1887

Abstract

A novel, strictly anaerobic, methylotrophic marine methanogen, strain SLH33, was isolated from deep sediment samples covered by an orange microbial mat collected from the Napoli Mud Volcano. Cells of strain SLH33 were Gram-stain-negative, motile, irregular cocci that occurred singly. Cells utilized trimethylamine, dimethylamine, monomethylamine, methanol, betaine, ,-dimethylethanolamine and choline (,,-trimethylethanolamine) as substrates for growth and methanogenesis. The optimal growth temperature was 30 °C; maximum growth rate was obtained at pH 7.0 in the presence of 0.5 M Na. The DNA G+C content of strain SLH33 was 43.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain SLH33 within the genus . The novel isolate was related most closely to TMA-10 (98.8 % 16S rRNA gene sequence similarity) but distantly related to DSM 6242 (97.6 %) and AK-5 (97.6 %). DNA–DNA hybridization studies indicated that strain SLH33 represents a novel species, given that it shared less than 16 % DNA–DNA relatedness with TMA-10. The name sp. nov. is proposed for this novel species, with strain SLH33 ( = DSM 26966 = JCM 19278) as the type strain. An emended description of the genus is also proposed.

Funding
This study was supported by the:
  • HERMES (Award GOCECT- 2005-511234-1)
  • HERMIONE (Award 226354)
  • European Union (Award 311975)
  • UBO
  • CNRS
  • Ifremer
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2014-06-01
2024-03-29
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References

