1887

Abstract

A Gram-negative, facultatively anaerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated Gsoil 042, was isolated from a soil sample of a ginseng field in Pocheon province (South Korea) and was characterized taxonomically by using a polyphasic approach. The isolate was positive for catalase and oxidase, but negative for gelatinase and production of indole and HS. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The major cellular fatty acids were summed feature 4 (C 7 and/or iso-C 2-OH; 35.7 %), iso-C (24.3 %) and iso-C 3-OH (11.6 %). Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 042 fell within the radiation of the cluster comprising species. On the basis of 16S rRNA gene sequence similarities, the phylogenetically closest recognized species of the genus to strain Gsoil 042 included DSM 2366 (98.1 %), DSM 12126 (97.8 %) and LMG 22862 (97.2 %). The 16S rRNA gene sequence similarity with other recognized species of the genus was less than 96.1 %. DNA–DNA hybridization experiments showed that the DNA–DNA relatedness between strain Gsoil 042 and its phylogenetically closest neighbours was less than 43 %. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 042 should be classified as representing a novel species in the genus , for which the name sp. nov. is proposed. The type strain is Gsoil 042 (=KCTC 12594=LMG 23400).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.64693-0
2007-02-01
2024-03-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/57/2/381.html?itemId=/content/journal/ijsem/10.1099/ijs.0.64693-0&mimeType=html&fmt=ahah

References

  1. Atlas R. M. 1993 Handbook of Microbiological Media Edited by Parks L. C. Boca Raton, FL: CRC Press;
    [Google Scholar]
  2. Buck J. D. 1982; Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993
    [Google Scholar]
  3. Cappuccino J. G., Sherman N. 2002 Microbiology: a Laboratory Manual , 6th edn. San Francisco: Benjamin Cummings;
    [Google Scholar]
  4. 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]
  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. Gallego V., García M. T., Ventosa A. 2006; Pedobacter aquatilis sp. nov., isolated from drinking water, and emended description of the genus Pedobacter . Int J Syst Evol Microbiol 56:1853–1858 [CrossRef]
    [Google Scholar]
  8. 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]
  9. 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 [CrossRef]
    [Google Scholar]
  10. Hwang C. Y., Choi D. H., Cho B. C. 2006; Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter . Int J Syst Evol Microbiol 56:1831–1836 [CrossRef]
    [Google Scholar]
  11. Im W.-T., Jung H.-M., Cui Y.-S., Liu Q.-M., Zhang S.-L., Lee S.-T. 2005; Cultivation of the three hundreds of bacterial species from the soil of the ginseng field and mining the novel lineage bacteria. In Proceedings of the International Meeting of the Federation of Korean Microbiological Societies , abstract A035p. 169 Seoul: Federation of Korean Microbiological Societies;
    [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
    [Google Scholar]
  13. Kimura M. 1983 The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press;
    [Google Scholar]
  14. Kouker G., Jaeger K.-E. 1987; Specific and sensitive plate assay for bacterial lipases. Appl Environ Microbiol 53:211–213
    [Google Scholar]
  15. 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]
  16. Margesin R., Spröer C., Schumann P., Schinner F. 2003; Pedobacter cryoconitis sp. nov., a facultative psychrophile from alpine glacier cryoconite. Int J Syst Evol Microbiol 53:1291–1296 [CrossRef]
    [Google Scholar]
  17. 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]
  18. Moore D. D., Dowhan D. 1995; Preparation and analysis of DNA. In Current Protocols in Molecular Biology pp  2–11 Edited by Ausubel F. W., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. New York: Wiley;
    [Google Scholar]
  19. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  20. Sasser M. 1990 Identification of bacteria by gas chromatography of cellular fatty acids , MIDI Technical Note 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  21. Shivaji S., Chaturvedi P., Reddy G. S. N., Suresh K. 2005; Pedobacter himalayensis sp. nov., from the Hamta glacier located in the Himalayan mountain ranges of India. Int J Syst Evol Microbiol 55:1083–1088 [CrossRef]
    [Google Scholar]
  22. Stackebrandt E., Goebel B. M. 1994; Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849 [CrossRef]
    [Google Scholar]
  23. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A. D., Kämpfer P., Maiden M. C. J., Nesme X., Rosselló-Mora R., Swings J. other authors 2002; Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047 [CrossRef]
    [Google Scholar]
  24. 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 [CrossRef]
    [Google Scholar]
  25. 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 [CrossRef]
    [Google Scholar]
  26. 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 [CrossRef]
    [Google Scholar]
  27. Ten L. N., Im W.-T., Kim M.-K., Lee S.-T. 2005; A plate assay for simultaneous screening of polysaccharide- and protein-degrading microorganisms. Lett Appl Microbiol 40:92–98 [CrossRef]
    [Google Scholar]
  28. Ten L. N., Liu Q.-M., Im W.-T., Lee M., Yang D.-C., Lee S.-T. 2006; Pedobacter ginsengisoli sp. nov., a Dnase-producing bacterium isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 56:2565–2570 [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. Tschech A., Pfennig N. 1984; Growth yield increase linked to caffeate reduction in Acetobacterium woodii . Arch Microbiol 137:163–167 [CrossRef]
    [Google Scholar]
  31. Vanparys B., Heylen K., Lebbe L., De Vos P. 2005; Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum. Int J Syst Evol Microbiol 55:1315–1318 [CrossRef]
    [Google Scholar]
  32. 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]
  33. Widdel F., Bak F. 1992; Gram-negative mesophilic sulfate reducing bacteria. In The Prokaryotes , 2nd edn. pp  3352–3378 Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K.-H. New York: Springer;
    [Google Scholar]
  34. Widdel F., Kohring G., Mayer F. 1983; Studies in dissimilatory sulfate-reducing bacteria that decompose fatty acids. III. Characterization of the filamentous gliding Desulfonema limicola gen.nov. sp. nov., and Desulfonema magnum sp. nov.. Arch Microbiol 134:286–294 [CrossRef]
    [Google Scholar]
  35. Yoon J.-H., Lee M.-H., Kang S.-J., Park S.-Y., Oh T.-K. 2006; Pedobacter sandarakinus sp. nov., isolated from soil. Int J Syst Evol Microbiol 56:1273–1277 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.64693-0
Loading
/content/journal/ijsem/10.1099/ijs.0.64693-0
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