DNA 173

forespore 184

formaldehyde 230, 234, 235, 236, 240, 272

formaldehyde dehydrogenase 234

formate 115, 150, 234, 259, 260, 272, 273, 277, 320, 324, 328, 330, 333, 374

formate dehydrogenase 45, 107, 234, 309, 322, 330, 332, 333, 336, 374

formate dehydrogenase I 277

formate dehydrogenase II 277

formate hydrogen-lyase operon 434

formate metabolism in facultative anaerobes 278

formate:hydrogen lyase 277, 434

formation of acetoin and 2,3-butanediol by Bacillus subtilis 243

formation of one gram of Escherichia coli cells 190

formimino (-CH=NH) 157

formiminoglycine 287

formyl (-CHO) 157

formyl tetrahydrofolate 149

formyl-carrier 322

formyl-H₄F synthetase 334

formylkynurenine 220

formyl-MF 325

formyl-MF dehydrogenase 324, 325, 326

formyltetrahydrofolate 282

formyltetrahydrofolate synthase 334

F-pilus 12, 16, 443

F-plasmid 12

Frankia alni 129

free energy 93, 95, 96, 97, 98, 101, 102, 105, 106, 114

free energy change 93, 94, 95, 97, 98, 99, 114, 115

free energy from NADH oxidation coupled to electron acceptors used by prokaryotes 299

free energy of an oxidation/reduction reaction 95

free energy of formation (ΔG_f^0′) 94

free radicals 150, 491

freshwater 304, 309, 360, 368, 389

fructose 65, 73, 188, 205, 206, 330, 357, 378

fructose diphosphatase 68, 69

fructose permease 357, 378

fructose-1,6-diphosphatase 61, 63, 65, 66, 67, 68, 370, 416

fructose-1,6-diphosphate (FDP) 206, 370, 417, 419, 460, 463, 464, 483

fructose-1,6-diphosphate aldolase 63, 236, 330

fructose-1,6-phosphate 377

fructose-1-phosphate 65, 206

fructose-6-phosphate 61, 63, 66, 68, 71, 75, 76, 77, 161, 163, 206, 235, 236, 240, 259, 370, 374, 483

fructose-6-phosphate phosphoketolase 77

fruiting bodies 490, 492

fuel cell 308

fumarase 87

fumarate 87, 91, 96, 106, 115, 217, 227, 228, 277, 279, 284, 303, 339, 340, 342, 444, 455

fumarate binding 342

fumarate nitrate reductase 442

fumarate reductase 91, 92, 115, 116, 252, 277, 278, 279, 284, 373, 442

fumarate reduction 298

fumarate/succinate 97

fumarylpyruvate 228

fungal cell walls 205

fungi 224, 304, 484

Fusarium oxysporum 304

Fusarium solani 304

Fusobacterium nucleatum 263

Fusobacterium spp. 263

futile cycle 66, 69, 463, 486, 487

G box 428

galactokinase 206, 434, 435

galactose 12, 41, 161, 188, 206, 207, 394, 411, 434, 435

galactose operon 434

galactose-1-phosphate 206

galactose-1-phosphate uridylytransferase 434

galactosyl diglyceride 394, 395

galacturonate 205

Gallionella ferruginea 362, 363

Gardnerella vaginalis 77

gas constant 95, 96, 97, 102

GcrA (cell cycle regulator) 187

GDP 66, 149, 488

Gemmata obscuriglobus 28

gene derepression 458

gene expression 420, 423, 430, 435, 459

general secretory pathway (GSP) 43, 43–45, 47

genes 29

genetic code of mRNA 176

genome analysis 324

genome sequences 1, 46, 357, 372, 451, 467

gentisate 227, 228, 342

gentisate dioxygenase 228

gentisate pathway 227, 228, 231

Geobacter chapellei 307

Geobacter grbiciae 341

Geobacter hydrogenophilus 307

Geobacter metallireducens 307, 308, 341

Geobacter spp. 117, 310, 312, 336

Geobacter sulfurreducens 17, 307, 308, 336

Geoglobus ahangari 307

Geospirillum barnesii 307, 335

Geothrix fermentans 307

Geovibrio ferrireducens 307

Gibberella fujikuroi 304

GlcNAc 167

Glc-NAc-N-acetlymuramylpentapeptide-(gly)₅ 167

global control system 135

global gene regulation

global regulation 67, 187, 410, 415, 418, 431, 435, 436, 438, 466

global regulation: responses to environmental stress 435–459

Gloeocapsa spp. 129

glucitol 417

glucoamylase 203

gluconate 60, 72, 73, 74, 188, 417, 419

gluconate dehydrogenase 73, 74

gluconate/glucose 97

gluconeogenesis 63, 66, 67, 67–69, 87, 89, 161, 189, 267, 319, 329, 330, 333, 374, 416, 432, 464

gluconeogenesis in archaea 68

Gluconobacter oxydans 242

Gluconobacter spp. 71, 241, 242

glucosamine 15, 205

glucosamine-6-phosphate 163

glucose 41, 60, 61, 63, 65, 66, 69, 70, 71, 72, 73, 74, 75, 77, 78, 79, 98, 156, 187, 188, 189, 202, 203, 205, 207, 208, 214, 259, 262, 263, 264, 265, 272, 275, 277, 278, 305, 330, 403, 411, 413, 414, 415, 416, 417, 419, 426, 435, 442, 465, 483, 484, 489

glucose degradation in Escherichia coli 79

glucose dehydrogenase 73, 74, 234

glucose dimer 484

glucose fermentation 265

glucose fermentation by Leuconostoc mesenteroides 75

glucose oxidation 62, 94

glucose transport 415, 426

glucose utilization 74

glucose:galactose-1-phosphate uridylyltransferase 206

glucose-1-phosphate 161, 165, 205, 206, 484

glucose-6-phosphate 61, 66, 67, 69, 70, 71, 72, 75, 161, 206, 259, 267, 484

glucose-6-phosphate dehydrogenase 70, 71, 76, 446, 485

glucose-6-phosphate isomerase 61

glucose-6-phosphate synthesis 67–69

glucose-fructose oxidoreductase 46

glucose-mineral salts medium 89, 126, 127, 187, 191, 419

glutaconyl-CoA 283

glutaconyl-CoA decarboxylase 115, 283

glutamate 87, 118, 128, 137, 140, 141, 142, 148, 159, 163, 188, 215, 217, 220, 243, 283, 289, 457, 461, 463

glutamate dehydrogenase 137, 138, 141, 215, 289, 440, 441, 461, 464, 465

glutamate fermentation by Acidaminococcus fermentans and Peptostreptococcus asaccharolyticus 284

glutamate fermentation by Clostridium tetanomorphum 283

glutamate mutase 283

glutamate synthase 137, 461

glutamate transport 39

glutamate-binding protein 39

glutamate-tRNA 159

glutamine 137, 138, 140, 141, 148, 149, 217, 440, 441, 461, 462

glutamine dehydrogenase 440

glutamine synthetase 135, 137, 138, 140, 435, 440, 441, 461, 462, 464, 465

glutamine synthetase adenylyltransferase/removase 461

glutamine: 2-oxoglutarate aminotranferase (GOGAT) 137, 141

glutamyl-tRNA 159

glutaredoxin 150, 446

glutaryl-CoA 220

glutathione (GSH) 97, 361, 446

glutathione reductase 446

glyceraldehyde 74

glyceraldehyde:ferredoxin oxidoreductase 332

glyceraldehyde-3-phosphate 63, 66, 67, 70, 71, 72, 75, 159, 236, 240, 242, 259, 289, 368, 370, 419

glyceraldehyde-3-phosphate dehydrogenase 63, 64, 370

glyceraldehyde-3-phosphate:ferredoxin oxidoreductase 66

glycerate pathway 210, 212

glycerol 26, 152, 206, 214, 262, 263, 274, 275, 306, 426

glycerol fermentation by Klebsiella pneumoniae 275

glycerol teichoic acid 164

glycerol-3-phosphate 18, 156, 157, 164, 167, 486

glycerol-3-phosphate acyltransferase 157

glycerol-3-phosphate dehydrogenase 106, 156

glycerol-P-N-acetylglucosamine-P 167

glycerol-P-N-acetylglucosamine-P-P-undecaprenyl 167

glycerophospholipids 23

glycine 17, 63, 141, 149, 159, 212, 217, 236, 237, 282, 286

glycine fermentation by Peptostreptococcus micros 282

glycine reductase 282, 287, 309

glycoaldehyde 76

glycocalyx 12

glycogen 29, 61, 126, 127, 161, 165, 166, 189, 203, 206, 403, 483, 487

glycogen biosynthesis 67, 165, 432, 464, 483

glycogen phosphorylase 432, 483

glycogen synthase 165, 166, 432, 483

glycolate 210

glycolipid 224

glycolysis 41, 60–80, 78, 105, 257, 264, 271, 299, 305, 330, 334, 402, 416, 432, 488

glycolysis in Bacillus subtilis 79

glycolytic enzymes 416

glycolytic genes 67

glycolytic pathway in some Gram-negative bacteria 72

glycoprotein 13

glycosyl (4→6) transferase 165, 166

glycyl radical 150

glycyl-tRNA 167

glyoxalase 64

glyoxylate 89, 210, 212, 217, 223, 236, 237, 375, 376, 377

glyoxylate cycle 89, 90, 91, 100, 208, 209, 376, 402, 416, 461

glyoxylate metabolism 212, 213

GMP 149, 459

Gordonia spp. 486

gramicidin A 35, 36

Gram-negative bacteria 11, 12, 13, 14, 16, 17, 19, 38, 43, 44, 45, 46, 47, 49, 72, 73, 88, 161, 182, 230, 234, 302, 355, 358, 362, 366, 410, 414, 415, 417, 418, 427, 452, 453, 486, 493

Gram-negative bacterial outer membrane 169

Gram-negative facultative anaerobes 107, 272, 274

Gram-negative spore-formers 330

Gram-negative syntrophic bacterium 339

Gram-positive bacteria 12, 13, 14, 17, 18, 20, 29, 44, 67, 88, 167, 169, 184, 185, 368, 410, 414, 417, 418, 427, 428, 439, 451, 452, 453, 454, 466, 489, 490, 492, 493

Gram-positive denitrifiers 302

Gram-positive methylotrophs 234

green bacteria 387, 388, 389, 390, 392, 394, 395, 400, 401

green gliding bacterium 375

green sulfur bacteria 387, 388, 392, 394, 395, 398, 400, 402, 403

green sulfur photosynthetic bacteria 372

group translocation (phosphotransferase system) 35, 37, 39–40, 61, 63, 74, 206, 263, 414, 417, 418

growth 182, 182–192

growth factors 10, 156, 257, 259, 387

growth medium 128

growth rate 182, 189, 192, 437, 466

growth rate and regulation 466

growth yield 187, 189, 192

growth yield of fermentative microorganisms 188

growth yield using different electron acceptors and maintenance energy 189

GSP system 51, 169

GSP-independent membrane integration 170

GTP 87, 149, 174, 177, 178, 189

GTPase 434

guanine 64, 221, 287, 428

guanine auxotrophs 467

guanine deaminase 221

guanine-cytosine 170

guanosine-3′-diphosphate-5′-diphosphate (guanosine tetraphosphate, ppGpp) 437

guanosine-3′-diphosphate-5′-triphosphate (guanosine pentaphosphate, pppGpp) 271, 437, 488

guanylic acid 149

H⁺ 8, 36, 38, 40, 95, 102, 103, 104, 105, 106, 107, 111, 112, 113, 114, 115, 116, 253, 260, 262, 269, 271, 289, 301, 302, 318, 340, 357, 364, 403, 404, 405

H⁺ permeability 110

H⁺ translocation 111

H⁺ translocation through the Q-cycle 112

H⁺ transport 114

H⁺/ATP stoichiometry 114, 189

H⁺/H₂ 96, 97

H⁺/O ratio 113, 189, 302

H⁺-ATPase 113

H⁺-dependent acetogens 334

H⁺-symport 41

H₂ 115, 131, 132, 253, 257, 263, 264, 265, 267, 268, 269, 270, 271, 272, 277, 289, 304, 310, 312, 315, 317, 318, 320, 325, 327, 330, 333, 334, 340, 354, 364, 365, 366, 378

H₂ + CO₂ 365

H₂ + CO₂ mixture 364

H₂ evolution 267

H₂-consuming sulfidogens 333

H₂O₂ 445, 446

H₂O₂-sensing regulator 445

H₂-oxidizing anaerobic chemolithotrophs 365

H₂-oxidizing bacteria 304, 377

H₂-oxidizing carboxydobacteria 366

H₂-producing hydrogenase 270

H₂S 107, 289

H₄F 157, 159, 235

H₄MPT 327

H₄MPT 234, 235, 322, 323, 325

Haemophilus influenzae 1

Haemophilus parainfluenzae 109

hairpin (stem-and-loop) structures 177, 420, 421, 422, 426, 429, 430, 431, 432, 446, 448

