1887

Abstract

A cold-adapted, piezophilic, slightly halophilic bacterium, designated as N102, was isolated from a deep-sea (4700 m) sediment sample collected from the New Britain Trench. Strain N102 was Gram-stain-negative, rod-shaped, oxidase- and catalase-positive, and grew optimally at 28 °C (range, 4–40 °C), pH 7.0–7.5 (range, 6.0–9.0) and 3–4 %(w/v) NaCl (range, 2–15 %). The optimum pressure for growth was 10 MPa with tolerance up to 70 MPa. 16S rRNA gene sequence analysis showed that strain N102 was most closely related to Alteromonas addita R10SW13 (97.2 %), Alteromonas stellipolaris LMG 21861 (97.1 %), Alteromonas gracilis 9a2 (97.1 %), Salinimonas lutimaris DPSR-4 (96.1 %) and Salinimonas chungwhensis BH030046 (95.4 %). Phylogenetic analyses based on 16S rRNA gene, gyrB gene and whole-genome sequences placed strain N102 within the genus Salinimonas . Genomic comparisons based on average nucleotide identity and tetranucleotide signature frequencies corroborated the results of the phylogenetic analyses. The principal fatty acids were summed feature 3 (C16 : 1 ω7c/C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c/C18 : 1ω6c). The major respiratory quinone was ubiquinone 8. The predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid. The G+C content of the genomic DNA was 48.2 mol%. On the basis of phenotypic, chemotaxonomic and molecular data, we conclude that strain N102 represents a novel species of the genus Salinimonas , for which the name Salinimonas sediminis sp. nov. is proposed (type strain N102=MCCC 1K03497=KCTC 62440).

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2018-10-26
2019-12-11
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References

  1. Jeon CO, Lim JM, Park DJ, Kim CJ. Salinimonas chungwhensis gen. nov., sp. nov., a moderately halophilic bacterium from a solar saltern in Korea. Int J Syst Evol Microbiol 2005;55:239–243 [CrossRef][PubMed]
    [Google Scholar]
  2. Yoon JH, Kang SJ, Lee SY. Salinimonas lutimaris sp. nov., a polysaccharide-degrading bacterium isolated from a tidal flat. Antonie van Leeuwenhoek 2012;101:803–810 [CrossRef][PubMed]
    [Google Scholar]
  3. Cao J, Gayet N, Zeng X, Shao Z, Jebbar M et al. Pseudodesulfovibrio indicus gen. nov., sp. nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of four species of the genus Desulfovibrio. Int J Syst Evol Microbiol 2016;66:3904–3911 [CrossRef][PubMed]
    [Google Scholar]
  4. Lai Q, Cao J, Yuan J, Li F, Shao Z. Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov. Int J Syst Evol Microbiol 2014;64:4160–4167 [CrossRef][PubMed]
    [Google Scholar]
  5. Chin CS, 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]
    [Google Scholar]
  6. Koren S, Schatz MC, Walenz BP, Martin J, Howard JT et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 2012;30:693–700 [CrossRef][PubMed]
    [Google Scholar]
  7. 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 [CrossRef][PubMed]
    [Google Scholar]
  8. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016;32:929–931 [CrossRef][PubMed]
    [Google Scholar]
  9. Zuo G, Hao B. CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genomics Proteomics Bioinformatics 2015;13:321–331 [CrossRef][PubMed]
    [Google Scholar]
  10. 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]
  11. 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]
  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]
    [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  14. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992;9:945–967
    [Google Scholar]
  15. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993;10:1073–1095 [CrossRef][PubMed]
    [Google Scholar]
  16. Venkateswaran K, Moser DP, Dollhopf ME, Lies DP, Saffarini DA et al. Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol 1999;49:705–724 [CrossRef][PubMed]
    [Google Scholar]
  17. Dong X, Cai M. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  18. Kato C, Sato T, Horikoshi K. Isolation and properties of barophilic and barotolerant bacteria from deep-sea mud samples. Biodivers Conserv 1995;4:1–9 [CrossRef]
    [Google Scholar]
  19. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: MIDI; 1990
    [Google Scholar]
  20. Wu YH, Xu L, Zhou P, Wang CS, Oren A et al. Brevirhabdus pacifica gen. nov., sp. nov., isolated from deep-sea sediment in a hydrothermal vent field. Int J Syst Evol Microbiol 2015;65:3645–3651 [CrossRef][PubMed]
    [Google Scholar]
  21. Tindall B, Sikorski J, Smibert R, Krieg N. 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, USA: ASM Press; 2007; pp.330–393
    [Google Scholar]
  22. Ivanova EP, Bowman JP, Lysenko AM, Zhukova NV, Gorshkova NM et al. Alteromonas addita sp. nov. Int J Syst Evol Microbiol 2005;55:1065–1068 [CrossRef][PubMed]
    [Google Scholar]
  23. van Trappen S, Tan TL, Yang J, Mergaert J, Swings J. Alteromonas stellipolaris sp. nov., a novel, budding, prosthecate bacterium from Antarctic seas, and emended description of the genus Alteromonas. Int J Syst Evol Microbiol 2004;54:1157–1163 [CrossRef][PubMed]
    [Google Scholar]
  24. Matsuyama H, Minami H, Sakaki T, Kasahara H, Baba S et al. Alteromonas gracilis sp. nov., a marine polysaccharide-producing bacterium. Int J Syst Evol Microbiol 2015;65:1498–1503 [CrossRef][PubMed]
    [Google Scholar]
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