Modern Topics in the Phototrophic Prokaryotes, DOI 10.1007/978-3-319-46261-5 482 Index

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Index

A Candidatus Thermochlorobacter Acaryochloris marina, 15 aerophilum, 115–117 Acidic habitats, 447 Chloracidobacterium thermophilum, Acidicophilic phototrophic bacteria, 447–448 113–115 Acidiphilium rubrum, 117 metagenomic and metatranscriptomic Acidobacteria, 89, 90, 97, 112, 113, 123, 164 analysis, 112 Acidophiles, 469–470 types, 112 Adenosine A2a receptor (A2aR), 405 Alka(e)ne production, 381–382 Aerobic anoxygenic phototrophic bacteria Alkaline soda lakes. See Alkaliphilic (AAPB), 117 phototrophic bacteria Aerobic anoxygenic phototrophs (AAP), Alkaliphiles, 470 311, 312 Alkaliphilic phototrophic bacteria apparatus, photosynthetic, 208 Big Soda Lake, 457 BChl a, 194 Böddi-szék Soda Lake in Ungary, 458 carbon metabolic pathways, 201–203 brackish water and seawater salinities, 449 carotenoid, 195 halophilic purple sulfur bacterium, 449 characteristics, 198 harbor massive developments, 449 distribution and enumeration, 195–197 Mono Lake, 458 LH1 and LH2 complexes, 209 pH values, 448 morphology, 200 soap lakes, 456–457 photosynthetic electron transport chain, soda lakes, 448 209, 210 Kulunda Steppe (Altai Krai), 451 photosynthetic pigments Mongolian, 451 BChl a synthesis, 205–207 Transbaikal Region, 452 carotenoids, 207, 208 Wadi el-Natrun, 452–456 phylogenetic conundrums, 197, 199 sulfur-oxidizing chemotrophic PNSB, 195 bacteria, 449 toxic heavy metal(loid) oxides, 203–205 Allophycocyanin, 98, 101 zooplankton grazing, 201 Alphaproteobacteria, 449 Aerobic anoxygenic purple bacteria (AAPB) Alphaproteobacteria, purple nonsulfur alkaline, acidic, cold and warm bacteria, 50–54 habitats, 118 Amino acid modifications, 368 α-, β- and γ-proteobacteria, 118 Anaerobic phototrophic purple bacteria. Aerobic chlorophototrophic bacteria See Phototrophic purple bacteria bioinformatic analysis, 112 Anaerolineae, 90, 97, 103, 109, 112

Angiosperms and cyanobacteria α- and β-proteobacteria, 118 Gunnera PSB genera, 117 cyanobionts, 273 retinalophototrophy and EF nectaries, 274, 275 chlorophototrophy, 117 fossil history, 272 Thermochromatium tepidum, 119 heterocysts, 273 Antarctic seawater, 444 Myrothamnus, 272 Aphanizomenonaceae, 31–33 Nostoc, 272, 273 Aphanothece sensu lato sugars accumulation, 274 subgenera, 18

N2 fixation, 275 from tropical to polar areas, 16 Nostoc hormogonia, 275 AT1aR. See Angiotensin AT1a receptor (AT1aR) Angiotensin AT1a receptor (AT1aR), 405 Autofluorescence, 99, 100, 106, 108, 110, 114, Anhydrobiosis, 227, 228 120, 121, 123 Anoxygenic photosynthesis Azolla symbiosis, 267–269

CO2 fixation, 307 DCMU, 307 FeS, 307 B green sulfur bacteria, 309 B2R. See Bradykinin B2 receptor (B2R)

