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Volume 58, Issue 5

sp. nov., a bacterium isolated from soil in a ginseng field Free

Abstract

Strain DCY16, a Gram-positive, spore-forming, rod-shaped, motile bacterium, was isolated from soil and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain DCY16 belonged to the genus ; highest sequence similarities were with JCM 9077 (94.4 %), WN9 (94.4 %), DSM 14203 (94.2 %), KCTC 3748 (92.8 %) and KCTC 10016BP (92.4 %). Chemotaxonomic data revealed that strain DCY16 possessed menaquinone MK-7 and the predominant fatty acids were C anteiso, C anteiso, C and C iso. The DNA G+C content of strain DCY16 was 50.9 mol%. Results of physiological and biochemical tests clearly demonstrated that strain DCY16 represents a distinct species. Based on these data, DCY16 (=KCTC 13141 =JCM 14928) should be classified as the type strain of a novel species, for which the name sp. nov. is proposed.

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2008-05-01
2024-04-16
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References

  1. Ash, C., Farrow, J. A. E., Wallbanks, S. & Collins, M. D.(1991). Phylogenetic heterogeneity of the genus Bacillus as revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett Appl Microbiol 13, 202–206. [Google Scholar]
  2. Ash, C., Priest, F. G. & Collins, M. D.(1993). Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie van Leeuwenhoek 64, 253–260. [Google Scholar]
  3. Buck, J. D.(1982). Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44, 992–993. [Google Scholar]
  4. Cappuccino, J. G. & Sherman, N.(2002).Microbiology: a Laboratory Manual, 6th edn. Menlo Park, CA: Benjamin Cummings.
  5. Claus, D. & Berkeley, R. C. W.(1986). Genus Bacillus Cohn 1872. In Bergey's Manual of Systematic Bacteriology, vol. 2, pp. 1105–1140. Edited by P. H. A. Sneath, N. S. Mair, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
  6. 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]
  7. Daane, L. L., Harjono, I., Barns, S. M., Launen, L. A., Palleroni, N. J. & Häggblom, M. M.(2002). PAH-degradation by Paenibacillus spp. and description of Paenibacillus naphthalenovorans sp. nov., a naphthalene-degrading bacterium from the rhizosphere of salt marsh plants. Int J Syst Evol Microbiol 52, 131–139. [Google Scholar]
  8. Felsenstein, J.(1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef] [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. Heyndrickx, M., Vandemeulebroecke, K., Scheldeman, P., Hoste, B., Kersters, K., De Vos, P., Logan, N. A., Aziz, A. M., Ali, N. & Berkeley, R. C. W.(1995).Paenibacillus (formerly Bacillus) gordonae (Pichinoty et al. 1986) Ash et al. 1994 is a later subjective synonym of Paenibacillus (formerly Bacillus) validus (Nakamura 1984) Ash et al. 1994: emended description of P. validus. Int J Syst Bacteriol 45, 661–669.[CrossRef] [Google Scholar]
  11. Heyndrickx, M., Lebbe, L., Kersters, K., De Vos, P., Forsyth, G. & Logan, N. A.(1998).Virgibacillus: a new genus to accommodate Bacillus pantothenticus (Proom and Knight 1950). Emended description of Virgibacillus pantothenticus. Int J Syst Bacteriol 48, 99–106.[CrossRef] [Google Scholar]
  12. Kim, D.-S., Bae, C.-Y., Jeon, J.-J., Chun, S.-J., Oh, H. W., Hong, S. G., Baek, K.-S., Moon, E. Y. & Bae, K. S.(2004).Paenibacillus elgii sp. nov., with broad antimicrobial activity. Int J Syst Evol Microbiol 54, 2031–2035.[CrossRef] [Google Scholar]
  13. 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]
  14. Kimura, M.(1983).The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  15. Kumar, S., Tamura, K., Jakobsen, I.-B. & Nei, M.(2001).mega2: molecular evolutionary genetics analysis software. Bioinformatics 17, 1244–1245.[CrossRef] [Google Scholar]
  16. Lee, J.-S., Pyun, Y.-R. & Bae, K. S.(2004). Transfer of Bacillus ehimensis and Bacillus chitinolyticus to the genus Paenibacillus with emended descriptions of Paenibacillus ehimensis comb. nov. and Paenibacillus chitinolyticus comb. nov. Int J Syst Evol Microbiol 54, 929–933.[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. Montes, M. J., Mercade, E., Bozal, N. & Guinea, J.(2004).Paenibacillus antarcticus sp. nov., a novel psychrotolerant organism from the Antarctic environment. Int J Syst Evol Microbiol 54, 1521–1526.[CrossRef] [Google Scholar]
