1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 62, Issue Pt_8

sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus , , , , and Free

Abstract

A Gram-stain-negative, short rod-shaped, motile (by gliding) bacterial strain, designated A12, was isolated from tundra soil collected from Ny-Ålesund, in the Arctic region of Norway. The temperature, NaCl and pH ranges for growth were 4–25 °C (optimum, 18 °C), 0–2 % (optimum, 0 %) and pH 6–9 (optimum, pH 7). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the Arctic isolate belonged to the genus and showed highest sequence similarity (94.4 %) to KCTC 12637. The DNA G+C content (38.3 mol%), polar lipid profile, presence of sphingolipid, MK-7 as the only respiratory quinone, and summed feature 3 (comprising Cω7 and/or Cω6), iso-C and iso-C 3-OH as major fatty acids supported the allocation of strain A12 to the genus as a representative of a novel species, for which the name sp. nov. is proposed. The type strain is A12 ( = CCTCC AB 2010223 = NRRL B-59457). Emended descriptions of the genus and of , , , and are also given.

  • Published Online:
Funding
This study was supported by the:
  • National Basic Research Program of China (Award 2011CB808800)
  • R&D Infrastructure and Facility Development Program from the Ministry of Science and Technology of the People’s Republic of China and the State Oceanic Administration, PR China (Award 10/11YR06)
© 2012 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.031104-0
2012-08-01
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/62/8/1963.html?itemId=/content/journal/ijsem/10.1099/ijs.0.031104-0&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 [View Article][PubMed]
     [Google Scholar]
  2. Baik K. S., Park Y.-D., Kim M. S., Park S. C., Moon E. Y., Rhee M. S., Choi J. H., Seong C. N. 2007; Pedobacter koreensis sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 57:2079–2083 [View Article][PubMed]
     [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 52:1049–1070 [View Article][PubMed]
     [Google Scholar]
  4. Böhmer L. H., Pitout M. J., Steyn P. L., Visser L. 1990; Purification and characterization of a novel heparinase. J Biol Chem 265:13609–13617[PubMed]
     [Google Scholar]
  5. Chun J., Lee J.-H., Jung Y., Kim M., Kim S., Kim B. K., Lim Y. W. 2007; EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259–2261 [View Article][PubMed]
     [Google Scholar]
  6. 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 [View Article][PubMed]
     [Google Scholar]
  7. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
     [Google Scholar]
  8. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [View Article]
     [Google Scholar]
  9. 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 [View Article][PubMed]
     [Google Scholar]
  10. 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 [View Article][PubMed]
     [Google Scholar]
  11. 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 [View Article][PubMed]
     [Google Scholar]
  12. Jeon Y., Kim J. M., Park J. H., Lee S. H., Seong C.-N., Lee S.-S., Jeon C. O. 2009; Pedobacter oryzae sp. nov., isolated from rice paddy soil. Int J Syst Evol Microbiol 59:2491–2495 [View Article][PubMed]
     [Google Scholar]
  13. Jung Y.-T., Lee S.-Y., Choi W.-C., Oh T.-K., Yoon J.-H. 2012; Pedobacter boryungensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 62:13–17 [View Article][PubMed]
     [Google Scholar]
  14. Kato M., Muto Y., Tanaka-Bandoh K., Watanabe K., Ueno K. 1995; Sphingolipid composition in Bacteroides species. Anaerobe 1:135–139 [View Article][PubMed]
     [Google Scholar]
  15. Payza A. N., Korn E. D. 1956; The degradation of heparin by bacterial enzymes. I. Adaptation and lyophilized cells. J Biol Chem 223:853–858[PubMed]
     [Google Scholar]
  16. Kumar S., Tamura K., Nei M. 2004; mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163 [View Article][PubMed]
     [Google Scholar]
  17. 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 [View Article][PubMed]
     [Google Scholar]