Haloarcula spp. 302

Haloarcula vallismortis 65

Halobacterium halobium 129

Halobacterium saccharovorum 73, 74, 75

Halobacterium salinarium 286

Halobacterium spp. 21, 403

Halococcus saccharolyticus 60, 73

Halococcus spp. 21

halogenated compounds 334, 335

halogenated hydrocarbons 298, 320, 330

halogens 298, 335, 336

Halophaga foetida 331

halophiles 24, 104

halophilic 68, 74, 150

halophilic archaea 7, 21, 37, 60, 65, 74, 105, 152, 386, 388, 403, 404, 405

halophilic archaeal membranes 27

halorhodopsin 404

Halothiobacillus neapolitanus 371, 373

Halothiobacillus spp. 359

Hansenula spp. 240

HAO 356

HCHO 236

heat 492

heat shock proteins (HSP) 431, 446, 447

heat shock response (HSR) 409, 437, 446–448

helicase 171, 172

Helicobacter pylori 50, 51, 451

Heliobacillus spp. 388

heliobacteria 387, 388, 389, 390, 392, 394, 400, 401, 403

heliobacteria and aerobic anoxygenic phototrophic bacteria 395

Heliobacterium chlorum 129

Heliobacterium spp. 388

Heliophilum spp. 388

helix destabilizing protein (HDP) 171

heme 107, 109, 159, 279, 356

heme biosynthetic pathway from 5-aminolevulinic acid (ALA) to protoheme 162

heme biosynthesis 159

hemicellulase 204

hemicellulose 204

hemin 10, 257, 260

hemoproteins 107

Hermovibrio ammonificans 304

heterocystous cyanobacteria 133, 134, 387, 487

heterocysts 133, 134, 387, 487, 490, 492

heterodimer 357

heterodisulfide 325

heterodisulfide reductase 324, 325, 326, 327

heterofermentative bacteria 75, 258, 286

heterofermentative lactic acid bacteria (LAB) 74, 75, 76, 256, 257, 259, 260, 263

heterofermentative Lactobacillus spp. 262

heterolactate fermentation 257

heteropolysaccharide 204

heterotrophic metabolism 189, 241

heterotrophic metabolism on substrates other than glucose 202–243

heterotrophic methylotrophs 230, 232, 235

heterotrophs 8, 60, 310, 362

hexokinase 61, 66, 205, 206

hexosamines 13

hexose fermentation 76

hexose metabolism 206, 207

hexose metabolism by homoacetogens 332

hexose monophosphate (HMP) pathway 60, 63, 69–72, 75, 77, 78, 79, 207, 323, 370

hexose phosphate 63, 67, 161, 235, 259

hexoses 13, 75, 204, 206, 256, 257, 259, 272, 330, 333

hexulose-6-phosphate 235

high energy bonds 99, 105, 486

high energy phosphate bonds 99, 100, 102

high osmotic pressure 484

high-affinity sugar-binding 39

histidase 216

histidine 135, 141, 145, 216, 217, 286, 420, 426, 441

histidine biosynthesis 145, 148

histidine deamination 217

histidine degradation 218

histidine protein kinase 457

histidine residue 428, 441, 445, 454, 455

histone-like DNA-binding protein 434

holin-like protein 493

homoacetogenesis 330–334, 341

homoacetogens 315, 329, 330, 331, 333, 334, 340, 365, 367, 368, 374

homoacetogens and their electron donors 331

homocysteine 216

homofermentative lactic acid fermentation 258, 271

homofermentative lactic-acid bacteria (LAB) 74, 75, 257, 258

homogentisate oxidase 227

homolactate fermentation 187, 252, 257, 259

homoserine acyltransferase 459

homoserine dehydrogenase 424, 459

homoserine kinase 424

hook 10, 11, 181, 455

hook protein 11

hopanoids 23, 24

hot springs 389

housekeeping σ-factor 410

HPr protein 417

HPr(ser) kinase 417, 418

HPr(Ser-P) 417

HS⁻ 360, 365

HS₂O₃⁻ 360

HS-CoB 325

HS-CoM 325

HSO₃⁻ 360

HSO₄⁻/HSO₃⁻ 139, 312

HS⁻-oxidizing enzyme 361

humic acid 308, 336

humic substances 118

hydride ion (H⁻) 357

hydrocarbon degradation 229

hydrocarbon monooxygenase 224

hydrocarbon oxidation 341

hydrocarbon transport 224

hydrocarbons 223, 224, 225, 341, 484, 486

hydrocarbon-utilizing microbes 224

hydrogen 7, 189, 253, 282, 304, 326, 333, 336, 337, 339, 340, 360, 364, 366

hydrogen bacteria 366

hydrogen bonding 177, 203

hydrogen bonds 171

hydrogen cycling in sulfate reduction by Desulfovibrio spp. 314

hydrogen cycling mechanism 318

hydrogen in fermentation 252

hydrogen oxidation 364–366

hydrogen partial pressure 264

hydrogen peroxide (H₂O₂) 240, 253, 254, 260, 434, 445, 492

hydrogen sulfide 304, 312

hydrogen utilization 445

hydrogen utlization by Ralstonia eutropha (Alcaligenes eutrophus) 366

hydrogenase 45, 46, 107, 132, 263, 264, 277, 282, 314, 317, 322, 326, 336, 364, 365, 366, 441, 442

hydrogen-consuming methanogens 340

Hydrogenobacter thermophilus 92, 304, 364, 365, 366, 377

Hydrogenobacterium thermophilus 373

Hydrogenobaculum sp. 367

Hydrogenomonas thermophila 304, 312, 365

hydrogenotrophic methanogenesis 324

hydrogenotrophic methanogens 320, 325, 326, 328

Hydrogenovibrio marinus 364, 365, 371, 373, 377

hydrogen-oxidizing bacteria 364, 365, 366

hydrolases 205, 207, 484

hydrolysis 113, 114

hydrolysis of crystalline cellulose 204

hydrolysis of polymers 202–206

hydrolysis of proteins, nucleic acids and lipids 206

hydrolyzing enzymes 17

hydrophobic glycolipids 224

hydrothermal vents 304, 310, 368, 389

hydroxamates 43

hydroxyaspartate pathway 223

hydroxyhydroquinone 343

hydroxyl radical (OH·) 445

hydroxylamine (NH₂OH) 356

hydroxylamine oxidation 356

hydroxylamine oxidoreductase (HAO) 356

hydroxylase 224

hydroxypropionate cycle 377

hydroxypyruvate 237

hyperosmolarity 437

hyperthermophiles 24

hyperthermophilic archaea 25, 26, 65, 68, 71, 74, 288, 310, 322, 332, 363

hyperthermophilic archaeal fermentation 287

hyperthermophilic archaeal membranes 26

hyperthermophilic bacteria 203

Hyphomicrobium vulgare 300

Hyphomonas spp. 187

hypochlorous acid (HOCl) 445

hypoxanthine 221, 467

Ideonella dechloratans 336

IMP 149

inclusion bodies 485

incomplete oxidation 241–243

incomplete oxidizers 306, 310, 311, 317

incomplete oxidizing sulfidogens 339

incomplete TCA fork 71, 87, 91, 92, 242, 267, 268, 276, 319, 329, 378, 442, 463

indole-3-glycerol phosphate 142

inducer 411, 412, 413

inducer exclusion 417

inducer exclusion/expulsion mechanism 417

inducer expulsion 417

inducible and constitutive enzymes 411

inducible enzymes 411

induction mechanism of the lac operon in Escherichia coli 412

induction of enzymes 411–413

induction of enzymes of arabinose metabolism in Escherichia coli 413

induction of β-galactosidase by lactose in Escherichia coli 411

inhibitors 110, 464

inhibitors of electron transport phosphorylation 110

inhibitors of murein synthesis 167

initial activation reactions during anaerobic degradation of saturated aliphatic and aromatic hydrocarbons 342

initiation 176

initiation and elongation 177

initiation codon 176, 177

initiation complex 177

initiation factors 177

initiation residue 178

injection of toxin proteins 51

inorganic electron donors 108, 110

inorganic nitrogen 127

inorganic phosphate 205

inorganic phosphate specific transporter (PST) 441

inorganic sulfur source 139

inosinic acid 149

inositol 157

integral proteins 23, 26, 169

interconversion of ATP 101

internal pH 103, 104, 114, 363

interspecies hydrogen transfer 337

intine 29

intracellular membrane structures 230

intracellular pH 257, 274

intracellular storage materials 29

intracellular vacuoles 360

intron 174

invasins 51

invertase 207

iodate 298, 336

ion transport mechanisms 37

ionic strength 461

ionizing radiation 29

ionophores 35, 105, 114

ions 39

iron 8, 43, 46, 130, 131, 132, 300, 304, 306, 357

iron bacteria 362

iron porphyrins 335

iron superoxide dismutase 434

isoamylase 203

isobutyryl-ACP 154

isocitrate 87, 89, 90, 461

isocitrate dehydrogenase 69, 87, 90, 91, 100, 443, 461, 464, 485

isocitrate lyase 89, 90, 91

isoenzymes 153, 423, 459, 460

isoleucine 141, 217, 274, 286, 423, 424, 459

isoleucine biosynthesis 141, 216

isomerases 70, 207

isopentenyl pyrophosphate (IPP) 159

Isophaera pallida 28

isoprenoid compounds 23, 25, 159, 160, 486

isoprenoid synthesis 159

isoprenoid units 107

isopropanol 214, 269

isorenieratene 390

isozymes 153

Janus green 97

K⁺ 36, 63

KDPG aldolase 72

keto acid dehydrogenase 214

ketones 214, 225, 242, 269, 320

ketoses 207

keto-sugars 15

key enzymes of the Calvin cycle 370

kimchi 260

kinase activity 440

kinase-phosphatase 90, 91

kinases 333

Klebsiella aerogenes 118, 489

Klebsiella oxytoca 47, 274

Klebsiella pneumoniae 109, 115, 129, 132, 135, 209, 261, 274, 275, 276, 489

Klebsiella spp. 273, 274

Krebs cycle 86

Kuenenia stuttgartiensis 305

kynurenine 220

L box 428

LAB and their fermentation mode 258

LAB fermented foods 260

lac operon 412, 413, 437

lac repressor 437

lactate 40, 64, 68, 74, 75, 77, 115, 116, 257, 259, 260, 261, 262, 265, 267, 268, 271, 272, 273, 274, 278, 279, 280, 281, 305, 306, 310, 313, 315, 317, 320, 330

lactate dehydrogenase 75, 257, 260, 267, 273, 278, 313, 460, 463

lactate fermentation 257–263

lactate fermentation by Clostridium butyricum 265

lactate gradient 116

lactate oxidation 267, 271, 318

lactate/H⁺ symport 116, 117, 252, 260

lactate–acetate fermentation 267

lactate–acetate fermentation to butyrate by Clostridium butyricum 266

lactic acid bacteria (LAB) 10, 40, 41, 75, 116, 117, 214, 219, 257, 259, 260, 261, 265, 268, 273, 275, 277, 279, 460