  19. Priest, F. G.(1981). DNA homology in the genus Bacillus. In The Aerobic Endospore-forming Bacteria, pp. 33–57. Edited by R. C. W. Berkeley & M. Goodfellow. London: Academic Press.
  20. Saha, P., Mondal, A. K., Mayilraj, S., Krishnamurthi, S., Bhattacharya, A. & Chakrabarti, T.(2005).Paenibacillus assamensis sp. nov., a novel bacterium isolated from a warm spring in Assam, India. Int J Syst Evol Microbiol 55, 2577–2581.[CrossRef] [Google Scholar]
  21. Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  22. Sánchez, M. M., Fritze, D., Blanco, A., Spröer, C., Tindall, B. J., Schumann, P., Kroppenstedt, R. M., Diaz, P. & Pastor, F. I.(2005).Paenibacillus barcinonensis sp. nov., a xylanase-producing bacterium isolated from a rice field in the Ebro River delta. Int J Syst Evol Microbiol 55, 935–939.[CrossRef] [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. Shida, O., Takagi, H., Kadowaki, K. & Komagata, K.(1996). Proposal for two new genera, Brevibacillus gen. nov. and Aneurinibacillus gen. nov. Int J Syst Bacteriol 46, 939–946.[CrossRef] [Google Scholar]
  25. Shida, O., Takagi, H., Kadowaki, K., Nakamura, L. K. & Komagata, K.(1997). Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int J Syst Bacteriol 47, 289–298.[CrossRef] [Google Scholar]
  26. 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]
  27. Slepecky, R. A. & Hemphill, H. E.(1992). The genus Bacillus – nonmedical. In The Prokaryotes, 2nd edn, pp. 1663–1696. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York: Springer.
  28. Spring, S., Ludwig, W., Marquez, M. C., Ventosa, A. & Schleifer, K.-H.(1996).Halobacillus gen. nov., with descriptions of Halobacillus litoralis sp. nov., and Halobacillus trueperi sp. nov., and transfer of Sporosarcina halophila to Halobacillus halophilus comb. nov. Int J Syst Bacteriol 46, 492–496.[CrossRef] [Google Scholar]
  29. Stackebrandt, E. & Liesack, W.(1993). Nucleic acids and classification. In Handbook of New Bacterial Systematics, pp. 152–189. Edited by M. Goodfellow & A. G. O'Donnell. London: Academic Press.
  30. 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]
  31. Ten, L. N., Baek, S. H., Im, W. T., Lee, M. J., Oh, H. W. & Lee, S. T.(2006).Paenibacillus panacisoli sp. nov., a xylanolytic bacterium isolated from soil in a ginseng field in South Korea. Int J Syst Evol Microbiol 56, 2677–2681.[CrossRef] [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, 4876–4882.[CrossRef] [Google Scholar]
  33. Wainø, M., Tindall, B. J., Schumann, P. & Ingvorsen, K.(1999).Gracilibacillus gen. nov., with description of Gracilibacillus halotolerans gen. nov., sp. nov.; transfer of Bacillus dipsosauri to Gracilibacillus dipsosauri comb. nov., and Bacillus salexigens to the genus Salibacillus gen. nov., as Salibacillus salexigens comb. nov. Int J Syst Bacteriol 49, 821–831.[CrossRef] [Google Scholar]
  34. Weisburg, W. G., Barns, S. M., Pelletier, D. A. & Lane, D. J.(1991). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173, 697–703. [Google Scholar]
  35. Wisotzkey, J. D., Jurtshuk, P., Jr, Fox, G. E., Deinhard, G. & Poralla, K.(1992). Comparative sequence analyses on the 16S rRNA (rDNA) of Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus and proposal for creation of a new genus, Alicyclobacillus gen. nov. Int J Syst Bacteriol 42, 263–269.[CrossRef] [Google Scholar]
  36. Yoon, J.-H., Seo, W.-T., Shin, Y. K., Kho, Y. H., Kang, K. H. & Park, Y.-H.(2002).Paenibacillus chinjuensis sp. nov., a novel exopolysaccharide-producing bacterium. Int J Syst Evol Microbiol 52, 415–421. [Google Scholar]
  37. Yoon, J. H., Kang, S. J., Yeo, S. H. & Oh, T. K.(2005).Paenibacillus alkaliterrae sp. nov., isolated from an alkaline soil in Korea. Int J Syst Evol Microbiol 55, 2339–2344.[CrossRef] [Google Scholar]
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Paenibacillus ginsengihumi sp. nov., a bacterium isolated from soil in a ginseng field
Int J Syst Evol Microbiol 58, 1164 (2008); https://doi.org/10.1099/ijs.0.65378-0
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vol. , part 5, pp. 1164 - 1168

Extended neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showing the phylogenetic relationships of strain DCY16 and type strains of all species. [PDF](30 KB)

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