1887

Abstract

A psychrophilic, Gram-stain-positive, rod-shaped bacterium, designated Hh39, was isolated from Xinjiang No. 1 glacier in PR China. Strain Hh39 was catalase-positive, oxidase-negative and could grow at 0–18 °C, pH 6.0–11.0 and in the presence of 0–2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Hh39 belonged to the genus . The highest level of 16S rRNA gene sequence similarities were found to the type strains of (99.01 %), (98.90 %), (98.90 %) and (98.75 %). However, the low average nucleotide identity (80.65–81.89 %) and digital DNA–DNA hybridization values (22.1–23.8 %) between strain Hh39 and its four closest relatives indicated that it represents a novel species of the genus . The predominant fatty acids were anteiso-C, anteiso-C, iso-C and anteiso-C. The major menaquinone was MK-10. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unidentified lipid and one unidentified glycolipid. On the basis of results of phenotypic, genotypic and phylogenetic analyses, a novel species, sp. nov., is proposed, with Hh39 (=NBRC 107884=CGMCC 1.11212) as the type strain.

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2019-10-01
2019-10-21
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References

  1. Suzuki K, Sasaki J, Uramoto M, Nakase T, Komagata K. Cryobacterium psychrophilum gen. nov., sp. nov., nom. rev., comb. nov., an obligately psychrophilic actinomycete to accommodate "Curtobacterium psychrophilum" Inoue and Komagata 1976. Int J Syst Bacteriol 1997;47:474–478 [CrossRef][PubMed]
    [Google Scholar]
  2. Liu Q, Zhou YG, Xin YH. High diversity and distinctive community structure of bacteria on glaciers in China revealed by 454 pyrosequencing. Syst Appl Microbiol 2015;38:578–585 [CrossRef][PubMed]
    [Google Scholar]
  3. Liu Q, Liu HC, Zhou YG, Xin YH. Genetic diversity of glacier-inhabiting Cryobacterium bacteria in China and description of Cryobacterium zongtaii sp. nov. and Arthrobacter glacialis sp. nov. Syst Appl Microbiol 2019;42:168–177 [CrossRef][PubMed]
    [Google Scholar]
  4. Reddy GS, Pradhan S, Manorama R, Shivaji S. Cryobacterium roopkundense sp. nov., a psychrophilic bacterium isolated from glacial soil. Int J Syst Evol Microbiol 2010;60:866–870 [CrossRef][PubMed]
    [Google Scholar]
  5. Liu Q, Liu H, Wen Y, Zhou Y, Xin Y. Cryobacterium flavum sp. nov. and Cryobacterium luteum sp. nov., isolated from glacier ice. Int J Syst Evol Microbiol 2012;62:1296–1299 [CrossRef][PubMed]
    [Google Scholar]
  6. Liu Q, Liu H, Zhang J, Zhou Y, Xin Y et al. Cryobacterium levicorallinum sp. nov., a psychrophilic bacterium isolated from glacier ice. Int J Syst Evol Microbiol 2013;63:2819–2822 [CrossRef][PubMed]
    [Google Scholar]
  7. Liu Q, Xin YH, Chen XL, Liu HC, Zhou YG et al. Cryobacterium aureum sp. nov., a psychrophilic bacterium isolated from glacier ice collected from the ice tongue surface. Int J Syst Evol Microbiol 2018;68:1173–1176 [CrossRef][PubMed]
    [Google Scholar]
  8. 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]
  9. 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]
  10. Turner S, Pryer KM, Miao VP, Palmer JD. Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol 1999;46:327–338 [CrossRef][PubMed]
    [Google Scholar]
  11. 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]
  12. 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 [CrossRef][PubMed]
    [Google Scholar]
  13. 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]
  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 [CrossRef][PubMed]
    [Google Scholar]
  15. 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 [CrossRef][PubMed]
    [Google Scholar]
  16. Na SI, Kim YO, Yoon SH, Ha SM, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018;56:280–285 [CrossRef][PubMed]
    [Google Scholar]
  17. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013;30:772–780 [CrossRef][PubMed]
    [Google Scholar]
  18. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015;32:268–274 [CrossRef][PubMed]
    [Google Scholar]
  19. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018;9:5114 [CrossRef][PubMed]
    [Google Scholar]
  20. 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 [CrossRef][PubMed]
    [Google Scholar]
  21. Tatusova T, Dicuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016;44:6614–6624 [CrossRef][PubMed]
    [Google Scholar]
  22. 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]
  23. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  24. Komagata K, Suzuki K. 4 Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988;161–207
    [Google Scholar]
  25. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; pp.267–284
    [Google Scholar]
  26. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101. Newark, DE: MIDI; 1990
    [Google Scholar]
  27. Schumann P. 5 - Peptidoglycan Structure. In Rainey F, Oren A. (editors) Methods in Microbiology Academic Press; 2011; pp.101–129
    [Google Scholar]
  28. Liu Q, Zhou YG, Xin YH. et al. Cryobacterium. In Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J, Hedlund B. (editors) Bergey's Manual of Systematics of Archaea and Bacteria New York: John Wiley and Sons; 2018
    [Google Scholar]
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