Journal of Microbiology

, Volume 55, Issue 4, pp 253–259 | Cite as

Hymenobacter daeguensis sp. nov. isolated from river water

  • Leonid N. Ten
  • Yeon-Hee Lee
  • Jae-Jin Lee
  • Su-Jin Park
  • Seung-Yeol Lee
  • Sangkyu Park
  • Dae Sung Lee
  • In-Kyu Kang
  • Hee-Young Jung
Microbial Systematics and Evolutionary Microbiology


A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, aerobic bacterial strain, designated 16F3Y-2T, was isolated from the Han River, South Korea, and was characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 16F3Y-2T belonged to the family Cytophagaceae in the phylum Bacteroidetes and was most closely related to ‘Hymenobacter terrae’ DG7A (98.01%), H. soli PB17T (97.26%), H. glaciei VUG-A130T (96.78%), H. antarcticus VUG-A42aaT (96.72%), H. ruber PB156T (96.61%), and H. saemangeumensis GSR0100T (95.77%). The G+C content of the genomic DNA of strain 16F3Y-2T was 62.9 mol%. The isolate contained MK-7 as the predominant respiratory quinone, and summed feature 3 (C16:1 ω7c/C16:1 ω6c; 35.5%), C15:0 iso (16.9%), C16:1 ω5c (10.9%), and C15:0 anteiso (9.9%) as major fatty acids. The major polar lipid was phosphatidylethanolamine. Phenotypic and chemotaxonomic data supported the affiliation of strain 16F3Y-2T with the genus Hymenobacter. However, strain 16F3Y-2T exhibited relatively low levels of DNA-DNA relatedness with ‘H. terrae’ KCTC 32554 (44.1%) and H. soli KCTC 12607T (24.3%), clearly indicating that the isolate constitutes a new genospecies. Strain 16F3Y-2T could be differentiated from its phylogenetic neighbors on the basis of several phenotypic, genotypic, and chemotaxonomic features. Therefore, strain 16F3Y-2T represents a novel species in the genus Hymenobacter, for which the name Hymenobacter daeguensis sp. nov. is proposed. The type strain is 16F3Y-2T (=KCTC 52537T =JCM 31654T).


