sp. nov., isolated from Antarctic intertidal sediment Free

Abstract

A Gram-reaction-negative, aerobic, flagellated and coccoid-shaped bacterial strain, designated SM1702, was isolated from Antarctic intertidal sediment collected off Ardely Island, West Antarctica. The strain grew at 0–30 °C and with 0.5–5.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences and single-copy orthologous clusters both showed that strain SM1702, together with , occupied an independent phylogenetic branch, sharing the highest 16S rRNA gene sequence similarity with type strain of the latter (95.6 %). The major fatty acids were summed feature 3 (C 7 and/or C 6), summed feature 8 (C 7 and/or C 6), C, and summed feature 2 (C 3-OH and/or iso-C I). Polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA G+C content of strain SM1702 was 27.1 mol%. Based on the results of the polyphasic characterisation for strain SM1702, it is identified as the representative of a novel species of , for which the name sp. nov. is proposed. The type strain of is SM1702 (=MCCC 1K03471=KCTC 62796).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003539
2019-09-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/9/2717.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003539&mimeType=html&fmt=ahah

References

  1. Vandamme P, de Ley J, Ley D. Proposal for a new family, Campylobacteraceae . Int J Syst Bacteriol 1991; 41:451–455 [View Article]
    [Google Scholar]
  2. Pérez-Cataluña A, Salas-Massó N, Diéguez AL, Balboa S, Lema A et al. Revisiting the taxonomy of the Genus Arcobacter: getting order from the chaos. Front Microbiol 2018; 9:9 [View Article][PubMed]
    [Google Scholar]
  3. Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2019; 69:5–9 [View Article]
    [Google Scholar]
  4. Lane DJ. 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics 1991 pp. 115–175
    [Google Scholar]
  5. 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]
  6. 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]
  7. 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]
  8. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  9. 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]
  10. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  11. 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 [View Article][PubMed]
    [Google Scholar]
  12. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673–679 [View Article][PubMed]
    [Google Scholar]
  13. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article][PubMed]
    [Google Scholar]
  14. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article][PubMed]
    [Google Scholar]
  15. 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]
  16. 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]
  17. Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF et al. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics 2011; 12:124 [View Article][PubMed]
    [Google Scholar]
  18. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  19. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992; 8:275–282 [View Article][PubMed]
    [Google Scholar]
  20. Diéguez AL, Balboa S, Magnesen T, Romalde JL. Arcobacter lekithochrous sp. nov., isolated from a molluscan hatchery. Int J Syst Evol Microbiol 2017; 67:1327–1332 [View Article][PubMed]
    [Google Scholar]
  21. Komagata K, Suzuki K. Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  22. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
    [Google Scholar]
  23. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) In Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 607–654
    [Google Scholar]
  24. Murray RGE, Doetsch RN, Robinow CF. Determinative and cytological light microscopy. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) In Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 21–41
    [Google Scholar]
  25. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria London: Cambridge University Press; 1965
    [Google Scholar]
  26. Baumann P, Baumann L. The marine Gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas and Alcaligenes . In Starr MP, Stolp H, Trüper HG, Balows A, Schleger H et al. (editors) The Prokaryotes vol 2 Heidelberg: Springer; 1981 pp. 1302–1331
    [Google Scholar]
  27. Levican A, Collado L, Aguilar C, Yustes C, Diéguez AL et al. Arcobacter bivalviorum sp. nov. and Arcobacter venerupis sp. nov., new species isolated from shellfish. Syst Appl Microbiol 2012; 35:133–138 [View Article][PubMed]
    [Google Scholar]
  28. Figueras MJ, Collado L, Levican A, Perez J, Solsona MJ et al. Arcobacter molluscorum sp. nov., a new species isolated from shellfish. Syst Appl Microbiol 2011; 34:105–109 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003539
Loading
/content/journal/ijsem/10.1099/ijsem.0.003539
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed