381

Index

a Anabaena 289 ABC transporter 297 – azollae 85 acetate 311f. anabolic metabolism 288 acetic acid bacteria 124 anammox 89 Acetobacter xylinum 124 animal Acetobacterium woodii 292, 318 – bacteria 203ff. acetone 105ff., 321 anthrax 209f. acetone-butanol fermentation 321f. antibiotic 151ff., 338f. acetyl-CoA 313 – resistance gene 160ff. Acidianus ambivalens 282ff. antimicrobial 150 Acinetobacter Aquifex aeolicus 289 – baumannii 215 Arc system 307ff. – calcoaceticus 313 archaea 7, 17ff., 53, 278, 281ff. – species 249 – metabolism 283 acyclovir (Zovirax) 227 – methane 93 adenine 268 – methanogenic 292 adenosine 5′-diphosphate (ADP) 9, 60, – phylogenetic tree 282 330 Archaeoglobus fulgidus 284 adenosine 5′-triphosphate (ATP) 9, 60, Arthrobacter simplex 313 274f., 301, 317, 330 ascorbic acid (vitamin C) 124f. – synthesis in microbes 301 Aspergillus species 215 Agrobacterium tumefaciens 165ff., 291 ATP, see adenosine 5′-triphosphate AIDS (acquired immunodefi ciency ATP synthase 60, 66, 303 syndrome) 222ff. autotrophic growth 316 D-alanine 123 Azoarcus 85, 185 L-alanine 123 Azolla 85 Alcanivorax Azospirillum 85, 185 – borkumensis 313 Azotobacter vinelandii 293 – species 249 alcohol dehydrogenase 111ff. b alcohol fermentation 318ff. Bacillus 156, 194ff. – via the EMP and the ED pathways 321 – anthracis 149, 186, 209, 290ff. Ames test 33 – licheniformis 194, 290ff., 334f. amino acid 271 – subtilis 194, 240, 274, 293, 325f. – fermentation 321 – thuringensis (Bt) 167, 293 ammonia 87ff. bacteria 53f., 73f. ammonia monooxygenase 313 – animal 203ff. amphotericin 156 – climate 99f. amylase 300 – competence 139

Discover the World of Microbes: Bacteria, Archaea, and Viruses, First Edition. Gerhard Gottschalk. © 2012 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2012 by Wiley-VCH Verlag GmbH & Co. KGaA.

bbindex.inddindex.indd 381381 99/8/2011/8/2011 5:46:225:46:22 PMPM 382 Index

– deep sea 47f. c – diversity 289ff. c-AMP receptor protein (CRP) 328 – ethanol-producing 111 Calvin-Benson-Bassham (CBB) cycle 62, – food resource 203ff. 316f. – Gram-negative 152f., 274 cancer 215ff. – Gram-positive 152f., 274 candicidin 156 – human 203ff. Candida – methanotrophic 314 – albicans 76, 215 – nickel-resistant 131 – lipolytica 313 – nitrifying 313 – species 249 – phylogenetic tree 289f. capsid 221 – plant 217f. capsomer 221 – production factory 191ff. carbohydrate 311 – resistance 160ff. carbon cycle 56, 101 – sulfate-reducing 50 carbon dioxide 100ff., 111 – symbiotic 48 – fi xation 317ff. bacterial fermentation 318 carbon dioxide cycle 101 bacterial food 203 carbon metabolism 311ff. bacterial genome 239 carbon monoxide 246 bacterial growth 4ff., 261ff. Carboxydothermus hydrogenoformans 246, 277 bacterial sex life 133ff. carcinogenic compound 33f. bacterial spore 108 Carsonella bacterial sulfur cycle 284 – ruddii 333 bacteriophage 145ff. – species 187 bacteriorhodopsin 58f., 283, 304 cell membrane 273 Bacteroides fragilis 77 cell wall 273f. base pairing 269 cellulase 113f., 300 beer 115 cellulose 114 Beggiatoa 252 Cenarchaeum symbiosum 281 – alba 285 Cephalosporium 154ff. beta (β)-lactam antibiotic 153f. – roseum 313 beta (β)-lactamase 135 Che protein 306 Bifi dobacterium 79 cheese 121ff. bile acid 78 chemiosmotic mechanism 301 biodiesel 118 chemolithotrophic way of life 49 bioelement 127 chemostat 263 bioenergy 118 chemosynthetic symbiosis 48 bioethanol 114f. chemotaxis 306 biofi lm 182 chitinase 300 biofuel 102, 109, 111ff. Chlamydia pneumoniae 209 biogas 93ff., 117f. Chlorella 61f. bioinformatics 235 Chlorobium limicola 291 biological warfare 209f. Chlorofl exus bioluminescent bacteria 178 – aurantiacus 289 biomass 101, 109, 114, 117 chloroplast 187 biotechnology 191, 339f. cholera toxin (CTX) 211 Bordetella pertussis 204 Chondromyces robustus 294 Borrelia burgdorferi 206 Chromatium okenii 179, 285, 291 borreliosis 205 Citrobacter species 196f. bronchitis 209 Clamydia trachomatis 76 bubonic plague 205 cloning 173 Buchnera Clostridium – aphidicola 187 – aceticum 292, 318, 325 butanol 105ff., 117, 321 – acetobutylicum 105ff., 290ff., 321f., γ-butyrolactone 309 325