Hymenobacter Bacteroidetes polyphasic taxonomy 


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  1. Buck, J.D. 1982. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl. Environ. Microbiol. 44, 992–993.PubMedPubMedCentralGoogle Scholar
  2. 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.CrossRefPubMedGoogle Scholar
  3. Buczolits, S., Denner, E.B.M., Vybiral, D., Wieser, M., Kämpfer, P., and Buss, H.J. 2002. Classification of three airborne bacteria and proposal of Hymenobacter aerophilus sp. nov. Int. J. Syst. Evol. Microbiol. 52, 445–456.CrossRefPubMedGoogle Scholar
  4. Cappuccino, J.G. and Sherman, N. 2010. Microbiology: a Laboratory Manual, 9th edn, pp. 69–74 & 161–164. Benjamin Cummings, San Francisco, USA.Google Scholar
  5. Chung, A.P., Lopes, A., Nobre, M.F., and Morais, P.V. 2010. Hymenobacter perfusus sp. nov., Hymenobacter flocculans sp. nov. and Hymenobacter metalli sp. nov. three new species isolated from an uranium mine waste water treatment system. Syst. Appl. Microbiol. 33, 436–443.CrossRefPubMedGoogle Scholar
  6. 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.CrossRefGoogle Scholar
  7. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376.CrossRefPubMedGoogle Scholar
  8. Felsenstein, J. 1985. Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.CrossRefGoogle Scholar
  9. Fitch, W.M. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20, 406–416.CrossRefGoogle 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. 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.CrossRefGoogle 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.CrossRefPubMedGoogle Scholar
  13. Jin, L., Lee, H.G., Kim, S.G., Lee, K.C., Ahn, C.Y., and Oh, H.M. 2014. Hymenobacter ruber sp. nov., isolated from grass soil. Int. J. Syst. Evol. Microbiol. 64, 979–983.CrossRefPubMedGoogle Scholar
  14. Kang, J.Y., Chun, J., Choi, A., Moon, S.H., Cho, J.C., and Jahng, K.Y. 2013. Hymenobacter koreensis sp. nov. and Hymenobacter saemangeumensis sp. nov., isolated from estuarine water. Evol. Microbiol. 63, 4568–4573.CrossRefGoogle Scholar
  15. Kang, H., Kim, H., Joung, Y., Kim, K.J., and Joh, K. 2016a. Hymenobacter marinus sp. nov., isolated from coastal seawater. Int. J. Syst. Evol. Microbiol. 65, 4557–4562.Google Scholar
  16. Kang, J.W., Baik, K.S., Im, W.T., and Seong, C.N. 2016b. Hymenobacter coalescens sp. nov., isolated from wetland freshwater. Int. J. Syst. Evol. Microbiol. 66, 3546–3551.CrossRefPubMedGoogle Scholar
  17. 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., 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.CrossRefPubMedGoogle Scholar
  18. 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.CrossRefPubMedGoogle Scholar
  19. 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
  20. 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.CrossRefPubMedGoogle Scholar
  21. Kojima, H., Watanabe, M., Tokizawa, R., Shinohara, A., and Fukui, M. 2016. Hymenobacter nivis sp. nov., isolated from red snow in Antarctica. Int. J. Syst. Evol. Microbiol. 66, 4821–4825.CrossRefPubMedGoogle Scholar
  22. Komagata, K. and Suzuki, K.I. 1987. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol. 19, 161–205.CrossRefGoogle Scholar
  23. 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.CrossRefPubMedGoogle Scholar
  24. Liu, K., Liu, Y., Wang, N., Gu, Z., Shen, L., Xu, B., Zhou, Y., Liu, H., and Jiao, N. 2016. Hymenobacter glacieicola sp. nov., isolated from glacier. Int. J. Syst. Evol. Microbiol. 66, 3793–3798.CrossRefPubMedGoogle Scholar
  25. 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.Google Scholar
  26. 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.CrossRefGoogle Scholar
  27. 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.CrossRefPubMedGoogle Scholar
  28. Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.PubMedGoogle Scholar
  29. Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc, Newark, DE, USA.Google Scholar
  30. Smibert, R.M. and Krieg, N.R. 1994. Phenotypic characterization. In Gerhardt, P., Murray, R.G.E., Wood, W.A., and Krieg, N.R. (eds.), Methods for General and Molecular Bacteriology, pp. 607–654. American Society for Microbiology, Washington, USA.Google Scholar
  31. Srinivasan, S., Lee, J.J., Park, K.R., Park, S.H., Jung, H.Y., and Kim, M.K. 2015. Hymenobacter terrae sp. nov., a bacterium isolated from soil. Curr. Microbiol. 70, 643–650.CrossRefPubMedGoogle Scholar
  32. 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. Evol. Microbiol. 44, 846–849.CrossRefGoogle Scholar
  33. Tang, K., Yuan, B., Lai, Q., Wang, R., Bao, H., and Feng, F.Y. 2015. Hymenobacter terrenus sp. nov., isolated from biological soil crusts. Int. J. Syst. Evol. Microbiol. 65, 4557–4562.CrossRefPubMedGoogle Scholar
  34. 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.CrossRefPubMedPubMedCentralGoogle Scholar
  35. 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.CrossRefGoogle Scholar
  36. 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.CrossRefPubMedPubMedCentralGoogle Scholar
  37. 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
  38. Zhang, G., Niu, F., Busse, H.J., Ma, X., Liu, W., Dong, M., Feng, H., An, L., and Cheng, G. 2008. Hymenobacter psychrotolerans sp. nov., isolated from the Qinghai-Tibet Plateau permafrost region. Int. J. Syst. Evol. Microbiol. 58, 1215–1220.CrossRefPubMedGoogle Scholar

Copyright information

© The Microbiological Society of Korea and Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Leonid N. Ten
    • 1
  • Yeon-Hee Lee
    • 1
  • Jae-Jin Lee
    • 1
  • Su-Jin Park
    • 1
  • Seung-Yeol Lee
    • 1
  • Sangkyu Park
    • 1
  • Dae Sung Lee
    • 2
  • In-Kyu Kang
    • 3
  • Hee-Young Jung
    • 1
    • 4
  1. 1.School of Applied BiosciencesKyungpook National UniversityDaeguRepublic of Korea
  2. 2.Department of Environmental EngineeringKyungpook National UniversityDaeguRepublic of Korea
  3. 3.Department of Horticultural ScienceKyungpook National UniversityDaeguRepublic of Korea
  4. 4.Institute of Plant MedicineKyungpook National UniversityDaeguRepublic of Korea

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