Kosmotoga arenicorallina sp. nov. a thermophilic and obligately anaerobic heterotroph isolated from a shallow hydrothermal system occurring within a coral reef, southern part of the Yaeyama Archipelago, Japan, reclassification of Thermococcoides shengliensis as Kosmotoga shengliensis comb. nov., and emended description of the genus Kosmotoga

Archives of Microbiology

Volumn 192, Issue 10, 2010, Pages 811-819

  Nunoura, Takuro ^a   Hirai, Miho ^a   Imachi, Hiroyuki ^a   Miyazaki, Masayuki ^a   Makita, Hiroko ^a   Hirayama, Hisako ^a   Furushima, Yasuo ^a   Yamamoto, Hiroyuki ^a   Takai, Ken ^a  

^a JAPAN AGENCY FOR MARINE EARTH SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

Anaerobe; Hydrothermal; Kosmotoga; Thermococcoides; Thermophile; Thermotogales

Indexed keywords

RNA 16S; SODIUM CHLORIDE;

ANAEROBIC BACTERIUM; ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATE; CORAL REEF; DNA BASE COMPOSITION; GENE SEQUENCE; GRAM NEGATIVE ANAEROBIC BACTERIA; HYDROTHERMAL VENT SPECIES; JAPAN; KOSMOTOGA ARENICORALLINA; KOSMOTOGA OLEARIA; KOSMOTOGA SHENGLIENSIS; LIPID COMPOSITION; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; THERMOCOCCOIDES SHENGLIENSIS; THERMOPHILIC BACTERIUM; THERMOTOGALES;

BACTERIA, ANAEROBIC; BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; CORAL REEFS; CULTURE MEDIA; DNA, BACTERIAL; GENES, BACTERIAL; HOT TEMPERATURE; JAPAN; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; SULFUR-REDUCING BACTERIA; WATER MICROBIOLOGY;

ANTHOZOA; BACTERIA (MICROORGANISMS); OLEARIA; THERMOTOGALES;

EID: 77957885245     PISSN: 03028933     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00203-010-0611-7     Document Type: Article

References (36)

