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Abstract

A Gram-staining-negative, yellow-colony-forming, rod-shaped, non-flagellated and facultatively aerobic strain, designed HRA130-1, was isolated from a deep-sea polymetallic nodule from the Pacific Clarion-Clipperton Fracture Zone (CCFZ). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HRA130-1 belonged to the genus Polaribacter (96.3–93.2 % 16S rRNA gene sequence similarity), and exhibited 94 % 16S rRNA gene sequence similarity to Polaribacter filamentus KCTC 23135 (type species) and the highest sequence similarity to Polaribacter huanghezhanensis KCTC 32516 (96.3 %). Optimal growth occurred in the presence of 4 % (w/v) NaCl, at pH 7.0 and 16 °C. The DNA G+C content of strain HRA130-1 was 35.9 mol%. The major fatty acid was iso-C15 : 0. The predominant respiratory quinone was menaquinone-6 (MK-6). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid and an unidentified aminolipid. On the basis of data from the present taxonomic study using a polyphasic approach, strain HRA130-1 represents a novel species of the genus Polaribacter , for which the name Polaribacter pacificus sp. nov. is proposed. The type strain is HRA130-1 (=KCTC 52370=MCCC 1K03199=JCM 31460=CGMCC 1.15763).

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2017-08-22
2019-10-22
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References

