Skip to main content

Hymenobacter jeollabukensis sp. nov., isolated from soil

Abstract

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterial strain, designated 1-3-3-8T, was isolated from soil and characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 1-3-3-8T belongs to the family Cytophagaceae of phylum Bacteroidetes and is most closely related to Hymenobacter paludis KBP-30T (96.8% similarity), Hymenobacter ocellatus Myx2105T (96.8%), Hymenobacter coalescens WW84T (95.6%), and Hymenobacter deserti ZLB-3T (95.4%). The G + C content of the genomic DNA of strain 1-3-3-8T was 63.6 mol%. The isolate contained C15:0 iso (28.4%), summed feature 4 (C17:1 anteiso B/C17:1 iso I; 18.9%), and C15:0 anteiso (17.6%) as major fatty acids, MK-7 as the predominant respiratory quinone, and sym-homospermidine as the predominant polyamine. The major polar lipids were phosphatidylethanolamine and an unidentified lipid. The phenotypic and chemotaxonomic data supported the affiliation of strain 1-3-3-8T with the genus Hymenobacter. The DNA-DNA relatedness between strain 1-3-3-8T and H. paludis KCTC 32237T and H. ocellatus DSM 11117T were 24.5 and 27.4% respectively, clearly showing that the isolate is not related to them at the species level. Overall, the novel strain could be differentiated from its phylogenetic neighbors on the basis of several phenotypic, genotypic, and chemotaxonomic features. Therefore, strain 1-3-3-8T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter jeollabukensis sp. nov. has been proposed. The type strain is 1-3-3-8T (= KCTC 52741T = JCM 32192T).

This is a preview of subscription content, access via your institution.

References

  1. Bernardet, J.F., Nakagawa, Y., and Holmes, B. 2002 Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int. J. Syst. Evol. Microbiol. 52, 1049–1070

    PubMed  CAS  Google Scholar 

  2. Buczolits, S. and Busse, H.J. 2015 Hymenobacter, pp. 1–11 In Whitman, W.B. (ed.), Bergey’s Manual of Systematics of Archaea and Bacteria, John Wiley & Sons, Inc.

    Book  Google Scholar 

  3. Buczolits, S.E., Denner, B.M., Kämpfer, P., and Busse, H.J. 2006 Proposal of Hymenobacter norwichensis sp. nov., classification of ‘Taxeobacter ocellatus’, ‘Taxeobacter gelupurpurascens’ and ‘Taxeobacter chitinovorans’ as Hymenobacter ocellatus sp. nov., Hymenobacter gelipurpurascens sp. nov. and Hymenobacter chitinivorans sp. nov., respectively, and emended description of the genus Hymenobacter Hirsch et al. 1999 Int. J. Syst. Evol. Microbiol. 56, 2071–2078

    Article  PubMed  CAS  Google Scholar 

  4. Busse, H.J., Bunka, S., Hensel, A., and Lubitz, W. 1997 Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int. J. Syst. Bacteriol. 47, 698–708

    Article  CAS  Google Scholar 

  5. Cappuccino, J.G. and Sherman, N. 2010 Microbiology: A laboratory manual, 9th edn, pp. 69–74 and 161–164 Benjamin Cummings, San Francisco, USA.

    Google Scholar 

  6. Chen, W.M., Chen, Z.H., Young, C.C., and Sheu, S.Y. 2016 Hymenobacter paludis sp. nov., isolated from a marsh. Int. J. Syst. Evol. Microbiol. 66, 1546–1553

    Article  PubMed  CAS  Google Scholar 

  7. 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 

  8. Felsenstein, J. 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376

    Article  PubMed  CAS  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

    Article  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

    CAS  Google Scholar 

  11. Hiraishi, A., Ueda, Y., Ishihara, J., and Mori, T. 1996 Comparative lipoquinone analysis of influent sewage and activated sludge by high performance liquid chromatography and photodiode array detection. J. Gen. Appl. Microbiol. 42, 457–469

    Article  CAS  Google Scholar 

  12. Hirsch, P., Ludwig, W., Hethke, C., Sittig, M., Hoffmann, B., and Gallikowski, C.A. 1998 Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antarctic soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent. Syst. Appl. Microbiol. 21, 374–383

    PubMed  CAS  Google Scholar 

  13. Kang, J.W., Lee, J.H., Choe, H.N., and Seong, C.N. 2017 Hymenobacter tenuis sp. nov., isolated from wastewater of an acidic water neutralization facility. Int. J. Syst. Evol. Microbiol. 67, 2171–2177

    PubMed  Google Scholar 

  14. Kim, K.H., Im, W.T., and Lee, S.T. 2008 Hymenobacter soli sp. nov., isolated from grass soil. Int. J. Syst. Evol. Microbiol. 58, 941–945

    Article  PubMed  CAS  Google Scholar 

  15. Klassen, J.L. and Foght, J.M. 2011 Characterization of Hymenobacter isolates from victoria upper glacier, antarctica reveals five new species and substantial non-vertical evolution within this genus. Extremophiles 15, 45–57

    Article  PubMed  Google Scholar 

  16. Komagata, K. and Suzuki, K.I. 1987 Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol. 19, 161–205

    Article  CAS  Google Scholar 

  17. Kumar, S., Stecher, G., and Tamura, K. 2016 MEGA7 Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  18. Kwak, Y., Park, G.S., and Shin, J.H. 2016 High quality draft genome sequence of the type strain of Pseudomonas lutea OK2T, a phosphate-solubilizing rhizospheric bacterium. Stand. Genomic Sci. 11, 51