1. RI Amann BJ Binder RJ Olson SW Chisholm R Devereux DA Stahl 1990 Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations Appl Environ Microbiol 56 1919 1925 1:CAS:528:DyaK3cXkvFCgsrs%3D 2200342
2. WE Balch GE Fox LJ Magrum CR Woese RS Wolfe 1979 Methanogens: reevaluation of a unique biological group Microbiol Rev 43 260 296 1:CAS:528:DyaE1MXkvVKqurc%3D 390357
3. M Balk J Weijma AJM Stams 2002 Thermotoga lettingae sp. nov a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor Int J Syst Evol Microbiol 52 1361 1368 1:CAS:528: DC%2BD38Xmt1Grs70%3D 10.1099/ijs.0.02165-0 12148651 (Pubitemid 34851237)
4. AM Briones BJ Daugherty LT Angenent KD Rausch ME Tumbleson L Raskin 2007 Microbial diversity and dynamics in multi- and single-compartment anaerobic bioreactors processing sulfate-rich waste streams Environ Microbiol 9 93 106 1:CAS:528:DC%2BD2sXis1SltLk%3D 10.1111/j.1462-2920.2006.01119.x 17227415 (Pubitemid 46059002)
5. H Daims A Brühl RI Amann K Schleifer M Wagner 1999 The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set Syst Appl Microbiol 22 434 444 1:CAS:528:DyaK1MXmvVentrw%3D 10553296
6. ME Davey WA Wood R Key K Nakamura D Stahl 1993 Isolation of three species of Geotoga and Petrotoga: two new genera, representing a new lineage in the bacterial line of descent distantly related to the 'Thermotogales' Syst Appl Microbiol 16 191 200
7. EF DeLong 1992 Archaea in coastal marine environments Proc Natl Acad Sci USA 89 5685 5689 1:CAS:528:DyaK38Xks1Kntrs%3D 10.1073/pnas.89.12.5685 1608980
8. JL DiPippo CL Nesbø H Dahle WF Doolittle NK Birkland KM Noll 2009 Kosmotoga olearia gen. nov sp. nov a thermophilic, anaerobic heterotroph isolated from Troll B oil production fluid in the North Sea Int J Syst Evol Microbiol 59 2991 3000 1:CAS:528:DC%2BC3cXhtFOltbk%3D 10.1099/ijs.0.008045-0 19643902
9. JA Eisen 1995 The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species J Mol Evol 41 1105 1123 1:CAS:528:DyaK28XivFOguw%3D%3D 10.1007/BF00173192 8587109
10. Y Feng L Cheng X Zhang X Li Y Deng H Zhang 2010 Thermococcoides shengliensis gen. nov representing a novel genus of the order Thermotogales from oil-production fluid Int J Syst Evol Microbiol 60 932 937 1:CAS:528: DC%2BC3cXmvFWns7g%3D 10.1099/ijs.0.013912-0 19661500
11. Y Furushima M Nagao A Suzuki H Yamamoto T Maruyama 2009 Periodic behavior of the bubble jet (geyser) in the Taketomi submarine hot springs of the southern part of Yaeyama Archipelago, Japan Marine Technol Soc J 43 13 22 10.4031/MTSJ.43.3.1
12. Gillis M, Vandamme P, De Vos P, Swings J, Kersters K (2001) Polyphasic taxonomy. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1 (The Archaea and the deeply branching and phototrophic Bacteria). Springer, New York, pp 43-48
13. H Hirayama M Sunamura K Takai T Nunoura T Noguchi H Oida Y Furushima H Yamamoto T Oomori K Horikoshi 2007 Culture-dependent and -independent characterization of microbial communities associated with a shallow submarine hydrothermal system occurring within a coral reef off Taketomi Island, Japan Appl Environ Microbiol 73 7642 7656 1:CAS:528:DC%2BD2sXhsVeisL3J 10.1128/AEM.01258-07 17921273
14. R Huber TA Langworthy H Kölnig M Thomm CR Woese UB Sleytr KO Stetter 1986 Thermotoga maritima sp. nov. represents a new genus of uniquely extremely thermophilic eubacteria growing up to 90°C Arch Microbiol 144 324 333 1:CAS:528:DyaL28Xktlyqsr8%3D 10.1007/BF00409880
15. R Huber CR Woese TA Langworthy H Fricke KO Stetter 1989 Thermosipho africanus gen. nov represents a new genus of thermophilic eubacteria within the ''Thermotogales'' Syst Appl Microbiol 12 32 37
16. K Kubota A Ohashi H Imachi H Harada 2006 Improved in situ hybridization efficiency with locked-nucleic-acid-incorporated DNA probes Appl Environ Microbiol 72 5311 5317 1:CAS:528:DC%2BD28XosVKls7o%3D 10.1128/AEM.03039-05 16885281
17. Lane DJ (1985) 16S-23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Techniques in bacterial systematics. Wiley, Chichester, pp 115-175
18. MA Larkin G Blackshields NP Brown R Chenna PA McGettigan H McWilliam F Valentin IM Wallace A Wilm R Lopez JD Thompson TJ Gibson DG Higgins 2007 Clustal W and Clustal X version 2.0 Bioinformatics 23 2947 2948 1:CAS:528: DC%2BD2sXhtlaqsL%2FM 10.1093/bioinformatics/btm404 17846036 (Pubitemid 350162903)
19. G Lauerer JK Kristjansson TA Langworthy H König KO Stetter 1986 Methanothermus sociabilis sp. nov a second species within the Methanothermaceae growing at 97°C Syst Appl Microbiol 8 100 105
