1887

Abstract

A novel mesophilic, facultatively anaerobic, sulfur-oxidizing bacterial strain, designated gps61, was isolated from a surface rock sample collected from the hydrothermal field of Suiyo Seamount on the Izu-Bonin Arc in the Western Pacific Ocean. Cells of the isolate were rod-shaped with a single sheathed polar flagellum. Neither extensive internal membranes nor storage materials were present in the cells. In a 20 % CO atmosphere, strain gps61 grew using thiosulfate, sulfur or tetrathionate as electron donors and oxygen or nitrate as electron acceptors. Other substrates, including organic acids and sugars, did not support growth, indicating that strain gps61 was an obligate chemolithoautotroph. 16S rRNA gene sequence analysis revealed that strain gps61 was closely related to 106 (98.5 % sequence similarity) in the order . Phylogenetic trees grouped strain gps61 and in the same cluster along with and , but it was apparent from the analysis that the novel strain had definitely departed from the family lineage. On the basis of its phylogenetic position along with its morphological and physiological characteristics, strain gps61 ( = NBRC 101261  = DSM 18546) represents a novel species of the genus , for which the name sp. nov. is proposed. In addition, we propose a novel family name, , in the order , to accommodate the genera , and .

Funding
This study was supported by the:
  • Ministry of Education, Science & Technology (MEST) of Japan
  • Special Coordination Fund ‘Archaean Park Project’: International Research Project on Interaction Between SubVent Biosphere and Geo-Environments
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2011-10-01
2024-12-02
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References

  1. Adachi J., Hasegawa M. 1995; Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: heterogeneity among amino acid sites. J Mol Evol 40:622–628 [View Article][PubMed]
    [Google Scholar]
  2. Arakawa S., Sato T., Sato R., Zhang J., Gamo T., Tsunogai U., Hirota A., Yoshida Y., Usami R. et al. 2006; Molecular phylogenetic and chemical analyses of the microbial mats in deep-sea cold seep sediments at the northeastern Japan Sea. Extremophiles 10:311–319 [View Article][PubMed]
    [Google Scholar]
  3. Ashelford K. E., Chuzhanova N. A., Fry J. C., Jones A. J., Weightman A. J. 2006; New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72:5734–5741 [View Article][PubMed]
    [Google Scholar]
  4. Brinkhoff T., Muyzer G., Wirsen C. O., Kuever J. 1999; Thiomicrospira chilensis sp. nov., a mesophilic obligately chemolithoautotrophic sulfur-oxidizing bacterium isolated from a Thioploca mat. Int J Syst Bacteriol 49:875–879 [View Article][PubMed]
    [Google Scholar]
  5. Cavanaugh C. M., Gardiner S. L., Jones M. L., Jannasch H. W., Waterbury J. B. 1981; Prokaryotic cells in the hydrothermal vent tube worm Riftia pachyptila Jones: possible chemoautotrophic symbionts. Science 213:340–342 [View Article][PubMed]
    [Google Scholar]
  6. Corre E., Reysenbach A. L., Prieur D. 2001; ϵ-Proteobacterial diversity from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge. FEMS Microbiol Lett 205:329–335[PubMed]
    [Google Scholar]
  7. Di Meo C. A., Wilbur A. E., Holben W. E., Feldman R. A., Vrijenhoek R. C., Cary S. C. 2000; Genetic variation among endosymbionts of widely distributed vestimentiferan tubeworms. Appl Environ Microbiol 66:651–658 [View Article][PubMed]
    [Google Scholar]
  8. Distel D., Felbeck H., Cavanaugh C. 1994; Evidence for phylogenetic congruence among sulfur-oxidizing chemoautotrophic bacterial endosymbionts and their bivalve hosts. J Mol Evol 38:533–542 [View Article]
    [Google Scholar]
  9. Durand P., Reysenbach A.-L., Prieur D., Pace N. 1993; Isolation and characterization of Thiobacillus hydrothermalis sp. nov., a mesophilic obligately chemolithotrophic bacterium isolated from a deep-sea hydrothermal vent in Fiji Basin. Arch Microbiol 159:39–44 [View Article]
    [Google Scholar]
  10. Ezaki T., Hashimoto Y., Takeuchi N., Yamamoto H., Liu S. L., Miura H., Matsui K., Yabuuchi E. 1988; Simple genetic method to identify viridans group streptococci by colorimetric dot hybridization and fluorometric hybridization in microdilution wells. J Clin Microbiol 26:1708–1713[PubMed]
    [Google Scholar]
  11. Ezaki T., Hashimoto Y., Yabuuchi E. 1989; Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229 [View Article]