H2S, 307 Bacteriochlorophylls (BChls) photosystem I-dependent, 306 BChl a, 91, 103, 105, 107, 109, 110, 116, polysulfides, 310 117, 121 purple sulfur bacteria, 308, 309 BChl b, 89, 98, 117 sulfide, 306 BChl c, 89, 103, 105, 108, 110 Thiocapsa roseopersicina, 309 BChl d, 89, 116 thiosulfate, 310 BChl e, 89 T. roseopersicina, 308, 309 BChl f, 89 Anoxygenic phototrophic bacteria, 140, 297, BChl g, 89, 98, 122 299, 300 BChls a, 89 disadvantages, 429 Bacteriorhodopsin, 88, 107, 109 extreme thermophiles and extreme Baltic Sea Ice, 444–445 halophiles, 428 BChl a-binding protein, FMO, 113, 116 fmoA gene, 429 Betaproteobacteria, purple nonsulfur bacteria, 55 green sulfur bacteria, 308 Biodiesel production, 351 harsh and extreme conditions, 428 Biodiversity analysis. See Phototrophic purple microbial ecology, 429 bacteria microorganisms, 428 Bioenergy production, 322, 323 molecular methods, 428 Biofuel production, 364, 379 morphological and physiological Biomass derived substrates, 340–342 characterization, 429 Blastochloris sp., 98, 117, 118, 122 physicochemical conditions, 428 Bradykinin B2 receptor (B2R), 405 physiological properties, 428 Bryophyta, mosses, 267 pufM gene, 429 Bryophytes purple sulfur bacteria, 308 fossil record, 259 ribosomal RNA gene sequences, 429 Hornworts, 264, 265 visible mass developments, 428 liverworts, 259, 260, 262, 263 Anoxygenic phototrophic proteobacteria mosses, 266 AAPB, 118 1-Butanol production, 372, 375–377 Blastochloris sp., 122 Candidatus Elioraea thermophila, 119–121 Candidatus Roseovibrio tepidum, 120–122 C Chl pigment, 117 Calvin–Benson–Bassham (CBB) cycle, 110, Chromatiaceae and 117, 118, 354 Ectothiorhodospiraceae, 117 Candidatus physiological groups, 118 Chloroploca asiatica, 110 Index 483

Chlorothrix halophila, 110 Chloroflexus Elioraea thermophila, 119–121 C. aggregans, 107 Roseilinea gracile, 90, 97, 103, 109 C. aurantiacus, 90, 104, 107, 110, 147, Roseovibrio tepidum, 119 149, 151, 430, 432 Symbiobacter mobilis, 145 Chloroflexus-like bacteria, 462–463 Thermochlorobacter aerophilum, Chlorogloeopsidaceae, 34 115–117 Chloroherpeton thalassium, 116 Capsosiraceae, 35 Chloronema giganteum, 110 Carbamoyl phosphate synthetase Chlorophototrophs, 90–95, 98–103 (see also (CPS), 359 Aerobic chlorophototrophic Carbon assimilation, 354–362 bacteria; Anoxygenic phototrophic Carbon concentrating mechanism (CCM), Proteobacteria; Chloroflexi phylum) 355, 360–362 Chls and BChls, 89 Carbon flux rerouting, 362 FAPs, 97 Carbonic anhydrase, 361 Heliobacterium modesticaldum, 122 Carboxysomal carbonic anhydrase metagenomic and isolation studies, 97 (CsoSCA), 361 oxygenic (see Oxygenic chlorophototrophs) β-Carotene, 88, 104, 107, 108, 110 oxygenic cyanobacteria, 97 γ-Carotene, 88, 104, 108, 110 phyla, 90 Carotenoid-binding protein (CbpA), 113 reaction centers, 89 Carotenoids, 88, 104, 108, 113, 117, 118, 124, in YNP (see Yellowstone National 127, 195, 204, 207–209 Park (YNP)) Chamaesiphon, 15–16 Chlorophyll (Chl) Chemotaxis, 299 Chl a, 89, 101, 113 Chloracidobacterium thermophilum, 90, 97, Chl b, 89 101, 113, 115, 125 Chl d, 89 Chloroacidobacterium thermophilum, Chl f, 89 437–438 Chlorosomes, 103, 108, 110, 113, 116 Chlorobaculum tepidum, 115, 142, 144, 145, Chromatiaceae, 117, 119 433, 438, 442, 447, 469 Chromatiales, 117 Chlorobi, 89, 98, 112, 113, 115, 116, 123 Chroococcales Chlorobiaceae, 142 (see also Green sulfur Aphanothece sensu lato, 16–18 bacteria (GSB)) aquatic and terrestrial environments, 16 Chlorobium (Chl.), 141–143, 145 Chroococcus, 18–19 Chlorochromatium aggregatum, 145 families, 16 Chloroflexaceae, 435 Gloeocapsa, 19 diversity, 147 Gloeothece, 18 ecology, 150, 151 Gomphospaericeae family, 20 FAPs, 147 Microcystis, 16 genomics, 151 Stichosiphonaceae family, 19 photosystems, 149 unicellular cyanobacteria, 16 phylogeny, 148 Chroococcidiopsidales physiology, 149 environments, 20 Chloroflexales, 103, 105, 112 heterocystous cyanobacteria, 20 Chloroflexi phylum Chroococcidiopsis, 222, 225, 226, bacteria, deep-branching lineage, 103 231, 234 Candidatus Chloranaerofilum corporosum, Chroococcus 109–112 aerophytic, subaerophytic/submerged Candidatus Roseilinea gracile, 109 substrates, 18 Chloroflexus sp., 104–108 Chroococcus sensu stricto, 18 chlorophototrophic and non-phototrophic, 103 Limnococcus, 18 FAPs, 103 Clostridial pathway, 375 low and high light conditions, 104 Cold waters. See Sea ice Roseiflexus spp., 104, 105, 107 Combinatorial biosynthesis, 412, 413 484 Index