lactobacillic acid 24, 156

Lactobacillus acidophilus 17

Lactobacillus arabinosus 24, 156

Lactobacillus brevis 258, 260

Lactobacillus bulgaricus 41, 258

Lactobacillus casei 187, 188, 259, 337

Lactobacillus curvantus 258

Lactobacillus delbrueckii 258, 259, 261

Lactobacillus fermentum 258

Lactobacillus plantarum 188, 254, 258, 259, 260, 261

Lactobacillus spp. 40, 257, 258

Lactococcus (Streptococcus) lactis 254

Lactococcus cremoris 116, 258, 260

Lactococcus lactis 116, 258, 260, 261, 466

Lactococcus lactis subsp. diacetylactis 261

Lactococcus spp. 257, 258, 259, 279, 417

lactonase 70, 71

lactose 41, 188, 207, 411, 412, 413, 415, 417

lactose/galactose antiport 41

lactyl-CoA 280

lag phase 182

L-alanine 163, 215

L-amino acids 215

large proteins 178

lateral gene transfer 322, 389

L-diaminopimelate 17

leader mRNA 420, 421, 426, 427, 428

leader sequence 420, 422, 425, 428

leghaemoglobin 132, 133

Legionella pneumophila 50, 51

legumes 129

Leptospirillum spp. 362, 363

Leptothirx discophora 368

leucine 141, 217, 286, 424

Leuconostoc cremoris 116, 260, 261

Leuconostoc dextranicum 258

Leuconostoc mesenteroides 75, 76, 77, 258, 259, 261

Leuconostoc oenos 261, 286

Leuconostoc spp. 40, 257, 258

levanase 417

L-glutamate 140, 215

L-glutamate 2–ketoglutarate 140, 206–207

L-glutamate-3-ketoglutarate 140

L-homoserine 17

lichenan 426

light 397

light emission 118

light energy 93, 116, 117

light reactions 396–401, 402, 403

light reactions in purple bacteria 401

light-driven electron transport 386

light-harvesting complex 386

lignin 225, 227, 229, 330, 333, 336

limited O₂ supply 404

lincomycin 323

linear and branched pathways in anaerobic fermentation 253

linear chromosomal DNA 171

linear DNA 28

linear fermentative pathways 253, 257, 271

lipases 47, 206

lipid A 13, 15, 16, 164, 165, 169

lipid A-core polysaccharide 170

lipid biosynthesis 152–159

lipid electron carriers 107

lipid II 167

lipid reserve materials 484–487

lipids 127, 190, 191, 192, 205, 206, 483, 487

lipoate 10

lipoglycan 17

lipopolysaccharide (LPS) 13, 15, 46, 127, 161, 164, 165, 169, 182, 190

lipopolysaccharide (LPS) translocation 169

lipoproteins 15, 16, 17, 169

liposomes 21, 22

lipoteichoic acid 17, 18

L-isoleucine 208

Listeria spp. 417

lithotrophs 8

L-lysine 17

L-ornithine 17

LPS exporter 170

L-serine 17

L-sorbose 242

luciferase 117, 118

luminescence 117, 452

luminescent bacteria 116, 117, 452

L-valine 208

lysine 64, 103, 141, 167, 220, 284, 405, 423, 428, 459

lysine biosynthesis 141

lysine biosynthesis in yeasts and fungi 143

lysine decarboxylases (CadA) 103

lysine degradation 221

lysine fermentation by Clostridium sticklandii 285

lysine/cadaverine antiporter (CadB) 103

lysozyme 13, 17, 21, 339

Macromonas spp. 359

magnesium 7

maintenance energy 182, 189, 192, 318, 464, 482

maintenance of nucleoid position 183

major elements 7–8, 8–9

major glycolytic pathways in prokaryotes 73

malate 40, 67, 68, 87, 89, 116, 189, 261, 262, 280, 416

malate decarboxylation reaction 116

malate dehydrogenase 87

malate enzyme 68

malate synthase 89, 90, 91

malate²⁻/lactate⁻ exchange 40, 41, 116, 261, 262

maleylpyruvate 228

malolactic fermentation 40, 116, 261, 262

malonate 209, 287

Malonomonas rubra 209, 287

malonyl group 153

malonyl transacylase 153

malonyl-ACP 153

malonyl-CoA 153, 209, 375

malonyl-CoA reductase 375

maltose 38, 39, 202, 203, 205, 207, 413

maltose phosphorylase 205

maltose transport 38, 39

maltose-binding protein (MBP) 39

malyl-CoA 237, 375, 377

malyl-CoA lyase 375

malyl-CoA lyase/erythro-3-methylmalyl-CoA lyase 377

manganese 9, 306

manganese superoxide dismutase 446

manganoprotein 398

mannitol 188, 278, 417, 419

mannose 12, 61, 206

mannose transport 40

mannose-6-phosphate 161, 206

mannose-6-phosphate isomerase 161

marine algae 334

marine environments 304, 368

master cell-cycle regulators 183

Mastigocladus laminosus 129

maximum growth yield (Y^max) 189, 192

mechanical energy 117

mechanisms regulating enzyme synthesis 408–435

megaplasmids 29

Megasphaera elsdenii 278, 280, 281

membrane diffusion 72

membrane fluidity 24, 26, 36, 155, 156, 451

membrane fusion protein (mfp) 47

membrane phospholipids 44, 102, 104, 451

membrane potential (Δψ) 37, 38, 102, 103, 104, 105, 357, 363

membrane proteins 21, 26–27, 35, 40, 45, 64, 102, 111, 178, 428, 442, 443

membrane structure 22–26

membrane transport 35–52

membrane vesicle formation 22

membrane-associated kinase 451

membrane-bound ATP synthase 103, 114, 149

membrane-bound desaturase (Des) 451

membrane-bound enzyme 324, 325

membrane-bound proteins

membrane-bound sensor protein 303, 444, 454, 455

membrane-bound sensor/kinase protein 453

membrane-spanning region 169

menaquinone 107, 108, 115, 284, 313, 318, 336

mercury 1

mercury(II) 309

mesaconyl-CoA 375

meso-diaminopimelate 163

mesophilic heterotrophic methanogens 372

messenger RNA (mRNA) 409

meta cleavage 228

meta cleavage of catechol and protocatechuate 231

Metabacterium polyspora 184, 185

Metabacterium polyspora 184

Metabacterium-like symbiont 185

metabolic engineering 467

metabolic intermediates 61

metabolic intermediates with high energy bonds 99

metabolic regulation 182, 408–467

metabolic regulation and growth 464–466

metabolic regulation and the fermentation industry 467

metabolic regulation by quorum sensing in Gram-negative bacteria 452

metabolism of fumarate by Syntrophobacter wolinii 339

metabolism of one-carbon compounds 233

metabolon 27

metal ions 101, 298, 306, 309, 310, 337, 344

metal ores 310

metal reduction 306–310, 341, 342

metal reduction and the environment 309

metal sulfides 360

metal toxicity 306

metalloids 306, 309, 335

Metallosphaera sedula 375, 376

metal-reducing bacteria 306, 309, 310, 335, 336, 341

metals 306, 308, 360

methane 223, 229, 230, 233, 240, 298, 320, 322, 324, 325, 326, 327, 328, 337, 340

methane monooxygenase 233

Methanobacteriales 321

Methanobacterium bryantii 255

Methanobacterium spp. 21, 320, 321, 329

Methanobacterium thermoautotrophicum 129, 255, 322, 372

Methanobrevibacter spp. 321

Methanocalculus spp. 321

Methanocaldococcus spp. 321

Methanoccus capsulatus 232

Methanococcales 321

Methanococcoides spp. 321

Methanococcus jannaschii 371

Methanococcus maripaludis 129, 372

Methanococcus spp. 329

Methanocorpusculum spp. 320, 321

Methanoculleus spp. 320, 321

methanofuran (MF) 157, 315, 322, 323, 324, 329

methanogenesis 298, 309, 310, 320–330, 328, 341, 342

methanogenic archaea 26, 68, 225, 226, 255, 322, 327, 372

methanogenic coenzymes 71, 234, 323

methanogenic cofactors and their structures 323

methanogenic conditions 337

methanogenic enzymes 324

methanogenic pathways 324

Methanogenium spp. 320, 321

methanogens 24, 46, 68, 71, 72, 129, 152, 157, 255, 309, 315, 320, 321, 322, 324, 325, 329, 330, 333, 334, 337, 338, 339, 340, 365, 367, 368, 374

Methanohalobium spp. 321

Methanohalophilus spp. 321

methanol 205, 229, 233, 234, 235, 240, 320, 322, 324, 325, 326, 327, 328, 330, 333

methanol dehydrogenase 234

methanol dehydrogenase and the electron transport chain of a methylotroph 234

methanol oxidase 240, 241

methanol oxidation 233

methanol oxidation by Methylobacterium extorquens 235

methanol utilization 240

Methanolacinia spp. 320, 321

Methanolobus spp. 321, 322

Methanomicrobiales 321

Methanomicrobium spp. 321

methanophenazine 322

Methanoplanus spp. 321

Methanopyrales 321

Methanopyrus kandleri 29

Methanopyrus spp. 321

Methanosaeta spp. 321, 322, 326, 327

Methanosalsum spp. 321

Methanosarcina acetivorans 372

Methanosarcina barkeri 129, 254, 255, 327, 372

Methanosarcina mazei 326, 372

Methanosarcina spp. 21, 321, 322, 326, 327, 329

Methanosarcinales 321, 322

Methanosphaera spp. 321, 322

Methanospirillum hungatei 339

Methanospirillum spp. 320, 321

Methanothermobacter spp. 321

Methanothermococcus spp. 321

Methanothermus spp. 321

Methanotorris spp. 321

methanotrophs 225, 229, 230, 233

methanotrophy 230–235

methanotrophy and methylotrophy 229

methenyl (-CH=) 157

methenyl tetrahydrofolate 149

methionine 139, 141, 159, 176, 216, 217, 423, 428, 459

methionine adenosyltransferase 159

methyl (-CH₃) group 157, 216

methyl compounds 322

methyl group donor 156, 322

methyl group transfer 325

methyl transferase 325

methyl viologen 97, 117

methyl-accepting chemotaxis proteins (MCPs) 457

methylamines 229, 320, 322, 325, 328

methylated nucleotides 174

methylation 154, 156, 157, 173, 461

Methylbacterium organophilum 232

methylcitrate cycle 208, 214, 217

methyl-CoM 325, 327, 328

methyl-CoM reductase 322, 325

methyl-corrinoid 374

methylene (-CH₂-) 157

methylene blue 97

methylene-H₄F 236, 282

methylene-H₄F reductase 334

methylene-tetrahydrofolate 282

methylene-tetrahydrofolate reductase 375

methylesterase CheB 457

methylglyoxal 64

methylglyoxal accumulation 64

methylglyoxal bypass 64

methylglyoxal synthase 64

methyl-group carrier

methyl-H₄F 315, 330, 331, 374

methyl-H₄MPT:CoM-methyltransferase 325, 326, 328

methyl-H₄MPT 329

methylmalonyl-ACP 154

methylmalonyl-CoA 279, 280, 375

methylmalonyl-CoA mutase 279

methylmalonyl-CoA pathway 208

methylmalonyl-CoA:pyruvate transcarboxylase 279, 280

Methylobacter spp. 233

Methylobacterium extorquens 72, 212, 232, 235, 323

Methylobacterium spp. 232, 233

Methylococcus capsulatus 129

Methylococcus spp. 233

Methylocystis spp. 232, 233

Methylomonas methanica 232

Methylomonas methanooxidans 232

Methylomonas spp. 233

Methylophilus methylotrophus 232, 235

Methylosinus spp. 233

Methylosinus trichosporium 129, 232, 236

methylotrophic methanogenesis 325

methylotrophic methanogens 320, 322, 326, 327

methylotrophic yeasts 230, 235, 240

methylotrophs 72, 226, 229, 230, 235, 323

methyltransferase CheR 457

mevalonate pathway 159, 160

mevalonate-independent pathway 159, 160

Mg²⁺ 8, 16, 18, 61, 63, 99, 101, 390, 392

micelles 21, 22

Michaelis-Menten kinetics 37

microaerophiles 253, 304, 312, 362

microaerophilic H₂-oxidizers 366

Microbacterium ammoniaphilum 468

microbial growth 126

Micrococcus luteus 19, 491

Micrococcus lysodeikticus 19

Micrococcus radiodurans 254

Micrococcus spp. 486, 489

Microcyclus aquaticus 365

Micromonospora spp. 486

Microvigula aerodenitrificans 305

milk 261

Min system 186

mineral surface 308

minor elements 8, 9

miscellaneous electron acceptors 336

mitochondria 106, 107, 109, 111, 113, 177

mitochondrial and bacterial electron transport systems 109

mitochondrial electron transport chain 105, 106

mitochondrial inner membrane 105, 106, 112, 113

mixed acid and butanediol fermentation 242, 272–277

mixed acid fermentation by some Gram-negative facultative anaerobic bacteria 273

mixed cultures 337, 341

mixed function oxidase 224

mixotrophy 354, 362

Mn nodules 368

Mn(II) 368

Mn(II) oxidation 368

Mn(II)-oxidizing bacteria 368

Mn(IV) 299, 307, 309, 310

Mn(IV) reducers 306

Mn²⁺ 464

MnO₂ → Mn²⁺ 299

Mo(VI) 309

mobile carrier model 35, 36

model of dissimilatory nitrate reductase in Escherichia coli 301

model of trp operon attenuation 425

modified ED pathways 65, 66, 72, 73, 330

modified ED pathways in archaea 74, 75

modified EMP pathways 64–66, 73, 288

modified EMP pathways in archaea 65–66

modified glycolytic pathways 60

modified TCA cycle 308, 312, 313, 318, 335

modified TCA cycle in complete oxidizing sulfidogens 315

modulation of gene expression by the FNR protein in Escherichia coli 444

modulation of translation and stability of mRNA by protein 431

modulation of translation and stability of mRNA by small RNA and small RNA–protein complex: riboregulation 433

modulator protein 441

modulon 437, 444

moisture content of the cell 127

molar growth yield 187

molecular chaperones 44, 446

molecular composition of an Escherichia coli cell 127

molecular composition of bacterial cells 126–127

molecular oxygen and anaerobes 253

molecular oxygen and N₂ fixation 132

molecular syringe 47

molybdenum 9, 45, 46, 130, 131, 300, 309, 332, 357, 361

molybdenum-limited conditions 132

molybdoferredoxin 130, 131, 135, 136

molybdopterin 45, 300

monomer biosynthesis 126, 127, 183, 189

monomers 128, 161, 189, 202, 257, 259, 485, 487

monomers of murein 163

monomers of teichoic acid 164

mononucleotides 149

monooxygenase 117, 224, 357

monosaccharide 204, 205

monosodium glutamate 243

monoxygenase 214, 225, 227

Moorella glycerine 331

Moorella thermoacetica 305, 331, 332, 333, 334

Moorella thermoautotrophica 331, 334

Moraxella spp. 486

Mot complex 11

Mothanofollis spp. 321

motility 11, 93, 98, 102, 116, 117, 183, 328, 404, 432, 452, 455

mRNA 145, 164, 174, 175, 176, 177, 178, 420, 421, 426, 429, 430, 433, 434, 446

mRNA complex 178

mRNA editing 174

mRNA structure 431

mRNA turnover 192, 430

mRNAs 431, 432, 448, 451

MS ring 181

Mucor rouxii 205

multicellularity 492

multicopper oxidase 368

multifunctional enzymes 375

multigene system 135, 436

multiple codons 176

multiple enzymes 423

multiple fission 184, 185–187, 186, 187

multiple intracellular offspring 184–185

multiple nucleoids 186

multiple ribosomes 178

multiple spores 186

multivalent attenuation 424

murein 13, 17, 18, 19, 20, 21, 29, 63, 127, 137, 141, 163, 164, 165, 167, 168, 169, 181, 191

murein hydrolase 492, 493

murein in Escherichia coli 18

murein synthesis and cell wall assembly 167

murein synthesis in a Gram-positive bacterium 168

mutation rates 173

mutations 173

Mycobacterium flavium 129

Mycobacterium genitalium 451

Mycobacterium gordonae 365

Mycobacterium smegmatis 72, 224, 226, 323

Mycobacterium spp. 19, 72, 366, 486

Mycobacterium tuberculosis 366, 492

mycolic acid 19

Mycoplasma spp. 286, 417

mycoplasmas 13, 23, 46, 87, 418

Mycoplasmataceae 19

myoglobin 133

myxobacteria 490

N utilization substance protein A 449

N,N′-dicyclohexylcarbodiimide (DCCD) 110, 327

N₂ 128, 130, 132, 137, 300, 302, 304, 387, 388

N₂ fixation 9, 127, 128, 130, 131, 132, 134, 136, 437, 445

N₂ fixation in heterocysts of heterocystous cyanobacteria 134

N₂ fixation in unicellular cyanobacteria 134

N₂-fixing conditions 133, 134, 387

N₂-fixing cyanobacteria 132

N₂O (nitrous oxide) 299, 302, 304

N₂O/N₂ 303

N₂-reduction by the nitrogenase complex 131

Na⁺ 40, 104, 114, 115, 283, 325

Na⁺/H⁺ antiporter 103, 104, 105, 115, 328

Na⁺-ATPase 104, 113, 328, 334

Na⁺-dependent acetogens 334

Na⁺-dependent decarboxylase 105, 115, 116, 252

Na⁺-dependent decarboxylation 298

Na⁺-dependent enzyme 277, 325

Na⁺-dependent ETP 104

Na⁺-dependent methylmalonyl-CoA decarboxylase 118

Na⁺-dependent motility 104

Na⁺-dependent NADH-quinone reductase complex 104

N-acetylglucosamine 17, 21, 137, 205

N-acetylglucosamine (GlcNAc) transferase 167

N-acetylglucosamine-6-phosphate 163

N-acetylglutamate-acetylornithine acetyltransferase 141

N-acetylmuramate 17

N-acetylmuramic acid 137

N-acetylornithine deacetylase 141

N-acetyltalosaminuronate 21

NaCl 403

N-acyl homoserine lactones (AHL) 117, 452

NAD 66, 71, 75, 85, 86, 87, 106, 110, 135, 220, 259, 260, 277, 364, 378, 463, 485

NAD/NADH 242, 264, 333

NADH 60, 63, 69, 71, 75, 76, 85, 87, 88, 91, 105, 106, 110, 111, 117, 137, 233, 257, 259, 260, 264, 277, 279, 330, 371, 375, 378, 463, 485