bbindex.inddindex.indd 382382 99/8/2011/8/2011 5:46:225:46:22 PMPM Index 383

– acidiurici 325 – restriction enzyme 169ff. – botulinum 290ff., 323 – sequence 236 – diffi cile 77, 211 – transfer 136ff. – histolyticum 204, 323 DNA polymerase 174, 228 – ljungdahlii 277, 292, 318 DNA virus 225 – pasteurianum 325 Dunaliella 45f. – perfringens 204 – species 196 e – sporogenes 323 Eco R1 169 – sticklandii 323 EET (extracellular electron transfer) 248 – tetani 204f., 238, 290ff., 326, 333 EHEC (enterohemorrhagic E. coli) 211f. – thermoaceticum 130 Embden-Meyerhof-Parnas (EMP) pathway cobalt 127 302, 311, 321ff. coenzyme B 95 endosymbiont 185ff.

coenzyme B12 128 endosymbiosis 70f.

coenzyme F430 94, 127 energy 297ff. coenzyme M 95 energy conservation 117ff. cold seep 50 Enterococcus cold vent 50 – aecium 215 combustible air 91ff. – faecalis 215 competence Entner-Doudoroff (ED) pathway 311ff. – bacteria 139 enzyme 9, 269 complementary DNA (cDNA) 224 – anaerobic 321 conjugation 140ff. enzyme activity conjugative plasmid 142 – regulation 330 coral bleaching 186 epidemics 221 Corynebacterium glutamicum 179, 192 Epstein-Barr virus (EBV) 227, 344 Crenarchaeota 281 Erwinia uredovora 167 CTP (cytidine 5′-triphosphate) 330 erythromycin 155 cyanobacteria 31ff., 69f. Escherichia coli 76f., 94, 145ff., 179, 196, cyclic AMP (cAMP) 328 213ff., 291, 326ff. cytoplasmic membrane 273 ETEC (enterotoxigenic E. coli) 211f. cytosine 268 ethanol 111 Eubacterium rectale 77 d eukaryotic cell 13 deep-sea vent 48 Euryarchaeota 281 Deinococcus radiodurans 245f., 289 exoenzyme 300 denitrifi cation 304 extremozyme 200 Desulfobacterium autotrophicum 285, 304, 318 f Desulfovibrio vulgaris 179, 285 F-factor 159 Desulfurococcales 281 fermentation Desulfuromonas acetoxidans 285 – acetone-butanol 105ff., 318ff., 321f. diabetes 194f. – alcohol 318ff. diarrhea 210 – amino acid 321 dicarboxylic azobenzene (DCAB) 134 – butyrate 321 dihydroxyacetone phosphate (DAP) – homoacetate 319, 321 316 – lactic acid 318 DNA (deoxyribonucleic acid) 7ff., 267 – mixed acid 321ff. – base 268 – propionate 123 – complementary (cDNA) 224 ferredoxin 119 – methylation 171, 326 Firmicutes 293 – mitochondrial (mtDNA) 187f. fl agella 179f., 306 – regulation 326 fl avin adenine dinucleotide (FAD) 303 – replication 10, 270 food chain 291

