1887

Abstract

A red-pigmented, non-motile, Gram-stain-negative, rod-shaped bacterium, strain R2-28, was isolated from a soil sample collected from Ardley Island, South Shetland Islands, Antarctica, and was characterized taxonomically by using a polyphasic approach. The organism grew optimally at 18 °C in TSB. On the basis of phylogenetic analyses of the 16S rRNA gene sequence, strain R2-28 was most closely related to the genus of the family . The highest levels of 16S rRNA gene sequence similarity were found with respect to NWER-II11 (95.6 %) and DS-57 (95.2 %). The DNA G+C content was 39.9 mol%, and MK-7 was the only respiratory quinone. The major polar lipids were phosphatidylethanolamine and a sphingolipid. The predominant cellular fatty acids were iso-C, anteiso-C, iso-C 3-OH and summed feature 3 (comprising Cω7 and/or Cω6). These chemotaxonomic and phylogenetic data supported the allocation of strain R2-28 to the genus . Additionally, the results of physiological and biochemical tests allowed phenotypic differentiation of strain R2-28 from species of the genus with validly published names. Therefore, strain R2-28 represents a novel species within the genus , for which the name sp. nov. is proposed. The type strain is R2-28 ( = CCTCC AB 2013365 = LMG 28255).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000504
2015-11-01
2019-10-15
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/11/3841.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000504&mimeType=html&fmt=ahah