NADH dehydrogenase 106, 110, 111

NADH oxidase 260

NADH/NAD⁺ 261

NADH:ferredoxin oxidoreductase 264

NADH–ubiquinone reductase 106, 112

NADH–ubiquinone reductase complex 113

NADP 69, 70, 71, 74, 86, 87, 105, 110, 215, 221, 252, 270, 318, 354, 356, 364, 367, 394, 398, 400

NADP reductase 74, 322

NADP/NADPH 97, 354

NADPH 60, 69, 70, 71, 90, 110, 136, 140, 150, 153, 155, 156, 163, 182, 189, 253, 270, 277, 289, 318, 354, 357, 370, 371, 375, 401, 402, 442

nanobacteria 492

naphthalene 227, 231

near-UV irradiation 437

needle 49

neelaredoxin 255

negative control 412, 413

negative regulation 435

negative regulation of translation 429

neopullulanase 203

neptunium(V) 309

neurosporene 390

neutral proteases 206

neutral red 97, 117, 118

neutrophiles 103, 104, 105

neutrophilic sulfur bacteria 360

N-formylmethionine 176

N-formylmethionyl residue 177

N-formylmethionyl-tRNA 177

–NH₂ donor 140, 142–145

–NH₂ group 148, 149, 215

NH₂OH 356

NH₂OH/NH₃ 356

NH₃ 287, 302, 356

NH₄⁺ 137, 302, 304, 305

nickel 9, 46

nicotinamide nucleotide transhydrogenase 110

nicotinate 10

nif regulon 135

nif regulon in Klebsiella pneumoniae 136

Ni–Fe centres 45

nisin 466

nitrate (NO₃^–) 9, 70, 88, 117, 127, 135, 136, 137, 277, 298, 299, 302, 303, 304, 305, 310, 312, 333, 337, 340, 355, 357, 360, 363, 365, 366, 441, 444

nitrate ammonification 305, 333, 341, 360

nitrate assimilation 441

nitrate metabolism 444

nitrate reductase 135, 136, 137, 277, 299, 300, 302, 303, 304, 442

nitrate reduction 135, 304, 305, 309, 368

nitrate-accumulating sulfur bacteria 360

nitric oxide (NO) 299, 302, 445

nitric oxide reductase 299, 300, 302, 304

nitric oxide reductase and nitrous oxide reductase 302

nitrification 355–358

nitrifiers 233, 305, 355, 377

nitrite oxidizers 356, 357, 358

nitrite oxidoreductase (NOR) 357

nitrite reductase (NiR) 135, 136, 137, 299, 300, 302, 304

nitrite(NO₂^–) 137, 299, 302, 304, 355, 356, 357, 358

Nitrobacter hamburgensis 357

Nitrobacter winogradskyi 357, 358

Nitrococcus mobilis 357

nitrogen (N₂) 1, 7, 8, 9, 64, 127, 128, 130, 133, 298, 299, 302, 306, 344, 354, 360, 439, 465, 483, 485, 487

nitrogen and sulfur transformations 182

nitrogen control gene products 136

nitrogen control genes 135

nitrogen cycle 128, 130, 355

nitrogen dioxide (NO₂) 305, 358

nitrogen fertilizer 299

nitrogen reduction 129, 132

nitrogen source 70

nitrogenase 107, 109, 130, 131, 132, 133, 134, 135, 387, 441, 463, 464

nitrogenase activity 134

nitrogenase assay 131

nitrogenase complex 130, 131

nitrogenase complex of Rhizobium 131

nitrogen-fixing bacteria 440, 490

nitrogen-fixing conditions 109, 132, 133

nitrogen-fixing cyanobacterium 129

nitrogen-fixing prokaryotes 129

nitrogen-limited conditions 486, 487

nitrogenous compounds 127

Nitromonas europaea 305, 358

nitropropanol 337

nitropropionate 337

Nitrosococcus nitrosus 357

Nitrosococcus oceanus 357

Nitrosolobus multiformis 357

Nitrosomonas europaea 356, 357, 378

Nitrosospira (Nitrosovibrio) tenuis 357

Nitrosospira briensis 357

Nitrosospira tenuis 355

Nitrospina gracilis 357

Nitrospira marina 357

nitrous oxide (N₂O) 299, 302

nitrous oxide reductase 45, 299, 302, 304

nitroxyl (NOH) 356

NO (nitric oxide) 299, 302

NO/1/2N₂O 303

NO₂⁻/NO 303

NO₃⁻/NO₂⁻ 97, 303, 364

Nocardia autotrophica 364, 365

Nocardia petroleophila 224, 225

Nocardia spp. 323, 486

nodules 132

non-butyrate clostridial fermentation 268

noncoding RNAs (ncRNAs) 433

non-cyclic electron transport 398, 399

non-heme irons 107

nonitol 26

non-ribosomal peptide synthesis process 164

nonsense codons 176, 178

non-sporulating bacteria 431

non-sugar electron donors 418

Nostoc spp. 133

Np(V) 309

nuclear body 28

nuclear power plants 309

nucleases 220

nucleic acid bases 10, 127, 137, 259, 281, 439

nucleic acid biosynthesis 98

nucleic acid turnover 145

nucleic acids 64, 202, 433, 487

nucleoid 28, 181, 182, 186

nucleoid assembly 182

nucleoid occlusion 186

nucleosidase 220

nucleoside triphosphate 489

nucleosides 17

nucleotidase 220

nucleotide biosynthesis 145–150

nucleotide kinases 149

nucleotide sequence 170

nucleotide triphosphate 488

nucleotides 138, 145, 148

nutrient broth 214

nutrient concentration 182

nutrient depletion 186

nutrient import systems 42

nutrient uptake 35, 41

nutrient-limited conditions 437, 439, 492

nutrient-rich conditions 437, 492

nutritional stresses 437

O/R values 272

O₂/H₂O 97, 363, 398

O-acetyl-L-serine sulfhydrylase 140

O-antigen 13, 15, 164, 165, 169, 170

O-antigen ligase 165, 169

obligate aerobes 360

obligate anaerobes 132, 253, 257, 263, 310, 395

obligate chemolithotrophs 29, 284, 357, 358, 362, 363, 366, 373, 377, 378

obligate methylotrophs 230, 232, 233, 235

obligate proton-reducing acetogens 337

obligately chemolithotrophic colourless sulfur bacteria 362

obligately chemolithotrophic hydrogen bacterium 371

obligately photolithotrophic cyanobacteria 403

obligately syntrophic bacteria 338, 339

OH⁻ 105

Okazaki fragment 172, 173

oligomers 202

oligomycin 110, 113

oligomycin-binding site 113

oligopeptide transport 434

oligosaccharides 65, 66, 165, 411

oligotroph 492

oligotrophic 482

one-step reaction 326

organelles 27

organic acid utilization 208–212

organic acids 217, 357

organic acids more oxidized than acetate 210

organic compounds 340

organic electron donors 108

organic nitro compounds 336

organic nitrogen 127, 135, 137, 439, 441

organic sulfonate 336

organic sulfur compounds 139, 455

organotrophs 8

ornithine 41, 141, 286

orotate 149, 287

ortho and meta cleavage 227, 228

ortho cleavage (3-keodipate pathway) of catechol and protocatechuate 230

Oscillatoria group 387

osmoregulatory responses 26

osmotic pressure 17, 29, 97, 434, 454, 485, 490

osmotic shock 22, 26, 38

outer membrane (OM) 12, 13–17, 19, 43, 47, 49, 51, 161, 165, 169, 170, 181, 182, 308

outer membrane (OM) of Gram-negative bacteria 16

outer membrane assembly 169

outer membrane channel 50

outer membrane c-type cytochrome 363

outer membrane L ring 181

outer membrane protein F 434, 454

outer membrane proteins (OMP) 44, 45, 47, 169, 434, 453

oxalate 210, 212, 213, 287

oxalate metabolism in Pseudomonas oxalaticus 213

oxalate/formate antiporter 41

oxaloacetate (OAA) 61, 67, 68, 87, 88, 89, 116, 140, 141, 212, 217, 237, 242, 261, 267, 272, 275, 279, 280, 313, 329, 378, 462

oxaloacetate decarboxylase 275

Oxalobacter formigenes 41, 287

oxalyl-CoA 212

oxidases 105, 108, 216, 221, 227, 362

oxidation 95

oxidation of acetate through the acetyl-CoA pathway in sulfidogens 316

oxidation of acetyl-CoA to glyoxylate in the SIL pathway 239

oxidation of aliphatic hydrocarbons 223–225

oxidation of aliphatic hydrocarbons by Nocardia petroleophila 225

oxidation of aliphatic hydrocarbons by Pseudomonas oleovorans 224

oxidation of aromatic amino acids 225

oxidation of aromatic compounds 225–229

oxidation of aromatic hydrocarbons under anaerobic conditions 341

oxidation of formaldehyde through the ribulose monophosphate cycle in Methylophilus methylotrophus 236

oxidation of propionate, lactate and ethanol to acetate by strains of Desulfobulbus 317

oxidation of propionyl-CoA to pyruvate through the methylcitrate cycle 211

oxidation of sulfur compounds by Thiobacillus ferrooxidans 361

oxidation of xenobiotics under denitrifying conditions 306

oxidation of xenobiotics under sulfidogenic conditions 320

oxidation reduction (redox) potential (E^0′) 95, 96

oxidation/reduction (O/R) balance 272

oxidation/reduction potential of compounds of biological interest 97

oxidation/reduction reactions 95, 96, 102, 105, 107, 115, 340

oxidation–reduction balance in the acetone-butanol-ethanol fermentation 272

oxidative deamination 281

oxidative decarboxylation 87

oxidative decarboxylation of pyruvate 78, 85, 86

oxidative HMP cycle 71, 242, 403, 404

oxidative phosphorylation 27, 85, 86, 91, 102

oxidative stress 434, 437, 445, 445–446

oxidative TCA fork 329

oxygen (O₂) 7, 8, 9, 88, 96, 105, 106, 107, 109, 113, 114, 115, 117, 132, 133, 137, 155, 156, 221, 224, 225, 229, 252, 253, 254, 255, 257, 260, 277, 298, 302, 303, 304, 305, 309, 324, 341, 354, 357, 358, 360, 362, 366, 367, 372, 386, 387, 388, 398, 402, 403, 443, 444, 445, 451, 454

oxygen consumption 110, 114

oxygen metabolism in LAB 260

oxygenase and aromatic compound oxidation 229

oxygenases 229, 341, 372

oxygenic photosynthesis 110, 133, 386, 398

oxygenic photosystem II 133

oxygen-limited conditions 27, 104, 109, 299, 303, 443, 445, 485, 486

P450 356

P-460 heme 356

P680 398

P700 398

paddy fields 309

palladium(II) 309

palmitate degradation to acetyl-CoA through β-oxidation 210

palmitic (hexadecanoic) acid 451

palmitoleic (cis-9-hexadecenoic) acid 451

pamamycin 466

p-aminobenzoate 10, 159

Pantoea agglomerans 307

pantothenate 10

PAPS 139

PAPS reductase 139

Paracoccus (Thiobacillus) pantotrophicus 361

Paracoccus carboxydivorans 232

Paracoccus denitrificans 109, 212, 213, 232, 234, 300, 301, 362, 365

Paracoccus spp. 299, 359

Paracoccus tentotrophus 360

particulate hydrogenase 364, 365

paryphoplasm 28

passenger domain 52

pathogens 453

pectin 204, 205

pectin esterase 205

pectin methylesterase 17

pectinase 205, 432

Pediococcus damnosus 258

Pediococcus halophilus 116, 260, 261, 275, 276

Pediococcus spp. 40, 257, 258

Pedomicrobium manganicum 368

Pedomicrobium spp. 187

Pelobacter carbinolicus 214, 307

Pelobacter ventianus 290

penicillin 467

Penicillium notatum 467

penta-glycine crossbridge 169

pentasulfide 313

pentose 259

pentose fermentation 76

pentose phosphate pathway 69

pentose utilization 207

pentose-5-phosphate 60, 69, 70, 75

pentoses 70, 71, 75, 204, 206, 207, 257, 259, 272

PEP 40, 61, 63, 66, 67, 68, 69, 71, 87, 88, 89, 90, 99, 102, 140, 141, 163, 210, 237, 242, 272, 280, 329, 371, 374, 417, 419, 464, 483

