1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 64, Issue Pt_11

sp. nov., isolated from bank soil Free

Abstract

A Gram-stain-negative, rod-shaped, yellow, non-motile, aerobic bacterium (strain S27) was isolated from bank soil of the Xixi wetland in Zhejiang province, PR China. Phylogenetic analysis, based on its 16S rRNA gene sequence, revealed that strain S27 could represent a novel species of the genus showing highest similarity to WPCB189 (95.45 %), followed by ‘’ TDMA-5 (95.22 %). The temperature, pH and NaCl concentration ranges for growth were 6–37 °C (optimum 28 °C), pH 5.0–9.0 (optimum pH 7.5) and 0–3 % (w/v) [optimum 0.5 % (w/v)], respectively. The DNA G+C content was 36.1 mol%, MK-7 was the only respiratory quinone, and iso-C, iso-C 3-OH and summed feature 3 (Cω7 and/or iso-C 2-OH) were the major fatty acids. These data all support the affiliation of strain S27 to the genus . The polar lipids of strain S27 comprised phosphatidylethanolamine, one unidentified aminophospholipid, four unidentified aminolipids and three unidentified lipids. However, strain S27 could be distinguished from other members of the genus due to its physiological and biochemical characteristics. Therefore, strain S27 represents a novel species of the genus , for which the name sp. nov. is proposed; the type strain is S27 ( = CGMCC 1.12803 = NBRC 110388).

  • Published Online:
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 21077090 and 21137003)
  • 973 Programme (Award 2014CB441103)
© 2014 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.065946-0
2014-11-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/11/3683.html?itemId=/content/journal/ijsem/10.1099/ijs.0.065946-0&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. 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. [View Article] [PubMed]
    [Google Scholar]
  3. 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]
  4. Derichs J., Kämpfer P., Lipski A. ( 2014 ). Pedobacter nutrimenti sp. nov., isolated from chilled food. . Int J Syst Evol Microbiol 64, 1310–1316. [View Article] [PubMed]
    [Google Scholar]
  5. Dong X. Z., Cai M. Y. ( 2001 ). Common Manual of Systematic Bacteriology. Beijing:: Science Press;.
     [Google Scholar]
  6. Fautz E., Reichenbach H. ( 1980 ). A simple test for flexirubin-type pigments. . FEMS Microbiol Lett 8, 87–91. [View Article]
    [Google Scholar]
  7. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368–376. [View Article] [PubMed]
    [Google Scholar]
  8. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783–791. [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. Hoang V.-A., Kim Y.-J., Nguyen N.-L., Min J.-W., Yang D.-C. ( 2013 ). Pedobacter ginsengiterrae sp. nov., isolated from soil of a ginseng field. . Int J Syst Evol Microbiol 63, 1273–1279. [View Article] [PubMed]
    [Google Scholar]
  12. Huang Y. L., Ki J. S., Case R., Qian P. Y. ( 2008 ). Diversity and acyl-homoserine lactone production among subtidal biofilm-forming bacteria. . Aquat Microb Ecol 52, 185–193. [View Article]
    [Google Scholar]
  13. Huo Y. Y., Xu X. W., Cui H. L., Wu M. ( 2010 ). Gracilibacillus ureilyticus sp. nov., a halotolerant bacterium from a saline-alkaline soil. . Int J Syst Evol Microbiol 60, 1383–1386. [View Article] [PubMed]
    [Google Scholar]
  14. 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]
  15. 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]
  16. Jeon Y. S., Lee K., Park S. C., Kim B. S., Cho Y. J., Ha S. M., Chun J. ( 2014 ). EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. . Int J Syst Evol Microbiol 64, 689–691. [View Article] [PubMed]
    [Google Scholar]
  17. 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]
  18. 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]
    [Google Scholar]
  19. 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, 716–721. [View Article] [PubMed]
    [Google Scholar]
  20. Kimura M. ( 1983 ). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  21. Komagata K., Suzuki K. ( 1987 ). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19, 161–207. [View Article]
    [Google Scholar]
  22. Kook M. C., Park Y. J., Yi T. H. ( 2014 ). Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter . . Int J Syst Evol Microbiol 64, 1789–1794. [View Article] [PubMed]
    [Google Scholar]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. Margesin R., Zhang D. C. ( 2013 ). Pedobacter ruber sp. nov., a psychrophilic bacterium isolated from soil. . Int J Syst Evol Microbiol 63, 339–344. [View Article] [PubMed]
    [Google Scholar]
  28. 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]
  29. Mesbah M., Whitman W. B. ( 1989 ). Measurement of deoxyguanosine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine + cytosine of DNA. . J Chromatogr A 479, 297–306. [View Article] [PubMed]
    [Google Scholar]
  30. 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, 233–241. [View Article]
    [Google Scholar]
  31. 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]
  32. Oh H. W., Kim B. C., Park D. S., Jeong W. J., Kim H., Lee K. H., Kim S. U. ( 2013 ). Pedobacter luteus sp. nov., isolated from soil. . Int J Syst Evol Microbiol 63, 1304–1310. [View Article] [PubMed]
    [Google Scholar]
  33. Qiu X., Qu Z. H., Jiang F., Ren L. Z., Chang X. L., Kan W. J., Fang C. X., Peng F. ( 2014 ). Pedobacter huanghensis sp. nov. and Pedobacter glacialis sp. nov., isolated from Arctic glacier foreland. . Int J Syst Evol Microbiol 64, 2431–2436. [CrossRef]
    [Google Scholar]
  34. 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]
  35. 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]
  36. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE:: MIDI Inc;.
     [Google Scholar]
  37. 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]
  38. 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]
  39. 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. [View Article] [PubMed]
    [Google Scholar]
  40. 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]
  41. Thompson J. D., Higgins D. G., Gibson T. J. ( 1994 ). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. . Nucleic Acids Res 22, 4673–4680. [View Article] [PubMed]
    [Google Scholar]
  42. Urios L., Intertaglia L., Magot M. ( 2013 ). Pedobacter tournemirensis sp. nov., isolated from a fault water sample of a deep Toarcian argillite layer. . Int J Syst Evol Microbiol 63, 303–308. [View Article] [PubMed]
    [Google Scholar]
  43. 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]
  44. Yang J.-E., Son H.-M., Lee J. M., Shin H.-S., Park S.-Y., Lee D.-G., Kook M. C., Yi T.-H. ( 2013 ). Pedobacter ginsenosidimutans sp. nov., with ginsenoside-converting activity. . Int J Syst Evol Microbiol 63, 4396–4401. [View Article] [PubMed]
    [Google Scholar]
  45. 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]
  46. 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]
  47. 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]
  48. 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]
  49. 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]
  50. Zhang D.-C., Schinner F., Margesin R. ( 2010 ). Pedobacter bauzanensis sp. nov., isolated from soil. . Int J Syst Evol Microbiol 60, 2592–2595. [View Article] [PubMed]
    [Google Scholar]
  51. 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. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.065946-0
Loading
Pedobacter xixiisoli sp. nov., isolated from bank soil
Int J Syst Evol Microbiol 64, 3683 (2014); https://doi.org/10.1099/ijs.0.065946-0
/content/journal/ijsem/10.1099/ijs.0.065946-0
/content/journal/ijsem/10.1099/ijs.0.065946-0
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