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Hymenobacter terrigena sp. nov., isolated from soil

  • Microbial Systematics and Evolutionary Microbiology
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Abstract

A Gram-stain-negative, non-motile, non-spore-forming, rodshaped, aerobic bacterial strain, designated S1-2-2-5T, was isolated from the Jeollabuk-do province, Republic of Korea, and was characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain S1-2-2-5T belonged to the family Cytophagaceae in phylum Bacteroidetes, and was most closely related to Hymenobacter terrae DG7AT (98.2%), Hymenobacter rubidus DG7BT (98.0%), Hymenobacter soli PB17T (97.7%), Hymenobacter daeguensis 16F3Y-2T (97.2%) and Hymenobacter saemangeumensis GSR0100T (97.0%). The G + C content of the genomic DNA of strain S1-2-2-5T was 59.4 mol%. The detection of menaquinone MK-7 as the predominant respiratory quinone, a fatty acid profile with summed feature 3 (C16:1ω7c/C16:1ω6c; 32.0%), C15:0 iso (19.0%), and C15:0 anteiso (15.0%) as the major components, and a polar lipid profile with phosphatidylethanolamine as the major component supported the affiliation of strain S1-2-2-5T to the genus Hymenobacter. The DNA-DNA relatedness between strain S1-2-2-5T and H. terrae KCTC 32554T, H. rubidus KCTC 32553T, H. soli KCTC 12607T, H. daeguensis KCTC 52537T, and H. saemangeumensis KACC 16452T were 49.5, 48.2, 34.1, 28.1, and 31.8% respectively, clearly showing that the isolate is not related to them at the species level. Strain S1-2-2-5T could be clearly differentiated from its closest neighbors on the basis of its phenotypic, genotypic and chemotaxonomic features. Therefore, strain S1-2-2-5T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter terrigena sp. nov. is proposed. The type strain is S1-2-2-5T (= KCTC 52737T = JCM 32195T).

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References

  • 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 

  • Beveridge, T.J., Lawrence, J.R., and Murray, R.G.E. 2007. Sampling and staining for light microscopy, pp. 19–33. In Reddy, C.A., Beveridge, T.J., Breznak, J.A., Marzluf, G., Schmidt, T.M., and Snyder, L.R. (eds). Methods for General and Molecular Microbiology. American Society for Microbiology, Washington, D.C., USA.

  • 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.

  • 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 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • 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 

  • 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 

  • 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 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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 

  • 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.

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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 

  • 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 

  • Lee, J.J., Joo, E.S., Kim, E.B., Jeon, S.H., Srinivasan, S., Jung, H.Y., and Kim, M.K. 2016. Hymenobacter rubidus sp. nov., bacterium isolated form a soil. J. Microbiol. 109, 457–466.

    CAS  Google Scholar 

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

    Article  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • 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 

  • 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.

    Article  PubMed  CAS  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. Evol. Microbiol. 39, 159–167.

    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 

  • 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.

    Article  PubMed  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.

    PubMed  CAS  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 

  • 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.

  • Srinivasan, S., Kim, M., Joo, E., Lee, S.Y., Lee, D.S., and Jung, H.Y. 2015b. 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 

  • Srinivasan, S., Lee, J.J., Park, K.R., Park, S.H., Jung, H.Y., and Kim, M.K. 2015a. Hymenobacter terrae sp. nov., a bacterium isolated from soil. Curr. Microbiol. 70, 643–650.

    Article  PubMed  CAS  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 

  • 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 

  • 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 

  • 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 

  • 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 

  • 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 

  • 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 

  • 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.

  • 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 

  • Yoon, M.H., Ten, L.N., and Im, W.T. 2007. Cohnella panacarvi sp. nov., a xylanolytic bacterium isolated from the ginseng cultivating soil. J. Microbiol. Biotechnol. 17, 913–918.

    PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. School of Food Science and Biotechnology, Kyungpook National University, Daegu, 41566, Republic of Korea

    Jeong-Eun Ohn & Byung-Oh Kim

  2. School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea

    Leonid N. Ten & Hee-Young Jung

  3. Department of Horticulture and Life Science, Yeungnam University, Gyeongbuk, 38541, Republic of Korea

    Kyeung Il Park

  4. Department of Horticultural Science, Kyungpook National University, Daegu, 41566, Republic of Korea

    Jeung-Sul Han

  5. Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea

    Hee-Young Jung

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  1. Jeong-Eun Ohn
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Correspondence to Jeung-Sul Han or Hee-Young Jung.

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Ohn, JE., Ten, L.N., Park, K.I. et al. Hymenobacter terrigena sp. nov., isolated from soil. J Microbiol. 56, 231–237 (2018). https://doi.org/10.1007/s12275-018-8029-z

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  • DOI: https://doi.org/10.1007/s12275-018-8029-z

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