Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 59, Issue 11

sp. nov., a -glucosidase-producing bacterium isolated from soil of a ginseng field Free

Abstract

Strain DCY24, a Gram-reaction-positive, aerobic, rod-shaped, motile bacterium, was isolated from soil of a ginseng field in South Korea. According to 16S rRNA gene sequence analysis, it was closely related to DSM 15131 (95.1 % similarity), KCTC 9106 (95.0 %), DSM 15529 (94.8 %) and DSM 19082 (94.7 %). Chemotaxonomic data revealed that strain DCY24 possessed MK-8(H) as the predominant menaquinone, -2,6-diaminopimelic acid as the diagnostic diamino acid, phosphatidylglycerol and diphosphatidylglycerol as predominant polar lipids and iso-C, iso-C and C 9 as predominant fatty acids. The DNA G+C content was 71.0 mol%. Based on evidence from this polyphasic study, strain DCY24 (=KCTC 19265 =LMG 24128) should be classified as the type strain of a novel species, for which the name sp. nov. is proposed.

  • Published Online:
Keyword(s): TEM, transmission electron microscopy
© SGM
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.008821-0
2009-11-01
2025-03-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/59/11/2724.html?itemId=/content/journal/ijsem/10.1099/ijs.0.008821-0&mimeType=html&fmt=ahah

