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Abstract

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped, manganese-oxidizing bacterial strain, designated DY2–5, was isolated from surface sediment of Pacific Clarion-Clipperton Fracture Zone (CCFZ). Growth occurred at 0–37 °C (optimum 28 °C), pH 6.5–9.0 (optimum pH 7.0–7.5) and in the presence of 1–11 % (w/v) NaCl (optimum 3–4 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel strain was most closely related to ZXM137 with 96.13 % sequence similarity, and had 16S rRNA gene sequence similarities in the range 93.89–95.87 % with other species of the genus . The dominant fatty acids were summed feature 8 (Cω7 and/or Cω6) and C. The polar lipids of strain DY2–5 comprised phosphatidylglycerol, phosphatidylcholine and two unknown aminolipids. The major respiratory quinone was ubiquinone–10 (Q–10). The DNA G+C content of strain DY2–5 was 64.8 mol%. On the basis of the phenotypic, genotypic and physiological evidence, strain DY2–5 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is DY2–5 ( = JCM 19384 = KCTC 32473).

Funding
This study was supported by the:
  • , China Ocean Mineral Resources Research & Development Association , (Award DY125-15-R-03)
  • , National High Technology Research & Development Program of China , (Award 2012AA091605)
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2015-11-01
2020-09-20
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References

  1. Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. (editors) ( 1995). Short Protocols in Molecular Biology: a Compendium of Methods from Current Protocols in Molecular Biology , 3rd edn.., New York: Wiley;.
    [Google Scholar]
  2. Baek K., Choi A., Kang I., Cho J.C. ( 2014;). Celeribacter marinus sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 64 13231327 [CrossRef] [PubMed].
    [Google Scholar]
  3. Bernardet J.-F., Nakagawa Y., Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes ( 2002;). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52 10491070 [CrossRef] [PubMed].
    [Google Scholar]
  4. Beveridge T.J., Lawrence J.R., Murray R.G.E. ( 2007;). Sampling and staining for light microscopy. . In Methods for General and Molecular Microbiology, pp. 1933. Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G., Schmidt T. M., Snyder L. R. , 3rd edn.., Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  5. Boogerd F.C., de Vrind J.P.M. ( 1987;). Manganese oxidation by Leptothrix discophora . J Bacteriol 169 489494 [PubMed].
    [Google Scholar]
  6. Collins M.D. ( 1994;). Isoprenoid quinones. . In Chemical Methods in Prokaryotic Systematics, pp. 265309. Edited by Goodfellow M., O'Donnell A. G. Chichester: Wiley;.
    [Google Scholar]
  7. Ghiorse W.C., Hirsch P. ( 1979;). An ultrastructural study of ion and manganese deposition associated with extracellular polymers of pedomicrobium-like budding bacteria. Arch Microbiol 123 213226 [CrossRef].
    [Google Scholar]
  8. Ivanova E.P., Webb H., Christen R., Zhukova N.V., Kurilenko V.V., Kalinovskaya N.I., Crawford R.J. ( 2010;). Celeribacter neptunius gen. nov., sp. nov., a new member of the class Alphaproteobacteria . Int J Syst Evol Microbiol 60 16201625 [CrossRef] [PubMed].
    [Google Scholar]
  9. Kim O.S., Cho Y.J., Lee K., Yoon S.H., Kim M., Na H., Park S.C., Jeon Y.S., Lee J.H., other authors. ( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62 716721 [CrossRef] [PubMed].
    [Google Scholar]
  10. Kimura M. ( 1980;). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16 111120 [CrossRef] [PubMed].
    [Google Scholar]
  11. Lai Q., Zhong H., Wang J., Yuan J., Sun F., Wang L., Zheng T., Shao Z. ( 2011;). Roseovarius indicus sp. nov., isolated from deep-sea water of the Indian Ocean. Int J Syst Evol Microbiol 61 20402044 [CrossRef] [PubMed].
    [Google Scholar]
  12. Lai Q., Cao J., Yuan J., Li F., Shao Z. ( 2014;). Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophilus as Celeribacter halophilus comb. nov. Int J Syst Evol Microbiol 64 41604167 [CrossRef] [PubMed].
    [Google Scholar]
  13. Lee K., Choo Y.-J., Giovannoni S.J., Cho J.-C. ( 2007;). Maritimibacter alkaliphilus gen. nov., sp. nov., a genome-sequenced marine bacterium of the Roseobacter clade in the order Rhodobacterales . Int J Syst Evol Microbiol 57 16531658 [CrossRef] [PubMed].
    [Google Scholar]
  14. Lee S.Y., Park S., Oh T.K., Yoon J.H. et al., ( 2012;). Celeribacter baekdonensis sp. nov., isolated from seawater, and emended description of the genus Celeribacter Ivanova .2010. Int J Syst Evol Microbiol 62 13591364 [CrossRef] [PubMed].
    [Google Scholar]
  15. Mesbah M., Whitman W.B. ( 1989;). Measurement of deoxyguanosine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine + cytosine of DNA. J Chromatogr A 479 297306 [CrossRef] [PubMed].
    [Google Scholar]
  16. Minnikin D.E., O'Donnell A.G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J.H. ( 1984;). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2 233241 [CrossRef].
    [Google Scholar]
  17. Montero-Calasanz M., del C., Göker M., Rohde M., Spröer C., Schumann P., Busse H.J., Schmid M., Tindall B.J., Klenk H.P., Camacho M. ( 2013;). Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobac-terium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium. Int J Syst Evol Microbiol 63 43864395 [CrossRef] [PubMed].
    [Google Scholar]
  18. Oh Y.-S.S., Lim H.-J.J., Cha I.-T.T., Im W.-T.T., Yoo J.-S.S., Kang U.G., Rhee S.-K.K., Roh D.-H.H. ( 2009;). Roseovarius halotolerans sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 59 27182723 [CrossRef] [PubMed].
    [Google Scholar]
  19. Sasser M. ( 1990). Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc;.
    [Google Scholar]
  20. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30 27252729 [CrossRef] [PubMed].
    [Google Scholar]
  21. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. ( 1997;). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25 48764882 [CrossRef] [PubMed].
    [Google Scholar]
  22. Tindall B.J., Sikorski J., Smibert R.M., Krieg N.R. ( 2007;). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Microbiology, pp. 330393. Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G., Schmidt T. M., Snyder L. R. , 3rd edn.., Washington, DC: American Society for Microbiology; [CrossRef].
    [Google Scholar]
  23. Wang H., Zhang X., Yan S., Qi Z., Yu Y., Zhang X.H. ( 2012;). Huaishuia halophilus gen. nov., sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 62 223228 [CrossRef] [PubMed].
    [Google Scholar]
  24. Weisburg W.G., Barns S.M., Pelletier D.A., Lane D.J. ( 1991;). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173 697703 [PubMed].
    [Google Scholar]
  25. Zhang R., Lai Q., Wang W., Li S., Shao Z. ( 2013;). Thioclava dalianensis sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 63 29812985 [CrossRef] [PubMed].
    [Google Scholar]
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