1887

Abstract

A novel Gram-staining-positive, aerobic bacterium, designed DCY80, was isolated from soil of a ginseng field in the Republic of Korea. 16S rRNA gene sequence analysis revealed that strain DCY80 belonged to the genus (95.8–98.2 % similarity) and was most closely related to DSM 4810 (98.2 %). Colonies were circular, entire, low-convex, opaque and 0.5–1.0 mm in diameter after growth for 2 days on TSA at 30 °C. Growth occurred at 4–34 °C (optimum, 25 °C), at pH 5.0–10.0 (optimum, pH 6.5–7.0) and in the presence of 0–7.0 % NaCl. Strain DCY80 produced siderophores and was sensitive to penicillin G, erythromycin, cefazolin, oleandomycin, ceftazidime, vancomycin, tetracycline, novobiocin, carbamicillin, rifampicin and neomycin. The DNA G+C content was 71.0 mol%. Levels of DNA–DNA relatedness between strain DCY80 and DSM 4810, KCTC 9916, DSM 23186 and KCTC 9915 were 46.9±0.5, 28.9±0.6, 20.4±0.9 and 17.3±0.4 %, respectively. The cell-wall peptidoglycan of strain DCY80 contained -diaminopimelic acid as the diagnostic diamino acid. The menaquinones were MK-7 (85.8 %) and MK-8 (14.2 %). The major cellular fatty acids were anteiso-C (69.1 %) and anteiso-C (12.2 %). Phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid, two unidentified phospholipids and five unidentified polar lipids were found. On the basis of our phenotypic and genotypic analyses, strain DCY80 represents a novel species of the genus , for which the name sp. nov. is proposed (type strain DCY80 = KCTC 29226 = JCM 19356).

Funding
This study was supported by the:
  • Korea Institute of Planning & Evaluation for Technology in Food, Agriculture, Forestry & Fisheries (Award 309019-03-3-SB010)
  • Next-Generation BioGreen 21 Program, Republic of Korea (Award PJ009529032014)
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2014-09-01
2024-03-28
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References

