1887

Abstract

A Gram-reaction-negative, strictly aerobic, rod-shaped, non-motile strain, designated 2-1-2, was isolated from perchloroethylene/trichloroethene-contaminated soil in Suwon, South Korea. A polyphasic approach was used to study the taxonomic position of strain 2-1-2. Strain 2-1-2 showed highest 16S rRNA gene sequence similarities to TR6-04 (97.9 %) and ATCC 33299 (97.1 %); sequence similarities to other species were less than 93.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 2-1-2 belonged to the clade formed by members of the genus in the family . The G+C content of the genomic DNA was 36.6 mol%. Strain 2-1-2 showed the typical chemotaxonomic features of the genus , with the presence of a ceramide phosphorylethanolamine (CerPE-2) as the major ceramide, menaquinone 7 (MK-7) as the predominant respiratory quinone and iso-C, iso-C 3-OH and summed feature 3 (comprising iso-C 2-OH and/or Cω7) as the major fatty acids. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, and DNA–DNA relatedness, strain 2-1-2 represents a novel species of the genus , for which the name sp. nov. is proposed; the type strain is 2-1-2 ( = KEMC 2241-005 = JCM 16704). Emended descriptions of and are also proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.024737-0
2012-11-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/62/11/2559.html?itemId=/content/journal/ijsem/10.1099/ijs.0.024737-0&mimeType=html&fmt=ahah

