1887

Abstract

A polyphasic taxonomic study was performed on strain YM26-026, which was isolated from acid-treated sediment in Kamaishi, Japan. The bacterial cells were pale-pink-pigmented, Gram-negative, obligately aerobic, non-spore-forming, spherical and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel isolate was a member of the phylum ‘’ and shared approximately 84–87 % sequence similarity with strains of the class that have been cultivated to date. Strain YM26-026 produced pale-pink pigments of carotenoid. -Lactam antibiotic susceptibility tests and amino acid analysis of cell-wall hydrolysates indicated that the novel isolate did not contain muramic acid or diaminopimelic acid in the cell wall, suggesting that the strain lacks peptidoglycan. The G+C content of the DNA of strain YM26-026 was 54.0 mol%. Menaquinone-7 was the major quinone and C and C 9 were the major fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strain YM26-026 represents a new genus of the family within the phylum ‘’, for which the name gen. nov., sp. nov. is proposed. The type strain is YM26-026 (=MBIC08280=KCTC 12870).

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2007-09-01
2024-12-09
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References

  1. Chin K.-J., Hahn D., Hengtsmann U., Liesack W., Janssen P. H. 1999; Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms. Appl Environ Microbiol 65:5042–5049
    [Google Scholar]
  2. Chin K.-J., Liesack W., Janssen P. H. 2001; Opitutus terrae gen. nov., sp. nov., to accommodate novel strains of the division ‘ Verrucomicrobia ’ isolated from rice paddy soil. Int J Syst Evol Microbiol 51:1965–1968 [CrossRef]
    [Google Scholar]
  3. Choo Y.-J., Lee K., Song J., Cho J.-C. 2007; Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam.nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum ‘ Verrucomicrobia ’. Int J Syst Evol Microbiol 57:532–537 [CrossRef]
    [Google Scholar]
  4. 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]
  5. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
    [Google Scholar]
  6. 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]
  7. 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 Boone D. R., Castenholz R. W., Garrity G. M. New York: Springer;
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  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. Janssen P. H., Schuhmann A., Mörschel E., Rainey F. A. 1997; Novel anaerobic ultramicrobacteria belonging to the Verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil. Appl Environ Microbiol 63:1382–1388
    [Google Scholar]
  14. 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]
  15. 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]
  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;
    [Google Scholar]
  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 micro-organisms. 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. 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 Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
  22. Rappé M. S., Giovannoni S. J. 2003; The uncultured microbial majority. Annu Rev Microbiol 57:369–394 [CrossRef]
    [Google Scholar]
  23. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  24. Sakai T., Ishizuka K., Kato I. 2003; Isolation and characterization of a fucoidan-degrading marine bacterium. Mar Biotechnol 5:409–416 [CrossRef]
    [Google Scholar]
  25. Schleifer K. H., Kandler O. 1972; Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477
    [Google Scholar]
  26. Shieh W. Y., Jean W. D. 1998; Alterococcus agarolyticus , gen. nov., sp. nov. a halophilic thermophilic bacterium capable of agar degradation. Can J Microbiol 44:637–645 [CrossRef]
    [Google Scholar]
  27. 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]
  28. 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]
  29. 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]
  30. Yokota A., Tamura T., Nishii T., Hasegawa T. 1993 Kineococcus aurantiacus gen. nov., sp. nov., a new aerobic, Gram-positive, motile coccus with meso -diaminopimelic acid and arabinogalactan in the cell wall. Int J Syst Bacteriol 4352–57 [CrossRef]
  31. Yoon J., Yasumoto-Hirose M., Katsuta A., Sekiguchi H., Matsuda S., Kasai H., Yokota A. 2007a; Coraliomargarita akajimensis gen. nov., sp. nov. a novel member of the phylum ‘ Verrucomicrobia ’ isolated from seawater in Japan. Int J Syst Evol Microbiol 57:959–963 [CrossRef]
    [Google Scholar]
  32. Yoon J., Yasumoto-Hirose M., Matsuo Y., Nozawa M., Matsuda S., Kasai H., Yokota A. 2007b; 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]
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