Combined dark/photofermentation processes keystone species, 225 (co-cultures), 337–339 macro-cyanobacterial taxon, North Complex redox proteins America, 8 active SorAB enzyme, 407 MLST, 7 cofactor-loaded holoproteins, 407 monophyletic species concept, 8 cytochrome oxidase subunit II-encoding morphological traits, 4 gene, 408 myriad secondary metabolites/bioactive FCSD, 408 compounds, 4 FeS clusters, FeMoco and [NiFe] nitrogen fixation, 231 see( also Nostocales; cofactor, 407 Oscillatoriales; Oxygenic fructose-inducible promoter chlorophototrophs) Pfru, 409 oxygenic photosynthesis, 3, 7 heterologous proteins, 407 phylogenetic and morphological HupS subunits, 408 analysis, 225 MADH biosynthesis, 408 phylogenetic reconstructions, 7, 8 periplasmic space location, 407 phylogenomic reconstruction, 9, 10 TREX system, 409 plants, fungi and eukaryotic algae Cross feeding, 221 relationship, 4 Cryptogamic crusts, 220, 223 pleurocapsales, 5, 20–22 CsoSCA. See Carboxysomal carbonic (see also Pleurocapsales) anhydrase (CsoSCA) polyphasic approach, 37 Cyanobacteria primary producers on Earth, 4 aerobic life forms, 3 prokaryotic genome sequencing, 7 akinetes, 5 resuscitation dynamics, 229 arid grasslands, 225 species diversity and evolution, 7 (see also biological activities, 4 Spirulinales; Synechococcales) biological soil crusts, 226 systematics, 8 blooms formation, 4 taxonomy, 5, 6 cell ultrastructures, 5 thylakoids, 7 (see also Chroococcales) tropical regions, 37 Chroococcidiopsidales, 20 unicellular, 5 cryptogenera, 8 UV radiation, 230, 231 desert crusts wastewater plants, 4 Chroococcidiopsis, 234 Cyanobacterial carbon transporter Colorado Plateau, 232 systems, 352 Gloeocapsopsis, 234 Cyanobacterial Hup-hydrogenases, 365 Microcoleus, 233 Cyanolichens Nostocales, 232 ascolichens, 253, 255 Pseudoanabaenales, 234 ascomycetes, 249 desiccation tolerance basidiolichens, 253, 255 dehydration, 227 bipartite cyanolichens, 251 preferential exclusion, 227, 228 cephalodiate cyanolichens, 251 PSII, 228 definition, 248 diversity/endemism based analysis, 36 ecology, 255, 257 endolithic, 227 fungi, 249 environment and human endeavors, 4 lichen thallus evolution, 8 crustose cyanolichens, 249 exopolysaccharides, 229, 230 division, 249 filamentous, 5 fruticose cyanolichens, 249 geothermal environments, 36 genetic regulation, 251 groups, 36 jelly lichens, 251 heterocytes, 5 photosymbiodemes, 253 hypolithic, 226 Cycad symbioses, 269–271 Index 485