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Lee, J.J., Lee, Y.H., Park, S.J., Lee, S.Y., Park, S., Kim, M.K., Ten, L.N., and Jung, H.Y. 2017a. Hymenobacter seoulensis sp. nov., isolated from river water. Int. J. Syst. Evol. Microbiol. 67, 596–601

    Article  PubMed  Google Scholar 

  20. Lee, J.J., Park, S.J., Lee, Y.H., Lee, S.Y., Ten, L.N., and Jung, H.Y. 2017b. Hymenobacter aquaticus sp. nov., a radiation-resistant bacterium isolated from a river. Int. J. Syst. Evol. Microbiol. 67, 1206–1211

    Article  PubMed  Google Scholar 

  21. Lee, M., Woo, S.G., Chae, M., Shin, M.C., Jung, H.M., and Ten, L.N. 2011 Stenotrophomonas daejeonensis sp. nov., isolated from sewage. Int. J. Syst. Evol. Microbiol. 61, 598–604

    Article  PubMed  CAS  Google Scholar 

  22. 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. Evol. Microbiol. 39, 159–167

    CAS  Google Scholar 

  23. Minnikin, D.E., O’Donnella, A.G., Goodfellowb, M., Aldersonb, G., Athalyeb, M., Schaala, 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 

  24. Reddy, G.S.N. and Garcia-Pichel, F. 2013 Description of Hymenobacter arizonensis sp. nov. from the southwestern arid lands of the United States of America. Antonie van Leeuwenhoek 103, 321–330

    PubMed  Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

    Google Scholar 

  27. Sedlácek, I., Králová, S., Kýrová, K., Mašlanová, I., Busse, H.J., Stanková, E., Vrbovská, V., Nemec, M., Barták, M., Holochová, P., et al. 2017 Red-pink pigmented Hymenobacter coccineus sp. nov., Hymenobacter lapidarius sp. nov. and Hymenobacter glacialis sp. nov., isolated from rocks in Antarctica. Int. J. Syst. Evol. Microbiol. 67, 1975–1983

    PubMed  Google Scholar 

  28. Smibert, R.M. and Krieg, N.R. 1994 Phenotypic characterization, pp. 607–654 In Gerhardt, P., Murray, R.G.E., Wood, W.A., and Krieg, N.R. (eds.), Methods for general and molecular bacteriology, American Society for Microbiology, Washington, USA.

    Google Scholar 

  29. Srinivasan, S., Kim, M., Joo, E., Lee, S.Y., Lee, D.S., and Jung, H.Y. 2015 Complete genome sequence of Rufibacter sp. DG31D, a bacterium resistant to gamma and UV radiation toxicity. Mol. Cell. Toxicol. 11, 415–421

    CAS  Google Scholar 

  30. Stackebrandt, E. and Ebers, J. 2006 Taxonomic parameters revisited: tarnished gold standards. Microbiol. Today 33, 152–155

    Google Scholar 

  31. 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 

  32. Ten, L.N., Jung, H.M., Yoo, S.A., Im, W.T., and Lee, S.T. 2008 Lysobacter daecheongensis sp. nov., isolated from sediment of stream near the Daechung dam in South Korea. J. Microbiol. 46, 519–524

    PubMed  CAS  Google Scholar 

  33. Ten, L.N., Lee, J.J., Lee, Y.H., Park, S.J., Lee, S.Y., Park, S., Lee, D.S., Kang, I.K., Kim, M.K., and Jung, H.Y. 2017a. Hymenobacter knuensis sp. nov., isolated from river water. Curr. Microbiol. 74, 515–521

    Article  PubMed  CAS  Google Scholar 

  34. Ten, L.N., Lee, Y.H., Lee, J.J., Park, S., Lee, S.Y., Park, S., Lee, D.S., Kang, I.K., and Jung, H.Y. 2017b. Hymenobacter daeguensis sp. nov. isolated from river water. J. Microbiol. 55, 253–259

    Article  PubMed  CAS  Google Scholar 

  35. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  36. Tittsler, R.P. and Sandholzer, L.A. 1936 The use of semi-solid agar for the detection of bacterial motility. J. Bacteriol. 31, 575–580

    PubMed  PubMed Central  CAS  Google Scholar 

  37. 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., et al. 1987 International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Evol. Microbiol. 37, 463–464

    Google Scholar 

  38. 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  39. Wilson, K. 1997 Preparation of Genomic DNA from Bacteria. In Ausubel, F.M., et al. (eds.), Current protocols in molecular biology, Wiley InterScience, 2.4.1–2.4.5 Supplement 27

    Google Scholar 

  40. Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., and Chun, J. 2017 Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613–1617

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Affiliations

Authors

Corresponding authors

Correspondence to Jeung-Sul Han or Hee-Young Jung.

Additional information

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

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Ten, L.N., Han, Y.E., Park, K.I. et al. Hymenobacter jeollabukensis sp. nov., isolated from soil. J Microbiol. 56, 500–506 (2018). https://doi.org/10.1007/s12275-018-8085-4

Download citation

Keywords

  • Hymenobacter
  • Bacteroidetes
  • soil bacteria