1887

Abstract

A mesophilic, hydrogenotrophic methanogen, strain S3Fa, was isolated from sediments collected by Ocean Researcher I cruise ORI-934 in 2010 near the submarine mud volcano MV4 located at the upper slope of south-west Taiwan. The methanogenic substrates utilized by strain S3Fa were formate and H/CO but not acetate, secondary alcohols, methylamines, methanol or ethanol. Cells of strain S3Fa were non-motile, irregular cocci, 0.5–1.0 μm in diameter. The surface-layer protein showed an Mr of 128 000.The optimum growth conditions were 37 °C, pH 7.1 and 0.17 M NaCl. The DNA G+C content of the genome of strain S3Fa was 62.3 mol %. Phylogenetic analysis revealed that strain S3Fa was most closely related to JR1 (99.3 % 16S rRNA gene sequence similarity). Genome relatedness between strain S3Fa and JR1 was computed using both genome-to-genome distance analysis (GGDA) and average nucleotide identity (ANI) with values of 46.3–55.5 % and 93.08 %, respectively. Based on morphological, phenotypic, phylogenetic and genomic relatedness data, it is evident that strain S3Fa represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is S3Fa ( = BCRC AR10044 = DSM 29354).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.000233
2015-07-01
2019-09-15
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/7/2141.html?itemId=/content/journal/ijsem/10.1099/ijs.0.000233&mimeType=html&fmt=ahah

