1887

Abstract

A methanogenic organism, designated strain HB-1, from the domain Archaea was isolated from groundwater sampled from a subsurface Miocene formation located in Horonobe, Hokkaido, Japan. The strain grew on methanol, dimethylamine, trimethylamine, dimethylsulfide and acetate but not on monomethylamine, H/CO, formate, 2-propanol, 2-butanol or cyclopentanol. Cells were Gram-reaction-negative, non-motile, irregular cocci that were 1.4–2.9 µm in diameter and occurred singly or in pairs. The strain grew at 20–42 °C (optimum 37 °C), at pH 6.0–7.75 (optimum pH 7.0–7.25) and in 0–0.35 M NaCl (optimum 0.1 M). The G+C content of the genomic DNA was 41.4 mol%. 16S rRNA gene sequencing revealed that the strain was a member of the genus but that it clearly differed from all recognized species of this genus (93.1–97.9 % sequence similarity). The phenotypic and phylogenetic features of strain HB-1 indicate that it represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is HB-1 ( = DSM 21571  = JCM 15518  = NBRC 102577).

Funding
This study was supported by the:
  • Ministry of Economy, Trade and Industry (METI) of Japan
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.028548-0
2011-10-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/61/10/2503.html?itemId=/content/journal/ijsem/10.1099/ijs.0.028548-0&mimeType=html&fmt=ahah