References

  1. Altmann L., Neuhann H. F., Krämer U., Witten J., Jermann E. 1995; Neurobehavioral and neurophysiological outcome of chronic low-level tetrachloroethene exposure measured in neighborhoods of dry cleaning shops. Environ Res 69:83–89 [View Article][PubMed]
    [Google Scholar]
  2. Atlas R. M. 1993 Handbook of Microbiological Media Edited by Parks L. C. Boca Raton, FL: CRC Press;
    [Google Scholar]
  3. Buck J. D. 1982; Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993[PubMed]
    [Google Scholar]
  4. Cappuccino J. G., Sherman N. 2002 Microbiology: a Laboratory Manual, 6th edn. San Francisco: Benjamin Cummings;
    [Google Scholar]
  5. 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 [View Article]
    [Google Scholar]
  6. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  7. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [View Article]
    [Google Scholar]
  8. Folch J., Lees M., Sloane Stanley G. H. 1957; A simple method for the isolation and purification of total lipids from animal tissues. J Biol Chem 226:497–509[PubMed]
    [Google Scholar]
  9. Hall T. A. 1999; BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
    [Google Scholar]
  10. Hiraishi A., Ueda Y., Ishihara J., Mori T. 1996; Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469 [View Article]
    [Google Scholar]
  11. Holmes B., Hollis D. G., Steigerwalt A. G., Pickett M. J., Brenner D. J. 1983; Flavobacterium thalpophilum, a new species recovered from human clinical material. Int J Syst Bacteriol 33:677–682 [View Article]
    [Google Scholar]
  12. Kim M. K., Im W.-T., Ohta H., Lee M., Lee S.-T. 2005; Sphingopyxis granuli sp. nov., a β-glucosidase-producing bacterium in the family Sphingomonadaceae in α-4 subclass of the Proteobacteria . J Microbiol 43:152–157[PubMed]
    [Google Scholar]
  13. Kim K.-H., Ten L. N., Liu Q.-M., Im W.-T., Lee S.-T. 2006; Sphingobacterium daejeonense sp. nov., isolated from a compost sample. Int J Syst Evol Microbiol 56:2031–2036 [View Article][PubMed]
    [Google Scholar]
  14. Kimura M. 1983 The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; [CrossRef]
    [Google Scholar]
  15. Klaassen C. D. (editor) 2001 Casarett and Doull’s Toxicology: The Basic Science of Poisons New York: McGraw Hill;
    [Google Scholar]
  16. Kumar S., Tamura K., Nei M. 2004; mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163 [View Article][PubMed]
    [Google Scholar]
  17. Kuykendall L. D., Roy M. A., O’Neill J. J., Devine T. E. 1988; Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . Int J Syst Bacteriol 38:358–361 [View Article]
    [Google Scholar]
  18. Liu R., Liu H., Zhang C. X., Yang S. Y., Liu X. H., Zhang K. Y., Lai R. 2008; Sphingobacterium siyangense sp. nov., isolated from farm soil. Int J Syst Evol Microbiol 58:1458–1462 [View Article][PubMed]
    [Google Scholar]
  19. Matsuyama H., Katoh H., Ohkushi T., Satoh A., Kawahara K., Yumoto I. 2008; Sphingobacterium kitahiroshimense sp. nov., isolated from soil. Int J Syst Evol Microbiol 58:1576–1579 [View Article][PubMed]
    [Google Scholar]
  20. Mehnaz S., Weselowski B., Lazarovits G. 2007; Sphingobacterium canadense sp. nov., an isolate from corn roots. Syst Appl Microbiol 30:519–524 [View Article][PubMed]
    [Google Scholar]
  21. 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 [View Article]
    [Google Scholar]
  22. Minnikin D. E., Patel P. V., Alshamaony L., Goodfellow M. 1977; Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 27:104–117 [View Article]
    [Google Scholar]
  23. Moran M. J., Zogorski J. S., Squillace P. J. 2007; Chlorinated solvents in groundwater of the United States. Environ Sci Technol 41:74–81 [View Article][PubMed]
    [Google Scholar]
  24. Naka T., Fujiwara N., Yano I., Maeda S., Doe M., Minamino M., Ikeda N., Kato Y., Watabe K. et al. 2003; Structural analysis of sphingophospholipids derived from Sphingobacterium spiritivorum, the type species of genus Sphingobacterium . Biochim Biophys Acta 1635:83–92[PubMed] [CrossRef]
    [Google Scholar]
  25. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
  26. Sasser M. 1990; Identification of bacteria by gas chromatography of cellular fatty acids. . Technical Note 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  27. Shivaji S., Ray M. K., Rao N. S., Saisree L., Jagannadham M. V., Kumar G. S., Reddy G. S. N., Bhargava P. M. 1992; Sphingobacterium antarcticus sp. nov., a psychrotrophic bacterium from the soils of Schirmacher Oasis, Antarctica. Int J Syst Bacteriol 42:102–106 [View Article]
    [Google Scholar]
  28. Steyn P. L., Segers P., Vancanneyt M., Sandra P., Kersters K., Joubert J. J. 1998; Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov.. Int J Syst Bacteriol 48:165–177 [View Article][PubMed]
    [Google Scholar]
  29. Takeuchi M., Yokota A. 1992; Proposals of Sphingobacterium faecium sp. nov., Sphingobacterium piscium sp. nov., Sphingobacterium heparinum comb. nov., Sphingobacterium thalpophilum comb. nov., and two genospecies of the genus Sphingobacterium and synonymy of Flavobacterium yabuuchiae and Sphingobacterium spiritivorum . J Gen Appl Microbiol 38:465–482 [View Article]
    [Google Scholar]
  30. Tamaoka J., Komagata K. 1984; Determination of DNA base composition by reversed phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128 [View Article]
    [Google Scholar]
  31. Ten L. N., Im W.-T., Kim M.-K., Kang M.-S., Lee S.-T. 2004; Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. J Microbiol Methods 56:375–382 [View Article][PubMed]
    [Google Scholar]
  32. Ten L. N., Liu Q.-M., Im W.-T., Aslam Z., Lee S.-T. 2006; Sphingobacterium composti sp. nov., a novel DNase-producing bacterium isolated from compost. J Microbiol Biotechnol 16:1728–1733
    [Google Scholar]
  33. 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 [View Article][PubMed]
    [Google Scholar]
  34. 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. et al. 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 [View Article]
    [Google Scholar]
  35. Wei W., Zhou Y., Wang X., Huang X., Lai R. 2008; Sphingobacterium anhuiense sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 58:2098–2101 [View Article][PubMed]
    [Google Scholar]
  36. Yabuuchi E., Kaneko T., Yano I., Moss C. W., Miyoshi N. 1983; Sphingobacterium gen. nov., Sphingobacterium spiritivorum comb. nov., Sphingobacterium multivorum comb. nov., Sphingobacterium mizutae sp. nov., and Flavobacterium indologenes sp. nov.: glucose-nonfermenting gram-negative rods in CDC groups IIk-2 and IIb. Int J Syst Bacteriol 33:580–598 [View Article]
    [Google Scholar]
  37. Yoo S. H., Weon H. Y., Jang H. B., Kim B. Y., Kwon S. W., Go S. J., Stackebrandt E. 2007; Sphingobacterium composti sp. nov., isolated from cotton-waste composts. Int J Syst Evol Microbiol 57:1590–1593 [View Article][PubMed]
    [Google Scholar]
  38. Yoshida N., Asahi K., Sakakibara Y., Miyake K., Katayama A. 2007; Isolation and quantitative detection of tetrachloroethene (PCE)-dechlorinating bacteria in unsaturated subsurface soils contaminated with chloroethenes. J Biosci Bioeng 104:91–97 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.024737-0
Loading
/content/journal/ijsem/10.1099/ijs.0.024737-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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