1887

Abstract

A Gram-stain-negative, strictly aerobic, rod-shaped bacterium, designated W1-2-1, was isolated from tap water in South Korea. The strain was characterized by a polyphasic approach to clarify its taxonomic position. Strain W1-2-1 grew at 18–42 °C and at pH 6.0–10.0 on R2A medium. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Sphingomonas and is most closely related to the Sphingomonas oligophenolica JCM 12082 (97.2 % similarity), Sphingomonas asaccharolytica NBRC 15499 (96.8 %), Sphingomonas desiccabilis CP1D (96.8 %), Sphingomonas pruni NBRC 15498 (96.8 %), Sphingomonas hankookensis ODN7 (96.4 %) and Sphingomonas yabuuchiae DSM 14562 (95.8 %). Chemotaxonomic data [major ubiquinone – Q10, major polyamine – homospermidine, major fatty acids – summed feature 8 (C18  : 1ω7c/ω6c), C16 : 0 and C14 : 0 2-OH and presence of sphingoglycolipid] supported the affiliation of the strain to the genus Sphingomonas . The G+C content of genomic DNA was 67.1 mol%. However, low level of DNA–DNA relatedness value between strain W1-2-1 and S. oligophenolica JCM 12082 and the results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain W1-2-1 from other Sphingomonas species with validly published names. Therefore, the isolate represents a novel species, for which the name Sphingomonas aquatica sp. nov. (type strain W1-2-1=KACC 18309=LMG 28596) is proposed.

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2017-05-05
2019-10-14
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References