bbindex.inddindex.indd 383383 99/8/2011/8/2011 5:46:225:46:22 PMPM 384 Index

Frankia 85, 185 Herpes simplex virus 227 furanosyl borate ester 309 Herpes virus 8 (HHV-8) 231 heterodisulfi de 95 g HIV (human immunodefi ciency virus) GC content 335 228ff. gene 333 homoacetate fermentation 321 gene cloning 173 homoserine lactone 309 gene technology 171 horizontal gene transfer 137, 333 gene therapy 232 human gene transfer 137, 142, 333f. – bacteria 73ff., 203ff. – horizontal 333, 137 hydrocarbon 250 genetic code 272 – degradation 315 genetic engineer 165ff. hydrochlorofl uorocarbon (HCFC) 99 genetic engineering 196 hydrogen sulfi de 49 genome 333 Hydrogenobacter thermophilus 318 genomics 235ff. hyper cycle 27 Geobacter metallireducens 304 hyperthermophiles 281 glacier ice 244 global warming potential (GWP) i 103f. Ignicoccus hospitalis 255, 281 Gloeocapsa 290 immunotherapy 149 Gluconobacter oxydans (Gluconobacter infection 204 oxidans) 124, 316 – in hospital 215 glucose 313 infl uenza virus 222ff. glucose isomerase enzyme 192 – infection cycle 226 glyceraldehyde 3-phosphate (GAP) informational macromolecule 267 316f. insulin 195 glyoxylic acid (glyoxylate) cycle 311f. interbacterial relationship 177ff. GMO (genetically modifi ed microorganism) intestinal microfl ora 78 219 isoamyl alcohol 105 Gram-negative bacteria 152f., 274 Gram-positive bacteria 152f., 274 k green manuring 84 Klebsiella 197f. green sulfur bacteria 67 – aerogenes 325 growth – pneumoniae 331 – aerobic heterotrophic 311 Korachaeota 281 – microbial 4ff., 261ff. guanine 268 l β-lactam antibiotic 153f. h β-lactamase 135 HAART (highly active antiretroviral therapy) lactic acid bacteria 121 231 lactic acid fermentation 318 habitat 283 Lactobacillus Haemophilus infl uenzae 76, 235ff., 305 – bulgaricus 121, 318 Haloarcula marismortui 46, 283 – helveticus 318 Halobacteriales 283 – lactis 318 Haloferax volcanii 46 – species 196 Haloraptus utahensis 42 lambda (λ) bacteriophage 147f. Halorubrum sodomense 47 Legionella pneumophila 206ff. Helicobacter pylori 74, 216, 291 Legionnaire’s disease 206 Heliobacterium 290ff. Leuconostoc mesenteroides 318 hemagglutinin (HA, H) 225f. lignocellulose 113 hemicellulose 114 lipase 300 Herpes 222 Listeria monocytogenes 214

bbindex.inddindex.indd 384384 99/8/2011/8/2011 5:46:225:46:22 PMPM Index 385

listeriosis 214 Methylobacterium 104, 218 LUCA (last universal common ancestor) Methylomonas 104 15ff., 277 methylotrophy 217f. Lyme disease 205 microbe – ATP synthesis 301 m – climate maker 99ff. macromolecule – incredible 245ff. – informational 267 – resistance to radiation 245 Magnetospirillum gryphiswaldense 247 microbial growth 261ff. malaria 205 – batch culture 261 MCP (methyl-accepting chemotaxis protein) – condition 263 306f. – continuous culture 263 membrane 297ff. – logarithmic 261 metabolism microbial metabolism – anabolic 288 – regulation 325ff. – archaea 283 microbial shape 264 – carbon 311ff. microbial size 264 – microbial 325 microorganism metagenomic library 242 – aerobic 264 metagenomics 241f. – anaerobic 264 metal needle effect 94 – chemotrophic 264 methane 91ff., 103, 117, 313f. – dead sea 45ff. – aerobic oxidation 314 – facultative anaerobic 264 – anaerobic oxidation 50 Miller-Urey soup 24 methane monooxygenase 313 mitochondria 187 methane seep 50 mitochondrial DNA (mtDNA) 187f. methane-oxidizing archaea 51 mixed acid fermentation 321ff. methanoarchaea 50, 93f., 118 molybdenum 83 Methanobrevibacter smithii 282 Moorella thermoacetica 130, 318 Methanocaldococcus jannaschii 282, 292 motility 305 Methanococcus 53 MRSA (methicillin-resistant Staphylococcus methanogen 318 aureus, multiresistant Staphylococcus methanogenesis 94, 285 aureus) 161, 215 methanogenic archaea 292 Mycobacterium methanogenic pathway 286f. – smegmatis 313 Methanohalobium evestigatum 282 – species 249 methanol 313 – tuberculosis 186, 206ff., 290 Methanopyrus kandleri 282 Mycoderma aceti 123ff. Methanosaeta concilli 282 Mycoplasma Methanosarcina 305 – genitalium 238 – acetivorans 282 – mycoides 256 – barkeri 282 – pneumoniae 209 – mazei 282, 292, 326, 334 Myxobacteria 293 Methanosarcinales 285 Methanosphera stadtmanae 282 n Methanospirillum hungatei 253 NADH 302ff., 330 Methanothermobacter Nanoarchaeota 281 – marburgensis 282 Nanoarchaeum equitans 255, 281 – thermoautotrophicus 282 Natronomonas pharaonis 42, 254, 283 methanotroph 313 (connected on p. 254) methanotrophic bacteria 314 Neisseria meningitides 76 methicillin-resistant Staphylococcus aureus neuraminidase (NA, N) 225f. (MRSA) 215 nickel 94, 127ff. methyl-coenzyme M 95 nickel-resistant bacteria 131