D RuBP carboxylation, 355 Dapisostemonaceae, 33 SbtA, 361 Desert crusts secretion mechanisms, 364 biotechnological aspects, 235 stress responses, 364 climate change, 234, 235 Ethanol production, 372–374 Colorado plateau, 219 Exopolysaccharides, 229–230 cyanobacteria, 217, 218, 220, 221, 232 Expression of clustered genes, 397 desiccation, 220, 222 (see also Complex redox proteins) diversity Expression vectors, 397, 415 archaea, 224 Extracellular polysaccharide, 228, 229, 231 bacteria, 223 Extreme environments. See Anoxygenic biogeographic issues, 221 phototrophic bacteria fungi, 224 Extremophilic property, 428 green algae, 222 drylands distribution, 218 GeoChip technology, 220 F hot and cold desert, 219 Fatty acid alkyl ester production, 382–383 Microcoleus vaginatus, 221 Fatty acid derivatives, 377 nitrogen fixation, 220, 221 Fatty acid synthesis (FAS), 378 Desertification, 218, 230 Fatty alcohol production, 380–381 Diatoms, 297, 298 Fenna–Matthew–Olson (FMO), 143 Diazotrophic bacteria, 243 Filamentous anoxygenic chlorophototrophy. Diel cycle, 94, 102, 112, 118, 124 See Chloroflexi phylum Dimethylallyl pyrophosphate (DMAPP), 410 Filamentous anoxygenic phototrophs (FAPs), Dynamic sensor-regulator system (DSRS), 383 97, 103, 147 Firmicutes, 89, 90, 98, 112, 122–123 Fluorescence in situ hybridization E (FISH), 108 Echinenone, 108 Fossil fuel limitation, 351 Ectothiorhodospiraceae, 117, 449 Free fatty acid (FFA), 355 Elioraea tepidiphila, 119 Engineering cyanobacteria alcohols, 371–377 G BicA, 360 Gammaproteobacteria, 449 biofuel compounds, 353 Geitlerinema, 304, 306 biomass accumulation, 354 Gemmatimonadetes, 89, 90, 112, 123 1-butanol production, 375 Gemmatimonas phototrophica, 112, 167 carbonic anhydrase, 361 Genetic instability, 363 CBB cycle, 354 GeoChip technology, 220 CO2/HCO3−transporters, 360–361 Geosiphon pyriformis, 257–259 ethanol, 372 Gliding movement, 299 FAEE production, 383 Gloeocapsa FAS, 378 aerophytic/subaerophytic populations, 19 fatty acid derivatives, 377 colonial cyanobacteria, 19 FeS clusters, 369 genera, 19 fossil fuel limitation, 351 Gloeocapsopsis, 234 Hox-hydrogenase, 369 Gloeothece hydrogen production, 365–371 aerophytic/subaerophytic communities, 18 isopropanol, 374 types, 18 light, 353 Gloeotrichiaceae, 35 N2-fixation, 367 Glycolate, 105, 126 photosynthesis, 352 GNS. See Green nonsulfur bacteria (GNS) PSII/PSI ratios, 354 Godleyaceae, 35 486 Index

G. phototrophica H AP64, 168 Haloalkaliphilic Ectothiorhodospiraceae, bacteriochlorophyll biosynthesis, 459, 460 177–178 Halochromatium glycolicum, 460 biochemical and chemotaxonomic Halophiles, 471 characteristics, 170, 171 Halophilic phototrophic bacteria, 459 carotenoid biosynthesis pathway, 174 Halorhodopsin, 88 chlorophototrophic species, 179 Halorhodospira cultivation and physiology, 170 H. halochloris, 117 gene composition and arrangement, H. halophila, 449 181, 182 Halothece, 227 genome Hapalosiphonaceae, 34 characteristics, 173 Heliobacillus mobilis, 438 cyanophycin, 179 Heliobacteria, 122, 140, 438 orthologs, 178 anoxygenic phototrophs, 152 PGC, 173–175 diversity TBLASTN searching, 178 16S rRNA gene sequences, 154 infra-red epifluorescence microscopy, alkaliphilic, 153 167, 168 morphological variation, 154 Longimicrobium terrae, 168 neutrophilic, 153 morphology, 169, 170 ecology, 155, 156 PGB genomics, 156, 157 acsF fragments, 185, 188 HbRC, 155 alphaproteobacterial AcsF, 187 photoheterotrophic metabolism, 141 gemmatimonadetes-AcsF, 183, 184, 187 photosystems, 151, 154, 155 metagenomes, 184 Heliobacteriaceae. See Heliobacteria methodological limitations, Heliobacterial reaction center (HbRC), 155 182, 183 Heliobacterium modesticaldum, 122, 123, PGCs, 189 152, 156, 438 phylogenetic analysis, 185, 186 Heliorestis, 154, 156 physiology and ecology, 188 H. baculata, 449, 450, 452 photosynthesis genes, 180 H. convoluta, 152 phototrophic properties H. daurensis, 449, 450, 452, 458 carotenoids, 171 Heliothrix oregonensis, 436 infra-red BChl, 171 High temperatures radioactive assays, 173 accumulation, compatible solutes, respiration assays, 172 443–444 phylogenetic analysis, 180 discrepancy, 441 16S rRNA gene sequences, 168 purple nonsulfur bacteria, 441 Green nonsulfur bacteria. See Chloroflexaceae structural adaptation, malate Green nonsulfur bacteria (GNS), 112 dehydrogenase, 442 Green sulfur bacteria (GSB), 115, 116 Horizontal gene transfer, 305 autotrophic, 140 Hot springs. See Thermophilic phototrophic Bchl a, 143 bacteria carotenoid, 143 Hox-hydrogenase, 365, 369, 370 chlorosomes, 140 Hup-hydrogenase, 365, 366 diversity, 141 Hydrogen producing systems ecology, 144, 145 and bioenergy, 322, 323 epibiont, 145 non-nitrogen fixing conditions, 324 genomics, 145, 146 Hydrogenase-PsaE fusion, 371 photosystem, 142 Hydrotaxis, 220 phylogeny, 142 3-Hydroxypropionate bi-cycle, 105, 107, 108, physiology, 143 110, 125, 126 Index 487