    [Google Scholar]
  12. Felbeck H. 1981; Chemoautotrophic potential of the hydrothermal vent tube worm, Riftia pachyptila Jones (Vestimentifera). Science 213:336–338 [View Article][PubMed]
    [Google Scholar]
  13. Feldman R. A., Black M. B., Cary C. S., Lutz R. A., Vrijenhoek R. C. 1997; Molecular phylogenetics of bacterial endosymbionts and their vestimentiferan hosts. Mol Mar Biol Biotechnol 6:268–277[PubMed]
    [Google Scholar]
  14. Glasby G. P., Iizasa K., Yuasa M., Usui A. 2000; Submarine hydrothermal mineralization on the Izu-Bonin Arc, south of Japan: an overview. Mar Georesour Geotechnol 18:141–176 [CrossRef]
    [Google Scholar]
  15. Hanada S., Takaichi S., Matsuura K., Nakamura K. 2002; Roseiflexus castenholzii gen. nov., sp. nov., a thermophilic, filamentous, photosynthetic bacterium that lacks chlorosomes. Int J Syst Evol Microbiol 52:187–193[PubMed] [CrossRef]
    [Google Scholar]
  16. Hasegawa M., Kishino H., Yano T. A. 1985; Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160–174 [View Article][PubMed]
    [Google Scholar]
  17. Hattori S., Kamagata Y., Hanada S., Shoun H. 2000; Thermacetogenium phaeum gen. nov., sp. nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium. Int J Syst Evol Microbiol 50:1601–1609 [View Article][PubMed]
    [Google Scholar]
  18. Heising S., Richter L., Ludwig W., Schink B. 1999; Chlorobium ferrooxidans sp. nov., a phototrophic green sulfur bacterium that oxidizes ferrous iron in coculture with a “Geospirillum” sp. strain. Arch Microbiol 172:116–124 [View Article][PubMed]
    [Google Scholar]
  19. Hewitt E. J., Nicholas D. J. D. 1964; Enzymes of inorganic nitrogen metabolism. In Modern Methods of Plant Analysis pp. 167–172 Edited by Linskens H. F., Sanwal B. D., Tracey M. V. Berlin: Springer;
    [Google Scholar]
  20. 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 [View Article][PubMed]
    [Google Scholar]
  21. Imhoff J. F. 2005a; Family I. Chromatiaceae Bavendamm 1924, 125AL emend. Imhoff 1984b, 339. In Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol. 2B pp. 3–9 Edited by Brenner D. J., Krieg N. R., Staley J. T. New York: Springer;
    [Google Scholar]
  22. Imhoff J. F. 2005b; Family I. Ectothiorhodospiraceae Imhoff 1984b, 339VP. In Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol. 2B pp. 41–43 Edited by Brenner D. J., Krieg N. R., Staley J. T. New York: Springer;
    [Google Scholar]
  23. Inagaki F., Tsunogai U., Suzuki M., Kosaka A., Machiyama H., Takai K., Nunoura T., Nealson K. H., Horikoshi K. 2004; Characterization of C1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, southern Ryukyu Arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes. Appl Environ Microbiol 70:7445–7455 [View Article][PubMed]
    [Google Scholar]
  24. Ito T., Sugita K., Yumoto I., Nodasaka Y., Okabe S. 2005; Thiovirga sulfuroxydans gen. nov., sp. nov., a chemolithoautotrophic sulfur-oxidizing bacterium isolated from a microaerobic waste-water biofilm. Int J Syst Evol Microbiol 55:1059–1064 [View Article][PubMed]
    [Google Scholar]
  25. Li L., Kato C., Horikoshi K. 1999; Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench. Mar Biotechnol (NY) 1:391–400 [View Article][PubMed]
    [Google Scholar]
  26. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S. et al. 2004; arb: a software environment for sequence data. Nucleic Acids Res 32:1363–1371 [View Article][PubMed]
    [Google Scholar]
  27. Marteinsson V. T., Birrien J. L., Kristjánsson J. K., Prieur D. 1995; First isolation of thermophilic aerobic non-sporulating heterotrophic bacteria from deep-sea hydrothermal vents. FEMS Microbiol Ecol 18:163–174 [View Article]
    [Google Scholar]
  28. Meyer B., Imhoff J. F., Kuever J. 2007; Molecular analysis of the distribution and phylogeny of the soxB gene among sulfur-oxidizing bacteria – evolution of the Sox sulfur oxidation enzyme system. Environ Microbiol 9:2957–2977 [View Article][PubMed]
    [Google Scholar]
  29. Mori K., Suzuki K.-i. 2008; Thiofaba tepidiphila gen. nov., sp. nov., a novel obligately chemolithoautotrophic, sulfur-oxidizing bacterium of the Gammaproteobacteria isolated from a hot spring. Int J Syst Evol Microbiol 58:1885–1891 [View Article][PubMed]
    [Google Scholar]
  30. Mori K., Yamamoto H., Kamagata Y., Hatsu M., Takamizawa K. 2000; Methanocalculus pumilus sp. nov., a heavy-metal-tolerant methanogen isolated from a waste-disposal site. Int J Syst Evol Microbiol 50:1723–1729[PubMed]