PEP carboxykinase 68, 280, 416

PEP carboxylase 89, 237, 272, 273

PEP carboxytransphosphorylase 280

PEP synthesis 67

PEP synthetase 67, 374

peptidase 26, 44

peptide bonds 177, 206

peptide synthesis 176, 177, 437

peptide synthesis – translation 179

peptides 16, 175, 178, 214, 452, 453, 487

peptidoglycan 17

peptidyl site (P) 177, 178

Peptostreptococcus asaccharolyticus 283

Peptostreptococcus prevotii 282

Peptostreptococcus productus 331

Peptostretococcus micros 282

Peptostreptococcus spp. 24

perchlorate 298, 336, 366

perchlorate-reducing bacteria 364

peripheral proteins 23, 26

periplasm 17, 19, 38, 43, 45, 49, 51, 73, 102, 165, 167, 169, 170, 181, 186, 300, 302, 317, 336, 363, 454

periplasmic binding protein 434

periplasmic chaperone 47

periplasmic enzymes 181, 361

periplasmic glucan 19

periplasmic ligand interaction domain 456

periplasmic p ring 181

periplasmic proteins 45, 448, 449

permeases 35, 412

peroxidase 254, 255, 260

peroxidase-negative aerobic organisms 260

peroxisome 241

pertechnetate [Tc(VII)] 308

petrochemical intermediates 275

petroleum 140, 225, 320

petroleum refineries 310

pH 182, 461

pH 6.0 enzyme 274

pH 8.0 enzyme 274

pH and osmotic homeostasis 183

phage receptor 13

phage recognition 15

phagocytosis 12

PHB degradation 487

PHB degradation and its regulation in Azotobacter beijerinckii 487

PHB depolymerase 485

PHB synthesis 485

phenazine methosulfate 97

phenol 227, 306, 308, 335, 343

phenylalanine 141, 142, 220, 225, 286, 287

phenylalanine monooxygenase 225

phenylpyruvate 141

pheophytin 389, 392, 393, 394, 398

pheophytin-quinone type reaction centres 387, 389, 392, 400, 401

pheromones 452

phloroglucinol 343

pho system 441, 454, 455, 488

phosphatase 139, 167, 313, 489

phosphatase activity 440

phosphate (P_i) 16, 64, 90, 98, 102, 128, 157, 206, 298, 303, 310, 337, 394, 428, 441, 442, 443, 444, 445, 453, 454, 455, 486, 487, 488

phosphate compounds 26

phosphate donor 488

phosphate excess conditions 457

phosphate linkages in ATP 99

phosphate receptor 455

phosphate transfers 490

phosphate-limited conditions 64, 441, 454, 457, 458

phosphatidate cytidyltransferase 157

phosphatidate phosphatase 486

phosphatidic acid 154, 157, 486

phosphatidic acid derivatives 157

phosphatidyl choline 157

phosphatidyl ethanolamine 157

phosphatidyl glycerol 157

phosphatidyl inositol 157

phosphatidyl serine 154, 157

phosphatidylethanolamine 157

phosphine 337

phosphodiester bonds 174

phosphodiesterase 415

phosphofructokinase (PFK) 61, 62, 66, 67, 68, 78, 416

phosphoglucomutase 206

phosphogluconolactone 72

phosphoglycerate 141

phosphoglycerate mutase 63

phosphoglycolate 210, 372

phosphoketolase 75, 76, 259

phosphoketolase (PK) pathways 60, 74–77, 257, 259

phosphoketolases 77, 259

phospholipase 26

phospholipid biosynthesis 156, 158, 486

phospholipid membrane 105

phospholipid translocation 170

phospholipids 13, 15, 16, 21, 22, 23–26, 35, 63, 127, 152, 156, 157, 169, 170, 394, 451

phospholipids in archaea 25

phospholipids in bacteria 24

phospholipids in halophilic archaea 25

phospholipids in methanogenic archaea 25

phosphomannoisomerase 206

phospho-N-acetylmuramylpentapeptide (phosphor-MurNAc- pentapeptide) 167

phosphorelay 434, 455, 490

phosphoribosyltransferase 147, 149

phosphoribulokinase 370, 371, 401

phosphoroclastic reaction 263, 264, 267, 313, 330

phosphorus 1, 7, 8, 127, 306

phosphoryl donor 39, 40

phosphorylases 205, 207, 318

phosphorylation 461

phosphorylation potential (ΔGp) 95, 101, 114, 327

phosphorylation site 417

phosphotransacetylase 259, 260, 269, 313, 326, 327, 330

phosphotransacylase and kinase 282

phosphotransfer 457

phosphotransferase (PT) system 40, 61, 414, 416, 417, 418

Photobacterium fischerii 116, 117, 118

photoinduced charge separation 397

photolithotrophic sulfur bacteria 358

photolithotrophs 9, 368, 371, 401, 403

photon exciting an electron of a light-absorbing pigment molecule 397

photons 397, 398, 399, 400

photoorganotrophic cyanobacteria 403, 404

photoorganotrophic growth 402

photoorganotrophic metabolism 402

photoorganotrophs 9, 401, 402

photooxidation 390

photophosphorylation 386, 388, 404

photophosphorylation in halophilic archaea 403

photorespiration 210, 372

photosynthesis 93, 102, 103, 114, 115, 366, 386–405, 445

photosynthetic apparatus 386, 390, 394, 394–395, 430, 445

photosynthetic apparatus in purple bacteria 396

photosynthetic bacteria 27, 129, 373, 386, 387, 388, 389, 392, 393, 402, 430

photosynthetic electron transport 91

photosynthetic electron transport chains of cyanobacteria 399

photosynthetic electron transport in green bacteria 400

photosynthetic flexibacteria 388

photosynthetic green bacteria 387

photosynthetic green sulfur bacteria 92, 373

photosynthetic microorganisms 128, 132, 386–389

photosynthetic organelle 395

photosynthetic pigments 27, 387, 389, 389–394, 397, 398

photosynthetic proteins 27

photosynthetic structure 431

photosystem I 133, 394, 398

photosystem I and II in cyanobacteria 398

photosystem II 132, 133, 387, 394, 398

phototaxis 27, 405

phototrophs 9, 116, 117, 386, 401

phycobilins 161

phycobiliproteins 389, 392, 393, 394

phycobilisomes 394, 395, 398

phycocyanin 392, 487, 488

phycoerythrin 392

p-hydroxyphenylpyruvate 142, 225

phylloquinone 398

physical modification 461, 463

physical stresses 104

physiological pH 96

physiological temperature 446, 447

P_i 64, 66, 68, 95, 101, 105, 139, 313, 377

piericidin A 110

PII (regulatory protein in nitrogen metabolism) 464

pili 12, 47, 48

Pirellula marina 28

PK 76, 78

PK pathways 75, 78

Planctomyces maris 28

Planctomycetaceae 27

Planctomycetes 20, 28, 187, 358

plant pathogenic fungi 205

plants 371, 386, 389, 432

plasmalogens 24

plasmids 28, 29, 228, 271, 277, 364, 428

plastocyanin 398

pleiotropic control 436

Pleurocapsa group 387

Pleurocapsa spp. 186

poly(propylene adipate) 278

poly-3-phosphoglycerate 69

polyalcohol 152

polyamine 191

polyaromatic hydrocarbons (PAH) 342, 343

polyaspartate 487

polychlorinated biphenyls (PCBs) 335

polyethyleneglycol 290

polyglucose 377, 378

polyhydroxyalkanoate 189

polyhydroxybutyrate 233

polyisoprenoid alcohols 152

polymannuronic acid 29

polymer synthesis 243

polymerization monomers 126, 183, 189

polymers 17, 202, 206, 259, 483, 485

polynucleotide phosphorylase 449

polypeptides 483

polypeptides as reserve materials 487

polyphosphatase 489

polyphosphate 29, 318, 483, 487, 488–489

polyphosphate glucokinase 489

polyphosphate hydrolysis 488

polyphosphate kinase 488

polyphosphate synthesis 488

polyphosphate: AMP phosphotransferase 488

polysaccharide biosynthesis and the assembly of cell surface structures 165–170

polysaccharide hydrolases 204

polysaccharide hydrolysis 206

polysaccharide synthesis 67

polysaccharides 12, 161, 165, 191, 192, 202, 205, 411, 432, 483

polysome 29, 178

polysulfides 313, 361

polythionate 358, 359

poly-β-1,4-N-acetylglucosamine 205

poly-β-hydroxyalkanoate (PHA) 29, 484, 485, 486, 487

poly-β-hydroxybutyrate (PHB) 126, 483, 485, 486

pore model 35

pore-forming carrier protein 36

porin 15, 434, 453, 454

porin-like structure 51

porins 17, 39

porphobilinogen 161

porphyrin synthesis 87

Porphyrobacter neustonensis 389

Porphyrobacter spp. 389

Porphyromonas gingivalis 23

positive and negative control 413

positive control 413

positive regulation 429

post-replicational modification 173

post-transcriptional control 430, 456

post-transcriptional processing 174

post-transcriptional processing of RNA 175

post-transcriptional processor 208

post-transcriptional regulation 430, 435

post-transcriptional regulation of gene expression 430–435

post-translational modification and protein folding 178

potassium 7, 8

potential energy 117

ppGpp 432

PP_i 98, 99, 139, 313, 318, 377, 489

PP_i-dependent phosphofructokinase 66

PQQ 74, 105, 234, 242

precursor activation 67, 460

precursor of lipopolysaccharide 164

precursor/product antiport 40–41

precursor/product antiport systems of lactic acid bacteria 41

Prevotella melaninogenicus 23

Prevotella ruminicola 23, 64

primary alcohol 213, 214, 224, 225

primary binding proteins 182

primary H⁺ (Na⁺) pumps in fermentative metabolism 115

primary H⁺(Na⁺) active transport 115

primary production 93

primary sodium pump 104

primary transport 37

primase 171

primer RNA 173

probiotic 268

producing hydrogenase 270

product/proton symport 298

programmed cell death (PCD) in bacteria 439, 482, 492, 493

prokaryotic DNA 170

prokaryotic electron transport 108, 109

proline 135, 141, 220, 286, 287, 429, 430

proline degradation 220

proline dehydrogenase 220, 428, 429, 430

proline oxidase 220

proline permease 220, 430

promoter 174, 409, 410

promoter activity 411

promoter region 174, 416

propagation 183

propanediol 214

properties of light 397

propionate 115, 208, 278, 279, 280, 281, 282, 305, 315, 337, 339, 441, 489

propionate fermentation 278–280

propionate oxidation pathway 339

propionate oxidizing syntrophic bacterium 339

propionate producers 278, 284

propionate-producing anaerobes 305

Propionibacterium freudenreichii 118

Propionibacterium pentosaceum 300

Propionibacterium shermanii 68, 279, 489

Propionibacterium spp. 24, 115, 116, 278, 280, 315, 489

Propionispora vibrioides 278

propionyl-CoA 208, 214, 217, 279, 280, 282, 375, 377

propionyl-CoA synthase 375, 377

proposed metabolic routes of the benzoyl-CoA pathway 344

propylbenzene 343

propylene 72, 225, 323

propylene oxidation by Rhodococcus rhodochrous 226

prosthecate Alphaproteobacteria 187

prosthetic group 74, 76, 87, 106, 107, 256, 263, 325, 356

proteases 26, 47, 51, 178, 206

protein 127, 191, 192

protein A 15

protein conduction channel 44

protein folding 178, 180, 446

protein injection into a host cell 50

protein secretion 35, 43, 51

protein secretion in Gram-negative bacteria 48

protein synthesis 29, 409, 437, 448

protein translocation 44, 169

protein translocation across the outer membrane in Gram-negative bacteria 46–47

protein transport 43–52

protein Z 183

protein-aided termination/antitermination process 426

proteins 12, 21, 22, 27, 28, 103, 169, 170, 175, 178, 181, 202, 205, 482, 483, 485, 487, 490, 491

proteobacteria 185, 187, 368, 386

proteolysis 51, 492

proteolytic clostridia 263, 281, 286

Proteus mirabilis 189

Proteus vulgaris 216

protocatechuate 227, 228

protoheme 161

proton (acid internal pH) gradient 37

proton (sodium) motive force generation 261

proton consumption 363

proton export 27, 37, 104, 110

proton gradient (ΔpH) 38, 102, 103, 105, 363

proton motive force (Δp) 11, 26, 37, 38, 40, 86, 88, 98, 101, 102–105, 110, 111, 112, 113, 114, 137, 252, 260, 261, 262, 268, 277, 279, 284, 298, 299, 302, 305, 306, 310, 317, 318, 319, 324, 325, 326, 327, 328, 334, 354, 355, 356, 360, 363, 366, 378, 394, 395, 398, 399, 400, 401, 403, 404, 405, 482, 485, 489, 492, 493

