1887

Abstract

A Gram-stain-negative, rod-shaped, green-pigmented, aerobic and motile bacterium, strain R3-44, was isolated from Arctic tundra soil. Stain R3-44 clustered closely with members of the genus , which belongs to the family , and showed the highest 16S rRNA sequence similarity to AR2 (96.10%). Strain R3-44 grew optimally at pH 7.0, 28 °C and in the presence of 0–0.5 % (w/v) NaCl. The predominant respiratory isoprenoid quinone of strain R3-44 was identified as ubiquinone Q-8. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, unidentified aminolipid and unidentified phospholipid. The main fatty acids were summed feature 3 (comprising C ω7 and/or C ω6, 40.6 %) and C (29.3 %). The DNA G+C content of strain R3-44 was 60.8 mol%. On the basis of the evidence presented in this study, strain R3-44 represents a novel species of the genus , for which the name sp. nov. is proposed, with the type strain R3-44 (=CCTCC AB 2010422=KCTC 72602).

Funding
This study was supported by the:
  • Fang Peng , Chinese Polar Scientific Strategy Research Fund , (Award IC201706)
  • Fang Peng , National Natural Science Foundation of China , (Award 31270538)
  • Fang Peng , the R&D Infrastructure and Facility Development Program of the Ministry of Science and Technology of the People’s Republic of China , (Award NIMR-2019-8)
  • Fang Peng , National Key R&D Program of China , (Award 2018YFC1406701)
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2020-05-04
2020-06-02
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References

  1. Chang S-C, Wang J-T, Vandamme P, Hwang J-H, Chang P-S et al. Chitinimonas taiwanensis gen. nov., sp. nov., a novel chitinolytic bacterium isolated from a freshwater pond for shrimp culture. Syst Appl Microbiol 2004; 27:43–49 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  2. Kim B-Y, Weon H-Y, Yoo S-H, Chen W-M, Kwon S-W et al. Chitinimonas koreensis sp. nov., isolated from greenhouse soil in Korea. Int J Syst Evol Microbiol 2006; 56:1761–1764 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  3. Joung Y, Lee B-I, Kang H, Kim H, Joh K. Chitinimonas viridis sp. nov., isolated from a mesotrophic artificial lake. Int J Syst Evol Microbiol 2014; 64:1123–1126 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  4. Padakandla SR, Chae J-C. Chitinimonas naiadis sp. nov., Isolated from a freshwater river. J Microbiol Biotechnol 2017; 27:1300–1305 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  5. Yang DJ, Choi HS, Hong J-K. Chitinimonas lacunae sp. nov., isolated from artificial pond in Korea. Int J Syst Evol Microbiol 2017; 67:4323–4327 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  6. Li Y, Zhu H, Lai Q, Lei X, Chen Z et al. Chitinimonas prasina sp. nov., isolated from lake water. Int J Syst Evol Microbiol 2014; 64:3005–3009 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  7. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  8. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  9. Chun J, Lee J-H, Jung Y, Kim M, Kim S et al. Eztaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259–2261 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  10. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  11. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 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][PubMed]
    [Google Scholar]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  14. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [CrossRef]
    [Google Scholar]
  15. 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][PubMed]
    [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  17. 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]
  18. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50 Pt 5:1861–1868 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  19. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  20. Moore DD, Dowhan D et al. Preparation and analysis of DNA. In Ausubel FW, Brent R, Kingston RE, Moore DD, Seidman JG et al. (editors) Current Protocols in Molecular Biology New York: Wiley; 1995 pp 2–11
    [Google Scholar]
  21. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [CrossRef]
    [Google Scholar]
  22. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  23. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [CrossRef]
    [Google Scholar]
  24. Kates M. Techniques of Lipidology Isolation, Analysis and Identification of Lipids, 2nd ed. rev. Amsterdam: Elsevier; 1986 pp 106–107
    [Google Scholar]
  25. Roberts RJ, Carneiro MO, Schatz MC. The advantages of SMRT sequencing. Genome Biol 2013; 14:405 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  26. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  27. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  28. Miller JR, Delcher AL, Koren S, Venter E, Walenz BP et al. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 2008; 24:2818–2824 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  29. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  30. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  31. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  32. Zuo G, Hao B. CVTree3 web server for Whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genom Proteom Bioinf 2015; 13:321–331 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  33. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  34. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [CrossRef][PubMed][PubMed]
    [Google Scholar]
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