References

  1. Achenbach L., Woese C. 1995; 16S and 23S rRNA-like primers. In Archaea: A Laboratory Manual: Methanogens pp. 521–523 Edited by Sowers K. R., Schreier H. J. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  2. Blotevogel K. H., Fischer U., Lüpkes K. H. 1986; Methanococcus frisius sp. nov., a new methylotrophic marine methanogen. Can J Microbiol 32:127–131 [View Article]
    [Google Scholar]
  3. Bryant M. P., Boone D. R. 1987; Emended description of strain MST (DSM 800T), the type strain of Methanosarcina barkeri . Int J Syst Bacteriol 37:169–170 [View Article]
    [Google Scholar]
  4. Christian J., Olivier N., Erwan C., Agnes G. L. 2005; Hyperthermophilic and methanogenic archaea in oil fields. In Petroleum Microbiology pp. 55–69 Edited by Ollivier B., Magot M. Washington: American Society for Microbiology;
    [Google Scholar]
  5. Doerfert S. N., Reichlen M., Iyer P., Wang M., Ferry J. G. 2009; Methanolobus zinderi sp. nov., a methylotrophic methanogen isolated from a deep subsurface coal seam. Int J Syst Evol Microbiol 59:1064–1069 [View Article][PubMed]
    [Google Scholar]
  6. Dojka M. A., Hugenholtz P., Haack S. K., Pace N. R. 1998; Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64:3869–3877[PubMed]
    [Google Scholar]
  7. 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]
  8. Fukusawa H. 1987; [The site of sedimentation of Late Neogene bedded siliceous rock in northern Hokkaido, Japan]. J Geol Soc Japan 93:37–55 (in Japanese with English abstract) [CrossRef]
    [Google Scholar]
  9. Hamamoto M., Nakase T. 1995; Ballistosporous yeasts found on the surface of plant materials collected in New Zealand. Antonie van Leeuwenhoek 67:151–171 [View Article][PubMed]
    [Google Scholar]
  10. Iwatsuki T., Ishii E., Niizato T. 2009; Scenario development of long-term evolution for deep hydrochemical conditions in Horonobe area, Hokkaido, Japan. J Geog 118:700–716 [View Article]
    [Google Scholar]
  11. Katayama-Fujimura Y., Komatsu Y., Kuraishi H., Kaneko T. 1984; Estimation of DNA base composition by high performance liquid chromatography of its nuclease P1 hydrolysate. Agric Biol Chem 48:3169–3172 [View Article]
    [Google Scholar]
  12. Kotelnikova S., Macario A. J. L., Pedersen K. 1998; Methanobacterium subterraneum sp. nov., a new alkaliphilic, eurythermic and halotolerant methanogen isolated from deep granitic groundwater. Int J Syst Bacteriol 48:357–367[PubMed] [CrossRef]
    [Google Scholar]
  13. Kumar S., Nei M., Dudley J., Tamura K. 2008; mega: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299–306 [View Article][PubMed]
    [Google Scholar]
  14. Lane D. J. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp. 115–175 Edited by Stackebrandt E., Goodfellow M. New York: Wiley;
    [Google Scholar]
  15. Lane D. J., Pace B., Olsen G. J., Stahl D. A., Sogin M. L., Pace N. R. 1985; Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82:6955–6959 [View Article][PubMed]
    [Google Scholar]
  16. Lyimo T. J., Pol A., Op den Camp H. J. M., Harhangi H. R., Vogels G. D. 2000; Methanosarcina semesiae sp. nov., a dimethylsulfide-utilizing methanogen from mangrove sediment. Int J Syst Evol Microbiol 50:171–178 [View Article][PubMed]
    [Google Scholar]
  17. Maestrojuán G. M., Boone D. R. 1991; Characterization of Methanosarcina barkeri MST and 227, Methanosarcina mazei S-6T, and Methanosarcina vacuolata Z-761T . Int J Syst Bacteriol 41:267–274 [View Article]
    [Google Scholar]
  18. Maestrojuán G. M., Boone J. E., Mah R. A., Menaia J. A. G. F., Sachs M. S., Boone D. R. 1992; Taxonomy and halotolerance of mesophilic Methanosarcina strains, assignment of strains to species, and synonymy of Methanosarcina mazei and Methanosarcina frisia . Int J Syst Bacteriol 42:561–567 [View Article]
    [Google Scholar]
  19. Mah R. A., Kuhn D. A. 1984; Transfer of the type species of the genus Methanococcus to the genus Methanosarcina, naming it Methanosarcina mazei (Barker 1936) comb. nov. et emend. and conservation of the genus Methanococcus (Approved List 1980) with Methanococcus vannielii (Approved List 1980) as the type species. Int J Syst Bacteriol 34:263–265 [View Article]
    [Google Scholar]
  20. Marmur J. 1961; A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208–218 [View Article]
    [Google Scholar]
  21. Mikucki J. A., Liu Y., Delwiche M., Colwell F. S., Boone D. R. 2003; Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of Methanoculleus submarinus sp. nov.. Appl Environ Microbiol 69:3311–3316 [View Article][PubMed]
    [Google Scholar]
  22. Mochimaru H., Tamaki H., Hanada S., Imachi H., Nakamura K., Sakata S., Kamagata Y. 2009; Methanolobus profundi sp. nov., a methylotrophic methanogen isolated from deep subsurface sediments in a natural gas field. Int J Syst Evol Microbiol 59:714–718 [View Article][PubMed]
    [Google Scholar]
  23. Ni S. S., Boone D. R. 1991; Isolation and characterization of a dimethyl sulfide-degrading methanogen, Methanolobus siciliae HI350, from an oil well, characterization of M. siciliae T4/MT, and emendation of M. siciliae . Int J Syst Bacteriol 41:410–416 [View Article][PubMed]
    [Google Scholar]
  24. Ni S., Woese C. R., Aldrich H. C., Boone D. R. 1994; Transfer of Methanolobus siciliae to the genus Methanosarcina, naming it Methanosarcina siciliae, and emendation of the genus Methanosarcina . Int J Syst Bacteriol 44:357–359 [View Article][PubMed]
    [Google Scholar]
  25. Shimizu S., Akiyama M., Ishijima Y., Hama K., Kunimaru T., Naganuma T. 2006; Molecular characterization of microbial communities in fault-bordered aquifers in the Miocene formation of northernmost Japan. Geobiology 4:203–213 [View Article]
    [Google Scholar]
  26. Simankova M. V., Parshina S. N., Tourova T. P., Kolganova T. V., Zehnder A. J. B., Nozhevnikova A. N. 2001; Methanosarcina lacustris sp. nov., a new psychrotolerant methanogenic archaeon from anoxic lake sediments. Syst Appl Microbiol 24:362–367 [View Article][PubMed]
    [Google Scholar]
  27. Sowers K. R., Baron S. F., Ferry J. G. 1984; Methanosarcina acetivorans sp. nov., an acetotrophic methane-producing bacterium isolated from marine sediments. Appl Environ Microbiol 47:971–978[PubMed]
    [Google Scholar]
  28. von Klein D., Arab H., Völker H., Thomm M. 2002; Methanosarcina baltica, sp. nov., a novel methanogen isolated from the Gotland Deep of the Baltic Sea. Extremophiles 6:103–110 [View Article][PubMed]
    [Google Scholar]
  29. Zhilina T. N., Zavarzin G. A. 1987; Methanosarcina vacuolata sp. nov., a vacuolated methanosarcina. Int J Syst Bacteriol 37:281–283 [View Article]
    [Google Scholar]
  30. Zinder S. H., Mah R. A. 1979; Isolation and characterization of a thermophilic strain of Methanosarcina unable to use H2-CO2 for methanogenesis. Appl Environ Microbiol 38:996–1008[PubMed]
    [Google Scholar]
  31. Zinder S. H., Sowers K. R., Ferry J. G. 1985; Methanosarcina thermophila sp. nov., a thermophilic, acetotrophic, methane-producing bacterium. Int J Syst Bacteriol 35:522–523 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.028548-0
Loading
/content/journal/ijsem/10.1099/ijs.0.028548-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error