proton motive force generation by heterodisulfide reductase during methanogenesis 326

proton motive force generation during methanol reduction to methane by Methanosarcina barkeri 328

proton motive force in acidophiles and alkalophiles 104

proton pumps 111, 112

proton translocation 113

protonophores 104, 114

protoplasts 22

protoporphyrin IX 161

Providencia rettgeri 276, 277

PRPP 145, 149

PRPP amidotransferase 149

PRPP synthetase 143, 145

pseudoazurin 302

Pseudomonas (Oligotropha) carboxidovorans 367

Pseudomonas acidovorans 225

Pseudomonas aeruginosa 19, 49, 89, 141, 205, 206, 211, 224, 453

Pseudomonas arsenitoxidans 367

Pseudomonas aureofaciens 302

Pseudomonas azotogensis 129

Pseudomonas carboxidoflava (Hydrogenovibrio pseudoflava) 367

Pseudomonas carboxidohydrogena 367

Pseudomonas carboxydoflava 304, 366

Pseudomonas chitinovorans 205

Pseudomonas facilis 365

Pseudomonas fluorescens 209, 224, 300

Pseudomonas gazotropha 367

Pseudomonas hydrogenovara 365

Pseudomonas MA 232

Pseudomonas nautical 305

Pseudomonas oxalaticus 212, 232

Pseudomonas putida 219, 225, 234, 368, 455

Pseudomonas saccharophila 64, 72, 73, 206

Pseudomonas stutzeri 46

Pseudomonas spp. 72, 73, 74, 137, 202, 203, 210, 212, 225, 254, 299, 359

pseudomurein 20, 21

pseudopetidoglycan 20

psychrophiles 23

pteridine 159

pullulan 203

pullulanase 47, 203

pure culture 2, 320, 339, 340, 342

purine bases 223, 287

purine degradation 210

purine fermenters 287

purine nucleotides 149

purple bacteria 386, 387, 388, 389, 390, 392, 394, 395, 400, 401, 402

purple bacteria, heliobacteria and aerobic anoxygenic photosynthetic bacteria 402

purple non-sulfur bacteria 387, 400, 402, 403, 445, 462, 489

purple proteins 404

purple sulfur and non-sulfur bacteria 484

purple sulfur bacteria 387, 400

pyridine nucleotide biosynthesis 149

pyridine nucleotides 132, 149, 378, 422, 464

pyridozine 10

pyrimidine bases 223, 287

pyrimidine nucleotide biosynthesis through a de novo pathway 148

pyrimidine nucleotide synthesis 148

pyrimidine nucleotides 149

pyrite (FeS₂) 358, 363

Pyrobaculum aerophilum 300, 307

Pyrobaculum arsenaticum 308

Pyrobaculum islandicum 307

Pyrobaculum spp. 312

Pyrococcus furiosus 29, 65, 66, 203, 255, 288

Pyrococcus woesei 29, 288

pyrophosphatase 98, 280, 318

pyrophosphate (PP_i) 98, 143, 280, 313, 489

pyrophosphate (PP_i)-dependent phosphofructokinase 66, 68

pyrophosphate fructokinase 489

pyrophosphate fructokinase (diphosphate-fructose-6-phosphate 1-phosphotransferase) 489

pyrophosphate phosphohydrolase 489

pyrrole rings 390

pyrroles 220, 390, 392

pyrroloquinoline quinone (PQQ) 74, 234, 242

pyruvate 60, 61, 64, 66, 67, 68, 69, 71, 72, 74, 75, 78, 85, 88, 89, 90, 98, 140, 141, 187, 188, 189, 208, 215, 216, 217, 228, 236, 241, 255, 256, 257, 259, 260, 261, 262, 263, 264, 265, 267, 271, 272, 273, 274, 275, 277, 278, 279, 280, 282, 283, 289, 305, 306, 313, 315, 319, 329, 330, 357, 374, 375, 377, 402, 416, 417, 424, 442, 463, 483, 489

pyruvate carboxylase 88, 89, 267

pyruvate decarboxylase 256, 257

pyruvate dehydrogenase 256, 263, 264, 442

pyruvate dehydrogenase activity 85

pyruvate dehydrogenase complex 85, 86, 214, 259, 277

pyruvate kinase 7, 66, 67, 460

pyruvate orthophosphate dikinase 280

pyruvate oxidase 259

pyruvate oxidation 267

pyruvate synthase 322, 329

pyruvate/lactate half reaction 97, 267

pyruvate:ferredoxin 282

pyruvate:ferredoxin oxidoreductase 107, 132, 256, 263, 267, 289, 305, 313, 319, 374, 402

pyruvate:formate lyase 259, 261, 273, 277, 442

pyruvate phosphate dikinase 68, 489

Q/QH₂ 333

Q-cycle 111, 112

QH 112

QH₂ 112

Q-loop 111, 112

quasi-photosynthetic bacteria 368, 389

quinol 299, 300, 400

quinones 105, 107, 108, 110, 159, 301, 309, 336, 378, 394

quinoproteins 74, 242

quorum sensing 117, 432, 452–453, 454, 466

quorum sensing in Gram-positive bacteria 453

radiation-resistant bacterium 309

radiorespirometry 78–80

raffinose 411

Ralstonia eutropha (Alcaligenes eutrophus) 73, 208, 214, 300, 364, 365, 370, 378, 460, 485

Ralstonia spp. 299

rare codons 178

RCI 398

RCII 398

reaction centre pigment 389

reaction centre proteins 430

reaction centres 386, 387, 394, 395, 396, 397, 398, 399, 400, 401, 430, 431

reactive oxygen species (ROS) 255, 390, 445

receptor methylation 457

receptor molecules 12

receptor proteins 15, 17, 457

receptor-coupling factor 457

receptors 16, 17

recognition site 44

recombinase A 449

redox potential 96, 105, 107, 139, 234, 242, 253, 255, 264, 267, 302, 303, 310, 318, 333, 334, 335, 337, 354, 355, 356, 358, 362, 363, 367, 398, 399, 400, 444, 446

redox potential of inorganic electron donors used by chemolithotrophs 355

redox potentials and ATP yield of denitrification reactions 303

redox-regulated genes 445

reduced electron carriers 241

reduction 95

reduction half-reaction 299

reduction of methanol and carbon dioxide to methane 324

reduction of sulfate and sulfur 312

reductive deamination 281

reductive TCA cycle 91, 92, 319, 329, 354, 362, 363, 366, 368, 372, 373, 375, 377, 402

RegB/RegA operons 445

RegB/RegA system in purple non-sulfur photosynthetic bacteria 445

regulation by molecular oxygen in facultative anaerobes 442–445

regulation by the arc system 443

regulation in central metabolism 464

regulation of amino acid biosynthesis 145

regulation of catabolism and anabolism 101

regulation of denitrification 303

regulation of extracytoplasmic function sigma factor σ^E activity by anti-σ factor and anti-anti-σ factor 449

regulation of fatty acid biosynthesis 156

regulation of gene expression 173, 488

regulation of genes by multiple end products 423–424

regulation of gluconeogenesis 69

regulation of glutamine synthetase activity 138

regulation of glutamine synthetase activity in Escherichia coli 460, 462

regulation of glycogen synthesis and hydrolysis 484

regulation of N₂ fixation 134

regulation of phosphofructokinase 66

regulation of pyruvate kinase 67

regulation of the EMP pathway 66

regulation of the glyoxylate cycle 90

regulation of the HMP pathway 71

regulation of the pho system under phosphate-limited conditions 442

regulation of the TCA cycle 88

regulation of transcription by promoter structure and sigma (σ) factor activity 409–411

regulation through modulation of enzyme activity: fine regulation 459–464

regulation through physical modification and dissociation/association 463

regulator 420

regulator gene 413

regulator protein 455

regulatory mechanisms that control the synthesis and activity of enzymes 409

regulatory network 464

regulatory proteins 19, 423, 428, 446

regulons 413, 436, 437, 440, 441, 444

releasing factors 178

Renobacter vacuolatum 365

replicase 435

replication 171, 175

replication origin (oriC) 171, 173

replisome 170, 171

representative nitrifying bacteria 357

repression 419, 420, 422

repression and attenuation by final metabolic products 419–423

repressor protein 412, 413, 415, 419, 420

repressors 174, 409, 420, 437

reserve materials 482, 483, 484, 485, 486, 487, 488

reserve materials in bacteria 483–489

resonance energy 397, 398

resonance transfer 397, 398

resorcinol 306, 343

respiration 93, 95, 102, 103, 114, 115, 252, 298, 443

respiratory inhibitors 309

respiratory metabolism 189

response regulator 457

response to ammonia limitation 439–441

response to changes in osmotic pressure 453

response to phosphate limitation: the pho system 441–442

resting cells 29–30, 233, 482, 489, 489–493

restriction enzymes 173

restriction-modification enzymes 173

resuscitation-promoting factor (RPF) 492

retinal 404, 405

reverse electron transport 98, 102, 110, 132, 313, 318, 319, 354, 355, 356, 357, 364, 367, 378, 400, 401

reverse electron transport to reduce NAD(P)⁺ in a nitrite oxidizer Nitrosococcus mobilis 355

reverse TCA cycle 91

reversibacteria 333, 338, 340

RFN element 428

rhamnose 411, 413

Rhizobium etli 428

Rhizobium japonicum 73, 129, 254, 365

Rhizobium spp. 129, 132, 133

rhodanese 361

Rhodobacter capsulatus 214, 371, 430, 445

Rhodobacter sphaeroides 39, 371, 373, 445

Rhodococcus opacus 364, 365, 486

Rhodococcus rhodochrous 225, 323

Rhodococcus spp. 486

Rhodomicrobium vannielii 214

Rhodopseudomonas gelatinosa 462, 463

Rhodopseudomonas palustris 343

Rhodopseudomonas sphaeroides 74

Rhodopseudomonas viridis 129

Rhodopseudomonas spp. 232

rhodopsin I 404

rhodopsin II 404

rhodopsins 27, 404, 405

rhodopsins and their functions in halophilic archaea 405

Rhodospirillum rubrum 129, 489

ribitol dehydrogenase 459

ribitol phosphate 18

ribitol teichoic acid 164

riboflavin 10, 107, 428

riboflavin synthesis 428

ribonuclease 429

ribonucleic anti-terminator (RAT) 426

ribonucleoside diphosphates 149

ribonucleoside monophosphate 220

ribonucleotide reductase 149

ribonucleotide reductases and their characteristics 152

ribonucleotides 149, 174, 190

riboplasm 28

ribose 98, 150, 188, 207, 220

ribose-5-phosphate 61, 70, 140, 141, 143, 164, 207

ribosomal pathway 437

ribosomal proteins (r-proteins) synthesis 177, 182, 429, 466

ribosomal RNA sequences 359, 386

ribosomal RNAs (rRNA) 429

ribosome assembly 182

ribosome-binding factor A 449

ribosome-binding site 177, 434

ribosomes 27, 28, 29, 164, 177, 178, 181, 182, 420, 421, 423, 429, 431, 432, 437, 446, 451, 466

riboswitch 423, 424

ribulose 207

ribulose monophosphate (RMP) pathway 230, 232, 233, 235–236, 237, 240, 241

ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) 29, 368, 370, 371, 372, 402

ribulose-1,5-bisphosphate 368, 370, 372

ribulose-5-phosphate 70, 75, 236, 259, 370

ring cleavage pathway 228

ring fission 228

ring structures 181

ristocetin 167

RNA 27, 28, 103, 126, 127, 174, 175, 191, 192, 206, 220, 408, 429, 430, 433, 466, 482, 483

RNA chaperones 435, 451

RNA gene sequences 305, 426

RNA polymerase 156, 171, 174, 175, 303, 409, 412, 420, 421, 425, 426, 435, 446, 490

RNA polymerase σ factors in Escherichia coli 410

RNA primer 171, 173

RNA stability 430

RNA synthesis 149, 174, 175, 409

RNA turnover 191

RNA-binding proteins 430

RNA-protein complexes 433

RNase 206, 430

RNase E 435

RNase II 432

rod structure 181

rod-shape determining protein 183

rod-shaped bacteria 183

ROS 445

Roseibium spp. 389

Roseivivax spp. 389

Roseobacter spp. 389

Roseococcus spp. 389

Roseovarious spp. 389

rotenone 110

rotor 181

r-proteins 429

rRNA 174, 182, 429, 430

RsmA (repressor of stationary phase metabolites) protein 431

RuBisCO 372, 373

rubredoxin 97, 255

rubrerythrin 255

Rubrimonas spp. 389

rumen 337

rumen bacterium 64, 340

Ruminococcus albus 340

Ruminococcus flavefaciens 188

Ruminococcus hydrogenotrophicus 331

Ruminococcus productus 331, 334

Ruminococcus spp. 24

run-tumble behaviour 457

rusticyanin 363

S⁰ 289, 318, 360, 362, 365

S⁰/H₂S 318

saccharides 161

saccharolytic clostridia 104, 214, 256, 263, 268, 271, 281, 330

Saccharomyces cerevisiae 141, 156, 188, 208, 255

Saccharomyces rosea 188

S-adenosylmethionine (SAM) 156, 157, 159, 173, 322, 457

salicin 426

Salmonella spp. 272, 273

Salmonella typhimurium 15, 16, 103, 208, 214, 254, 261, 275, 276, 424, 455

salvage pathway 145, 149

Sandaracinobacter spp. 389

Sanguibacter inulinus 258

Sarcina ventriculi spp. 23, 188, 256

sarcosine 286

saturate acyl-ACP 153

saturated aliphatic hydrocarbons 342

saturated fatty acid synthesis 154

saturated fatty acids 153, 155, 451

S-box system 428

Scalindua brodae 305

Scalindua wagneri 305

Schiff’s base 404, 405

Se(VI) 309

Se(VI) → Se(IV) 299

seawater 336, 360

Sec system 43

SecB pathway 44, 45

second chromosomes 29

second codon 177

secondary alcohol 214, 225, 322

secondary alcohol dehydrogenase 214, 225

secondary binding proteins 182

secondary metabolism 271

secondary metabolites produced during cell differentiation 466

secondary metabolite production 452, 453, 466

secondary structure 178

secondary transport 37, 38

secretin 49

secretin complex 49

secretion pathways 43, 170

secreton 47, 49

sediments 368

segmented filamentous bacteria (SFB) 185

segregation process 173

selenate [Se(VI)] 307, 309, 335

Selenihalanaerobacter shriftii 307

selenium 1, 9, 306, 309

selenium-containing protein 282

selenocysteine 309

Selenomonas spp. 24

semiquinol (QH) 112

sensor protein 19, 428, 441, 453, 455

sensory transduction protein (LytR) 493

septum site-determining protein C 183

septum site-determining protein D 183

sequential induction 411

serine 63, 141, 142, 157, 215, 217, 236

serine dehydratase 215

serine residue 417

serine, glycine and cysteine biosynthesis 145

serine-isocitrate lyase (SIL) pathway 230, 232, 233, 234, 235, 236, 238, 239, 241

