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Current Microbiology

, Volume 74, Issue 4, pp 515–521 | Cite as

Hymenobacter knuensis sp. nov., Isolated From River Water

  • Leonid N. Ten
  • Jae-Jin Lee
  • Yeon-Hee Lee
  • Su-Jin Park
  • Seung-Yeol Lee
  • Sangkyu Park
  • Dae Sung Lee
  • In-Kyu Kang
  • Myung Kyum Kim
  • Hee-Young JungEmail author
Article

Abstract

A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, aerobic bacterial strain, designated 16F7C-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 16F7C-2T belonged to the family Cytophagaceae in the phylum Bacteroidetes and was most closely related to Hymenobacter algoricola VUG-A23aT (98.3%) and Hymenobacter fastidiosus VUG-A124T (97.7%). The G + C content of the genomic DNA of strain 16F7C-2T was 63.4 mol%. The detection of menaquinone MK-7 as the predominant respiratory quinone; a fatty acid profile with summed feature 3 (C16:1 ω7c/C16:1 ω6c; 19.5%), summed feature 4 (C17:1 iso I/C17:1 anteiso B; 15.9%), C15:0 iso (12.6%), C16:1 ω5c (10.5%), and C15:0 anteiso (10.4%) as the major components; and a polar lipid profile with phosphatidylethanolamine as the major component also supported the affiliation of strain 16F7C-2T to the genus Hymenobacter. The DNA–DNA relatedness between strain 16F7C-2T and H. algoricola JCM 17214T and H. fastidiosus JCM17224T were 45.2 ± 5.8 and 40.3 ± 2.9%, respectively, clearly showing that the isolate constitutes a new genospecies. Strain 16F7C-2T could be clearly differentiated from its closest neighbors on the basis of its phenotypic, genotypic, and chemotaxonomic features. Therefore, strain 16F7C-2T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter knuensis sp. nov. is proposed. The type strain is 16F7C-2T (=KCTC 52538T = JCM 31814T).

Keywords

Fatty Acid Profile Cellular Fatty Acid Isoprenoid Quinone Itaconate Major Polar Lipid 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

This work was supported by the Human Resource Training Program for Regional Innovation and Creativity through the Ministry of Education and National Research Foundation (NRF) of Korea (NRF-2014H1C1A1066929) and by the Brain Pool Program of 2016 (grant 162S-4-3-1727) through the Korean Federation of Science and Technology Societies (KOFST) funded by the Ministry of Science, ICT and Future Planning, Republic of Korea.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

284_2017_1216_MOESM1_ESM.docx (655 kb)
Supplementary material 1 (DOCX 655 KB)

References

  1. 1.
    Buck JD (1982) Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993PubMedPubMedCentralGoogle Scholar
  2. 2.
    Buczolits SE, Denner BM, Kämpfer P, Busse HJ (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 56:2189–2192CrossRefGoogle Scholar
  3. 3.
    Cappuccino JG, Sherman N (2010) Microbiology: a Laboratory Manual. 9th edn. Benjamin Cummings, San FranciscoGoogle Scholar
  4. 4.
    Ezaki T, Hashimoto Y, 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 39:224–229CrossRefGoogle Scholar
  5. 5.
    Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefPubMedGoogle Scholar
  6. 6.
    Felsenstein J (1985) Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  7. 7.
    Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  8. 8.
    Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  9. 9.
    Hiraishi A, Ueda Y, Ishihara J, 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 42:457–469CrossRefGoogle Scholar
  10. 10.
    Hirsch P, Ludwig W, Hethke C, Sittig M, Hoffmann B, Gallikowski CA (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 21:374–383CrossRefPubMedGoogle Scholar
  11. 11.
    Joung Y, Cho SH, Kim H, Kim SB, Joh K (2011) Hymenobacter yonginensis sp. nov., isolated from a mesotrophic artificial lake. Int J Syst Evol Microbiol 61:1511–1514CrossRefPubMedGoogle Scholar
  12. 12.
    Kang H, Kim H, Joung Y, Kim KJ, Joh K (2016) Hymenobacter marinus sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 65:4557–4562Google Scholar
  13. 13.
    Kang JY, Chun J, Choi A, Moon SH, Cho JC, Jahng KY (2013) Hymenobacter koreensis sp. nov. and Hymenobacter saemangeumensis sp. nov., isolated from estuarine water. Int J Syst Evol Microbiol 63:4568–4573CrossRefPubMedGoogle Scholar
  14. 14.
    Kang JW, Baik KS, Im WT, Seong CN (2016) Hymenobacter coalescens sp. nov., isolated from wetland freshwater. Int J Syst Evo Microbiol. doi: 10.1099/ijsem.0.001226 Google Scholar
  15. 15.
    Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721CrossRefPubMedGoogle Scholar
  16. 16.
    Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefPubMedGoogle Scholar
  17. 17.
    Klassen JL, Foght JM (2011) Characterization of Hymenobacter isolates from Victoria Upper Glacier, Antarctica reveals five new species and substantial non-vertical evolution within this genus. Extremophiles 15:45–57CrossRefPubMedGoogle Scholar
  18. 18.
    Kojima H, Watanabe M, Tokizawa R, Shinohara A, Fukui M (2016) Hymenobacter nivis sp. nov., isolated from red snow in Antarctica. Int J Syst Evo Microbiol. doi: 10.1099/ijsem.0.001435 Google Scholar
  19. 19.
    Komagata K, Suzuki KI (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–205CrossRefGoogle Scholar
  20. 20.
    Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefPubMedGoogle Scholar
  21. 21.
    Liu K, Liu Y, Wang N, Gu Z, Shen L, Xu B, Zhou Y, Liu H, Jiao N (2016) Hymenobacter glacieicola sp. nov., isolated from glacier. Int J Syst Evo Microbiol. doi: 10.1099/ijsem.0.001266 Google Scholar
  22. 22.
    Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167CrossRefGoogle Scholar
  23. 23.
    Minnikin DE, O’Donnella AG, Goodfellowb M, Aldersonb G, Athalyeb M, Schaala A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241CrossRefGoogle Scholar
  24. 24.
    Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  25. 25.
    Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc, NewarkGoogle Scholar
  26. 26.
    Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RG E, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, pp 607–654Google Scholar
  27. 27.
    Stackebrandt E, Goebel BM (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 44:846–849CrossRefGoogle Scholar
  28. 28.
    Tang K, Yuan B, Lai Q, Wang R, Bao H, Feng FY (2015) Hymenobacter terrenus sp. nov., isolated from biological soil crusts. Int J Syst Evo Microbiol 65:4557–4562CrossRefGoogle Scholar
  29. 29.
    Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464CrossRefGoogle Scholar
  31. 31.
    Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Wilson K (1997) Preparation of genomic DNA from bacteria. In: Ausubel FM et al (ed) Current protocols in molecular biology. Wiley, Hoboken, 2.4.1–2.4.5, Supplement 27Google Scholar

Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Leonid N. Ten
    • 1
  • Jae-Jin Lee
    • 1
  • Yeon-Hee Lee
    • 1
  • Su-Jin Park
    • 1
  • Seung-Yeol Lee
    • 1
  • Sangkyu Park
    • 1
  • Dae Sung Lee
    • 2
  • In-Kyu Kang
    • 3
  • Myung Kyum Kim
    • 4
  • Hee-Young Jung
    • 1
    • 5
    Email author
  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.Department of Bio and Environmental TechnologySeoul Women’s UniversitySeoulRepublic of Korea
  5. 5.Institute of Plant MedicineKyungpook National UniversityDaeguRepublic of Korea

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