Skip to main content
SpringerLink
Log in

Paenibacillus swuensis sp. nov., a bacterium isolated from soil

  • Microbial Systematics and Evolutionary Microbiology
  • Published:
Journal of Microbiology Aims and scope Submit manuscript

Abstract

Strain DY6T, a Gram-positive endospore-forming motile rod-shaped bacterium, was isolated from soil in South Korea and characterized to determine its taxonomic position. Phylogenetic analyses based on the 16S rRNA gene sequence of strain DY6T revealed that strain DY6T belongs to the genus Paenibacillus in the family Paenibacillaceae in the class Bacilli. The highest degree of sequence similarities of strain DY6T were found with Paenibacillus gansuensis B518T (97.9%), P. chitinolyticus IFO 15660T (95.3%), P. chinjuensis WN9T (94.7%), and P. rigui WPCB173T (94.7%). Chemotaxonomic data revealed that the predominant fatty acids were anteiso-C15:0 (38.7%) and C16:0 (18.0%). A complex polar lipid profile consisted of major amounts of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The predominant respiratory quinone was MK-7. Based on these phylogenetic, chemotaxonomic, and phenotypic data, strain DY6T (=KCTC 33026T =JCM 18491T) should be classified as a type strain of a novel species, for which the name Paenibacillus swuensis sp. nov. is proposed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Ash, C., Priest, F.G., and Collins, M.D. 1993. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Antonie van Leeuwenhoek 64, 253–260.

    Article  CAS  PubMed  Google Scholar 

  • Ash, C., Priest, F.G., and Collins, M.D. 1994. Paenibacillus gen. nov. In Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB, List no. 51. Int. J. Syst. Bacteriol. 44, 852.

    Article  Google Scholar 

  • Baik, K.S., Lim, C.H., Choe, H.N., Kim, E.M., and Seong, C.N. 2011. Paenibacillus rigui sp. nov., isolated from a freshwater wetland. Int. J. Syst. Evol. Microbiol. 61, 529–534.

    Article  CAS  PubMed  Google Scholar 

  • Collins, M.D. and Jones, D. 1981. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol. Rev. 45, 316–354.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ezaki, T., Hashimoto, Y., and 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.

    Article  Google Scholar 

  • Felsenstein, J. 1985. Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.

    Article  Google Scholar 

  • Fitch, W.M. 1971. Toward defining the course of evolution: minimum change for a specified tree topology. Syst. Zool. 20, 406–416.

    Article  Google Scholar 

  • Gerhardt, P., Murray, R.G.E., Wood, W.A., and Krieg, N.R. 1994. Methods for General and Molecular Bacteriology. American Society for Microbiology, Washington, D.C., USA.

    Google Scholar 

  • 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.

    CAS  Google Scholar 

  • Im, W.T., Jung, H.M., Ten, L.N., Kim, M.K., Bora, N., Goodfellow, M., Lim, S., Jung, J., and Lee, S.T. 2008. Deinococcus aquaticus sp. nov., isolated from fresh water, and Deinococcus caeini sp. nov., isolated from activated sludge. Int. J. Syst. Evol. Microbiol. 58, 2348–2353.

    Article  CAS  PubMed  Google Scholar 

  • Kempf, M.J., Chen, F., Kern, R., and Venkateswaran, K. 2005. Recurrent isolation of hydrogen peroxide-resistant spores of Bacillus pumilus from a spacecraft assembly facility. Astrobiology 5, 391–405.

    Article  CAS  PubMed  Google Scholar 

  • Kim, O.S., Cho, Y.J., Lee, K., Yoon, S.H., Kim, M., Na, H., Park, S.C., Jeon, Y.S., Lee, J.H., Yi, H., and 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, 716–721.

    Article  CAS  PubMed  Google Scholar 

  • Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, UK.

    Book  Google Scholar 

  • Komagata, K. and Suzuki, K. 1987. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol. 19, 161–207.

    Article  CAS  Google Scholar 

  • Kong, B.H., Liu, Q.F., Liu, M., Liu, Y., Liu, L., Li, C.L., Yu, R., and Li, Y.H. 2013. Paenibacillus typhae sp. nov., isolated from roots of Typha angustifolia L. Int. J. Syst. Evol. Microbiol. 63, 1037–1044.

    Article  CAS  PubMed  Google Scholar 

  • Lanyi, B. 1987. Classical and rapid identification methods for medically important bacteria. Methods Microbiol. 19, 1–67.

    Article  CAS  Google Scholar 

  • Lee, L.J., Lee, H.J., Jang, G.S., Yu, J.M., Cha, J.Y., Kim, S.J., Lee, E.B., and Kim, M.K. 2013. Deinococcus swuensis sp. nov., a gamma-radiation-resistant bacterium isolated from soil. J. Microbiol. 51, 305–311.