  18. 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 [View Article][PubMed]
     [Google Scholar]
  19. 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 [View Article][PubMed]
     [Google Scholar]
  20. 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 [View Article][PubMed]
     [Google Scholar]
  21. 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 [View Article][PubMed]
     [Google Scholar]
  22. 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 [View Article]
     [Google Scholar]
  23. Morita R. Y. 1975; Psychrophilic bacteria. Bacteriol Rev 39:144–167[PubMed]
     [Google Scholar]
  24. Muurholm S., Cousin S., Päuker O., Brambilla E., Stackebrandt E. 2007; Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet. Int J Syst Evol Microbiol 57:2221–2227 [View Article][PubMed]
     [Google Scholar]
  25. 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 [View Article][PubMed]
     [Google Scholar]
  26. 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]
  27. Sasser M. 1990; Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.;
  28. Shivaji S., Chaturvedi P., Reddy G. S. N., 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 [View Article][PubMed]
     [Google Scholar]
  29. Skerman V. B. D. 1967 A Guide to the Identification of the Genera of Bacteria, 2nd edn. Baltimore: Williams & Wilkins;
     [Google Scholar]
  30. 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]
  31. 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 [View Article][PubMed]
     [Google Scholar]
  32. Takeuchi M., Yokota A. 1992; Proposals of Sphingobacterium faecium sp. nov., Sphingobacterium piscium sp. nov., Sphingobacterium heparinum comb. nov., Sphingobacterium thalpophilum com. nov. and two genospecies of the genus Sphingobacterium, and synonymy of Flavobacterium yabuuchiae and Sphingobacterium spiritivorum . J Gen Appl Microbiol 38:465–482 [View Article]
     [Google Scholar]
  33. 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]
     [Google Scholar]
  34. Ten L. N., Liu Q.-M., Im W.-T., Lee M., Yang D.-C., Lee S.-T. 2006; Pedobacter ginsengisoli sp. nov., a DNase-producing bacterium isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 56:2565–2570 [View Article][PubMed]
     [Google Scholar]
  35. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [View Article][PubMed]
     [Google Scholar]
  36. Tindall B. J. 1990; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66:199–202 [View Article]
     [Google Scholar]
  37. 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 [View Article][PubMed]
     [Google Scholar]
  38. 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 [View Article][PubMed]
     [Google Scholar]
  39. Yoon J.-H., Lee M.-H., Kang S.-J., Park S.-Y., Oh T.-K. 2006; Pedobacter sandarakinus sp. nov., isolated from soil. Int J Syst Evol Microbiol 56:1273–1277 [View Article][PubMed]
     [Google Scholar]
  40. Yoon M.-H., Ten L. N., Im W. T., Lee S. T. 2007a; Pedobacter panaciterrae sp. nov., isolated from soil in South Korea. Int J Syst Evol Microbiol 57:381–386 [View Article][PubMed]
     [Google Scholar]
  41. Yoon J.-H., Kang S.-J., Oh H. W., Oh T.-K. 2007b; Pedobacter insulae sp. nov., isolated from soil. Int J Syst Evol Microbiol 57:1999–2003 [View Article][PubMed]
     [Google Scholar]
  42. Yoon J.-H., Kang S.-J., Park S., Oh T.-K. 2007c; Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov., isolated from soil. Int J Syst Evol Microbiol 57:2089–2095 [View Article][PubMed]
     [Google Scholar]
  43. Yoon J.-H., Kang S.-J., Oh T.-K. 2007d; Pedobacter terrae sp. nov., isolated from soil. Int J Syst Evol Microbiol 57:2462–2466 [View Article][PubMed]
     [Google Scholar]
  44. 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/ijs.0.031104-0
Loading
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 (2012); https://doi.org/10.1099/ijs.0.031104-0
/content/journal/ijsem/10.1099/ijs.0.031104-0
/content/journal/ijsem/10.1099/ijs.0.031104-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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