  1. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T et al. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol Immunol 1990;34:99–119 [CrossRef][PubMed]
    [Google Scholar]
  2. Busse HJ, Kämpfer P, Denner EB. Chemotaxonomic characterisation of Sphingomonas. J Ind Microbiol Biotechnol 1999;23:242–251 [CrossRef][PubMed]
    [Google Scholar]
  3. Wittich RM, Busse HJ, Kampfer P, Macedo AJ, Tiirola M et al. Sphingomonas fennica sp. nov. and Sphingomonas haloaromaticamans sp. nov., outliers of the genus Sphingomonas. Int J Syst Evol Microbiol 2007;57:1740–1746 [CrossRef]
    [Google Scholar]
  4. Euzéby JP. List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 1997;47:590–592 [CrossRef][PubMed]
    [Google Scholar]
  5. Park HK, Han JH, Kim TS, Joung Y, Cho SH et al. Sphingomonas aeria sp. nov. from indoor air of a pharmaceutical environment. Antonie van Leeuwenhoek 2015;107:47–53 [CrossRef][PubMed]
    [Google Scholar]
  6. Han SI, Lee JC, Ohta H, Whang KS. Sphingomonas oligoaromativorans sp. nov., an oligotrophic bacterium isolated from a forest soil. Int J Syst Evol Microbiol 2014;64:1679–1684 [CrossRef][PubMed]
    [Google Scholar]
  7. Huy H, Jin L, Lee KC, Kim SG, Lee JS et al. Sphingomonas daechungensis sp. nov., isolated from sediment of a eutrophic reservoir. Int J Syst Evol Microbiol 2014;64:1412–1418 [CrossRef][PubMed]
    [Google Scholar]
  8. Son HM, Kook M, Tran HT, Kim KY, Park SY et al. Sphingomonas kyeonggiense sp. nov., isolated from soil of a ginseng field. Antonie van Leeuwenhoek 2014;105:791–797 [CrossRef][PubMed]
    [Google Scholar]
  9. Feng GD, Yang SZ, Wang YH, Zhao GZ, Deng MR et al. Sphingomonas gimensis sp. nov., a novel Gram-negative bacterium isolated from abandoned lead–zinc ore mine. Antonie van Leeuwenhoek 2014;105:1091–1097 [CrossRef][PubMed]
    [Google Scholar]
  10. Zhu L, Si M, Li C, Xin K, Chen C et al. Sphingomonas gei sp. nov., isolated from roots of Geum aleppicum. Int J Syst Evol Microbiol 2015;65:1160–1166 [CrossRef][PubMed]
    [Google Scholar]
  11. Kim JH, Kim SH, Kim KH, Lee PC. Sphingomonas lacus sp. nov., an astaxanthin-dideoxyglycoside-producing species isolated from soil near a pond. Int J Syst Evol Microbiol 2015;65:2824–2830 [CrossRef][PubMed]
    [Google Scholar]
  12. Liu Y, Yao S, Lee YJ, Cao Y, Zhai L et al. Sphingomonas morindae sp. nov., isolated from noni (Morinda citrifolia L.) branch. Int J Syst Evol Microbiol 2015;65:2817–2823 [CrossRef][PubMed]
    [Google Scholar]
  13. Liu Q, Liu HC, Zhang JL, Zhou YG, Xin YH. Sphingomonas psychrolutea sp. nov., a psychrotolerant bacterium isolated from glacier ice. Int J Syst Evol Microbiol 2015;65:2955–2959 [CrossRef][PubMed]
    [Google Scholar]
  14. Huang J, Huang Z, Zhang ZD, He LY, Sheng XF. Sphingomonas yantingensis sp. nov., a mineral-weathering bacterium isolated from purplish paddy soil. Int J Syst Evol Microbiol 2014;64:1030–1034 [CrossRef][PubMed]
    [Google Scholar]
  15. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991;173:697–703 [CrossRef][PubMed]
    [Google Scholar]
  16. Kim JK, Kang MS, Park SC, Kim KM, Choi K et al. Sphingosinicella ginsenosidimutans sp. nov., with ginsenoside converting activity. J Microbiol 2015;53:435–441 [CrossRef][PubMed]
    [Google Scholar]
  17. Kim OS, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  18. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  19. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999;41:95–98
    [Google Scholar]
  20. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983;[CrossRef]
    [Google Scholar]
  21. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Bio Evol 1987;4:406–425
    [Google Scholar]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  23. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef]
    [Google Scholar]
  25. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982;44:992–993[PubMed]
    [Google Scholar]
  26. Cappuccino JG, Sherman N. Microbiology: a Laboratory Manual, 6th ed. CA: Pearson Education, Inc. Benjamin Cummings; 2002
    [Google Scholar]
  27. Atlas RM. In Parks LC. (editor) Handbook of Microbiological Media Boca Raton, FL: CRC Press; 1993
    [Google Scholar]
  28. Moore DD, Dowhan D. Preparation and analysis of DNA. In Ausubel FW, Brent R, Kingston RE, Moore DD, Seidman JG. et al. (editors) Current Protocols in Molecular Biology New York: Wiley; 1995; pp.2–11
    [Google Scholar]
  29. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989;39:159–167 [CrossRef]
    [Google Scholar]
  30. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  31. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996;42:457–469 [CrossRef]
    [Google Scholar]
  32. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984;2:233–241 [CrossRef]
    [Google Scholar]
  33. Schenkel E, Berlaimont V, Dubois J, Helson-Cambier M, Hanocq M. Improved high-performance liquid chromatographic method for the determination of polyamines as their benzoylated derivatives: application to P388 cancer cells. J Chromatogr Biomed Sci Appl 1995;668:189–197 [CrossRef]
    [Google Scholar]
  34. Ezaki T, Hashimoto Y, Yabuuchi E. 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 1989;39:224–229 [CrossRef]
    [Google Scholar]
  35. Takeuchi M, Hamana K, Hiraishi A. Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 2001;51:1405–1417 [CrossRef][PubMed]
    [Google Scholar]
  36. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International committee on systematic bacteriology. report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987;37:463–464[CrossRef]
    [Google Scholar]
  37. Ohta H, Hattori R, Ushiba Y, Mitsui H, Ito M et al. Sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations. Int J Syst Evol Microbiol 2004;54:2185–2190 [CrossRef][PubMed]
    [Google Scholar]
  38. Reddy GS, Garcia-Pichel F. Sphingomonas mucosissima sp. nov. and Sphingomonas desiccabilis sp. nov., from biological soil crusts in the Colorado Plateau, USA. Int J Syst Evol Microbiol 2007;57:1028–1034 [CrossRef][PubMed]
    [Google Scholar]
  39. Yoon JH, Park S, Kang SJ, Kim W, Oh TK. Sphingomonas hankookensis sp. nov., isolated from wastewater. Int J Syst Evol Microbiol 2009;59:2788–2793 [CrossRef][PubMed]
    [Google Scholar]
  40. Li Y, Kawamura Y, Fujiwara N, Naka T, Liu H et al. Sphingomonas yabuuchiae sp. nov. and Brevundimonas nasdae sp. nov., isolated from the Russian space laboratory Mir. Int J Syst Evol Microbiol 2004;54:819–825 [CrossRef][PubMed]
    [Google Scholar]
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