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Abstract

A novel Gram-stain-negative, straight or curved rod-shaped, non-spore-forming, strictly aerobic, motile bacterium with a single polar flagellum, designated D3211, was isolated from marine alga collected at the seashore of Yantai, PR China. The organism grew optimally at 24 °C, pH 7.0 and in the presence of 2.0 % (w/v) NaCl. Strain D3211 contained ubiquinone 8 as the major respiratory quinone and C 7 and/or C 6, C, iso-C and anteiso-C B and/or iso-C I as the major fatty acids. The predominant polar lipids of strain D3211 were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content of strain D3211 was 39.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was related most closely to BSs20135, JDTF-33, KCTC 32108, DSM 15026, JCM 13954 and ARK 150 with 97.6, 97.6, 97.5, 97.4, 97.3 and 97.1 % sequence similarities, respectively. Calculated average nucleotide identity and DNA–DNAhybridization values between strain D3211 and its phylogenetically related species were in the range 70.2–73.4 % and 19.1–20.4 %, respectively. On the basis of polyphasic analyses, strain D3211 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is D3211 (=KCTC 72122=MCCC 1K03603).

Funding
This study was supported by the:
  • the Foundation of He'nan Science and Technology Agency of China (Award 162102210404)
    • Principle Award Recipient: Jing Kang
  • the National Natural Sciences Foundation (Award 81903525)
    • Principle Award Recipient: Yan Wang
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2020-07-20
2024-12-04
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References

  1. Shivaji S, Reddy GS. Phylogenetic analyses of the genus Glaciecola: emended description of the genus Glaciecola, transfer of Glaciecola mesophila, G. agarilytica, G. aquimarina, G. arctica, G. chathamensis, G. polaris and G. psychrophila to the genus Paraglaciecola gen. nov. as Paraglaciecola mesophila comb. nov., P. agarilytica comb. nov., P. aquimarina comb. nov., P. arctica comb. nov., P. chathamensis comb. nov., P. polaris comb. nov. and P. psychrophila comb. nov., and description of Paraglaciecola oceanifecundans sp. nov., isolated from the Southern Ocean. Int J Syst Evol Microbiol 2014; 64:3264–3275 [View Article][PubMed]
    [Google Scholar]
  2. Parte AC. LPSN--list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–D616 [View Article][PubMed]
    [Google Scholar]
  3. Park S, Yoon J-H. Glaciecola aquimarina sp. nov., a gammaproteobacterium isolated from coastal seawater. Antonie Van Leeuwenhoek 2013; 103:1141–1148 [View Article][PubMed]
    [Google Scholar]
  4. Van Trappen S, Tan T-L, Yang J, Mergaert J, Swings J. Glaciecola polaris sp. nov., a novel budding and prosthecate bacterium from the Arctic Ocean, and emended description of the genus Glaciecola . Int J Syst Evol Microbiol 2004; 54:1765–1771 [View Article][PubMed]
    [Google Scholar]
  5. Yong J-J, Park S-J, Kim H-J, Rhee S-K. Glaciecola agarilytica sp. nov., an agar-digesting marine bacterium from the East Sea, Korea. Int J Syst Evol Microbiol 2007; 57:951–953 [View Article][PubMed]
    [Google Scholar]
  6. Matsuyama H, Hirabayashi T, Kasahara H, Minami H, Hoshino T et al. Glaciecola chathamensis sp. nov., a novel marine polysaccharide-producing bacterium. Int J Syst Evol Microbiol 2006; 56:2883–2886 [View Article][PubMed]
    [Google Scholar]
  7. Zhang Y-J, Zhang X-Y, Mi Z-H, Chen C-X, Gao Z-M et al. Glaciecola arctica sp. nov., isolated from Arctic marine sediment. Int J Syst Evol Microbiol 2011; 61:2338–2341 [View Article][PubMed]
    [Google Scholar]
  8. Park S, Choi SJ, Choi J, Yoon J-H. Paraglaciecola aestuariivivens sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2017; 67:4754–4759 [View Article][PubMed]
    [Google Scholar]
  9. Zhang D-C, Yu Y, Chen B, Wang H-X, Liu H-C et al. Glaciecola psychrophila sp. nov., a novel psychrophilic bacterium isolated from the Arctic. Int J Syst Evol Microbiol 2006; 56:2867–2869 [View Article][PubMed]
    [Google Scholar]
  10. Romanenko LA, Zhukova NV, Rohde M, Lysenko AM, Mikhailov VV et al. Glaciecola mesophila sp. nov., a novel marine agar-digesting bacterium. Int J Syst Evol Microbiol 2003; 53:647–651 [View Article][PubMed]
    [Google Scholar]
  11. Bech PK, Schultz-Johansen M, Glaring MA, Barbeyron T, Czjzek M et al. Paraglaciecola hydrolytica sp. nov., a bacterium with hydrolytic activity against multiple seaweed-derived polysaccharides. Int J Syst Evol Microbiol 2017; 67:2242–2247 [View Article][PubMed]
    [Google Scholar]
  12. Wang Y, Zhou C, Ming H, Kang J, Chen H et al. Pseudofulvibacter marinus sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2016; 66:1301–1305 [View Article][PubMed]
    [Google Scholar]
  13. Yoon S-H, Ha S-M, 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 [View Article][PubMed]
    [Google Scholar]
  14. 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 [View Article][PubMed]
    [Google Scholar]
  15. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  16. Rosselló-Móra R, Amann R. Past and future species definitions for bacteria and archaea. Syst Appl Microbiol 2015; 38:209–216 [View Article][PubMed]
    [Google Scholar]
  17. Kim M, Oh H-S, Park S-C, Chun J, Mincheol K. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  18. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
    [Google Scholar]
  19. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article][PubMed]
    [Google Scholar]
  20. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 2007; 23:673–679 [View Article][PubMed]
    [Google Scholar]
  21. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  22. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article][PubMed]
    [Google Scholar]
  23. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
    [Google Scholar]
  24. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  25. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article][PubMed]
    [Google Scholar]
  26. Richter M, Rosselló-Móra R, Michael R, Ramon RM. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  27. Beveridge TJ, Lawrence JR, Murray RGE. Sampling and staining for light microscopy. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology Washington, DC: ASM Press; 2007 pp 19–33
    [Google Scholar]
  28. Tindall BJ, Sikorski J, Smibert RM, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology Washington, DC: ASM Press; 2007 pp 330–393
    [Google Scholar]
  29. Lyman J, Fleming RH. Composition of seawater. J Mar Res 1940; 3:134–146
    [Google Scholar]
  30. 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 [View Article][PubMed]
    [Google Scholar]
  31. Breznak JA, Costilow RN. Physicochemical factors in growth. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: ASM Press; 1994 pp 137–154
    [Google Scholar]
  32. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101.. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  33. Collins MD. Isoprenoid quinones. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley Press; 1994 pp 265–309
    [Google Scholar]
  34. 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 [View Article]
    [Google Scholar]
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