1887

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Volume 69, Issue 12

sp. nov., isolated from glacier Free

Abstract

A Gram-stain-negative, aerobic, rod-shaped, devoid of flagella, orange–yellow-coloured bacterium (strain LB2P22) was isolated from an ice sample collected from the Laigu glacier on the Tibetan Plateau, PR China. The results of 16S rRNA gene sequence analysis indicated that strain LB2P22 belongs to the genus with highest similarity to LB2P30 (98.14 %), CGMCC 1.5380 (98.02 %), CCM 8827 (97.94 %) and CGMCC 1.10125 (97.91 %). Strain LB2P22 had 77.99–84.99 % average nucleotide identity and 22.3–29.3 % digital DNA–DNA hybridization values with its closest relatives, indicating that it represents a novel species of the genus . Strain LB2P22 grew at 0–25 °C, pH 7.0–8.0 and up to 1.0 % (w/v) NaCl. The main cellular fatty acids were iso-C, summed feature 3 (comprising Cω7/Cω6) and anteiso-C. The genomic DNA G+C content is 34.3 mol%. The predominant menaquinone was MK-6 and the polar lipids were phosphatidylethanolamine, one unidentified aminolipid and four unidentified lipids. Based on these data, a novel species, sp. nov., is proposed, with LB2P22 (=CGMCC 1.11361=NBRC 113777) as the type strain.

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  • Accepted:
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Keyword(s): Flavobacterium ranwuense , glacier and psychrotolerant
© 2019 Institute of Microbiology, Chinese Academy of Science
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2019-12-01
2024-04-25
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References