Serratia liquefaciens 205

Serratia marcescens 205

Serratia plymuthica 205

Serratia spp. 273, 274

sewage works 310

sex pilus 12

-SH donor 140

Shewanella alga 306, 307

Shewanella frigidimarina 307

Shewanella oneidensis 306, 307, 308, 309

Shewanella putrefaciens 17, 336

Shewanella saccharophilia 307

Shewanella spp. 310, 311

Shigella spp. 272, 273, 277

shikimate 141

Shine–Dalgarno (SD) sequence 177, 426, 427, 431, 432, 433, 435

shock-sensitive transport 39

siderophores 43

sigma factor (see also σ factors) 156, 433

signal molecules 452

signal peptidase 44, 45

signal peptide 43, 45, 47, 52, 178

signal recognition particle 433

signal recognition particle (SRP) pathway 44, 45, 170, 181

signal sequence 43, 45, 51

signal transducing pathway of chemotaxis 458

signal transduction 490

signal transduction cascade of ammonia availability regulating the transcription of glnA (glutamine synthetase gene) 440

signal-transducing system 441

silage 265

simple diffusion 37

simple media 10, 60

single accessory factor 51

single accessory pathways 52

single strand DNA 171

site 0 110

site 2 111

S-layer 12, 13, 20, 21, 429

S-layer protein 429

slime layer 12

small noncoding RNAs (sRNAs) 430, 433

small proteins 178

small RNAs (sRNAs) 178, 433

small stable RNA A 178

Smithella propionica 338, 339

SO₄²⁻→ HS⁻ 299

sodium 7, 8, 37, 38, 106

sodium gradient 38, 277

sodium motive force 11, 37, 38, 103, 104, 105, 113, 115, 284, 287, 324, 325, 328, 334, 375

sodium motive force generation by the methyl-H₄MPT:CoM- methyltransferase complex 325

soil 320, 360, 368

solubilization-immobilization cycles 310

soluble enzymes 367

soluble hydrogenase 364

solute transport 35, 37, 170

solute-binding protein-dependent transport 38

solute-binding proteins 19, 38

solventogenesis 269, 270, 271

solventogenic clostridia 270

solventogenic enzymes 271

solventogenic phase 269, 270

sorbitol 278

sortase 18, 169

sox gene cluster 361

SoxRS system 446

soybean sauce fermentation 260, 261

Sphingobacterium spiritivorum 23

sphingolipids 23, 24

Sphingomonas alaskensis 492

spirilloxanthin 390

spontaneous mutation 173

spore formation 409

spore-forming anaerobic Gram-positive bacteria 263

spore-forming bacteria 439

spore-forming Gram-positive bacteria 310

spores 29, 184, 233, 268, 439, 453, 489, 490

spore-specific structures 29

Sporolactobacillus spp. 257, 258

Sporomusa malonica 331

Sporomusa silvacetica 331

Sporomusa sphaeroides 331

Sporomusa spp. 330, 331

Sporomusa termitida 331

sporulation in Bacillus subtilis 490, 491

sporulation initiation phosphotransferase 490

sporulation kinase 490

sporulation process 184, 271, 466, 490

sRNA base-pairing with mRNAs 433

sRNA synthesis 435

sRNAs 432, 434, 435

SRP (signal recognition particle) pathway 44, 45, 170, 181

stability of mRNA of puf genes in photosynthetic Rhodobacter capsulatus 431

stable RNAs 430

stalled polypeptide chain 178

Stanieria spp. 186

Staphylococcus aureus 19, 167, 168, 206, 455, 492

Staphylococcus spp. 417

starch 65, 66, 202, 203, 411

Starkeya spp. 359

starvation conditions 482, 483, 484

stationary phase 182, 431, 432, 435, 437, 439, 491

stationary phase proteins 409, 439, 466

stationary phase σ-factor 411

stator 181

steroids 23

Stickland reaction 281, 286, 287

stimulon 437

storage materials 403

straight-chain fatty acid 154

Streptococcus agalactiae 188

Streptococcus faecalis 188

Streptococcus lactis 188, 337

Streptococcus pyogenes 188

Streptococcus thermophilus 41

Streptococcus spp. 40, 41, 417

Streptomyces alboniger 466

Streptomyces antibioticus 466

Streptomyces bikiniensis 466

Streptomyces griseus 205, 453, 466

Streptomyces lividans 28, 205

Streptomyces spp. 71, 171, 206, 226, 323, 410, 486, 492

streptomycetes 186

streptomycin 453, 466

stress conditions 434, 459

stress resistance 431

stress response 439

strict anaerobes 129, 253, 254, 255, 273, 305, 312, 365, 366

strictly anaerobic archaea 320, 366

stringent control 271

stringent response 432, 437, 437–439, 466, 488

structural genes 412, 413, 415

structural modification 460

structure and maximum absorbance of chlorophylls 391

structure of a [4Fe-4S] cluster 107

structure of a tRNA 177

structure of adenosine triphosphate (ATP) 99

structure of bilins in phycobiliproteins 392

structure of chlorophyll 390

structure of cyanophycin 487

structure of hemes of cytochromes 108

structure of microbial cells 10–30

structure of murein 19

structure of polyphosphate 488

structure of retinal bound to rhodopsins in species of Halobacterium 404

structure of the trp operon with the leader sequence for transcriptional control through attenuation 421

structure of the β-glucanase (lic) operon, and its control by a terminator/antiterminator mechanism in Bacillus subtilis 426

structure of ubiquinone and menaquinone 107

structure of undecaprenyl (bactoprenyl) phosphate 167

structure of valinomycin 36

structures of cobalamin and coenzyme B₁₂ 280

structures of some uncouplers 115

substrate receptor protein in chemotaxis 464

substrate-level phosphorylation (SLP) 38, 63, 87, 99, 101, 102, 103, 105, 114, 149, 252, 255, 260, 282, 287, 313, 314, 317, 318, 327, 334, 467

substrate–receptor protein 463

subtilisin 206

succinate 87, 89, 90, 91, 102, 106, 115, 220, 228, 272, 273, 277, 278, 280, 284, 287, 313, 318, 330, 339, 375, 378, 455

succinate decarboxylase 115

succinate dehydrogenase 87, 91, 92, 106, 242, 373, 377, 434

succinate dehydrogenase inhibitor 209

succinate oxidation 96

succinate thiokinase 87

succinate–propionate pathway 115, 278, 279, 280, 315

succinate–propionate pathway in the genus Propionibacterium 279

succinate–ubiquinone reductase complex 106

Succinispira mobilis 287

succinyl-CoA 61, 87, 91, 102, 159, 279, 375, 485, 486

succinyl-CoA synthetase 87, 102

succinyl-CoA:acetate CoA-SH transferase 313

sucrose 188, 205, 207, 419, 426

sucrose phosphorylase 205, 206

sugar 242

sugar alcohols 278

sugar fermentation by Pyrococcus furiosus 290

sugar fermentation by selected Clostridium species 271

sugar metabolism 330

sugar transport 37

sugars 39, 72, 161, 411

sulfate (SO₄²⁻) 9, 128, 139, 140, 288, 298, 304, 310, 312, 313, 317, 318, 320, 337, 340, 361

sulfate adenyltransferase 139

sulfate assimilation 139

sulfate reduction 309, 314, 318, 341

sulfate starvation induced (SSI) stimulon 140

sulfate-limited conditions 140, 455, 487

sulfate-reducing bacteria 139, 255, 310, 311, 315, 318, 320, 358

sulfhydrogenase 289

sulfide (HS^–) 9, 107, 139, 140, 216, 255, 305, 306, 313, 337, 358, 359, 360, 361, 362, 363, 395, 400

sulfidogenesis 298, 306, 310–320, 333, 341, 342

sulfidogenic conditions 320

sulfidogens 9, 310, 311, 320, 329, 331, 333, 337, 365, 368, 374

sulfite (HSO₃^–) 139, 140, 260, 313, 335, 358, 361

sulfite cytochrome reductase (SCR) 361

sulfite radicals 260

sulfite reductase 140, 313

Sulfolobus acidocaldarius 73, 75, 92, 103, 323, 333, 360, 362, 363

Sulfolobus metallicus 375, 376

Sulfolobus spp. 71, 74, 359, 362, 373

sulfonate compound 140, 337

sulfur (S⁰) 1, 7, 8, 9, 46, 127, 130, 139, 140, 287, 288, 298, 304, 306, 310, 312, 313, 318, 344, 354, 359, 360, 366, 388, 400

