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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 © Springer International Publishing Switzerland 2017 481 P.C. Hallenbeck (ed.), Modern Topics in the Phototrophic Prokaryotes, DOI 10.1007/978-3-319-46261-5 482 Index 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
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  • The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment

    The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment

    life Article The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment Sierra R. Athen, Shivangi Dubey and John A. Kyndt * College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; [email protected] (S.R.A.); [email protected] (S.D.) * Correspondence: [email protected] Abstract: The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique Citation: Athen, S.R.; Dubey, S.; inland salt marsh environment.
  • A Novel Species of the Marine Cyanobacterium Acaryochloris With

    A Novel Species of the Marine Cyanobacterium Acaryochloris With

    www.nature.com/scientificreports OPEN A novel species of the marine cyanobacterium Acaryochloris with a unique pigment content and Received: 12 February 2018 Accepted: 1 June 2018 lifestyle Published: xx xx xxxx Frédéric Partensky 1, Christophe Six1, Morgane Ratin1, Laurence Garczarek1, Daniel Vaulot1, Ian Probert2, Alexandra Calteau 3, Priscillia Gourvil2, Dominique Marie1, Théophile Grébert1, Christiane Bouchier 4, Sophie Le Panse2, Martin Gachenot2, Francisco Rodríguez5 & José L. Garrido6 All characterized members of the ubiquitous genus Acaryochloris share the unique property of containing large amounts of chlorophyll (Chl) d, a pigment exhibiting a red absorption maximum strongly shifted towards infrared compared to Chl a. Chl d is the major pigment in these organisms and is notably bound to antenna proteins structurally similar to those of Prochloron, Prochlorothrix and Prochlorococcus, the only three cyanobacteria known so far to contain mono- or divinyl-Chl a and b as major pigments and to lack phycobilisomes. Here, we describe RCC1774, a strain isolated from the foreshore near Roscof (France). It is phylogenetically related to members of the Acaryochloris genus but completely lacks Chl d. Instead, it possesses monovinyl-Chl a and b at a b/a molar ratio of 0.16, similar to that in Prochloron and Prochlorothrix. It difers from the latter by the presence of phycocyanin and a vestigial allophycocyanin energetically coupled to photosystems. Genome sequencing confrmed the presence of phycobiliprotein and Chl b synthesis genes. Based on its phylogeny, ultrastructural characteristics and unique pigment suite, we describe RCC1774 as a novel species that we name Acaryochloris thomasi. Its very unusual pigment content compared to other Acaryochloris spp.