References

  1. An D. S. , Kim S. G. , Ten L. N. , Cho C. H. . ( 2009;). Pedobacter daechungensis sp. nov., from freshwater lake sediment in South Korea. Int J Syst Evol Microbiol 59: 69–72 [CrossRef] [PubMed].
    [Google Scholar]
  2. Asker D. , Beppu T. , Ueda K. . ( 2008;). Nubsella zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Sphingobacteriaceae isolated from freshwater. Int J Syst Evol Microbiol 58: 601–606 [CrossRef] [PubMed].
    [Google Scholar]
  3. Bauer A. W. , Kirby W. M. M. , Sherris J. C. , Turck M. . ( 1966;). Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45: 493–496 [PubMed].
    [Google Scholar]
  4. Bernardet J. F. , Nakagawa Y. , Holmes B. . ( 2002;). Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52: 1049–1070 [CrossRef] [PubMed].
    [Google Scholar]
  5. Bowman J. P. . ( 2000;). 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 50: 1861–1868 [PubMed].[CrossRef]
    [Google Scholar]
  6. Doetsch R. N. . ( 1981;). Determinative methods of light microscopy. . In Manual of Methods for General Bacteriology, pp. 21–33. Edited by Gerhardt P. , Murray R. G. E. , Costilow R. N. , Nester E. W. , Wood W. A. , Krieg N. R. , Phillips G. H. . Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  7. Dorsch M. , Lane D. , Stackebrandt E. . ( 1992;). Towards a phylogeny of the genus Vibrio based on 16S rRNA sequences. Int J Syst Bacteriol 42: 58–63 [CrossRef] [PubMed].
    [Google Scholar]
  8. Felsenstein J. . ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791 [CrossRef].
    [Google Scholar]
  9. Fitch W. M. . ( 1971;). Towards defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20: 406–416 [CrossRef].
    [Google Scholar]
  10. Gallego V. , García M. T. , Ventosa A. . ( 2006;). Pedobacter aquatilis sp. nov., isolated from drinking water, and emended description of the genus Pedobacter . Int J Syst Evol Microbiol 56: 1853–1858 [CrossRef] [PubMed].
    [Google Scholar]
  11. Gordon N. S. , Valenzuela A. , Adams S. M. , Ramsey P. W. , Pollock J. L. , Holben W. E. , Gannon J. E. . ( 2009;). Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil. Int J Syst Evol Microbiol 59: 1720–1726 [CrossRef] [PubMed].
    [Google Scholar]
  12. Hwang C. Y. , Choi D. H. , Cho B. C. . ( 2006;). Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter . Int J Syst Evol Microbiol 56: 1831–1836 [CrossRef] [PubMed].
    [Google Scholar]
  13. Kato M. , Muto Y. , Tanaka-Bandoh K. , Watanabe K. , Ueno K. . ( 1995;). Sphingolipid composition in Bacteroides species. Anaerobe 1: 135–139 [CrossRef] [PubMed].
    [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. . ( 2012;). & other authors Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62: 716–721 [CrossRef] [PubMed].
    [Google Scholar]
  15. Kim D. U. , Kim Y. J. , Shin D. H. , Weon H. Y. , Kwon S. W. , Seong C. N. , Ka J. O. . ( 2013;). Pedobacter namyangjuensis sp. nov. isolated from soil and reclassification of Nubsella zeaxanthinifaciens Asker et al. 2008 as Pedobacter zeaxanthinifaciens comb. nov.. J Microbiol 51: 25–30 [CrossRef] [PubMed].
    [Google Scholar]
  16. Kwon S. W. , Kim B. Y. , Lee K. H. , Jang K. Y. , Seok S. J. , Kwon J. S. , Kim W. G. , Weon H. Y. . ( 2007;). Pedobacter suwonensis sp. nov., isolated from the rhizosphere of Chinese cabbage (Brassica campestris). Int J Syst Evol Microbiol 57: 480–484 [CrossRef] [PubMed].
    [Google Scholar]
  17. Kwon S. W. , Son J. A. , Kim S. J. , Kim Y. S. , Park I. C. , Bok J. I. , Weon H. Y. . ( 2011;). Pedobacter rhizosphaerae sp. nov. and Pedobacter soli sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris). Int J Syst Evol Microbiol 61: 2874–2879 [CrossRef] [PubMed].
    [Google Scholar]
  18. Lee H. G. , Kim S. G. , Im W. T. , Oh H. M. , Lee S. T. . ( 2009;). Pedobacter composti sp. nov., isolated from compost. Int J Syst Evol Microbiol 59: 345–349 [CrossRef] [PubMed].
    [Google Scholar]
  19. Luo X. , Wang Z. , Dai J. , Zhang L. , Li J. , Tang Y. , Wang Y. , Fang C. . ( 2010;). Pedobacter glucosidilyticus sp. nov., isolated from dry riverbed soil. Int J Syst Evol Microbiol 60: 229–233 [CrossRef] [PubMed].
    [Google Scholar]
  20. Margesin R. , Shivaji S. . ( 2011;). Pedobacter Steyn, Segers, Vancanneyt, Sandra, Kersters and Joubert 1998, 171VP . . In Bergey's Manual of Systematic Bacteriology, pp. 339–351. Edited by Krieg N. R. , Ludwig W. , Whitman W. , Hedlund B. P. , Paster B. J. , Staley J. T. , Ward N. , Brown D. , Parte A. . 4 , 2nd edn.., New York: Springer;.
    [Google Scholar]
  21. Margesin R. , Zhang D. C. . ( 2013;). Pedobacter ruber sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 63: 339–344 [CrossRef] [PubMed].
    [Google Scholar]
  22. Margesin R. , Spröer C. , Schumann P. , Schinner F. . ( 2003;). Pedobacter cryoconitis sp. nov., a facultative psychrophile from alpine glacier cryoconite. Int J Syst Evol Microbiol 53: 1291–1296 [CrossRef] [PubMed].
    [Google Scholar]
  23. Mesbah M. , Premachandran U. , Whitman W. B. . ( 1989;). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39: 159–167 [CrossRef].
    [Google Scholar]
  24. Roh S. W. , Quan Z. X. , Nam Y. D. , Chang H. W. , Kim K. H. , Kim M. K. , Im W. T. , Jin L. , Kim S. H. , other authors . ( 2008;). Pedobacter agri sp. nov., from soil. Int J Syst Evol Microbiol 58: 1640–1643 [CrossRef] [PubMed].
    [Google Scholar]
  25. Saitou N. , Nei M. . ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425 [PubMed].
    [Google Scholar]
  26. Sambrook J. , Fritsch E. F. , Maniatis T. . ( 1989;). Molecular Cloning: a Laboratory Manual , 2nd edn.., Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;.
    [Google Scholar]
  27. Sasser M. . ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical note 101 Newark, DE: MIDI Inc;.
    [Google Scholar]
  28. Shivaji S. , Chaturvedi P. , Reddy G. S. , Suresh K. . ( 2005;). Pedobacter himalayensis sp. nov., from the Hamta glacier located in the Himalayan mountain ranges of India. Int J Syst Evol Microbiol 55: 1083–1088 [CrossRef] [PubMed].
    [Google Scholar]
  29. Smibert R. M. , Krieg N. R. . ( 1994;). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by Gerhardt P. , Murray R. G. E. , Woods W. A. , Krieg N. R. . Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  30. Steyn P. L. , Segers P. , Vancanneyt M. , Sandra P. , Kersters K. , Joubert J. J. . ( 1998;). Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. Proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 48: 165–177 [CrossRef] [PubMed].
    [Google Scholar]
  31. Tamura K. , Peterson D. , Peterson N. , Stecher G. , Nei M. , Kumar S. . ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731–2739 [CrossRef] [PubMed].
    [Google Scholar]
  32. Tang Y. , Wang Y. , Ji S. , Zhang K. , Dai J. , Zhang L. , Peng F. , Fang C. . ( 2010;). Pedobacter xinjiangensis sp. nov., from desert, Xinjiang. J Microbiol Biotechnol 20: 397–402 [PubMed].[CrossRef]
    [Google Scholar]
  33. Tindall B. J. . ( 1990;). Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66: 199–202 [CrossRef].
    [Google Scholar]
  34. Vanparys B. , Heylen K. , Lebbe L. , De Vos P. . ( 2005;). Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum. Int J Syst Evol Microbiol 55: 1315–1318 [CrossRef] [PubMed].
    [Google Scholar]
  35. Xie C. H. , Yokota A. . ( 2003;). Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 49: 345–349 [CrossRef] [PubMed].
    [Google Scholar]
  36. Zhou Z. , Jiang F. , Wang S. , Peng F. , Dai J. , Li W. , Fang C. . ( 2012;). Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus . Int J Syst Evol Microbiol 62: 1963–1969 [CrossRef] [PubMed].
    [Google Scholar]
  37. Zimmermann J. J. , Langer R. , Cooney C. L. . ( 1990;). Specific plate assay for bacterial heparinase. Appl Environ Microbiol 56: 3593–3594 [PubMed].
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000504
Loading
/content/journal/ijsem/10.1099/ijsem.0.000504
Loading

Data & Media loading...

Supplementary Data



PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error