I thermophilic phototrophic and halophilic Immobilized systems, 339–340 bacteria, 460 The International Code for Nomenclature of uniform thalassohaline salts Prokaryotes (ICNP), 9 composition, 460 International Committee on Systematics of Membrane proteins Prokaryotes, 63 bacteria-based expression systems, 402 International Energy Agency, 351 biochemical and structural Intracytoplasmic membrane (ICM) characterization, 401

cytoplasmic membrane, O2 availability, 402 from natural sources, 402 photosynthesis apparatus, 396 ICM system, 402, 403 of Rhodobacter, 406 inclusion bodies, 402 vesicles, 403 living cells, physiology, 401 Iron photosynthesis, 310–311 Rba. sphaeroides and Rba. capsulatus, 403 Isopentenyl pyrophosphate (IPP), 410 Rhodobacter, protein expression, 404, 405 Isopropanol pathway, 363 Rhodospirillum rubrum, 405–406 Isopropanol production, 374–375 in vitro and in vivo systems, 402 Merismopedia, 15 Metatranscriptome, 108, 113 K 2-Methyl-d-erythritol 4-phosphate (MEP) Komvophoron genus, 25 pathway, 410 Microbial mats, 150 anaerobic processes, 300 L coastal microbial mat, 296 Leptolyngbya, 228, 229, 234 cyanobacterial/phototrophic, 296 filamentous cyanobacteria, 13 dark energy generation, 299–300 genus Nodosilinea, 13 distribution and migration, 298, 299 genus Oculatella, 13 diversity, 297 habitats, 13 fairy rings, 297, 298 L. laminosa, 102 FeS, 302 monophyly, 14 green sulfur bacteria, 300

Light harvesting system, 195, 207–209, H2 and N2, 300 353–354 living entity, 296 Lower Geyser Basin, 90, 92, 430 Microcoleus chthonoplastes, 303–305

Lyngbya genus, 26, 300 N2 fixation, 302, 303 oxygenic photosynthetic activity, 298 productions report, 297 M purple sulfur bacteria, 300 Mammoth Hot Springs, 103, 119 sulfate-reducing bacteria, 301 Marichromatium gracile, 439 sulfide, 300, 301 Marine salterns Microcoleus, 24, 300 anoxygenic phototrophic purple M. chthonoplastes, 303–305 bacteria, 460 M. vaginatus, 24, 221–223, 225, 226, 229, coastal lagoons, 460 230, 232, 233, 235 evaporation ponds, 458 Microcystis Great Salt Lake and Dead Sea, 464 cosmopolitan, bloom-forming and toxin Guerrero Negro, Baja California salterns, producing genus, 16 462–463 planktic, 16 Lake Chiprana, 463–464 specialized clones, 16 Salar de Atacama (Chile) salt lakes, MoFe-proteins, 367 464–467 Multilocus sequence typing (MLST), 7 Salinas at Santa Pola (Spain), 461–462 Mushroom spring (MS) Salin-de-Giraud salterns (France), 460–461 abiotic factors, 124 salinity, 458 alkaline, siliceous hot springs, 91 488 Index

