1887

Abstract

Six Gram-negative, non-motile, rod-shaped, chemoheterotrophic bacteria designated strains YM23-227, 06SJR1-1, AK18-024, 05IJR53-1, MN1-1037 and MN1-1047 were isolated from various marine environments and subjected to a polyphasic taxonomic study. Preliminary analysis based on 16S rRNA gene sequences revealed that the novel isolates could be affiliated with the family of the phylum ‘’. The strains shared approximately 94–100 % sequence similarity with each other and showed less than 94 % similarity with members of the family with validly published names. The DNA–DNA relatedness between strains YM23-227 and 06SJR1-1 was less than 70 %, a value that is accepted as a phylogenetic definition of a species. The cell wall peptidoglycan of the strains contained muramic acid and -diaminopimelic acid. The novel isolates produced carotenoid pigments and squalene. The DNA G+C contents of the six strains were 63–65 mol%. The major menaquinone was MK-9 and iso-C was the major fatty acid. Based on the evidence from the polyphasic taxonomic study, it was concluded that the six strains should be classified as representing a new genus and five novel species of the family within the phylum ‘’, for which the names gen. nov., sp. nov. (type strain 06SJR1-1=MBIC08340=KCTC 22201), sp. nov. (type strain YM23-227=MBIC08299=KCTC 22198), sp. nov. (type strain AK18-024=MBIC08341=KCTC 22200), sp. nov. (type strain 05IJR53-1=MBIC08342=KCTC 22199) and sp. nov. (type strain MN1-1037=MBIC08343=KCTC 22202) are proposed.

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2008-11-01
2019-10-19
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References

  1. Dedysh, S. N., Pankratov, T. A., Belova, S. E., Kulichevskaya, I. S. & Liesack, W. ( 2006; ). Phylogenetic analysis and in situ identification of Bacteria community composition in an acidic Sphagnum peat bog. Appl Environ Microbiol 72, 2110–2117.[CrossRef]
    [Google Scholar]
  2. 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]
  3. 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]
  4. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  5. 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]
  6. Garrity, G. M. & Holt, J. G. ( 2001; ). The road map to the Manual. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, pp. 119–166. Edited by D. R. Boone, R. W. Castenholz & G. M. Garrity. New York: Springer.
  7. 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]
  8. Haukka, K., Heikkinen, E., Kairesalo, T., Karjalainen, H. & Sivonen, K. ( 2005; ). Effect of humic material on the bacterioplankton community composition in boreal lakes and mesocosms. Environ Microbiol 7, 620–630.[CrossRef]
    [Google Scholar]
  9. Haukka, K., Kolmonen, E., Hyder, R., Hietala, J., Vakkilainen, K., Kairesalo, T., Haario, H. & Sivonen, K. ( 2006; ). Effect of nutrient loading on bacterioplankton community composition in lake mesocosms. Microb Ecol 51, 137–146.[CrossRef]
    [Google Scholar]
  10. Hedlund, B. P., Gosink, J. J. & Staley, J. T. ( 1997a; ). Verrucomicrobia div. nov., a new division of the bacteria containing three new species of Prosthecobacter. Antonie Van Leeuwenhoek 72, 29–38.[CrossRef]
    [Google Scholar]
  11. Hedlund, B. P., Gosink, J. J. & Staley, J. T. ( 1997b; ). Phylogeny of Prosthecobacter, the fusiform caulobacters: members of a recently discovered division of the Bacteria. Int J Syst Bacteriol 46, 960–966.
    [Google Scholar]
  12. 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]
  13. Joseph, S. J., Hugenholtz, P., Sangwan, P., Osborne, C. A. & Janssen, P. H. ( 2003; ). Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69, 7210–7215.[CrossRef]
    [Google Scholar]
  14. Kanokratana, P., Chanapan, S., Pootanakit, K. & Eurwilaichitr, L. ( 2004; ). Diversity and abundance of Bacteria and Archaea in the Bor Khlueng hot spring in Thailand. J Basic Microbiol 44, 430–444.[CrossRef]
    [Google Scholar]
  15. 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]
  16. 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]
  17. Kimura, M. ( 1983; ). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  18. 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]
  19. Marmur, J. ( 1961; ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208–218.[CrossRef]
    [Google Scholar]
  20. 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]
  21. Mincer, T. J., Jensen, P. R., Kauffman, C. A. & Fenical, W. ( 2002; ). Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments. Appl Environ Microbiol 68, 5005–5011.[CrossRef]
    [Google Scholar]
  22. Murray, R. G. E., Doetsch, R. N. & Robinow, 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.
  23. Rappé, M. S. & Giovannoni, S. J. ( 2003; ). The uncultured microbial majority. Annu Rev Microbiol 57, 369–394.[CrossRef]
    [Google Scholar]
  24. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  25. Scheuermayer, M., Gulder, T. A., 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]
  26. Schleifer, K. H. & Kandler, O. ( 1972; ). Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36, 407–477.
    [Google Scholar]
  27. Schlesner, H. ( 1987; ). Verrucomicrobium spinosum gen nov., sp. nov.; a fimbriated prosthecate bacterium. Syst Appl Microbiol 10, 54–56.[CrossRef]
    [Google Scholar]
  28. 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]
  29. 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]
  30. Vandekerckhove, T. T. M., Willems, A., Gillis, M. & Coomans, A. ( 2000; ). Occurrence of novel verrucomicrobial species, endosymbiotic and associated with parthenogenesis in Xiphinema americanum-group species (Nematoda, Longidoridae). Int J Syst Evol Microbiol 50, 2197–2205.[CrossRef]
    [Google Scholar]
  31. 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]
  32. 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]
  33. 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]
  34. Yoon, J., Matsuo, Y., Matsuda, S., Adachi, K., Kasai, H. & Yokota, A. ( 2007; ). 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]
  35. Yoon, J., Matsuo, Y., Matsuda, S., Adachi, K., Kasai, H. & Yokota, A. ( 2008a; ). Rubritalea sabuli sp. nov., a carotenoid- and squalene-producing member of the family Verrucomicrobiaceae, isolated from marine sediment. Int J Syst Evol Microbiol 58, 992–997.[CrossRef]
    [Google Scholar]
  36. Yoon, J., Matsuo, Y., Adachi, K., Nozawa, M., Matsuda, S., Kasai, H. & Yokota, A. ( 2008b; ). 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]
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