1887

Abstract

The taxonomic status of a verrucomicrobial strain isolated from marine sediment was established based on a polyphasic examination. The novel isolate, strain YM29-052, was obligately aerobic, Gram-negative, non-motile, coccoid or rod-shaped and chemoheterotrophic. Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that the new isolate shared approximately 94–99 % sequence similarity with members of genus of the family within the phylum ‘’. Genomic DNA–DNA hybridization between strain YM29-052 and HOact23 showed relatedness of <70 %, the value commonly accepted as the threshold for the phylogenetic definition of a species. Strain YM29-052 produces carotenoid compounds that render the cell biomass a pink colour; the strain also contains squalene. The cell-wall peptidoglycan of the novel strain contains muramic acid and -diaminopimelic acid. The DNA G+C content of strain YM29-052 was 47.7 mol%; MK-8 and MK-9 were the major menaquinones. The presence of iso-C, iso-C and C 7 as major cellular fatty acids supported the identification of the novel isolate as a member of the genus . On the basis of polyphasic taxonomic evidence, it was concluded that strain YM29-052 should be classified within a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YM29-052 (=MBIC08323 =KCTC 22127).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.65540-0
2008-04-01
2020-01-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/58/4/992.html?itemId=/content/journal/ijsem/10.1099/ijs.0.65540-0&mimeType=html&fmt=ahah