    [Google Scholar]
  31. Mori K., Kim H., Kakegawa T., Hanada S. 2003; A novel lineage of sulfate-reducing microorganisms: Thermodesulfobiaceae fam. nov., Thermodesulfobium narugense, gen. nov., sp. nov., a new thermophilic isolate from a hot spring. Extremophiles 7:283–290 [View Article][PubMed]
    [Google Scholar]
  32. Mori K., Maruyama A., Urabe T., Suzuki K.-i., Hanada S. 2008; Archaeoglobus infectus sp. nov., a novel thermophilic, chemolithoheterotrophic archaeon isolated from a deep-sea rock collected at Suiyo Seamount, Izu-Bonin Arc, western Pacific Ocean. Int J Syst Evol Microbiol 58:810–816 [View Article][PubMed]
    [Google Scholar]
  33. Nakagawa Y., Yamasato K. 1993; Phylogenetic diversity of the genus Cytophaga revealed by 16S rRNA sequencing and menaquinone analysis. J Gen Microbiol 139:1155–1161 [CrossRef]
    [Google Scholar]
  34. NBRC 2010 NBRC Catalogue of Biological Resources: Microorganisms, Microorganism-Related DNA Resources, and Human-Related DNA Resources., 2nd edn. Chiba, Japan: National Institute of Technology and Evaluation (NITE);
    [Google Scholar]
  35. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
  36. Santelli C. M., Orcutt B. N., Banning E., Bach W., Moyer C. L., Sogin M. L., Staudigel H., Edwards K. J. 2008; Abundance and diversity of microbial life in ocean crust. Nature 453:653–656 [View Article][PubMed]
    [Google Scholar]
  37. Sievert S. M., Heidorn T., Kuever J. 2000; Halothiobacillus kellyi sp. nov., a mesophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium isolated from a shallow-water hydrothermal vent in the Aegean Sea, and emended description of the genus Halothiobacillus . Int J Syst Evol Microbiol 50:1229–1237 [View Article][PubMed]
    [Google Scholar]
  38. Sorokin D. Y., Tourova T. P., Kolganova T. V., Sjollema K. A., Kuenen J. G. 2002; Thioalkalispira microaerophila gen. nov., sp. nov., a novel lithoautotrophic, sulfur-oxidizing bacterium from a soda lake. Int J Syst Evol Microbiol 52:2175–2182 [View Article][PubMed]
    [Google Scholar]
  39. Sorokin D. Y., Tourova T. P., Bezsoudnova E. Y., Pol A., Muyzer G. 2007; Denitrification in a binary culture and thiocyanate metabolism in Thiohalophilus thiocyanoxidans gen. nov. sp. nov. - a moderately halophilic chemolithoautotrophic sulfur-oxidizing Gammaproteobacterium from hypersaline lakes. Arch Microbiol 187:441–450 [View Article][PubMed]
    [Google Scholar]
  40. Sunamura M., Higashi Y., Miyako C., Ishibashi J., Maruyama A. 2004; Two bacteria phylotypes are predominant in the Suiyo seamount hydrothermal plume. Appl Environ Microbiol 70:1190–1198 [View Article][PubMed]
    [Google Scholar]
  41. Takai K., Horikoshi K. 1999; Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 152:1285–1297[PubMed]
    [Google Scholar]
  42. Takai K., Komatsu T., Inagaki F., Horikoshi K. 2001; Distribution of archaea in a black smoker chimney structure. Appl Environ Microbiol 67:3618–3629 [View Article][PubMed]
    [Google Scholar]
  43. Takai K., Inagaki F., Nakagawa S., Hirayama H., Nunoura T., Sako Y., Nealson K. H., Horikoshi K. 2003; Isolation and phylogenetic diversity of members of previously uncultivated ϵ-Proteobacteria in deep-sea hydrothermal fields. FEMS Microbiol Lett 218:167–174[PubMed]
    [Google Scholar]
  44. Takai K., Hirayama H., Nakagawa T., Suzuki Y., Nealson K. H., Horikoshi K. 2004; Thiomicrospira thermophila sp. nov., a novel microaerobic, thermotolerant, sulfur-oxidizing chemolithomixotroph isolated from a deep-sea hydrothermal fumarole in the TOTO caldera, Mariana Arc, Western Pacific. Int J Syst Evol Microbiol 54:2325–2333 [View Article][PubMed]
    [Google Scholar]
  45. Takai K., Miyazaki M., Hirayama H., Nakagawa S., Querellou J., Godfroy A. 2009; Isolation and physiological characterization of two novel, piezophilic, thermophilic chemolithoautotrophs from a deep-sea hydrothermal vent chimney. Environ Microbiol 11:1983–1997 [View Article][PubMed]
    [Google Scholar]
  46. Tamaki H., Hanada S., Kamagata Y., Nakamura K., Nomura N., Nakano K., Matsumura M. 2003; Flavobacterium limicola sp. nov., a psychrophilic, organic-polymer-degrading bacterium isolated from freshwater sediments. Int J Syst Evol Microbiol 53:519–526 [View Article][PubMed]
    [Google Scholar]
  47. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
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