20. W Ludwig O Strunk R Westram L Richter H Meier BA Yadhukumar T Lai S Steppi G Jobb W Förster I Brettske S Gerber AW Ginhart O Gross S Grumann S Hermann R Jost A König T Liss R Lümann M May B Nonhoff B Reichel R Strehlow A Stamatakis N Stuckmann A Vilbig M Lenke T Ludwig A Bode KH Schleifer 2004 ARB: a software environment for sequence data Nucleic Acids Res 32 1363 1371 1:CAS:528:DC%2BD2cXhvFSqu7k%3D 10.1093/nar/gkh293 14985472 (Pubitemid 38854737)
21. S Nakagawa F Inagaki Y Suzuki BO Steinsbu MA Lever K Takai B Engelen Y Sako CG Wheat K Horikoshi Integrated Ocean Drilling Program Expedition 301 Scientists 2006 Microbial community in black rust exposed to hot ridge flank crustal fluids Appl Environ Microbiol 72 6789 6799 1:CAS:528:DC%2BD28XhtFalsLnI 10.1128/AEM.01238-06 17021232 (Pubitemid 44582923)
22. T Nakamura SS Yamazaki K Sakai H Yamasaki Y Furushima H Yamamoto 2006 Acroporid corals growing over a methane-bubbling hydrothermal vent, Southern Ryukyu Archipelago Coral Reefs 25 382 10.1007/s00338-006-0107-8 (Pubitemid 44098579)
23. CL Nesbø M Dlutek O Zhaxybayeva WF Doolittle 2006 Evidence for existence of "mesotogas", members of the order Thermotogales adapted to low-temperature environments Appl Environ Microbiol 72 5061 5068 10.1128/AEM.00342-06 16820506 (Pubitemid 44078839)
24. BKC Patel HW Morgan RM Daniel 1985 Fervidobacterium nodosum gen. nov. and spec. nov a new chemoorganotrophic, caldoactive, anaerobic bacterium Arch Microbiol 141 63 69 1:CAS:528:DyaL2MXhsVGrs7k%3D 10.1007/BF00446741 (Pubitemid 15139561)
25. KG Porter YS Feig 1980 The use of DAPI for identifying and counting microflora Limnol Oceanogr 25 943 948 10.4319/lo.1980.25.5.0943
26. Reysenbach A-L (2001) Phylum BII. Thermotogae phy. nov. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey's manual of systematic bacteriology, 2nd edn, vol. 1 (The Archaea and the deeply branching and phototrophic Bacteria). Springer, New York, pp 369-387
27. Y Sako K Takai Y Ishida A Uchida Y Katayama 1996 Rhodothermus obamensis sp. nov a modern lineage of extremely thermophilic marine bacteria Int J Syst Bacteriol 46 1099 1104 1:STN:280:DyaK2s%2Fhs1yitA%3D%3D 10.1099/00207713-46-4- 1099 8863442
28. Y Sekiguchi Y Kamagata K Nakamura A Ohashi H Harada 1999 Fluorescence in situ hybridization using 16S rRNA-targeted oligonucleotides reveals localization of methanogens and selected uncultured bacteria in mesophilic and thermophilic sludge granules Appl Environ Microbiol 65 1280 1288 1:CAS:528:DyaK1MXhslWku7g%3D 10049894
29. K Takai A Sugai T Itoh K Horikoshi 2000 Palaeococcus ferrophilus gen. nov sp. nov a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney Int J Syst Evol Microbiol 50 489 500 1:CAS:528:DC%2BD3cXivFaju70%3D 10758851
30. K Takai H Hirayama T Nakagawa Y Suzuki KH Nealson K Horikoshi 2005 Lebetimonas acidiphila gen. nov sp. nov a novel thermophilic, acidophilic, hydrogen-oxidizing chemolithoautotroph within the 'Epsilonproteobacteria', isolated from a deep-sea hydrothermal fumarole in the Mariana Arc Int J Syst Evol Microbiol 55 183 189 1:CAS:528:DC%2BD2MXhs1aqsL4%3D 10.1099/ijs.0.63330-0 15653874 (Pubitemid 40185490)
31. K Takai M Miyazaki T Nunoura H Hirayama H Oida Y Furushima H Yamamoto K Horikoshi 2006 Sulfurivirga caldicuralii gen. nov sp. nov a novel microaerobic, thermophilic, thiosulfate-oxidizing chemolithoautotroph, isolated from a shallow marine hydrothermal system occurring in a coral reef, Japan Int J Syst Evol Microbiol 56 1921 1929 1:CAS:528:DC%2BD28XhtVSrsrbK 10.1099/ijs.0.64297-0 16902032 (Pubitemid 44288422)
32. J Tamaoka K Komagata 1984 Determination of DNA base composition by reverse-phase high-performance liquid chromatography FEMS Microbiol Lett 25 125 128 1:CAS:528:DyaL2MXitVGktg%3D%3D 10.1111/j.1574-6968.1984.tb01388.x
33. CC Thompson FL Thompson K Vandemeulebroecke B Hoste P Dawyndt J Swings 2004 Use of recA as an alternative phylogenetic marker in the family Vibrionaceae Int J Syst Evol Microbiol 54 919 924 1:CAS:528:DC%2BD2cXlt1emt7w%3D 10.1099/ijs.0.02963-0 15143042 (Pubitemid 38779711)
34. L Urios V Cueff-Gauchard P Pignet A Postec ML Fardeau B Ollivier G Barbier 2004 Thermosipho atlanticus sp. nov a novel member of the Thermotogales isolated from a Mid-Atlantic Ridge hydrothermal vent Int J Syst Evol Microbiol 54 1953 1957 1:CAS:528:DC%2BD2cXhtFGjs7rK 10.1099/ijs.0.63069-0 15545417 (Pubitemid 39585374)
35. N Wery F Lesongeur P Pignet V Derennes MA Cambon-Bonavita A Godfroy G Barbier 2001 Marinitoga camini gen. nov., sp. nov., a rod-shaped bacterium belonging to the order Thermotogales, isolated from a deep-sea hydrothermal vent Int J Syst Evol Microbiol 51 495 504 1:CAS:528:DC%2BD3MXivVOrur4%3D 11321096
36. S Yamamoto S Harayama 1998 Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes Int J Syst Bacteriol 48 813 819 1:CAS:528:DyaK1cXmt1Sgsb8%3D 10.1099/00207713-48-3-813 9734035