sulfur bacteria 358, 359, 360, 362, 371

sulfur bacteria and the oxidation of sulfur compounds 358–362

sulfur compound oxidation pathways 360, 361

sulfur compounds 358, 359, 362, 363, 386, 403

sulfur deposition 358

sulfur granules 387

sulfur oxidase 361

sulfur reducers 310, 311, 313, 318

sulfur reductase 313

sulfur-containing amino acids 140

sulfur-dependent archaea 288

Sulfurospirillum arcachonense 311

Sulfurospirillum arsenophilum 308

Sulfurospirillum barnesii 308

Sulfurospirillum spp. 310

sulfur-reducing archaea 310

supercoiled form of DNA 171, 173

superoxide (O₂·^–) 221, 253, 255, 260, 445

superoxide dismutase (SOD) 254, 255, 260

superoxide dismutase and catalase activities in selected prokaryotes 254

superoxide reductase 255

supply of carbon skeletons for biosynthesis in methanogens 329

surface structure of a prokaryotic cell 12

surfactant 224

surgeon fish 27

survival 452, 466, 483

survival and energy 482

survival strategy mechanisms 110, 437, 482

swarmer cells 490

switch 181

syc proteins 50

symbiotic association with legumes 132

symbiotic N₂ fixation 129, 133

symport 38

synchronous cell division 186

Synechocystis spp. 186

synthesis of acyl-ACP 154

synthesis of carbon skeletons for biosynthesis in homoacetogens 333

synthesis of deoxynucleotides 149

synthesis of glycerol teichoic acid 169

synthesis of isopentenyl pyrophosphate (IPP) 160

synthesis of P-antigen and lipopolysaccharide in Salmonella enterica 165

synthesis of peptide: initiation, elongation and termination 176

synthesis of saccharides and their derivatives 161–165

synthesis of UDP-N-acetylmuramylpentapeptide 164

synthetic gas 330

syntrophic associations 337, 337–340

syntrophic bacteria 333, 337, 338, 339

Syntrophobacter fumaroxidans 338, 340

Syntrophobacter wolinii 338, 339

Syntrophococcus sucromutans 331

Syntrophomonas sapovorans 338

Syntrophomonas wolfei 338, 339

Syntrophospora bryantii 338

Syntrophothermus lipocalidus 338, 340

Syntrophus aciditrophicus 338, 339

Syntrophus buswellii 338, 339

Syntrophus gentianae 338, 343

sythesis of murein monomers 163

TA variant 236

Talaromyces flavus 304

TAT pathway 45, 46

TAT signal sequence 45, 46

TAT-dependent protein export 46

taurine 337

T-box 427, 428

T-box transcription termination control system 427

Tc(IV) 309

Tc(VII) 306, 309

Tc(VIII) 309

TCA cycle enzymes 88, 277, 373, 375

TCA cycle intermediates 88

teichoic acid 13, 18, 20, 165, 167

teichoic acid synthesis 167

teichuronic acid 17, 18

tellurium(VI) 309

temperature 182

terminal electron acceptor 252

terminal oxidase 109, 363

termination 176, 178, 421

termination and antitermination 424–428

termination and antitermination aided by protein 424

termination and antitermination aided by tRNA 426

termination and antitermination mechanism aided by metabolites 427, 428

termination codon 178

termination site 174

termination steps 176

terminator 420, 421, 422, 425, 426, 427, 428

terminator hairpin 427

terminator region 173

terminator sequence 173

terminator/antiterminator mechanism 417, 418, 420, 424, 427

ternary fission 389

tertiary binding proteins 182

tertiary structures 178

tetrachloroethene 336

tetrachloroethene dehalogenase 45

tetracycline 323, 487

tetracycline biosynthesis 71

tetrahydrofolate (H₄F) 157, 158, 234, 236, 315, 322, 323, 329, 330, 374

tetrahydrofolate:B₁₂ methyltransferase 334

tetrahydromethanopterin (H₄MPT) 72, 157, 234, 315, 329

tetrahydrosarcinapterin 327

tetrapyrroles 159, 161

tetrasulfide 313

tetritol 26

Thauera aromatica 341, 343

Thauera selenatis 305, 307

theoretical maximum Y_ATP 189

Thermithiobacillus spp. 359

Thermoacetogenium phaeum 333, 338, 340

Thermoanaerobacter ethanolicus 203, 257

Thermoanaerobacter kivui 331, 334

Thermoanaerobium brockii 257

Thermococcus (formerly Pyrococcus) spp. 371

Thermococcus celer 65

Thermococcus kodakaraensis 371

Thermococcus litoralis 203, 288

Thermodesulfobacterium spp. 311

thermophiles 23, 60, 304, 310, 359

thermophilic anaerobes 64, 257

thermophilic archaea 60, 150, 152, 323, 371

thermophilic chemolithotroph 365

thermophilic chemolithotrophic hydrogen bacterium 304

thermophilic H₂ bacterium 373

thermophilic obligately chemolithotrophic bacteria 310

thermoplasma 74

Thermoplasma acidophilum 103

Thermoproteus spp. 74, 312, 373

Thermoproteus tenax 60, 66, 68, 73, 75, 98, 333

Thermosyntropha lipolytica 338

Thermoterrabacterium ferrireducens 307

Thermothrix spp. 359

Thermotoga maritima 60, 73

Thermovibrio ammonificans 312, 365

Thermovibrio ruber 304, 312, 365

Thermus spp. 367

Thermus thermophilus 113

THI box 428

Thialkalivibrio nitratireducens 304

Thialkalivibrio thiocyanodenitrificans 304

thiamine 10, 428

thiamine pyrophosphate (TPP) 76, 85, 256, 263, 274

Thimonas intermedia 371

Thioalkalimicrobium 359, 360

Thioalkalivibrio denitrificans 304

Thioalkalivibrio spp. 359, 360

thiobacilli 377

Thiobacillus denitrificans 300, 304, 360, 362, 368, 371

Thiobacillus ferrooxidans 73, 103, 129, 360, 362, 363

Thiobacillus intermedius 371

Thiobacillus neapolitanus 371

Thiobacillus novellas 71, 89, 403

Thiobacillus thiooxidans 360, 361, 362

Thiobacillus thioparus 361

Thiobacillus spp. 232, 358, 359, 360, 362

Thiobacterium spp. 359

thiocyanate 304, 359

thiol:disulfide oxidoreductase 181

thiols 140

Thiomargarita namibiensis 305, 360

Thiomicrospira denitrificans 304

Thiomicrospira spp. 359, 360, 362

Thiomonas spp. 359, 367

thiophene 140

Thioploca spp. 305, 359, 360

thioredoxin 140, 149, 150, 282

thioredoxin reductase 149

Thiosphaera pantotropha 214, 305, 362

Thiospira spp. 359

thiosulfate (HS₂O₃^–) 9, 304, 335, 358, 359

thiosulfate-oxidizing multienzyme complex 361

Thiothrix spp. 359

Thiovulum spp. 359

Thodococcus rhodochrous 72

threonine 141, 215, 216, 217, 282, 423, 424, 459

threonine dehydratase 215, 216, 282, 459

threonine synthase 424

thylakoids 27, 394, 395, 398

thylakoids of cyanobacteria 394

thymidylate synthase 150

TMAO reductase 46

tmRNA 178

tmRNA reading frame 178

toluene 306, 308, 341, 342, 343

toluidine 97

toluidine blue 488

topoisomerase 173

topoisomerase IV 173

Torulopsis colliculosa 224

Torulopsis spp. 240

total weight of a single cell 127

toxic metals 29, 309, 310, 344

toxin 50

toxins 29, 43, 46, 47, 51

trans-2,3-enoyl-ACP 154

transacetylase 412

transaldolase 70, 77, 236

transaminase 137, 138, 140, 142, 215

transamination 128, 138, 215, 220, 281

transcarboxylase 278

transcript turnover 430

transcription 145, 171, 174, 175, 408, 409, 410, 412, 415, 416, 420, 421, 422, 425, 428, 431, 435, 449, 451

transcription antiterminator (LicT) 417

transcription elongation 420, 421

transcription factors 409

transcription initiation 420, 430

transcription of genes for the synthesis of aspartate series amino acids 423

transcription pause site 422

transcription regulatory protein (LevR) 417

transcriptional activator 434, 446, 455

transcriptional control 430

transcriptional control of genes for the enzymes synthesizing isoleucine, valine and leucine by attenuation 424

transcriptional control of the proline dehydrogenase gene through autogenous regulation 429

transcriptional control of the trp operon through attenuation 422

transcriptional regulation 451

transcriptional regulation of heat shock protein genes in Escherichia coli at elevated temperature 447

transcriptional regulation of HSP in Escherichia coli 447

transcriptional regulation of the tryptophan operon through repression 419

transcriptional regulator 451, 452

transducer proteins 405

transformation of xenobiotics under anaerobic conditions 343

transglycosylase 167

transglycosylation reaction 166

transhydrogenase 110

transketolase 70, 77, 236, 240

translation 175, 176, 178, 408, 409, 421, 422, 428, 431, 432, 433, 449

translation and stability of mRNA encoding enzymes of glycogen metabolism 432

translation efficiency 430, 431

translation quality control process 178

translation regulation of glnA (glutamine synthetase gene) by antisense RNA in Clostridium acetobutylicum 436

translational activation 439

translational control 430

translocon 44

transmembrane receptors 456

transmethylase 216

transpeptidase 167

transpeptidation 167

transport 38, 93, 98, 116, 117, 165, 182, 191, 192, 223, 328, 455, 482

transport of cell wall precursor components through the membrane 167

transporters 19, 35

TRAP (tripartite ATP-independent periplasmic) transporter 39

TRAP (trp RNA binding attenuation protein) 424, 425, 426

trehalase 484

trehalose 411, 484

trehalose phosphorylase 484

trehalose-6-phosphatase 484

trehalose-6-phosphate 484

trehalose-6-phosphate synthase 484

triacylglyceride (TAG) 484, 485, 486

tricarboxylic acid (TCA) cycle 60, 68, 69, 70, 71, 79, 85, 86–91, 92, 100, 102, 105, 106, 208, 209, 212, 242, 243, 267, 275, 277, 299, 315, 319, 373, 376, 402, 416, 419, 442, 461, 464, 486

Trichoderma hamatum 304

Trichoderma reesei 204

Trichsporon cutaneum 304

trifunctional enzyme 375

trigger factor 178

triglycerides 157

trimethylamine N-oxide (TMAO) reductase 46

trimethylamine-N-oxide (TMAO) 444

trinitrotoluene 308

triokinase 240

triose phosphate 61, 63, 75, 235, 236, 240

triose-phosphate isomerase 63

tRNA 174, 176, 178, 430

tRNA-dependent transcription antitermination 426, 427

truncated mRNA 178

truncated peptide 178

tryptophan 141, 142, 176, 286, 419, 420, 421, 424, 425

tryptophan degradation 220, 221

tryptophan synthase 142

tryptophan-2,3-dioxygenase 220

tubulin 183

tungsten 8, 9, 332

turgor pressure 104

turnover 183

twin-arginine motif 45

twin-arginine translocation (TAT) pathway 43, 45–46

two alternative routes of carbon rearrangement in the RMP pathway 238

two-component response regulator 490

two-component signal transduction system 371

two-component system 27, 303, 304, 428, 441, 442, 444, 451, 453, 454, 455, 466, 493

two-component system with sensor-regulator proteins 428

two-step process 326

two-step reaction 289

type I pathway 47

type I pathway: ATP binding cassette (ABC) pathway 46, 47

type II pathway 46, 47, 49

type III excretion pathway 47, 49, 50, 110

type III flagellar export pathway 181

type IV pathway 47, 50, 51

type V pathway 47, 51

tyrocidin 466

tyrosine 141, 142, 220, 225, 356, 426

tyrosine radical 150

tyrosyl-tRNA synthetase 426

U 360

U(IV) 309, 364

U(VI) 306, 307, 309

ubiquinol-cytochrome c reductase (complex III) 106, 111, 112, 113

ubiquinone (coenzyme Q) 106, 107, 108, 333

ubiquinone/ubiquinol 97

UDP 167, 488

UDP-galactose 161, 206, 435

UDP-galactose epimerase (GalE) 434, 435

UDP-GlcNAc 167

UDP-glucose 161, 165, 206, 484

UDP-MurNAc-pentapeptide (lipid I) 167

UDP-N-acetylglucosamine 163

UDP-N-acetylmuramate 163, 164

UDP-N-acetylmuramylpentapeptide 163

UDP-sugar 161, 164

ultramicrobacteria 492

UMP 167, 206

uncouplers 36, 105, 110, 114, 192, 327, 328

undecaprenyl phosphate 164, 165, 167, 170

undecaprenyl pyrophosphate 167

undecaprenyl-GlcNAc-MurNAc-pentapeptide pyrophosphate (lipid II) 167

undecaprenyl-GlcNAc-MurNAc-pentapetide-(gly)₅ pyrophosphate 167

unicellular cyanobacteria 133, 134, 387

uninucleoid cells 186

uniport 38

uniporters 38

unsaturated acyl-ACP 154

unsaturated acyl-ACP synthesis by the anaerobic route 155

unsaturated fatty acid synthesis 153, 154, 156

unsaturated fatty acids 153, 154, 155, 156, 217, 451

unusual amino acids 178

uptake hydrogenase 270, 364

uracil 287

uranium (IV) oxidation 304, 368

urate 202, 223, 287

urea 223

urease 441

uridylylase/deuridylylase 440

urocanate 217

uroporphyrinogen III 161

usher 47

utilization of alcohols and ketones 213–214

utilization of methane and methanol 229–241

utilization of pentoses 71

utilization of sugars 207–208

UTP 149, 163, 164, 174

UV 490

vacuoles 113, 305, 360

valine 141, 217, 286, 424

valine synthesis 274

valinomycin 35, 36

vanadate [V(V)] 308, 309

vanadium 132

vancomycin 167

V-ATPase 113, 328

vegetative cell 490

vegetative growth 490

Veillonella alcalescens 254

Veillonella parvula 116

Veillonella spp. 24

vesicles 21

viability 101

viable but non-culturable (VBNC) cells 490, 491, 492

Vibrio alginolyticus 106

Vibrio cholerae biotype albensis 117

Vibrio furnissii 487

Vibrio harveyi 117

Vibrio spp. 117

Vibrio succinogenes 115

vinegar fermentation 104

virulence 452

virulence factor 432

virulence genes 439

virulence-related proteins 169

vitamin B₁₂ 10, 107, 279, 387

vitamin K 10

vitamins 10, 17, 257, 259

wastewater 308, 309, 320

wastewater treatment 299

water 110, 155, 257, 308, 386, 398, 445

water–oil interface 224

wax ester (WE) 484, 485, 486

wax ester (WE) and hydrocarbons 486

wax ester synthase 486

weak acids 114

wine 286

Wolinella spp. 310, 311

Wolinella succinogenes 45, 305, 307

Wood–Ljungdahl pathway 312, 315, 329, 374

xanthine 221

xanthine dehydrogenase 221

xanthine oxidase 221

Xanthobacter flavus 365

Xanthobacter spp. 72, 214, 359

Xanthomonas phaseoli 73, 79, 80

xenobiotics 289, 290, 306, 308, 309, 310, 320, 340, 343

xenobiotics metabolized under anaerobic conditions 341

Xenorhabdus nematophilus 117

xylanase 204

xylene 306, 308, 343

xylitol 278, 459

xylose 204, 207, 419

xylulose 207

xylulose monophosphate (XMP) pathway 230, 235, 240, 240–241

xylulose monophosphate pathway of methylotrophic yeasts 240

xylulose-5-phosphate 70, 75, 76, 77, 240, 259

Y_ATP 188, 189, 192, 318

yeast 156

Yersinia spp. 50

Y_glucose 260

Z interacting protein A 183

zinc 9, 46, 309

Zn²⁺ 390, 392

Z-ring assembly 186

Zymomonas anaerobia 187, 188

Zymomonas mobilis 46, 188, 255, 256

Zymomonas spp. 72

α-1,1-linkage 484

α-1,4 linkages 166, 483

α-1,4-glucoside 166

α-1,4-glucoside bonds 202, 203

α-1,4-polygalacturonate 205

α-1,6 side chain 166

α-1,6-glucoside bonds 202, 203

α-1,6-linkages 483

α-amylase 66, 202

α-glucan 203

α-glucosidase 66, 207

α-proteobacteria 367

β-1,4-glucoside bonds 203

β-1,4-linked glucose units 203

β-alanine 287

β-amylase 203

β-carotene 390

β-galactosidase 41, 207, 411, 412, 459

β-glucan 426

β-glucan cellobiohydrolase 203

β-glucanase 426

β-glucosidase 203, 207, 417

β-glycerol phosphate 459

β-glycoside bonds 204

β-lactam antibiotics 167

β-lactamase 19, 20

β-oxidation 208

Δp 114, 115, 116

Δp formation through fermentation product/H⁺ symport 116

ρ-factor 174

σ-amylase 65

σ-factors 174, 409, 410, 420, 432, 439, 440, 446, 448, 449, 455

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