  1. De Ley J., Cattoir H., Reynaerts A. ( 1970 ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12, 133142. [View Article] [PubMed]
    [Google Scholar]
  2. Franzmann P. D., Springer N., Ludwig W., Demacario E. C., Rohde M. ( 1992 ). A methanogenic archaeon from Ace lake Antartica: Methanococcoides burtonii sp. nov.. Syst Appl Microbiol 15, 573581. [View Article]
    [Google Scholar]
  3. Garcia J. L., Patel B. K. C., Ollivier B. ( 2000 ). Taxonomic, phylogenetic, and ecological diversity of methanogenic Archaea . . Anaerobe 6, 205226. [View Article] [PubMed]
    [Google Scholar]
  4. Hales B. A., Edwards C., Ritchie D. A., Hall G., Pickup R. W., Saunders J. R. ( 1996 ). Isolation and identification of methanogen-specific DNA from blanket bog peat by PCR amplification and sequence analysis. . Appl Environ Microbiol 62, 668675.[PubMed]
    [Google Scholar]
  5. Huß V. A., Festl H., Schleifer K. H. ( 1983 ). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. . Syst Appl Microbiol 4, 184192. [View Article] [PubMed]
    [Google Scholar]
  6. Iino T., Tamaki H., Tamazawa S., Ueno Y., Ohkuma M., Suzuki K., Igarashi Y., Haruta S. ( 2013 ). Candidatus Methanogranum caenicola: a novel methanogen from the anaerobic digested sludge, and proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a methanogenic lineage of the class Thermoplasmata . . Microbes Environ 28, 244250. [View Article] [PubMed]
    [Google Scholar]
  7. Kendall M., Boone D. ( 2006 ). The order Methanosarcinales . . In The Prokaryotes, pp. 244256. Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K.-H., Stackebrandt E. . New York:: Springer;. [View Article]
    [Google Scholar]
  8. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A. & other authors ( 2007 ). clustal w and clustal_x version 2.0. . Bioinformatics 23, 29472948. [View Article] [PubMed]
    [Google Scholar]
  9. Lazar C. S., L’Haridon S., Pignet P., Toffin L. ( 2011a ). Archaeal populations in hypersaline sediments underlying orange microbial mats in the Napoli mud volcano. . Appl Environ Microbiol 77, 31203131. [View Article] [PubMed]
    [Google Scholar]
  10. Lazar C. S., Parkes R. J., Cragg B. A., L’Haridon S., Toffin L. ( 2011b ). Methanogenic diversity and activity in hypersaline sediments of the centre of the Napoli mud volcano, Eastern Mediterranean Sea. . Environ Microbiol 13, 20782091. [View Article] [PubMed]
    [Google Scholar]
  11. Lomans B. P., Maas R., Luderer R., Op den Camp H. J., Pol A., van der Drift C., Vogels G. D. ( 1999 ). Isolation and characterization of Methanomethylovorans hollandica gen. nov., sp. nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol. . Appl Environ Microbiol 65, 36413650.[PubMed]
    [Google Scholar]
  12. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S. & other authors ( 2004 ). arb: a software environment for sequence data. . Nucleic Acids Res 32, 13631371. [View Article] [PubMed]
    [Google Scholar]
  13. Mesbah M., Premachandran U., Whitman W. B. ( 1989 ). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. . Int J Syst Bacteriol 39, 159167. [View Article]
    [Google Scholar]
  14. Oremland R. S., Taylor B. F. ( 1978 ). Sulfate reduction and methanogenesis in marine sediments. . Geochim Cosmochim Acta 42, 209214. [View Article]
    [Google Scholar]
  15. Pruesse E., Quast C., Knittel K., Fuchs B. M., Ludwig W., Peplies J., Glöckner F. O. ( 2007 ). silva: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with arb . . Nucleic Acids Res 35, 71887196. [View Article] [PubMed]
    [Google Scholar]
  16. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  17. Singh N., Kendall M. M., Liu Y., Boone D. R. ( 2005 ). Isolation and characterization of methylotrophic methanogens from anoxic marine sediments in Skan Bay, Alaska: description of Methanococcoides alaskense sp. nov., and emended description of Methanosarcina baltica . . Int J Syst Evol Microbiol 55, 25312538. [View Article] [PubMed]
    [Google Scholar]
  18. Sowers K. R. ( 2000 ). Genus II. Methanococcoides. . In the Bergey's Manual of Systematic Bacteriology , , 2nd edn., vol. 1, pp 276278. Edited by Boone D. R., Castenholz R. W., Garrity G. M. . New York:: Springer;.
    [Google Scholar]
  19. Sowers K. R., Ferry J. G. ( 1983 ). Isolation and characterization of a methylotrophic marine methanogen, Methanococcoides methylutens gen. nov., sp. nov.. Appl Environ Microbiol 45, 684690.[PubMed]
    [Google Scholar]
  20. Sprenger W. W., van Belzen M. C., Rosenberg J., Hackstein J. H. P., Keltjens J. T. ( 2000 ). Methanomicrococcus blatticola gen. nov., sp. nov., a methanol- and methylamine-reducing methanogen from the hindgut of the cockroach Periplaneta americana . . Int J Syst Evol Microbiol 50, 19891999. [View Article] [PubMed]
    [Google Scholar]
  21. Stackebrandt E., Ebers J. ( 2006 ). Taxonomic parameters revisited: tarnished gold standards. . Microbiol Today 33, 152155.
    [Google Scholar]
  22. Stamatakis A. ( 2006 ). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. . Bioinformatics 22, 26882690. [View Article] [PubMed]
    [Google Scholar]
  23. Tamura K., Dudley J., Nei M., Kumar S. ( 2007 ). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. . Mol Biol Evol 24, 15961599. [View Article] [PubMed]
    [Google Scholar]
  24. Teske A., Hinrichs K.-U., Edgcomb V., de Vera Gomez A., Kysela D., Sylva S. P., Sogin M. L., Jannasch H. W. ( 2002 ). Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. . Appl Environ Microbiol 68, 19942007. [View Article] [PubMed]
    [Google Scholar]
  25. Watkins A. J., Roussel E. G., Webster G., Parkes R. J., Sass H. ( 2012 ). Choline and N,N-dimethylethanolamine as direct substrates for methanogens. . Appl Environ Microbiol 78, 82988303. [View Article] [PubMed]
    [Google Scholar]
  26. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. & other authors ( 1987 ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37, 463464. [View Article]
    [Google Scholar]
  27. Yu I. K., Kawamura F. ( 1987 ). Halomethanococcus doii gen. nov., sp. nov., an obligately halophilic methanogenium bacterium from solar salt ponds. . J Gen Appl Microbiol 33, 303310. [View Article]
    [Google Scholar]
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