References

  1. Buck, J. D.(1982). Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44, 992–993. [Google Scholar]
  2. Cappuccino, J. G. & Sherman, N.(2002).Microbiology: a Laboratory Manual, 6th edn. Menlo Park, CA: Benjamin/Cummings.
  3. Choi, D. H., Kim, H. M., Noh, J.-H. & Cho, B. C.(2007).Nocardioides marinus sp. nov. Int J Syst Evol Microbiol 57, 775–779.[CrossRef] [Google Scholar]
  4. Collins, M. D. & Jones, D.(1981). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 45, 316–354. [Google Scholar]
  5. Collins, M. D., Dorsch, M. & Stackebrandt, E.(1989). Transfer of Pimelobacter tumescens to Terrabacter gen. nov. as Terrabacter tumescens comb. nov. and of Pimelobacter jensenii to Nocardioides as Nocardioides jensenii comb. nov. Int J Syst Bacteriol 39, 1–6.[CrossRef] [Google Scholar]
  6. Collins, M. D., Cockcroft, S. & Wallbanks, S.(1994). Phylogenetic analysis of a new ll-diaminopimelic acid-containing coryneform bacterium from herbage, Nocardioides plantarum sp. nov. Int J Syst Bacteriol 44, 523–526.[CrossRef] [Google Scholar]
  7. Dastager, S. G., Lee, J.-C., Ju, Y.-J., Park, D.-J. & Kim, C.-J.(2008).Nocardioides dilutes sp. nov. isolated from soil in Bigeum island, Korea. Curr Microbiol 56, 569–573.[CrossRef] [Google Scholar]
  8. Felsenstein, J.(1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef] [Google Scholar]
  9. 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]
  10. 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]
  11. 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]
  12. Kimura, M.(1983).The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  13. Kubota, M., Kawahara, K., Sekiya, K., Uchida, T., Hattori, Y., Futamata, H. & Hiraishi, A.(2005).Nocardioides aromaticivorans sp. nov., a dibenzofuran-degrading bacterium isolated from dioxin-polluted environments. Syst Appl Microbiol 28, 165–174.[CrossRef] [Google Scholar]
  14. 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]
  15. Lawson, P. A., Collins, M. D., Schumann, P., Tindall, B. J., Hirsch, P. & Labrenz, M.(2000). New ll-diaminopimelic acid-containing actinomycetes from hypersaline, heliothermal and meromictic Antarctic Ekho Lake: Nocardioides aquaticus sp. nov. and Friedmanniella lacustris sp. nov. Syst Appl Microbiol 23, 219–229.[CrossRef] [Google Scholar]
  16. Lee, S. D., Lee, D. W. & Kim, J.-S.(2008).Nocardioides hwasunensis sp. nov. Int J Syst Evol Microbiol 58, 278–281.[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. 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.[CrossRef] [Google Scholar]
  19. Moore, D. D. & Dowhan, D.(1995). Preparation and analysis of DNA. In Current Protocols in Molecular Biology, pp. 2–11. Edited by F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith & K. Struhl. New York: Wiley.
  20. O'Donnell, A. G., Goodfellow, M. & Minnikin, D. E.(1982). Lipids in the classification of Nocardioides: reclassification of Arthrobacter simplex (Jensen) Lochhead in the genus Nocardioides (Prauser) emend. O'Donnell et al. as Nocardioides simplex comb. nov. Arch Microbiol 133, 323–329.[CrossRef] [Google Scholar]
  21. Prauser, H.(1976).Nocardioides, a new genus of the order Actinomycetales. Int J Syst Bacteriol 26, 58–65.[CrossRef] [Google Scholar]
  22. Prauser, H.(1984).Nocardioides luteus spec. nov. Z Allg Mikrobiol 24, 647–648.[CrossRef] [Google Scholar]
  23. Prauser, H.(1989). Genus Nocardioides Prauser 1976. In Bergey's Manual of Systematic Bacteriology, vol. 4, pp. 2371–2375. Edited by S. T. Williams, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
  24. Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  25. Sasser, M.(1990).Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark, DE: MIDI Inc.
  26. Schleifer, K. H. & Kandler, O.(1972). Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36, 407–477. [Google Scholar]
  27. Shin, Y. K., Lee, J.-S., Chun, C. O., Kim, H.-J. & Park, Y.-H.(1996). Isoprenoid quinone profiles of the Leclercia adecarboxylata KCTC 1036T. J Microbiol Biotechnol 6, 68–69. [Google Scholar]
  28. Tamaoka, J. & Komagata, K.(1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125–128.[CrossRef] [Google Scholar]
  29. Tamura, T. & Yokota, A.(1994). Transfer of Nocardioides fastidiosa Collins and Stackebrandt 1989 to the genus Aeromicrobium as Aeromicrobium fastidiosum comb. nov. Int J Syst Bacteriol 44, 608–611.[CrossRef] [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, 4876–4882.[CrossRef] [Google Scholar]
  31. Urzì, C., Salamone, P., Schumann, P. & Stackebrandt, E.(2000).Marmoricola aurantiacus gen. nov., sp. nov., a coccoid member of the family Nocardioidaceae isolated from a marble statue. Int J Syst Evol Microbiol 50, 529–536.[CrossRef] [Google Scholar]
  32. Wang, Y. M., Zhang, Z. S., Xu, X. L., Ruan, J. S. & Wang, Y.(2001).Actinopolymorpha singaporensis gen. nov., sp. nov., a novel actinomycete from the tropical rainforest of Singapore. Int J Syst Evol Microbiol 51, 467–473. [Google Scholar]
  33. Yoon, J.-H., Lee, J.-S., Shin, Y. K., Park, Y.-H. & Lee, S. T.(1997). Reclassification of Nocardioides simplex ATCC 13260, ATCC 19565, and ATCC 19566 as Rhodococcus erythropolis. Int J Syst Bacteriol 47, 904–907.[CrossRef] [Google Scholar]
  34. Yoon, J.-H., Cho, Y.-G., Lee, S. T., Suzuki, K., Nakase, T. & Park, Y.-H.(1999).Nocardioides nitrophenolicus sp. nov., a p-nitrophenol-degrading bacterium. Int J Syst Bacteriol 49, 675–680.[CrossRef] [Google Scholar]
  35. Yoon, J.-H., Kim, I.-G., Lee, M.-H., Lee, C.-H. & Oh, T.-K.(2005).Nocardioides alkalitolerans sp. nov., isolated from an alkaline serpentinite soil in Korea. Int J Syst Evol Microbiol 55, 809–814.[CrossRef] [Google Scholar]
  36. Yoon, J.-H., Lee, J.-K., Jung, S.-Y., Kim, J.-A., Kim, H.-K. & Oh, T.-K.(2006).Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium. Int J Syst Evol Microbiol 56, 1783–1787.[CrossRef] [Google Scholar]
  37. Yoon, J.-H., Kang, S.-J., Lee, C.-H. & Oh, T.-K.(2007).Nocardioides insulae sp. nov., isolated from soil. Int J Syst Evol Microbiol 57, 136–140.[CrossRef] [Google Scholar]
/content/journal/ijsem/10.1099/ijs.0.008821-0
Loading
Nocardioides humi sp. nov., a β-glucosidase-producing bacterium isolated from soil of a ginseng field
Int J Syst Evol Microbiol 59, 2724 (2009); https://doi.org/10.1099/ijs.0.008821-0
/content/journal/ijsem/10.1099/ijs.0.008821-0
/content/journal/ijsem/10.1099/ijs.0.008821-0
Loading

Data & Media loading...

Supplements

Fatty acid compositions of strain DCY24 and closely related species. [PDF](72 KB)

PDF

Transmission electron micrographs of negatively stained cells of strain DCY24 . Bars, 1 µm.

IMAGE

Transmission electron micrographs of negatively stained cells of strain DCY24 . Bars, 1 µm.

IMAGE

Transmission electron micrographs of negatively stained cells of strain DCY24 . Bars, 1 µm.

IMAGE

Transmission electron micrographs of negatively stained cells of strain DCY24 . Bars, 1 µm.

IMAGE

Most cited Most Cited RSS feed

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