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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 8

sp. nov., sp. nov., and sp. nov. isolated from glaciers Free

Abstract

Three strains, designated as LB1R34, LB3P52 and ZT4R6, were isolated from glaciers located on the Tibetan Plateau, PR China. The strains were Gram-stain-negative, aerobic, rod-shaped, non-motile and yellow. Phylogenetic analysis based on the 16S rRNA gene and genomic sequences indicated that they were related to the members of the genus . The 16S rRNA gene sequences similarities between the three strains were 92.31–96.93 %. The average nucleotide identity values and digital DNA–DNA hybridization values between these three strains and their closest relatives were 76.80–91.33 % and 21.3–44.2 %, respectively. LB1R34, LB3P52 and ZT4R6 contained MK-6 as the major menaquinone, summed feature 3 (comprising Cω7 and/or Cω6) and -C as the major fatty acids. Phosphatidylethanolamine was present in their polar lipids profiles. On the basis of the phenotypic characteristics, he results of phylogenetic analysis and genotypic data, three novel species, sp. nov. (type strain=LB1 R34=CGMCC 1.11493=NBRC 113650), sp. nov. (type strain=LB3 P52=CGMCC 1.11446=NBRC 113776) and sp. nov. (type strain=ZT4 R6=CGMCC 1.11919=NBRC 113653) are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Flavobacterium restrictum , Flavobacterium rhamnosiphilum and Flavobacterium zepuense
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31670003)
    • Principle Award Recipient: Yu-Hua Xin
© 2020 Institute of Microbiology, Chinese Academy of Sciences
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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 JF, Bowman JP et al. Genus I. Flavobacterium . In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ et al. (editors) Bergey’s Manual of Systematic Bacteriology 4, 2nd ed. New York: Springer; 2011 pp 112–154
     [Google Scholar]
  3. Liu Q, Zhou Y-G, Xin Y-H. High diversity and distinctive community structure of bacteria on glaciers in China revealed by 454 pyrosequencing. Syst Appl Microbiol 2015; 38:578–585 [View Article][PubMed]
     [Google Scholar]
  4. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley and Sons; 1991 pp 115–175
     [Google Scholar]
  5. 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]
  6. 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 [View Article][PubMed]
     [Google Scholar]
  7. Kim M, Oh H-S, Park S-C, Chun J. 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]
  8. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
     [Google Scholar]
  9. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed]
     [Google Scholar]
  10. Yoon S-H, Ha S-M, 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]
  11. 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]
  12. Richter M, Rosselló-Móra R. 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]
  13. 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]
  14. 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 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]
  15. Yang L-L, Liu Q, Liu H-C, Zhou Y-G, Xin Y-H. 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]
  16. Lee SH, Kim JM, Lee JR, Park W, Jeon CO. Flavobacterium fluvii sp. nov., isolated from stream sediment. Int J Syst Evol Microbiol 2010; 60:353–357 [View Article][PubMed]
     [Google Scholar]
  17. Zhang G-Q, Liu Q, Liu H-C, Zhou Y-G, Xin Y-H. Flavobacterium ranwuense sp. nov., isolated from glacier. Int J Syst Evol Microbiol 2019; 69:38123817 [View Article][PubMed]
     [Google Scholar]
  18. Zhang D-C, Wang H-X, Liu H-C, Dong X-Z, Zhou P-J. 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]
  19. Aslam Z, Im W-T, Kim MK, Lee S-T. 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]
  20. Ali Z, Cousin S, Frühling A, Brambilla E, Schumann P et al. Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet. Int J Syst Evol Microbiol 2009; 59:2610–2617 [View Article][PubMed]
     [Google Scholar]
  21. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  22. 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]
  23. Collins MD. Isoprenoid quinone 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]
  24. Komagata K, Suzuki K. 4 Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol, 1988 pp. 161–207
     [Google Scholar]
  25. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101. Newark, DE: MIDI; 1990
     [Google Scholar]
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Flavobacterium restrictum sp. nov., Flavobacterium rhamnosiphilum sp. nov., and Flavobacterium zepuense sp. nov. isolated from glaciers
Int J Syst Evol Microbiol 70, 4583 (2020); https://doi.org/10.1099/ijsem.0.004317
/content/journal/ijsem/10.1099/ijsem.0.004317
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