Mushroom spring (MS) (cont.) heterocytes, 31 carbohydrate storage product, 125 molecular markers, 27 cellular pigments, 124 (see also monophyletic, 29 Chlorophototrophs) Nostocaceae, 35–36 communities and thermal gradient, 123 phylogenetic reconstruction, 31, 32 cyanobacterial photosynthetic activity, 125 Rivulariaceae, 34 dsrAB, 126 Scytonemataceae, 33 environmental parameters, 94 Stigonemataceae, 34 glycolate, 126 Symphyonemataceae, 33 hydrogen, 126 terrestrial, aquatic, subaerial and symbiotic in situ measurements, 94, 95 environments, 29 lipid biomarkers, 127 Tolypothrichaceae, 35 Lower Geyser Basin of YNP, 91, 92 ultrastructural features, 30 metabolic co-dependencies, 124 Nostoc symbiosis, 257–259 microbial ecologists, 90 Novel fermentation systems natural communities, 94 biomass derived substrates, 340–342 nitrogen-rich compounds, 125 co-culture system, 334, 337, 338 nutrients and energy sources, 123 immobilized systems, 339, 340 oxygen, 124 photobiological hydrogen production, 328 physicochemical parameters, 91, 93–94 single stage photofermentation processes, spectral scalar irradiance and absorbance 327–330 spectra, 94, 96 synthetic substrates, 343, 344 sulfate reduction and biogenic sulfide two stage system, 331–333, 335–337 production, 126 Taq DNA polymerase, 91 temperatures, 94 O unicellular, oxygenic and filamentous Octopus spring (OS). See Mushroom spring anoxygenic, 91 (MS) Mycosporine-like amino acids, 298 Oligotrophic soils, 220 Operational taxonomic units (OTUs), 107 Oscillatoria genus, 25–26, 225, 303 N Oscillatoriales

N2 fixation, 221 Geitlerinema sensu lato, 22 Nearest-Neighbor-Interchange (NNI), 148 Komvophoron, 25 NiFe-hydrogenase oxygen tolerance, 370, 371 Lyngbya, 26 Nitrogenase-based hydrogen evolution, 366 Microcoleus, 24 Nitrogenase complex, 367 Oscillatoria, 25–26 Nitrogen fixation, 221, 231, 243, 244 Phormidium sensu lato, 24 Non-coding RNAs (ncRNAs), 363 Planktothrix, 25 Non-halophilic/slightly halophilic bacteria, 428 polyphyletic, 22 Nostocaceae, 35–36 sheath and trichomes characteristics, Nostocales, 232–233 22, 23 akinetes, 27, 28, 31 Symplocastrum, 26 Aphanizomenonaceae, 31–33 Oscillochloris trichoides, 109, 110, 126 aquatic habitats, 29 Osmotic adaptation, 467–468 Capsosiraceae, 35 Oxidosqualene cyclases (OSCs), 410 cell division, types of, 30 2-Oxoglutarate, 113 Chlorogloeopsidaceae, 34 Oxygenic chlorophototrophs cyanobacterial researchers, 27 DGGE and 16S rRNA cloning Dapisostemonaceae, 33 experiments, 102 encountered lentic taxa, 29 MS and OS temperatures, 102 Gloeotrichiaceae, 35 SILVA Ref database release NR 123, 102 Godleyaceae, 35 Synechococcus spp. Hapalosiphonaceae, 34 amtB, narB and nirA, 102 Index 489