bbindex.inddindex.indd 385385 99/8/2011/8/2011 5:46:225:46:22 PMPM 386 Index

nif gene 331f. Picrophilus torridus 41, 255, 283, 333 nitrate 88f. plague 211 nitrifying bacteria 313 Planctomyces 291 nitrite 88f. plant Nitrobacter winogradskyi 291 – bacteria 217f. nitrogen 81ff. plasmid 159ff., 165ff. nitrogen cycle 88, 304 Plasmodium falciparum 205 nitrogen fi xation pneumonia 209 – symbiotic 84 Pocillopora damicornis 186 – regulation 331 polio virus 222ff. nitrogenase 82f. poly-beta-hydroxy fatty acid (PHF) 198ff. Nitrosomonas europaea 291, 313 poly-beta-hydroxybutyric acid (PHB) 198ff. Nocardia petroleophila 313 Prochlorococcus marinus 248f., 289 prokaryote 278 o prokaryotic cell 13 Oculina patagonica 186 prontosil 150 Oligotropha carboxydovorans 291 1,3-propanediol 196 “omics” era 235 propanediol dehydrogenase 197 oncogene 232 prophage 335 Oscillatoria 289 Propionibacterium acnes 73ff., 290 oxidation propionic acid bacteria 123 – aerobic 314 Propionigenium modestum 252, 305 – D-glucose 316 protease 193, 300 – incomplete 315 protein 269 oxygen 34ff., 278 proteomics 241ff. proton motive force 59, 302ff. p proton translocation P700 305 – light-driven 304 P840 305 Pseudomonas P870 system 304 – aeruginosa 76, 181, 209ff., 291, 309 Paracoccus denitrifi cans 325, 326 – fl uorescens 313 pathogenic microorganism 341 – lindneri, see Zymomonas mobilis pathogenicity island (PAI) 212f. – syringae 218, 291 PCR (polymerase chain reaction) 172ff. pullulanase 300 Pelagibacter ubique 249, 304 purple bacteria 66 penicillin 150ff. Pyrococcus 201 Penicillium 150ff. – furiosus 283 phage 145, 335 Pyrodictium occultum 39f., 255, 282 phosphoenolpyruvate (PEP) 298, 312, 330 Pyrolobus fumarii 282 phosphotransferase system (PTS) 298 pyruvate decarboxylase 111ff. Photobacterium phosphoreum 180 photosynthesis 29ff., 59, 65ff. q – aerobic (oxygenic) 31, 68f. quorum sensing 309 – anaerobic (anoxygenic) 31, 69, 291 – fi rst type 65 r – second type 59 radical 35 photosystem Ralstonia eutropha 199f., 291, 325 – PSI 305 Reclinomonas americana 189 – PSII 305 reducing equivalent 31 phototrophic bacteria 30 renewable resources 117 phototrophic microorganism 263 repair system 294 phylogenetic tree replication 10, 270 – archaea 282 resistance – bacteria 289f. – bacteria 160ff.