References

  1. Balch W.E. , Fox G.E. , Magrum L.J. , Woese C.R. , Wolfe R.S. . ( 1979;). Methanogens: reevaluation of a unique biological group. Microbiol Rev 43: 260–296 Medline.
    [Google Scholar]
  2. Blotevogel K.-H. , Gahl-Janβen R. , Jannsen S. , Fischer U. , Pilz F. , Auling G. , Macario A.J.L. , Tindall B.J. . ( 1991;). Isolation and characterization of a novel mesophilic, fresh-water methanogen from river sediment Methanoculleus oldenburgensis sp. nov.. Arch Microbiol 157: 54–59.[CrossRef]
    [Google Scholar]
  3. Chen S.C. , Hsu S.K. , Wang Y. , Chung S.H. , Chen P.C. , Tsai C.H. , Liu C.S. , Lin H.S. , Lee Y.W. . ( 2014;). Distribution and characters of the mud diapirs and mud volcanoes off southwest Taiwan. J Asian Earth Sci 92: 201–214 [CrossRef].
    [Google Scholar]
  4. Cheng L. , Qiu T.L. , Li X. , Wang W.D. , Deng Y. , Yin X.B. , Zhang H. . ( 2008;). Isolation and characterization of Methanoculleus receptaculi sp. nov. from Shengli oil field, China. FEMS Microbiol Lett 285: 65–71 [CrossRef] [PubMed].
    [Google Scholar]
  5. Chiu J.K. , Tseng W.H. , Liu C.S. . ( 2006;). Distribution of gassy sediments and mud volcanoes offshore southwestern Taiwan. Terr Atmos Ocean Sci 17: 703–722.
    [Google Scholar]
  6. Corder R.E. , Hook L.A. , Larkin J.M. , Frea J.I. . ( 1983;). Isolation and characterization of two new methane-producing cocci: Methanogenium olentangyi, sp. nov., and Methanococcus deltae, sp. nov.. Arch Microbiol 134: 28–32.[CrossRef]
    [Google Scholar]
  7. Dianou D. , Miyaki T. , Asakawa S. , Morii H. , Nagaoka K. , Oyaizu H. , Matsumoto S. . ( 2001;). Methanoculleus chikugoensis sp. nov., a novel methanogenic archaeon isolated from paddy field soil in Japan, and DNA-DNA hybridization among Methanoculleus species. Int J Syst Evol Microbiol 51: 1663–1669 [CrossRef] [PubMed].
    [Google Scholar]
  8. Dimitrov L.I. . ( 2002;). Mud volcanoes-the most important pathway for degassing deeply buried sediments. Earth Sci Rev 59: 49–76 [CrossRef].
    [Google Scholar]
  9. Ferguson T.J. , Mah R.A. . ( 1983;). Isolation and characterization of an H2-oxidizing thermophilic methanogen. Appl Environ Microbiol 45: 265–274 Medline.
    [Google Scholar]
  10. Goris J. , Konstantinidis K.T. , Klappenbach J.A. , Coenye T. , Vandamme P. , Tiedje J.M. . ( 2007;). DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57: 81–91 [CrossRef] [PubMed].
    [Google Scholar]
  11. Jarrell K.F. , Faguy D. , Hebert A.M. , Kalmokoff M.L. . ( 1992;). A general method of isolating high molecular weight DNA from methanogenic archaea (archaebacteria). Can J Microbiol 38: 65–68 [CrossRef] [PubMed].
    [Google Scholar]
  12. König H. . ( 1995;). Isolation and analysis of cell walls from methanogenic archaea. . In Archaea: a Laboratory Manual, Methanogens, pp. 315–328. Edited by Sowers K. R. , Schreier H. T. . Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;.
    [Google Scholar]
  13. Laemmli U.K. . ( 1970;). Cleavage of structural proteins during the assembly of the head of bacteriophage tbl4. Nature 227: 680–685 [CrossRef] [PubMed].
    [Google Scholar]
  14. Lai M.C. , Chen S.C. . ( 2001;). Methanofollis aquaemaris sp. nov., a methanogen isolated from an aquaculture fish pond. Int J Syst Evol Microbiol 51: 1873–1880 [CrossRef] [PubMed].
    [Google Scholar]
  15. Lai M.C. , Shih C.J. . ( 2001;). Characterization of Methanococcus voltaei strain P2F9701a: a new methanogen isolated from estuarine environment. Curr Microbiol 42: 432–437 [CrossRef] [PubMed].
    [Google Scholar]
  16. Lai M.C. , Yang D.R. , Chuang M.J. . ( 1999;). Regulatory factors associated with synthesis of the osmolyte glycine betaine in the halophilic methanoarchaeon Methanohalophilus portucalensis . Appl Environ Microbiol 65: 828–833 Medline.
    [Google Scholar]
  17. Lai M.C. , Chen S.C. , Shu C.M. , Chiou M.S. , Wang C.C. , Chuang M.J. , Hong T.Y. , Liu C.C. , Lai L.J. , Hua J.J. . ( 2002;). Methanocalculus taiwanensis sp. nov., isolated from an estuarine environment. Int J Syst Evol Microbiol 52: 1799–1806 [CrossRef] [PubMed].
    [Google Scholar]
  18. Lai M.C. , Lin C.C. , Yu P.H. , Huang Y.F. , Chen S.C. . ( 2004;). Methanocalculus chunghsingensis sp. nov., isolated from an estuary and a marine fishpond in Taiwan. Int J Syst Evol Microbiol 54: 183–189 [CrossRef] [PubMed].
    [Google Scholar]
  19. Meier-Kolthoff J.P. , Auch A.F. , Klenk H.P. , Göker M. . ( 2013;). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60 [CrossRef] [PubMed].
    [Google Scholar]
  20. 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 [CrossRef] [PubMed].
    [Google Scholar]
  21. Ollivier B.M. , Mah R.A. , Garcia J.L. , Boone D.R. . ( 1986;). Isolation and characterization of Methanogenium bourgense sp. nov. Int J Syst Bacteriol 36: 297–301 [CrossRef].
    [Google Scholar]
  22. Oung J.N. , Lee C.Y. , Lee C.S. , Kuo C.L. . ( 2006;). Geochemical study on hydrocarbon gases in seafloor sediments, southwestern offshore Taiwan-implications in the potential occurrence of gas hydrates. Terr Atmos Ocean Sci 17: 921–931.
    [Google Scholar]
  23. Rivard C.J. , Smith P.H. . ( 1982;). Isolation and characterization of a thermophilic marine methanogenic bacterium, Methanogenium thermophilicum sp. nov. Int J Syst Bacteriol 32: 430–436 [CrossRef].
    [Google Scholar]
  24. Romesser J.A. , Wolfe R.S. , Mayer F. , Spiess E. , Walther-Mauruschat A. . ( 1979;). Methanogenium, a new genus of marine methanogenic bacteria, and characterization of Methanogenium cariaci sp. nov. and Methanogenium marisnigri sp. nov. Arch Microbiol 121: 147–153 [CrossRef].
    [Google Scholar]
  25. Shimizu S. , Ueno A. , Tamamura S. , Naganuma T. , Kaneko K. . ( 2013;). Methanoculleus horonobensis sp. nov., a methanogenic archaeon isolated from a deep diatomaceous shale formation. Int J Syst Evol Microbiol 63: 4320–4323 [CrossRef] [PubMed].
    [Google Scholar]
  26. Sowers K.R. , Noll K.M. . ( 1995;). Techniques for anaerobic growth. . In Archaea: a Laboratory Manual, Methanogens, pp. 15–48. Edited by Sowers K. R. , Schreier H. T. . Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;.
    [Google Scholar]
  27. Tamura K. , Stecher G. , Peterson D. , Filipski A. , Kumar S. . ( 2013;). mega6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30: 2725–2729 [CrossRef] [PubMed].
    [Google Scholar]
  28. Tian J. , Wang Y. , Dong X. . ( 2010;). Methanoculleus hydrogenitrophicus sp. nov., a methanogenic archaeon isolated from wetland soil. Int J Syst Evol Microbiol 60: 2165–2169 [CrossRef] [PubMed].
    [Google Scholar]
  29. Weng C.Y. , Chen S.C. , Lai M.C. , Wu S.Y. , Lin S. , Yang T.F. , Chen P.C. . ( 2015;). Methanoculleus taiwanensis sp. nov., a methanogen isolated from deep marine sediment at deformation front area near Taiwan. Int J Syst Evol Microbiol 65: 1044–1049 [CrossRef] [PubMed].
    [Google Scholar]
  30. Wolin E.A. , Wolin M.J. , Wolfe R.S. . ( 1963;). Formation of methane by bacterial extracts. J Biol Chem 238: 2882–2886 Medline.
    [Google Scholar]
  31. Wu S.Y. , Lai M.C. . ( 2011;). Methanogenic archaea isolated from Taiwan's Chelungpu fault. Appl Environ Microbiol 77: 830–838 [CrossRef] [PubMed].
    [Google Scholar]
  32. Wu S.Y. , Chen S.C. , Lai M.C. . ( 2005;). Methanofollis formosanus sp. nov., isolated from a fish pond. Int J Syst Evol Microbiol 55: 837–842 [CrossRef] [PubMed].
    [Google Scholar]
  33. Zellner G. , Messner P. , Winter J. , Stackebrandt E. . ( 1998;). Methanoculleus palmolei sp. nov., an irregularly coccoid methanogen from an anaerobic digester treating wastewater of a palm oil plant in north-Sumatra, Indonesia. Int J Syst Bacteriol 48: 1111–1117 [CrossRef] [PubMed].
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.000233
Loading
/content/journal/ijsem/10.1099/ijs.0.000233
Loading

Data & Media loading...

Supplementary Data



PDF

Most Cited This Month

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