cultivation experiments, 101 Phototaxis, 299 cyanobacterial enrichment cultures, Phototrophic purple bacteria 98, 99 alpha-, beta, and gammaproteobacteria, dinitrogen fixation, 98 48, 63 light adaptations, 99 approaches, 61 low-light-adapted strains, 101 bacteriochlorophyll b-containing MS mats, 98, 100 Chromatiaceae, 65 nitrogen fixation, 102 chemoheterotrophic metabolism, 48 PS I and PS II, 98 ecological niches, 48 psaA sequences, ecotypes, 99 Ectothiorhodosinus mongolicus stable and radioactive isotopes, 99 clusters, 65 type A and B′ lineages, 98 environmental communities, 66–68 “uni-cyanobacterial” mixed cultures, 101 environmental samples/enrichment Thermosynechococcus sp., 103 cultures, 49 Oxygenic photosynthesis, 354 families, 64 Oxygen sensitivity, 371 freshwater and marine habitats, 62 functional genes, 67 generas, 49 P habitat, 48 PCC 7942 strain, 358 Baltic Sea Coastal Lagoon, Germany, Pelagibacter ubique, 117 71–73 Pelochromatium roseum, 145 examples, 68 PHA. See Polyhydroxyalkanoates (PHA) Lake Cadagno, Switzerland, 70–71 PHB. See Polyhydroxybutyrate (PHB) Sippewissett Salt Marsh, MA, USA, Phormidium, 225, 233 68–70 P. laminosum, 102 halophilic, 62 P. sensu lato heterogeneity of species, 61 Coleofasciculus, 24 marine and freshwater habitats, 56–60 Oxynema, 24 phenotypic and genetic similarities, 61 phylogenetic analysis, 24 ribosomal RNA sequences, 49 polyphyletic species, 24 saline and alkaline conditions, 65 Wilmottia, 24 species-specific diversity, 61 Phosphoenolpyruvate carboxylase (PEPc), 16S rRNA gene, 62 355, 359 sulfur vs. nonsulfur bacteria, 48 Photobiological hydrogen production, 371 taxonomic characterization, 62 Photobioreactors, 327 Phototrophs, 89 Photofermentation, 326 chlorophototrophs (see Chlorophototrophs) Photosynthesis retinalophototrophs, 88 FeS-based (type-1) reaction, 164 Phycocyanin, 7, 96, 98, 124 pheophytin-quinone (type-2) reaction, Phycoerythrin, 98 164–165 Phycoerythrocyanin, 98 Photosynthesis gene cluster (PGC) Planktothrix genus, 25 comparison, 181 Plectonema, 225 gemmatimonadetes-PGCs, 189 Pleurocapsales gene composition and arrangement, 181, 182 genome sequencing placed genome, 173, 175, 179 pleurocapsalean cyanobacteria, 20 Photosynthetic microorganisms, 352, 354, 364 Myxosarcina genus, 21 Photosynthetic α-proteobacteria, 401–409 order Chroococcales, 20, 21 photopigments, 396 PCC strains, 20, 21 photosynthetic complexes, 396 (see also Stanieria genus, 21 Recombinant carotenoid pathways; Xenococcus sequences, 22 Rhodobacter species) Polyhydroxyalkanoates (PHA), 125 target proteins (see Target proteins) Polyhydroxybutyrate (PHB), 325 Photosystem (PS) I and II reaction centers, 89 Polysulfide, 301, 308 490 Index

Prochlorococcus enriched membrane fractions, 404 ecological importance and evolutionary gene expression, vectors for, 397–400 impact, 12 gene in trans expression and synthetic ecotypes, 13 operons, 396 monophyletic, 13 gram-negative expression, 397 oligotrophic cyanobacterium, 12 heterologous production, 404 Proteobacteria, 89, 90, 98, 112 highly versatile, 396 Proteomics analysis, 370 membrane anchor, 406 Proteorhodopsin, 88, 89 metabolic network, 396 psaA sequences, 99 microbial and human membrane proteins, 405 PscA polypeptides, 113, 115 oriT, mob site, 397 PscB polypeptides, 113 plasmid-borne gene expression, 404

Pseudanabaena prominent Plac and PT7 promoters, 397 chromatoplasma, 14 PufX, Rhodobacter RC-LHI complex, 406 planktic cyanobacterium, 14 Rba. sphaeroides, 397 plankton and water bodies, 14 RBS, 397 polyphyletic, 14 recombinant puc promoter, 406 Pseudoanabaenales, 234 soluble proteins, 406 Purple non sulfur bacteria (PNSB), 117, 118, SQRs, 404 122, 311, 440–441 β subunit, LHII complex, 406 microanaerobic nitrogenase activity, 325 terpenoids, 414–416 PHB, 325 Rhodocista centenaria, 440 photofermentation process, 325 Rhodospirillum rubrum, 405–406 TCA cycle, 324 Rhodothalassium salexigens, 460 VFA, 326 Rhodovulum sulfidophilum, 404 Ribulose-1,5-biphosphate (RuBP) regeneration carboxylation, 355 R CBB cycle-based CO2 assimilation, R248H strain, 368 354–355 Reaction Centers (RCs), 89 regeneration capacity, 358 Recombinant carotenoid pathways Rivulariaceae, 34 amino acid residues, 413 Roseiflexus spp., 147–151, 430 colorimetric whole-cell biosensors, 414 β-carotene biosynthesis, 107 foreign isoprenoids, 412 genes encoding, 105 high-resolution NMR analysis, 414 mat photomixotrophy, 105 host desaturase CrtI, 413 metatranscriptomic analyses, 105 nutraceutical and pharmaceutical mushroom spring mats, 105, 106 applications, 413 putative ecological species, 107 species, 413 16S rRNA oligonucleotide probes, 105 terpenoid pathways, 411, 413 R. castenholzii, 436–437 TREX system, 413 temperature, light and chemical profiles, 107 Redox proteins. See Complex redox proteins undermat community and upper green Retinalophototrophs layer, 104 bop and blh genes, 88 RuBisCO, 110, 117, 195, 201, 307, disadvantages, 88 355–362, 408 light-induced trans-to-cis isomerization, 88 in marine environments, 88 physiological studies, 89 S retinal-binding proteins, 88 Salt lakes. See Marine salterns Reverse TCA cycle, 144 SbtA activity, 361 Rhodobaca/Rhodovulum, 449 Schizothrix, 225 Rhodobacter species Scytonema, 225, 226, 230–232 A2aR, AT1aR and B2R, 405 Scytonemataceae, 33 BioBrickTM compatible expression, 397 Scytonemin, 298 Index 491