  1. Anzai Y., Kim H., Park J. Y., Wakabayashi H., Oyaizu H. ( 2000 ). Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. . Int J Syst Evol Microbiol 50, 15631589. [View Article] [PubMed]
    [Google Scholar]
  2. Bauer A. W., Kirby W. M. M., Sherris J. C., Turck M. ( 1966 ). Antibiotic susceptibility testing by a standardized single disk method. . Am J Clin Pathol 45, 493496.[PubMed]
    [Google Scholar]
  3. 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]
  4. Buczolits S., Schumann P., Weidler G., Radax C., Busse H.-J. ( 2003 ). Brachybacterium muris sp. nov., isolated from the liver of a laboratory mouse strain. . Int J Syst Evol Microbiol 53, 19551960. [View Article] [PubMed]
    [Google Scholar]
  5. Chou J. H., Lin K. Y., Lin M. C., Sheu S.-Y., Wei Y. H., Arun A. B., Young C.-C., Chen W.-M. ( 2007 ). Brachybacterium phenoliresistens sp. nov., isolated from oil-contaminated coastal sand. . Int J Syst Evol Microbiol 57, 26742679. [View Article] [PubMed]
    [Google Scholar]
  6. Christensen W. B. ( 1946 ). Urea decomposition as a means of differentiating Proteus and paracolon cultures from each other and from Salmonella and Shigella types. . J Bacteriol 52, 461466.[PubMed]
    [Google Scholar]
  7. 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]
  8. Collins M. D., Brown J., Jones D. ( 1988 ). Brachybacterium faecium gen. nov., sp. nov., a coryneform bacterium from poultry litter. . Int J Syst Bacteriol 38, 4548. [View Article]
    [Google Scholar]
  9. Cowan S. T., Steel K. J. ( 1974 ). Manual for the Identification of Medical Bacteria. Cambridge:: Cambridge University Press;.
    [Google Scholar]
  10. 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]
  11. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  12. 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]
  13. Gontia I., Kavita K., Schmid M., Hartmann A., Jha B. ( 2011 ). Brachybacterium saurashtrense sp. nov., a halotolerant root-associated bacterium with plant growth-promoting potential. . Int J Syst Evol Microbiol 61, 27992804. [View Article] [PubMed]
    [Google Scholar]
  14. Gvozdyak O. R., Nogina T. M., Schumann P. ( 1992 ). Taxonomic study of the genus Brachybacterium: Brachybacterium nesterenkovii sp. nov.. Int J Syst Bacteriol 42, 7478. [View Article] [PubMed]
    [Google Scholar]
  15. 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]
  16. Heyrman J., Balcaen A., De Vos P., Schumann P., Swings J. ( 2002 ). Brachybacterium fresconis sp. nov. and Brachybacterium sacelli sp. nov., isolated from deteriorated parts of a medieval wall painting of the chapel of Castle Herberstein (Austria). . Int J Syst Evol Microbiol 52, 16411646. [View Article] [PubMed]
    [Google Scholar]
  17. 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, 152157.[PubMed]
    [Google Scholar]
  18. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. & other authors ( 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]
  19. Kimura M. ( 1983 ). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  20. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115176. Edited by Stackebrandt E., Goodfellow M. . Chichester:: Wiley;.
    [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, 159167. [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, 104117. [View Article]
    [Google Scholar]
  23. Park S. K., Kim M. S., Jung M. J., Nam Y. D., Park E. J., Roh S. W., Bae J. W. ( 2011 ). Brachybacterium squillarum sp. nov., isolated from salt-fermented seafood. . Int J Syst Evol Microbiol 61, 11181122. [View Article] [PubMed]
    [Google Scholar]
  24. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  25. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc.;
    [Google Scholar]
  26. Schleifer K. H., Kandler O. ( 1972 ). Peptidoglycan types of bacterial cell walls and their taxonomic implications. . Bacteriol Rev 36, 407477.[PubMed]
    [Google Scholar]
  27. Schubert K., Ludwig W., Springer N., Kroppenstedt R. M., Accolas J.-P., Fiedler F. ( 1996 ). Two coryneform bacteria isolated from the surface of French Gruyère and Beaufort cheeses are new species of the genus Brachybacterium: Brachybacterium alimentarium sp. nov. and Brachybacterium tyrofermentans sp. nov.. Int J Syst Bacteriol 46, 8187. [View Article] [PubMed]
    [Google Scholar]
  28. Schwyn B., Neilands J. B. ( 1987 ). Universal chemical assay for the detection and determination of siderophores. . Anal Biochem 160, 4756. [View Article] [PubMed]
    [Google Scholar]
  29. Skerman V. B. D. ( 1967 ). A Guide to the Identification of the Genera of Bacteria, , 2nd edn.. Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  30. Takeuchi M., Fang C. X., Yokota A. ( 1995 ). Taxonomic study of the genus Brachybacterium: proposal of Brachybacterium conglomeratum sp. nov., nom. rev., Brachybacterium paraconglomeratum sp. nov., and Brachybacterium rhamnosum sp. nov.. Int J Syst Bacteriol 45, 160168. [View Article]
    [Google Scholar]
  31. Tamura K., Dudley J., Nei M., Kumar S. ( 2007 ). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. . Mol Biol Evol 24, 15961599. [View Article] [PubMed]
    [Google Scholar]
  32. 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]
  33. 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, 463464. [View Article]
    [Google Scholar]
  34. Zhang G., Zeng G., Cai X., Deng S., Luo H., Sun G. ( 2007 ). Brachybacterium zhongshanense sp. nov., a cellulose-decomposing bacterium from sediment along the Qijiang River, Zhongshan City, China. . Int J Syst Evol Microbiol 57, 25192524. [View Article] [PubMed]
    [Google Scholar]
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