  1. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM et al. Genus II. Flavobacterium gen. nov. Bergey’s Manual of Determinative Bacteriology, 1st ed. Baltimore, MD: Williams and Wilkins; 1923 pp. 97–117
     [Google Scholar]
  2. Bernardet J-F, Segers P, Vancanneyt M, Berthe F, Kersters K et al. Cutting a gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996; 46:128–148 [View Article]
     [Google Scholar]
  3. Huq MA, Akter S, Lee SY. Flavobacterium chungangensis sp. nov., a bacterium isolated from soil of Chinese cabbage garden. Curr Microbiol 2018; 75:842–848 [View Article][PubMed]
     [Google Scholar]
  4. Hu G, Zhang J, Yang G, Li YY, Guan YT et al. Flavobacterium yanchengense sp. nov., isolated from soil. Int J Syst Evol Microbiol 2013; 63:2848–2852 [View Article][PubMed]
     [Google Scholar]
  5. Kang JY, Chun J, Jahng KY. Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium . Int J Syst Evol Microbiol 2013; 63:1633–1638 [View Article][PubMed]
     [Google Scholar]
  6. Sheu SY, Chen YL, Chen WM. Flavobacterium verecundum sp. nov., isolated from a freshwater river. Int J Syst Evol Microbiol 2016; 66:3337–3344 [View Article][PubMed]
     [Google Scholar]
  7. Song L, Liu H, Huang Y, Dai X, Zhou Y. Flavobacterium marinum sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2013; 63:3551–3555 [View Article][PubMed]
     [Google Scholar]
  8. Li DD, Liu C, Zhang YQ, Wang XJ, Wang N et al. Flavobacterium arcticum sp. nov., isolated from Arctic seawater. Int J Syst Evol Microbiol 2017; 67:1070–1074 [View Article][PubMed]
     [Google Scholar]
  9. Tamaki H, Hanada S, Kamagata Y, Nakamura K, Nomura N et al. Flavobacterium limicola sp. nov., a psychrophilic, organic-polymer-degrading bacterium isolated from freshwater sediments. Int J Syst Evol Microbiol 2003; 53:519–526 [View Article][PubMed]
     [Google Scholar]
  10. Zhang Y, Jiang F, Chang X, Qiu X, Ren L et al. Flavobacterium collinsense sp. nov., isolated from a till sample of an Antarctic glacier. Int J Syst Evol Microbiol 2016; 66:172–177 [View Article][PubMed]
     [Google Scholar]
  11. Zhang DC, Wang HX, Liu HC, Dong XZ, Zhou PJ. Flavobacterium glaciei sp. nov., a novel psychrophilic bacterium isolated from the China No.1 glacier. Int J Syst Evol Microbiol 2006; 56:2921–2925 [View Article][PubMed]
     [Google Scholar]
  12. Yang LL, Liu Q, Liu HC, Zhou YG, Xin YH. Flavobacterium laiguense sp. nov., a psychrophilic bacterium isolated from Laigu glacier on the Tibetan Plateau. Int J Syst Evol Microbiol 2019; 69:1821–1825 [View Article][PubMed]
     [Google Scholar]
  13. Zhu L, Liu Q, Liu H, Zhang J, Dong X et al. Flavobacterium noncentrifugens sp. nov., a psychrotolerant bacterium isolated from glacier meltwater. Int J Syst Evol Microbiol 2013; 63:2032–2037 [View Article][PubMed]
     [Google Scholar]
  14. Zhu F, Wang S, Zhou P. Flavobacterium xinjiangense sp. nov. and Flavobacterium omnivorum sp. nov., novel psychrophiles from the China No. 1 glacier. Int J Syst Evol Microbiol 2003; 53:853–857 [View Article][PubMed]
     [Google Scholar]
  15. Xu M, Xin Y, Tian J, Dong K, Yu Y et al. Flavobacterium sinopsychrotolerans sp. nov., isolated from a glacier. Int J Syst Evol Microbiol 2011; 61:20–24 [View Article][PubMed]
     [Google Scholar]
  16. Xin YH, Liang ZH, Zhang DC, Liu HC, Zhang JL et al. Flavobacterium tiangeerense sp. nov., a cold-living bacterium isolated from a glacier. Int J Syst Evol Microbiol 2009; 59:2773–2777 [View Article][PubMed]
     [Google Scholar]
  17. Dong K, Liu H, Zhang J, Zhou Y, Xin Y. Flavobacterium xueshanense sp. nov. and Flavobacterium urumqiense sp. nov., two psychrophilic bacteria isolated from glacier ice. Int J Syst Evol Microbiol 2012; 62:1151–1157 [View Article][PubMed]
     [Google Scholar]
  18. Bernardet JF, Nakagawa Y, Holmes B. 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 [View Article][PubMed]
     [Google Scholar]
  19. Bernardet JF, Bowman JP. Genus I. Flavobacterium . In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ et al. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 4 New York: Springer; 2010 pp. 112–154
     [Google Scholar]
  20. Liu Q, Liu HC, Zhang JL, Zhou YG, Xin YH. Nocardioides glacieisoli sp. nov., isolated from a glacier. Int J Syst Evol Microbiol 2015; 65:4845–4849 [View Article][PubMed]
     [Google Scholar]
  21. 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 [View Article][PubMed]
     [Google Scholar]
  22. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
     [Google Scholar]
  23. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  24. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  25. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  26. 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]
  27. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article]
     [Google Scholar]
  28. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
     [Google Scholar]
  29. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  30. Tatusova T, Dicuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article][PubMed]
     [Google Scholar]
  31. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  32. 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
     [Google Scholar]
  33. Gerhardt P, Murray RGE, Wood WA, King NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  34. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 607–654
     [Google Scholar]
  35. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101. Newark, DE: MIDI; 1990
     [Google Scholar]
  36. Collins MD. Isoprenoidquinone analysis in classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp. 267–287
     [Google Scholar]
  37. Komagata K, Suzuki K. 4 Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988161–207
     [Google Scholar]
  38. Aslam Z, Im WT, Kim MK, Lee ST. Flavobacterium granuli sp. nov., isolated from granules used in a wastewater treatment plant. Int J Syst Evol Microbiol 2005; 55:747–751 [View Article][PubMed]
     [Google Scholar]
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Flavobacterium ranwuense sp. nov., isolated from glacier
Int J Syst Evol Microbiol 69, 3812 (2019); https://doi.org/10.1099/ijsem.0.003687
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