bbindex.inddindex.indd 386386 99/8/2011/8/2011 5:46:225:46:22 PMPM Index 387

resistome 163 Staphylococcus respiratory chain – aureus 179, 204ff., 274, 290, 309 – aerobic 302f. – epidermidis 73, 215 restriction enzyme 169ff. Streptococcus 76 retrovirus 228ff. – cremoris 121 Rhizobium radiobacter 165 – infection 150 rhizosphere 96 – pneumonia 209 Rhodospirillum rubrum 291 – salivarius 76 ribonucleotide reductase 233 – thermophilus 121 ribozyme 26ff. Streptomyces 154ff., 193, 290 ribulose 1,5-bisphosphate 62, 316 – griseus 151ff. ribulose 1,5-bisphosphate carboxylase streptomycin 151ff. (rubisco) 63 stromatolite 35f. Rickettsia substrate-level phosphorylation 301 – prowazekii 186ff. sugar 111 – species 291 sulfate-reducing bacteria 50 RNA (ribonucleic acid) 7ff., 222ff. Sulfolobales 281 – 16S-rRNA 17ff., 55 Sulfolobus 252, 282 – messenger (mRNA) 267, 326ff. – acidocaldarius 281ff. – ribosomal (rRNA) 267 – solfataricus 246, 291 – small (sRNA) 329 sulfur cycle 284 – synthesis 12 survival strategy 292 – transfer (tRNA) 269 symbiont 186 – translation 272 symbiosis 185 – triplet 272 symbiotic bacteria 48 RNA polymerase 228 symbiotic nitrogen fi xation 84 RNA virus 225 symporter 297 RNA world 277 Syntrophus aciditrophus 252f. ROS (reactive oxygen species) 35, 278 Roseobacter 304 t T-DNA region 165 s T4 bacteriophage 147f. Saccharomyces cerevisiae 111, 197, Taq polymerase 174, 201 318 TCA, see tricarboxylic acid Salmonella TEM-1 β-lactamase 135f. – species 204ff. tetanus 204ff. – typhi 211ff., 291 tetracycline 155 – typhimurium 33, 179 Thermobacterium mobile, see Zymomonas saltpeter 87 mobilis salvarsan 150 Thermococcus 201 selenocysteine 130 thermophiles 281 sensor kinase 307ff. Thermoplasma acidophilum 283 sequencing Thermoproteales 281 – DNA 236 Thermoproteus 282 Shewanella oneidensis 248, 304 – tenax 179, 255, 277, 281, 318 shingles 227 Thermotoga maritima 289, 334 SHV-1 β-lactamase 135 thermozyme 42 Sinorhizobium meliloti 84 Thermus sodium glutamate 191 – aquaticus 39, 228, 289 sodium ion pump 305 – thermophilus 289 Sorangium cellulosum 333 Thiobacillus 252 Spanish infl uenza virus 224 – ferrooxidans 255 Sporomusa 109, 293 – thiooxidans 255, 285, 291 sporulation 294 thioester 26

bbindex.inddindex.indd 387387 99/8/2011/8/2011 5:46:225:46:22 PMPM 388 Index

Thiomargarita namibiensis 250f. vancomycin-resistant enterococci (VRE) 215 Thioploca 252 Varicella zoster 227 Thiospirillum jenense 180, 291 Vibrio thymine 268 – cholerae 210ff., 291 Ti plasmid 165 – fi scheri 180, 309 tobacco mosaic virus (TMV) 28 – harveyi 309 transcription 12, 326 – shiloi 185f. – regulation 327ff. vinegar 123ff. transformation 139 viral hypothesis 234 translation 12, 272, 326 virus 7, 145, 221ff., 343f.

– regulation 328f. vitamin B12 127 transport 297 vitamin C synthesis 124 – active 298 VRSA 215 – primary 297 – secondary 297 w tricarboxylic acid (TCA) cycle 302, 312 wine 115 Trichodesmium 289 Wood-Ljungdahl pathway 318f. tuberculosis 206ff. tungsten 129 x two-component system 307f. Xanthomonas campestris 218 typhoid fever 211 xylanase 300

u y UPEC (uropathogenic E. coli) 212 Yersinia pestis 205ff. uracil 269 yogurt 121 urease 94 z v Zooxanthellae 185f. vanadium 83 zovirax 227 vancomycin 215 Zymomonas mobilis 112f., 291, 318

bbindex.inddindex.indd 388388 99/8/2011/8/2011 5:46:225:46:22 PMPM