1887

Abstract

Two Gram-stain-negative, yellow, aerobic and rod-shaped bacterial isolates, designated THG-DN3.18 and THG-DN3.19, were isolated from an ancient tree trunk from Daejeon, South Korea. 16S rRNA gene sequence similarity showed that both strains belong to the genus within the family . Strain THG-DN3.18 exhibited maximum sequence similarity with KCTC 23344 (98.5 %) while strain THG-DN3.19 exhibited maximum sequence similarity with LMG 24260 (97.3 %). In DNA–DNA hybridization tests, the two strains showed less than 35 % relatedness with respect to closely related species of the genus . Both strains contained iso-C and Cω6 and/or Cω7 (summed feature 3) as the predominant fatty acids and MK-7 as the major isoprenoid quinone. The DNA G+C contents of strains THG-DN3.18 and THG-DN3.19 were 35.5 and 40.1 mol%, respectively. The genotypic analysis, biochemical properties, and phenotypic and chemotaxonomic characteristics indicate that strains THG-DN3.18 and THG-DN3.19 represent novel species of the genus , for which the names sp. nov. and sp. nov. are proposed. The type strains are THG-DN3.18 ( = KCTC 42230 = JCM 30352) and THG-DN3.19 ( = KCTC 42233 = JCM 30353), respectively.

Funding
This study was supported by the:
  • Ministry of Trade, Industry & Energy (MOTIE, Korea) (Award N0000888)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.000087
2015-04-01
2024-12-13
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/4/1241.html?itemId=/content/journal/ijsem/10.1099/ijs.0.000087&mimeType=html&fmt=ahah

References

  1. Bernardet J. F., Nakagawa Y., Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes ( 2002 ). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. . Int J Syst Evol Microbiol 52, 10491070. [View Article] [PubMed]
    [Google Scholar]
  2. Collins M. D. ( 1985 ). Isoprenoid quinone analyses in bacterial classification and identification. . In Chemical Methods in Bacterial Systematics, pp. 267287. Edited by Goodfellow M., Minnikin D. E. . London:: Academic Press;.
    [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, 224229. [View Article]
    [Google Scholar]
  4. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  5. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [View Article]
    [Google Scholar]
  6. Gillis M., De Ley J., De Cleene M. ( 1970 ). The determination of molecular weight of bacterial genome DNA from renaturation rates. . Eur J Biochem 12, 143153. [View Article] [PubMed]
    [Google Scholar]
  7. Gomori G. ( 1955 ). Preparation of buffers for use in enzyme studies. . Methods Enzymol 12, 138146. [View Article]
    [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, 9598.
    [Google Scholar]
  9. Joubert J. J., van Rensburg E. J., Pitout M. J. ( 1984 ). A plate method for demonstrating the breakdown of heparin and chondroitin sulfate by bacteria. . J Microbiol Methods 2, 197202. [View Article]
    [Google Scholar]
  10. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [View Article] [PubMed]
    [Google Scholar]
  11. Kimura M. ( 1983 ). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  12. Kook M., Park Y., Yi T. H. ( 2014 ). Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter . . Int J Syst Evol Microbiol 64, 17891794. [View Article] [PubMed]
    [Google Scholar]
  13. Luo X., Wang Z., Dai J., Zhang L., Li J., Tang Y., Wang Y., Fang C. ( 2010 ). Pedobacter glucosidilyticus sp. nov., isolated from dry riverbed soil. . Int J Syst Evol Microbiol 60, 229233. [View Article] [PubMed]
    [Google Scholar]
  14. Margesin R., Shivaji S. ( 2011 ). Genus II. Pedobacter Steyn, Segers, Vancanneyt, Sandra, Kersters, and Joubert 1998, 171VP . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 4, pp. 339351. Edited by Krieg N. R., Staley J. T., Brown D. R., Hedlund B. P., Paster B. J., Ward N. L., Ludwig W., Whitman W. B. . New York:: Springer;.
    [Google Scholar]
  15. Margesin R., Zhang D.-C. ( 2013 ). Pedobacter ruber sp. nov., a psychrophilic bacterium isolated from soil. . Int J Syst Evol Microbiol 63, 339344. [View Article] [PubMed]
    [Google Scholar]
  16. McConaughy B. L., Laird C. D., McCarthy B. J. ( 1969 ). Nucleic acid reassociation in formamide. . Biochemistry 8, 32893295. [View Article] [PubMed]
    [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, 159167. [View Article]
    [Google Scholar]
  18. Minnikin D. E., O’Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. ( 1984 ). An intergrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2, 233241. [View Article]
    [Google Scholar]
  19. Oh H. W., Kim B. C., Park D. S., Jeong W. J., Kim H., Lee K. H., Kim S. U. ( 2013 ). Pedobacter luteus sp. nov., isolated from soil. . Int J Syst Evol Microbiol 63, 13041310. [View Article] [PubMed]
    [Google Scholar]
  20. Qiu X., Qu Z., Jiang F., Ren L., Chang X., Kan W., Fang C., Peng F. ( 2014 ). Pedobacter huanghensis sp. nov. and Pedobacter glacialis sp. nov., isolated from Arctic glacier foreland. . Int J Syst Evol Microbiol 64, 24312436. [View Article] [PubMed]
    [Google Scholar]
  21. Reichenbach H. ( 1992 ). The order Cytophagales . . In The Prokaryotes, , 2nd edn., vol. 4, pp. 36313675. Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K. H. . New York:: Springer;. [View Article]
    [Google Scholar]
  22. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  23. Sasser M. . ( 1990 ). Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  24. Schmidt K., Connor A., Britton G. ( 1994 ). Analysis of pigments: carotenoids and related polyenes. . In Chemical Methods in Prokaryotic Systematics, pp. 403461. Edited by Goodfellow M., O’Donnell A. G. . Chichester:: Wiley;.
    [Google Scholar]
  25. Skerman V. B. D. ( 1967 ). A Guide to the Identification of the Genera of Bacteria, , 2nd edn.. Baltimore, MD:: Williams & Wilkins;.
    [Google Scholar]
  26. Stabili L., Gravili C., Tredici S. M., Piraino S., Talà A., Boero F., Alifano P. ( 2008 ). Epibiotic Vibrio luminous bacteria isolated from some hydrozoa and bryozoa species. . Microb Ecol 56, 625636. [View Article] [PubMed]
    [Google Scholar]
  27. 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, 846849. [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, 165177. [View Article] [PubMed]
    [Google Scholar]
  29. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 27312739. [View Article] [PubMed]
    [Google Scholar]
  30. 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, 48764882. [View Article] [PubMed]
    [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. 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, 463464. [View Article]
    [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, 697703.[PubMed]
    [Google Scholar]
  33. Yoon M. H., Ten L. N., Im W. T., Lee S. T. ( 2007 ). Pedobacter panaciterrae sp. nov., isolated from soil in South Korea. . Int J Syst Evol Microbiol 57, 381386. [View Article] [PubMed]
    [Google Scholar]
  34. Zhou Z., Jiang F., Wang S., Peng F., Dai J., Li W., Fang C. ( 2012 ). Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus . . Int J Syst Evol Microbiol 62, 19631969. [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijs.0.000087
Loading
/content/journal/ijsem/10.1099/ijs.0.000087
Loading

Data & Media loading...

Supplements

Supplementary Data

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