  1. Gosink JJ, Woese CR, Staley JT. Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of 'Flectobacillus glomeratus' as Polaribacter glomeratus comb. nov. Int J Syst Bacteriol 1998;48:223–235 [CrossRef][PubMed]
    [Google Scholar]
  2. Mcguire AJ, Franzmann PD, Mcmeekin TA. Flectobacillus glomeratus sp. nov., a curved, nonmotile, pigmented bacterium isolated from antarctic marine environments. Syst Appl Microbiol 1987;9:265–272 [CrossRef]
    [Google Scholar]
  3. Nedashkovskaya OI, Kim SB, Lysenko AM, Kalinovskaya NI, Mikhailov VV et al. Polaribacter butkevichii sp. nov., a novel marine mesophilic bacterium of the family Flavobacteriaceae. Curr Microbiol 2005;51:408–412 [CrossRef][PubMed]
    [Google Scholar]
  4. Park S, Park JM, Jung YT, Lee KC, Lee JS et al. Polaribacter marinivivus sp. nov., a member of the family Flavobacteriaceae isolated from seawater. Antonie Van Leeuwenhoek 2014;106:1139–1146 [CrossRef][PubMed]
    [Google Scholar]
  5. Yoon JH, Kang SJ, Oh TK. Polaribacter dokdonensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2006;56:1251–1255 [CrossRef][PubMed]
    [Google Scholar]
  6. Lee YS, Lee DH, Kahng HY, Sohn SH, Jung JS et al. Polaribacter gangjinensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2011;61:1425–1429 [CrossRef][PubMed]
    [Google Scholar]
  7. Hyun DW, Shin NR, Kim MS, Kim PS, Jung MJ et al. Polaribacter atrinae sp. nov., isolated from the intestine of a comb pen shell, Atrina pectinata. Int J Syst Evol Microbiol 2014;64:1654–1661 [CrossRef][PubMed]
    [Google Scholar]
  8. Kim BC, Oh HW, Kim H, Park DS, Hong SG et al. Polaribacter sejongensis sp. nov., isolated from antarctic soil, and emended descriptions of the genus Polaribacter, Polaribacter butkevichii and Polaribacter irgensii. Int J Syst Evol Microbiol 2013;63:4000–4005 [CrossRef][PubMed]
    [Google Scholar]
  9. Nedashkovskaya OI, Kukhlevskiy AD, Zhukova NV. Polaribacter reichenbachii sp. nov.: a new marine bacterium associated with the green alga Ulva fenestrata. Curr Microbiol 2013;66:16–21 [CrossRef][PubMed]
    [Google Scholar]
  10. Park S, Park JM, Jung YT, Lee KH, Yoon JH et al. Polaribacter undariae sp. nov., isolated from a brown alga reservoir. Int J Syst Evol Microbiol 2015;65:1679–1685 [CrossRef][PubMed]
    [Google Scholar]
  11. Kim E, Shin SK, Choi S, Yi H. Polaribacter vadi sp. nov., isolated from a marine gastropod. Int J Syst Evol Microbiol 2017;67:144–147 [CrossRef][PubMed]
    [Google Scholar]
  12. Li H, Zhang XY, Liu C, Lin CY, Xu Z et al. Polaribacter huanghezhanensis sp. nov., isolated from arctic fjord sediment, and emended description of the genus Polaribacter. Int J Syst Evol Microbiol 2014;64:973–978 [CrossRef][PubMed]
    [Google Scholar]
  13. Fukui Y, Abe M, Kobayashi M, Saito H, Oikawa H et al. Polaribacter porphyrae sp. nov., isolated from the red alga Porphyra yezoensis, and emended descriptions of the genus Polaribacter and two Polaribacter species. Int J Syst Evol Microbiol 2013;63:1665–1672 [CrossRef][PubMed]
    [Google Scholar]
  14. Sq J, Zhao R, Yin Q, Zhao Y, Liu C-G et al. Gel microbead cultivation with a subenrichment procedure can yield better bacterial cultivability from a seawater sample than standard plating method. J Ocean Univ China 2012;11:45–51[CrossRef]
    [Google Scholar]
  15. Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ et al. Cultivating the uncultured. Proc Natl Acad Sci USA 2002;99:15681–15686 [CrossRef][PubMed]
    [Google Scholar]
  16. Suzuki MT, Rappé MS, Haimberger ZW, Winfield H, Adair N et al. Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample. Appl Environ Microbiol 1997;63:983–989[PubMed]
    [Google Scholar]
  17. Ausubel F, Brent R, Kingston R, Moore D, Seidman J et al. Short Protocols in Molecular Biology: A Compendium of Methods From Current Protocols in Molecular Biology, 3rd ed. New York, NY: Wiley; 1995
    [Google Scholar]
  18. 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]
  19. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017;67:1613–1617 [CrossRef][PubMed]
    [Google Scholar]
  20. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG et al. 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]
  21. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  22. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  23. Stackebrandt E, Goebel BM. 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 1994;44:846–849 [CrossRef]
    [Google Scholar]
  24. Beveridge TJ, Lawrence JR, Murray RG. Sampling and staining for light microscopy. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR. et al. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007; pp.19–33
    [Google Scholar]
  25. Bernardet JF, Nakagawa Y, Holmes B..Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002;52:1049–1070 [CrossRef][PubMed]
    [Google Scholar]
  26. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR. et al. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007; pp.330–393
    [Google Scholar]
  27. Hsu SC, Lockwood JL. Powdered chitin agar as a selective medium for enumeration of actinomycetes in water and soil. Appl Microbiol 1975;29:422–426[PubMed]
    [Google Scholar]
  28. Yoon JH, Lee KC, Kho YH, Kang KH, Kim CJ et al. Halomonas alimentaria sp. nov., isolated from Jeotgal, a traditional korean fermented seafood. Int J Syst Evol Microbiol 2002;52:123–130 [CrossRef][PubMed]
    [Google Scholar]
  29. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.; 1990
    [Google Scholar]
  30. 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]
  31. Collins MD, Shah HN. Fatty acid, menaquinone and polar lipid composition of Rothia dentocariosa. Arch Microbiol 1984;137:247–249 [CrossRef]
    [Google Scholar]
  32. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987;19:161–207[CrossRef]
    [Google Scholar]
  33. Moore ERB, Arnscheidt A, Krü ger A, Strömpl C, Mau M et al. Simplified protocols for the preparation of genomic DNA from bacterial cultures. In Akkermans ADL, van Elsas JD, de Bruijn FJ. (editors) Molecular Microbial Ecology Manual 1.6.1. Dordrecht:: Kluwer; 1999; pp.1–15
    [Google Scholar]
  34. Mesbah M, Whitman WB. 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 1989;479:297–306 [CrossRef][PubMed]
    [Google Scholar]
  35. Montero-Calasanz MC, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium. Int J Syst Evol Microbiol 2013;63:4386–4395 [CrossRef][PubMed]
    [Google Scholar]
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