sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment Free

Abstract

A Gram-staining-negative, yellow-pigmented, aerobic, rod-shaped and non-motile bacterium, PAMC 27130, was isolated from the marine sediment of the Ross Sea, Antarctica. The temperature, pH and NaCl tolerance ranges for growth were 4–20 °C, pH 6.0–9.0 and 0.5–5.0 % (w/v) NaCl, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PAMC 27130 belonged to the genus and was closely related to and with 97.2, 94.7 and 94.2 % sequence similarities, respectively. Genomic relatedness analyses based on average nucleotide identity and genome-to-genome distance showed that strain PAMC 27130 could be clearly distinguished from other species of the genus . The genomic DNA G+C content was 32.7 mol%. The major fatty acids (>10 %) were Cω6 (13.2 %), iso-C (12.3 %), iso-C G (11.7 %) and iso-C 3-OH (10.0 %). The major respiratory isoprenoid quinone was menaquinone-6 (MK-6) and the polar lipids were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid, an unidentified aminophospholipid and three unidentified lipids. On the basis of genotypic and phenotypic data collected in this study, it is proposed that strain PAMC 27130 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is PAMC 27130 ( = KCTC 42128 = JCM 30228).

Funding
This study was supported by the:
  • Korea Polar Research Institute (Award PM11030 and PE14080)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.069740-0
2015-01-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/1/183.html?itemId=/content/journal/ijsem/10.1099/ijs.0.069740-0&mimeType=html&fmt=ahah

References

  1. Auch A. F., von Jan M., Klenk H.-P., Göker M. ( 2010 ). Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. . Stand Genomic Sci 2, 117134. [View Article] [PubMed]
    [Google Scholar]
  2. Bernardet J.-F., Nakagawa Y. ( 2006 ). An introduction to the family Flavobacteriaceae . . In The Prokaryotes: a Handbook on the Biology of Bacteria, , 3rd edn., vol. 7, pp. 455480. Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K. H., Stackebrandt E. . New York:: Springer;. [View Article]
    [Google Scholar]
  3. 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 ( 2002 ). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. . Int J Syst Evol Microbiol 52, 10491070. [View Article] [PubMed]
    [Google Scholar]
  4. Bowman J. P., McCammon S. A., Brown J. L., Nichols P. D., McMeekin T. A. ( 1997 ). Psychroserpens burtonensis gen. nov., sp. nov., and Gelidibacter algens gen. nov., sp. nov., psychrophilic bacteria isolated from antarctic lacustrine and sea ice habitats. . Int J Syst Bacteriol 47, 670677. [View Article] [PubMed]
    [Google Scholar]
  5. Cho J.-C., Giovannoni S. J. ( 2004 ). Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria . . Appl Environ Microbiol 70, 432440. [View Article] [PubMed]
    [Google Scholar]
  6. Choo Y.-J., Lee K., Song J., Cho J.-C. ( 2007 ). Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum ‘Verrucomicrobia’. . Int J Syst Evol Microbiol 57, 532537. [View Article] [PubMed]
    [Google Scholar]
  7. Cole J. R., Wang Q., Fish J. A., Chai B., McGarrell D. M., Sun Y., Brown C. T., Porras-Alfaro A., Kuske C. R., Tiedje J. M. ( 2014 ). Ribosomal Database Project: data and tools for high throughput rRNA analysis. . Nucleic Acids Res 42 (D1), D633D642. [View Article] [PubMed]
    [Google Scholar]
  8. Collins M. ( 1985 ). Analysis of isoprenoid quinones. . Methods Microbiol 18, 329366. [View Article]
    [Google Scholar]
  9. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  10. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [View Article]
    [Google Scholar]
  11. Gordon R. E., Barnett D. A., Handerhan J. E., Pang C. H.-N. ( 1974 ). Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. . Int J Syst Bacteriol 24, 5463. [View Article]
    [Google Scholar]
  12. Goris J., Konstantinidis K. T., Klappenbach J. A., Coenye T., Vandamme P., Tiedje J. M. ( 2007 ). DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. . Int J Syst Evol Microbiol 57, 8191. [View Article] [PubMed]
    [Google Scholar]
  13. Jukes T. H., Cantor C. R. ( 1969 ). Evolution of protein molecules. . In Mammalian Protein Metabolism, pp. 21132. Edited by Munro H. N. . New York:: Academic Press;. [View Article]
    [Google Scholar]
  14. Kim O. S., Cho Y.-J., Lee K., Yoon S.-H., Kim M., Na H., Park S.-C., Jeon Y. S., Lee J.-H. & other authors ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [View Article] [PubMed]
    [Google Scholar]
  15. Kwon K. K., Lee S. J., Park J. H., Ahn T.-Y., Lee H. K. ( 2006 ). Psychroserpens mesophilus sp. nov., a mesophilic marine bacterium belonging to the family Flavobacteriaceae isolated from a young biofilm. . Int J Syst Evol Microbiol 56, 10551058. [View Article] [PubMed]
    [Google Scholar]
  16. Lee Y. M., Kim G., Jung Y.-J., Choe C.-D., Yim J. H., Lee H. K., Hong S. G. ( 2012 ). Polar and Alpine Microbial Collection (PAMC): a culture collection dedicated to polar and alpine microorganisms. . Polar Biol 35, 14331438. [View Article]
    [Google Scholar]
  17. Lee D.-H., Cho S. J., Kim S. M., Lee S. B. ( 2013 ). Psychroserpens damuponensis sp. nov., isolated from seawater. . Int J Syst Evol Microbiol 63, 703708. [View Article] [PubMed]
    [Google Scholar]
  18. Lee Y. M., Jung Y.-J., Hong S. G., Kim J., Lee H. K. ( 2014 ). Diversity and physiological characteristics of culturable bacteria from marine sediments of Ross Sea, Antarctica. . Kor J Microbiol 50, 119127. [View Article]
    [Google Scholar]
  19. Minnikin D. E., O’Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. ( 1984 ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2, 233241. [View Article]
    [Google Scholar]
  20. Richter M., Rosselló-Móra R. ( 2009 ). Shifting the genomic gold standard for the prokaryotic species definition. . Proc Natl Acad Sci U S A 106, 1912619131. [View Article] [PubMed]
    [Google Scholar]
  21. Rosselló-Mora R., Amann R. ( 2001 ). The species concept for prokaryotes. . FEMS Microbiol Rev 25, 3967. [View Article] [PubMed]
    [Google Scholar]
  22. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  23. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characteristics. . In Methods for General and Molecular Biology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  24. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013 ). mega6: molecular evolutionary genetics analysis version 6.0. . Mol Biol Evol 30, 27252729. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.069740-0
Loading
/content/journal/ijsem/10.1099/ijs.0.069740-0
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF

Most cited Most Cited RSS feed