References

  1. Derrien, M., Vaughan, E. E., Plugge, C. M. & de Vos, W. M. ( 2004; ). Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol 54, 1469–1476.[CrossRef]
    [Google Scholar]
  2. 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.[CrossRef]
    [Google Scholar]
  3. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  4. Fitch, W. M. ( 1971; ). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406–416.[CrossRef]
    [Google Scholar]
  5. Harper, J. J. & Davis, G. H. G. ( 1979; ). Two-dimensional thin-layer chromatography for amino acid analysis of bacterial cell walls. Int J Syst Bacteriol 29, 56–58.[CrossRef]
    [Google Scholar]
  6. Hedlund, B. P., Gosink, J. J. & Staley, J. T. ( 1996; ). Phylogeny of Prosthecobacter, the fusiform caulobacters: members of a recently discovered division of the Bacteria. Int J Syst Bacteriol 46, 960–966.[CrossRef]
    [Google Scholar]
  7. Hedlund, B. P., Gosink, J. J. & Staley, J. T. ( 1997; ). Verrucomicrobia div. nov., a new division of the bacteria containing three new species of Prosthecobacter. Antonie van Leeuwenhoek 72, 29–38.[CrossRef]
    [Google Scholar]
  8. Hugenholtz, P., Goebel, B. M. & Pace, N. R. ( 1998; ). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180, 4765–4774.
    [Google Scholar]
  9. Kasai, H., Katsuta, A., Sekiguchi, H., Matsuda, S., Adachi, K., Kazutoshi, S., Yoon, J., Yokota, A. & Shizuri, Y. ( 2007; ). Rubritalea squalenifaciens sp. nov., a squalene-producing marine bacterium belonging to subdivision 1 of the phylum ‘Verrucomicrobia’. Int J Syst Evol Microbiol 57, 1630–1634.[CrossRef]
    [Google Scholar]
  10. Katsuta, A., Adachi, K., Matsuda, S., Shizuri, Y. & Kasai, H. ( 2005; ). Ferrimonas marina sp. nov. Int J Syst Evol Microbiol 55, 1851–1855.[CrossRef]
    [Google Scholar]
  11. Kimura, M. ( 1983; ). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  12. Kumar, S., Tamura, K. & Nei, M. ( 2004; ). mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef]
    [Google Scholar]
  13. Marmur, J. ( 1961; ). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3, 208–218.[CrossRef]
    [Google Scholar]
  14. 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, 159–167.[CrossRef]
    [Google Scholar]
  15. Murray, R. G. E., Doetsch, R. N. & Robinow, C. F. ( 1994; ). Determinative and cytological light microscopy. In Methods for General and Molecular Bacteriology, pp. 21–41. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
  16. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  17. Scheuermayer, M., Gulder, T. A. M., Bringmann, G. & Hentschel, U. ( 2006; ). Rubritalea marina gen. nov., sp. nov., a marine representative of the phylum ‘Verrucomicrobia’, isolated from a sponge (Porifera). Int J Syst Evol Microbiol 56, 2119–2124.[CrossRef]
    [Google Scholar]
  18. Schleifer, K. H. & Kandler, O. ( 1972; ). Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36, 407–477.
    [Google Scholar]
  19. Schlesner, H. ( 1987; ). Verrucomicrobium spinosum gen. nov., sp. nov.: a fimbriated prosthecate bacterium. Syst Appl Microbiol 10, 54–56.[CrossRef]
    [Google Scholar]
  20. Shindo, K., Mikami, K., Tamesada, E., Takaichi, S., Adachi, K., Misawa, N. & Maoka, T. ( 2007; ). Diapolycopenedioic acid xylosyl ester, a novel glyco-C30-carotenoic acid produced by a new marine bacterium Rubritalea squalenifaciens. Tetrahedron Lett 48, 2725–2727.[CrossRef]
    [Google Scholar]
  21. Staley, J. T., Bont, J. A. M. & Jonge, K. ( 1976; ). Prosthecobacter fusiformis nov. gen. et sp., the fusiform caulobacter. Antonie van Leeuwenhoek 42, 333–342.[CrossRef]
    [Google Scholar]
  22. 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.[CrossRef]
    [Google Scholar]
  23. 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, 463–464.[CrossRef]
    [Google Scholar]
  24. Weisburg, W. G., Barns, S. M., Pelletier, D. A. & Lane, D. J. ( 1991; ). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173, 697–703.
    [Google Scholar]
  25. Yokota, A., Tamura, T., Nishii, T. & Hasegawa, T. ( 1993; ). Kineococcus aurantiacus gen. nov., sp. nov., a new aerobic, gram-positive, motile coccus with diaminopimelic acid and arabinogalactan in the cell wall. Int J Syst Bacteriol 43, 52–57.[CrossRef]
    [Google Scholar]
  26. Yoon, J., Yasumoto-Hirose, M., Matsuo, Y., Nozawa, M., Matsuda, S., Kasai, H. & Yokota, A. ( 2007a; ). Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum ‘Verrucomicrobia’ isolated from seawater by in situ cultivation. Int J Syst Evol Microbiol 57, 1377–1385.[CrossRef]
    [Google Scholar]
  27. Yoon, J., Matsuo, Y., Matsuda, S., Adachi, K., Kasai, H. & Yokota, A. ( 2007b; ). Rubritalea spongiae sp. nov. and Rubritalea tangerina sp. nov., two carotenoid- and squalene-producing marine bacteria of the family Verrucomicrobiaceae within the phylum ‘Verrucomicrobia’ isolated from marine animals. Int J Syst Evol Microbiol 57, 2337–2343.[CrossRef]
    [Google Scholar]
  28. Yoon, J., Matsuo, Y., Adachi, K., Nozawa, M., Matsuda, S., Kasai, H. & Yokota, A. ( 2008; ). Description of Persicirhabdus sediminis gen. nov., sp. nov., Roseibacillus ishigakijimensis gen. nov., sp. nov., Roseibacillus ponti sp. nov., Roseibacillus persicicus sp. nov., Luteolibacter pohnpeiensis gen. nov., sp. nov. and Luteolibacter algae sp. nov., six marine members of the phylum ‘Verrucomicrobia’, and emended descriptions of the class Verrucomicrobiae, the order Verrucomicrobiales and the family Verrucomicrobiaceae. Int J Syst Evol Microbiol 58, 998–1007.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.65540-0
Loading
/content/journal/ijsem/10.1099/ijs.0.65540-0
Loading

Data & Media loading...

Most cited articles

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