Abstract
A novel thermophilic and sulfur-reducing bacterium, strain S304T, was isolated from the Taketomi submarine hot spring shallow hydrothermal field located at southern part of the Yaeyama Archipelago, Japan. The cells were non-motile short thick rods or oval cocci 1.1–2.7 μm in length and 1.1–1.9 μm in width. Strain S304T was an obligately anaerobic heterotroph and sulfur reduction stimulates growth. Growth was observed between 50–65°C (optimum 60°C), pH 6.2–8.0 (optimum pH 7.1), 1.0–6.0% NaCl concentration (optimum 3.0%). The fatty acid composition was C16:0 (71.4%), C18:0 (20.9%) and C18:1 (7.7%). The G + C content of genomic DNA was 40.8 mol%. The 16S rRNA gene sequence analysis indicated that strain S304T belonged to the genus Kosmotoga. Based on physiological and phylogenetic features of a new isolate, we propose new species in the genus Kosmotoga: the type strain of Kosmotoga arenicorallina sp. nov is S304T (=JCM 15790T = DSM22549T). Thermococcoides shengliensis 2SM-2T is phylogenetically associated with Kosmotoga olearia 14.5.1T. Based on the phylogenetic relationship between Thermococcoides shengliensis 2SM-2T and Kosmotoga olearia 14.5.1T, we propose the reclassification of Thermococcoides shengliensis as Kosmotoga shengliensis comb. nov. (type strain 2SM-2T). In addition, an emended description of the genus Kosmotoga is proposed.
Similar content being viewed by others
References
Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56:1919–1925
Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS (1979) Methanogens: reevaluation of a unique biological group. Microbiol Rev 43:260–296
Balk M, Weijma J, Stams AJM (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
Briones AM, Daugherty BJ, Angenent LT, Rausch KD, Tumbleson ME, Raskin L (2007) Microbial diversity and dynamics in multi- and single-compartment anaerobic bioreactors processing sulfate-rich waste streams. Environ Microbiol 9:93–106
Daims H, Brühl A, Amann RI, Schleifer K, Wagner M (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
Davey ME, Wood WA, Key R, Nakamura K, Stahl D (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
DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685–5689
DiPippo JL, Nesbø CL, Dahle H, Doolittle WF, Birkland NK, Noll KM (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
Eisen JA (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
Feng Y, Cheng L, Zhang X, Li X, Deng Y, Zhang H (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
Furushima Y, Nagao M, Suzuki A, Yamamoto H, Maruyama T (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
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
Hirayama H, Sunamura M, Takai K, Nunoura T, Noguchi T, Oida H, Furushima Y, Yamamoto H, Oomori T, Horikoshi K (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
Huber R, Langworthy TA, Kölnig H, Thomm M, Woese CR, Sleytr UB, Stetter KO (1986) Thermotoga maritima sp. nov. represents a new genus of uniquely extremely thermophilic eubacteria growing up to 90°C. Arch Microbiol 144:324–333
Huber R, Woese CR, Langworthy TA, Fricke H, Stetter KO (1989) Thermosipho africanus gen. nov represents a new genus of thermophilic eubacteria within the ‘‘Thermotogales’’. Syst Appl Microbiol 12:32–37
Kubota K, Ohashi A, Imachi H, Harada H (2006) Improved in situ hybridization efficiency with locked-nucleic-acid-incorporated DNA probes. Appl Environ Microbiol 72:5311–5317
Lane DJ (1985) 16S–23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Techniques in bacterial systematics. Wiley, Chichester, pp 115–175
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948
Lauerer G, Kristjansson JK, Langworthy TA, König H, Stetter KO (1986) Methanothermus sociabilis sp. nov a second species within the Methanothermaceae growing at 97°C. Syst Appl Microbiol 8:100–105
Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar BA, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüßmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371
Nakagawa S, Inagaki F, Suzuki Y, Steinsbu BO, Lever MA, Takai K, Engelen B, Sako Y, Wheat CG, Horikoshi K, 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
Nakamura T, Yamazaki SS, Sakai K, Yamasaki H, Furushima Y, Yamamoto H (2006) Acroporid corals growing over a methane-bubbling hydrothermal vent, Southern Ryukyu Archipelago. Coral Reefs 25:382
Nesbø CL, Dlutek M, Zhaxybayeva O, Doolittle WF (2006) Evidence for existence of “mesotogas”, members of the order Thermotogales adapted to low-temperature environments. Appl Environ Microbiol 72:5061–5068
Patel BKC, Morgan HW, Daniel RM (1985) Fervidobacterium nodosum gen. nov. and spec. nov a new chemoorganotrophic, caldoactive, anaerobic bacterium. Arch Microbiol 141:63–69
Porter KG, Feig YS (1980) The use of DAPI for identifying and counting microflora. Limnol Oceanogr 25:943–948
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
Sako Y, Takai K, Ishida Y, Uchida A, Katayama Y (1996) Rhodothermus obamensis sp. nov a modern lineage of extremely thermophilic marine bacteria. Int J Syst Bacteriol 46:1099–1104
Sekiguchi Y, Kamagata Y, Nakamura K, Ohashi A, Harada H (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
Takai K, Sugai A, Itoh T, Horikoshi K (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
Takai K, Hirayama H, Nakagawa T, Suzuki Y, Nealson KH, Horikoshi K (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
Takai K, Miyazaki M, Nunoura T, Hirayama H, Oida H, Furushima Y, Yamamoto H, Horikoshi K (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
Tamaoka J, Komagata K (1984) Determination of DNA base composition by reverse-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128
Thompson CC, Thompson FL, Vandemeulebroecke K, Hoste B, Dawyndt P, Swings J (2004) Use of recA as an alternative phylogenetic marker in the family Vibrionaceae. Int J Syst Evol Microbiol 54:919–924
Urios L, Cueff-Gauchard V, Pignet P, Postec A, Fardeau ML, Ollivier B, Barbier G (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
Wery N, Lesongeur F, Pignet P, Derennes V, Cambon-Bonavita MA, Godfroy A, Barbier G (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
Yamamoto S, Harayama S (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
Acknowledgments
We would like to thank Dr Katsuyuki Uematsu for assistance in taking electron micrographs. Part of this study was supported by Grant-in-Aid from the Ministry of Education, Culture, Sports, Science & Technology of Japan (No. 18658135).
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by Harald Huber.
Rights and permissions
About this article
Cite this article
Nunoura, T., Hirai, M., Imachi, H. et al. 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. Arch Microbiol 192, 811–819 (2010). https://doi.org/10.1007/s00203-010-0611-7
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00203-010-0611-7