Sea ice Tellurite, 203–205 Antarctic lakes and Fjords, 445–447 Terpenoids bacterial communities, 444 applications, 409 Baltic sea ice, 444–445 biosynthesis of, 410–412 deep ocean, 444 carotenoids, 412 dense microbial communities, 444 metabolites, 409 Sequential dark/photofermentation plant-based production processes, 335 routes, 412 Chlorella pyrenoidosa and cassava with Rhodobacter, 414–416 starch, 337 tailor-made phototrophic cell dark fermentation, 335 factories, 412 hydrogen production, 335 terpenes/isoprenoids, 409 hydrogenase, 335 Terrestrial symbiotic systems OMWW, 336 cyanobacterial adaptations photobiological hydrogen production, 336 Azolla, 248 thermophilic conditions, 336 hormogonium-repressing Spirulinales factors, 247 morphology and high halotolerance, 27 nonribosomal peptides, 248 solitary/colonial (mats), 27 Nostoc, 246, 247 trichomes/motile hormogonia, 27 vegetative cells, 247 Squalene epoxidase (SQE), 410 evolution, 276–278 Squalene synthase (SQS), 410 lichens (see Cyanolichens) Stigonemataceae, 34 nitrogen, 244 Sulfide-quinone reductases (SQRs), 404 Thermochromatium tepidum, 431, 439 Symbiotic cyanobacteria, 244–246 Thermophiles, 469 Symbiotic Nostoc, 246 Thermophilic phototrophic bacteria, 433 Symphyonemataceae, 33 Chloroacidobacterium thermophilum Symplocastrum genus, 26 (51 °C), 437–438 Synechococcales Chlorobaculum tepidum (48 °C), 438 Acaryochloris marina, 15 Chloroflexus and Chloroflexus aurantiacus Chamaesiphon, 15–16 (55 °C), 432–435 Leptolyngbya, 13–14 cyanobacteria, 430 Merismopedia, 15 green and purple sulfur bacteria, 430 parietal thylakoid arrangement, 9 Heliobacteria and Heliobacterium Prochlorococcus, 12, 13 modesticaldum (52 °C), 438 Pseudanabaena, 14 Heliothrix oregonensis, 436 Synechococcus, 11–13 Marichromatium gracile (<44 °C), 439 Synechocystis, 14–15 microbial mats, 430 unicellular and filamentous cyanobacteria, 9 purple nonsulfur bacteria (38–42 °C), Synechococcus, 226 440–441 clades of, 11, 12 Roseiflexus castenholzii (45–55 °C), hot springs, 11 436–437 pseudofilaments and involuted cells, 11 sulfide-dependent photoautotrophic Thermosynechococcus, 11 growth, 431 Synechocystis, 14–15 temperature tolerance, 430 Synthetic pathways, 376 Thermochromatium tepidum Synthetic substrates, 343, 344 (50 °C), 439 Yellowstone, 431–432 Thiocapsa, 301, 309 T Tolypothrichaceae, 35 Tamura–Nei model, 148 Tracheophytes, 276 Target proteins Transcriptomic responses, 363 complex redox (see Complex redox proteins) Transketolase (TK), 359 membrane (see Membrane proteins) Trehalose, 227, 228, 234 492 Index

Tricarboxylic acid (TCA) cycle, 324 Y Type-1 reaction centers (RCs), 89, 113, 116, Yellowstone National Park (YNP), 90, 431 165, 166, 180, 437 microbiological research, 90 Type-2 reaction centers (RCs), 89, 103, 108, MS (see Mushroom spring (MS)) 117, 165, 166, 180 OS (see Octopus spring (OS))

W Z Waste disposal, 342 Zymomonas mobilis, 373