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The Journal of Microbiology

, Volume 47, Issue 5, pp 524–529 | Cite as

Paenibacillus filicis sp. nov., isolated from the rhizosphere of the fern

  • Byung-Chun Kim
  • Mi Na Kim
  • Kang Hyun Lee
  • Sun Beom Kwon
  • Kyung Sook Bae
  • Kee-Sun ShinEmail author
Article

Abstract

A Gram-positive and endospore-forming bacterial strain, designated S4T, was isolated from the rhizosphere of ferns in Daejeon, Republic of Korea. This isolate is strictly aerobic, motile, and rod-like in shape, and it is positive for catalase, oxidase, esterase lipase, and β-galactosidase activities. In addition, this strain grows when cultured at temperatures between 15 and 37°C and at pH values ranging from 5.5 to 9.0. The DNA G+C content was determined to be 53.2 mol%. Strain S4T has meso-diaminopimelic acid in the cell-wall peptidoglycan; it also contains menaquinone 7 (MK-7) as the predominant isoprenoid quinone and anteiso-C15:0 (57.5%), iso-C16:0 (11.3%), and C16:0 (9.4%) as the major cellular fatty acids. Phylogenetic analysis based on alignments of the 16S rRNA gene sequence showed that S4T is affiliated with a cluster of strains within the genus Paenibacillaceae and is most closely related to Paenibacillus chinjuensis WN9T, with 96.8% similarity. Based on the phylogenetic and phenotypic characteristics of strain S4T, we believe that this isolate should be distinguished from all type species of the genus Paenibacillus and should thus represent a novel taxon within the genus Paenibacillus. We propose naming this type species Paenibacillus filicis sp. nov. for the rhizosphere isolate; the type strain will be known as S4T (=KCTC 13693T =KACC 14197T =JCM 16417T).

Keywords

novel bacterium fern rhizosphere Paenibacillus filicis 

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References

  1. Ash, C., F.G. Priest, and M.D. Collins. 1993. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Antonie van Leeuwenhoek 64, 253–260.CrossRefPubMedGoogle Scholar
  2. Atlas, R.M. 1993. Handbook of Microbiological Media. In L.C. Parks (ed.). CRC Press. Boca Raton, FL, USA.Google Scholar
  3. Chakrabarty, A.N., S. Adhya, and M.K. Pramanik. 1970. The hydrolysis of Tween 80 by vibrios and aeromonads. J. Appl. Bacteriol. 33, 397–402.PubMedGoogle Scholar
  4. Cole, J.R., B. Chai, T.L. Marsh, R.J. Farris, Q. Wang, S.A. Kulam, S. Chandra, D.M. McGarrell, T.M. Schmidt, G.M. Garrity, and J.M. Tiedje. 2003. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31, 442–443.CrossRefPubMedGoogle Scholar
  5. Collins, M.D. and D. Jones. 1981. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol. Rev. 45, 316–354.PubMedGoogle Scholar
  6. Chun, J., J.H. Lee, Y. Jung, M. Kim, S. Kim, B.K. Kim, and Y.W. Lim. 2007. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol. 57, 2259–2261.CrossRefPubMedGoogle Scholar
  7. Euzeby, J.P. 1997. List of bacterial names with standing in nomenclature: a folder available on the Internet. Int. J. Syst. Bacteriol. 47, 590–592.PubMedGoogle Scholar
  8. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.CrossRefGoogle Scholar
  9. Felsenstein, J. 1993. PHYLIP (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.Google Scholar
  10. Heyndrickx, M., K. Vandemeulebroecke, P. Scheldeman, B. Hoste, K. Kersters, P. De Vos, N.A. Logan, A.M. Aziz, N. Ali, and R.C. Berkeley. 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.PubMedCrossRefGoogle Scholar
  11. Kim, D.S., C.Y. Bae, J.J. Jeon, S.J. Chun, H.W. Oh, S.G. Hong, K.S. Baek, E.Y. Moon, and K.S. Bae. 2004. Paenibacillus elgii sp. nov., with broad antimicrobial activity. Int. J. Syst. Evol. Microbiol. 54, 2031–2035.CrossRefPubMedGoogle Scholar
  12. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111–120.CrossRefPubMedGoogle Scholar
  13. Komagata, K. and K. Suzuki. 1987. Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol. 19, 161–203.CrossRefGoogle Scholar
  14. Park, M.J., H.B. Kim, D.S. An, H.C. Yang, S.T. Oh, H.J. Chung, and D.C. Yang. 2007. Paenibacillus soli sp. nov., a xylanolytic bacterium isolated from soil. Int. J. Syst. Evol. Microbiol. 57, 146–150.CrossRefPubMedGoogle Scholar
  15. Rivas, R., M. Sánchez, M.E. Trujillo, J.L. Zurdo-Piñeiro, P.F. Mateos, E. Martínez-Molina, and E. Velázquez. 2003. Xylanimonas cellulosilytica gen. nov., sp. nov., a xylanolytic bacterium isolated from a decayed tree (Ulmus nigra). Int. J. Syst. Evol. Microbiol. 53, 99–103.CrossRefPubMedGoogle Scholar
  16. Sambrook, J. and D.W. Russell. 2001. Molecular Cloning: a Laboratory Manual, 3rd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, N.Y., USA.Google Scholar
  17. Sasser, M. 1990. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. MIDI Inc., Newark, DE, USA.Google Scholar
  18. Shida, O., H. Takagi, K. Kadowaki, L.K. Nakamura, and K. Komagata. 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.PubMedCrossRefGoogle Scholar
  19. Shin, Y.K., J.S. Lee, C.O. Chun, H.J. Kim, and Y.H. Park. 1996. Isoprenoid quinone profiles of the Leclercia adecarboxylata KCTC 1036T. J. Microbiol. Biotechnol. 6, 68–69.Google Scholar
  20. Stackebrandt, E. and B.M. Goebel. 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.Google Scholar
  21. Tamaoka, J. and K. Komagata. 1984. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol. Lett. 25, 125–128.CrossRefGoogle Scholar
  22. Thompson, J.D., T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876–4882.CrossRefPubMedGoogle Scholar
  23. Wayne, L.G., D.J. Brenner, R.R. Colwell, P.A.D. Grimont, O. Kandler, M.I. Krichevsky, L.H. Moore, W.E.C. Moore, R.G.E. Murray, E. Stackerbrandt, M.P. Starr, and H.G. Truper. 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.Google Scholar
  24. Weisburg, W.G., S.M. Barns, D.A. Pelletier, and D.J. Lane. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173, 697–703.PubMedGoogle Scholar
  25. Yoon, J.H., W.T. Seo, Y.K. Shin, Y.H. Kho, K.H. Kang, and Y.H. Park. 2002. Paenibacillus chinjuensis sp. nov., a novel exopolysaccharideproducing bacterium. Int. J. Syst. Evol. Microbiol. 52, 415–421.CrossRefPubMedGoogle Scholar

Copyright information

© The Microbiological Society of Korea and Springer Berlin Heidelberg 2009

Authors and Affiliations

  • Byung-Chun Kim
    • 1
  • Mi Na Kim
    • 1
  • Kang Hyun Lee
    • 1
  • Sun Beom Kwon
    • 1
  • Kyung Sook Bae
    • 1
  • Kee-Sun Shin
    • 1
    Email author
  1. 1.Biological Resources CenterKRIBBDaejeonRepublic of Korea

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