    Article  CAS  PubMed  Google Scholar 

  • Lee, J.S., Pyun, Y.R., and 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.

    Article  CAS  PubMed  Google Scholar 

  • Lim, J.M., Jeon, C.O., Lee, J.C., Xu, L.H., Jiang, C.L., and Kim, C.J. 2006a. Paenibacillus gansuensis sp. nov., isolated from desert soil of Gansu Province in China. Int. J. Syst. Evol. Microbiol. 56, 2131–2134.

    Article  CAS  PubMed  Google Scholar 

  • Lim, S., Yoon, H., Ryu, S., Jung, J., Lee, M., and Kim, D. 2006b. A comparative evaluation of radiation-induced DNA damage using real-time PCR: influence of base composition. Radiat. Res. 165, 430–437.

    Article  CAS  PubMed  Google Scholar 

  • Lim, S., Song, D., Joe, M., and Kim, D. 2012. Development of a qualitative dose indicator for gamma radiation using lyophilized Deinococcus. J. Microbiol. Biotechnol. 22, 1296–1300.

    Article  CAS  PubMed  Google Scholar 

  • Mesbah, M., Premachandran, U., and 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.

    Article  CAS  Google Scholar 

  • Minnikin, D.E., O’Donnell, A.G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A., and Parlett, J.H. 1984. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J. Microbiol. Methods 2, 233–241.

    Article  CAS  Google Scholar 

  • Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.

    CAS  PubMed  Google Scholar 

  • Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc., Newark, DE, USA.

    Google Scholar 

  • Shin, Y.K., Lee, J.S., Chun, C.O., Kim, H.J., and Park, Y.H. 1996. Isoprenoid quinone profiles of the Leclercia adecarboxylata KCTC 1036T. J. Microbiol. Biotechnol. 6, 68–69.

    CAS  Google Scholar 

  • Smibert, R.M. and Krieg, N.R. 1994. Phenotypic characterization. Methods for General and Molecular Bacteriology, pp. 607–654. In Gerhardt, P. (ed.). American Society for Microbiology, Washington, D.C., USA.

    Google Scholar 

  • Srinivasan, S., Kim, M.K., Lim, S., Joe, M., and Lee, M. 2012a. Deinococcus daejeonensis sp. nov., isolated from sludge in a sewage disposal plant. Int. J. Syst. Evol. Microbiol. 62, 1265–1270.

    Article  CAS  PubMed  Google Scholar 

  • Srinivasan, S., Lee, J.J., Lim, S., Joe, M., and Kim, M.K. 2012b. Deinococcus humi sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol. 62, 2844–2850.

    Article  CAS  PubMed  Google Scholar 

  • Stackebrandt, E. and 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.

    Article  CAS  Google Scholar 

  • Tamaoka, J. and Komagata, K. 1984. Determination of DNA base composition by reversed phase high-performance liquid chromatography. FEMS Microbiol. Lett. 25, 125–128.

    Article  CAS  Google Scholar 

  • Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. 2011. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol. 28, 2731–2739.

    Article  CAS  PubMed  Google Scholar 

  • Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24, 4876–4882.

    Article  Google Scholar 

  • 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., Stackebrandt, E., and 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, 463–464.

    Article  Google Scholar 

  • Weisburg, W.G., Barns, S.M., Pelletier, D.A., and Lane, D.J. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173, 697–703.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Yoon, J.H., Seo, W.T., Shin, Y.K., Kho, Y.H., Kang, K.H., and Park, Y.H. 2002. Paenibacillus chinjuensis sp. nov., a novel exopolysaccharide-producing bacterium. Int. J. Syst. Evol. Microbiol. 52, 415–421.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Bio & Environmental Technology, Seoul Women’s University, Seoul, 139-774, Republic of Korea

    Jae-Jin Lee & Myung Kyum Kim

  2. Honor’s Class, Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul, 139-774, Republic of Korea

    Da-Hye Yang, Ye-Sil Ko, Jae-Kyoung Park, Eun-Young Im, Ju-Yeon Kim, Ka-Young Kwon, Yu-Jung Lee & Hyung-Mi Kim

Authors
  1. Jae-Jin Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Da-Hye Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ye-Sil Ko
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jae-Kyoung Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Eun-Young Im
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ju-Yeon Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ka-Young Kwon
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yu-Jung Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Hyung-Mi Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Myung Kyum Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Myung Kyum Kim.

Additional information

Supplemental material for this article may be found at http://www.springerlink.com/content/120956.

The NCBI GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain DY6T (=KCTC 33026T =JCM 18491T) is JQ958374.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lee, JJ., Yang, DH., Ko, YS. et al. Paenibacillus swuensis sp. nov., a bacterium isolated from soil. J Microbiol. 52, 106–110 (2014). https://doi.org/10.1007/s12275-014-3546-x

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12275-014-3546-x

Keywords

Search

Navigation