1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 63, Issue Pt_4

sp. nov., isolated from soil Free

Abstract

Two strains of Gram-staining-negative, rod-shaped bacteria that were motile by gliding, N7d-4 and B4a-b5, were isolated during a study of culturable bacteria in soil cultivated with potatoes. These isolates grew at 15–37 °C and at pH 6.5–7.0. The major cellular fatty acids were summed feature 3 (iso-C 2-OH and/or Cω7), anteiso-C, iso-C, iso-C 3-OH and iso-Cω9. The major polar lipids were phosphatidyl--methylethanolamine and phosphatidylethanolamine. The strains contained d-18 : 0 and d-19 : 0 sphingosines. The DNA G+C contents of strains N7d-4 and B4a-b5 were 48.5 and 46.9 mol% (HPLC), respectively. A phylogenetic analysis based on 16S rRNA gene sequences showed that strains N7d-4 and B4a-b5 were affiliated with species in the family . Strains N7d-4 and B4a-b5 shared 99.9 % sequence similarity, and the most closely related type strains were TR6-06 (96.5 and 96.7 % sequence similarity, respectively), N7 (95.4 and 95.6 %) and LMG 22862 (94.0 and 94.4 %). Phenotypic data and phylogenetic inference clearly distinguished the two isolates from other species. Based on these data, the isolates are considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is N7d-4 ( = KCTC 22699  = DSM 22385).

  • Published Online:
Funding
This study was supported by the:
  • KRIBB research initiative program (Award KBM4111022)
  • National Research Foundation of Korea (NRF) (Award 2007-2001776)
© 2013 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.033134-0
2013-04-01
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/4/1304.html?itemId=/content/journal/ijsem/10.1099/ijs.0.033134-0&mimeType=html&fmt=ahah

References

  1. Altenburger P., Kämpfer P., Makristathis A., Lubitz W., Busse H.-J. ( 1996 ). Classification of bacteria isolated from a medieval wall painting. . J Biotechnol 47, 39–52. [View Article]
    [Google Scholar]
  2. 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]
  3. Atlas R. M. ( 1993 ). Handbook of Microbiological Media. Edited by Parks L. C. . Boca Raton, FL:: CRC Press;.
     [Google Scholar]
  4. 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]
  5. Bernardet J. F., Nakagawa Y., Holmes B. ( 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]
  6. 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]
  7. Collins M. D., Jones D. ( 1981 ). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. . Microbiol Rev 45, 316–354.[PubMed]
    [Google Scholar]
  8. Ezaki T., Hashimoto Y., Takeuchi N., Yamamoto H., Liu S. L., Miura H., Matsui K., Yabuuchi E. ( 1988 ). Simple genetic method to identify viridans group streptococci by colorimetric dot hybridization and fluorometric hybridization in microdilution wells. . J Clin Microbiol 26, 1708–1713.[PubMed]
    [Google Scholar]
  9. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783–791. [View Article]
    [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. [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. Komagata K., Suzuki K. ( 1987 ). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19, 161–207. [View Article]
    [Google Scholar]
  15. 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]
  16. 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 the rhizosphere soil of Chinese cabbage (Brassica campestris). . Int J Syst Evol Microbiol 61, 2874–2879. [View Article] [PubMed]
    [Google Scholar]
  17. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by Stackebrandt E., Goodfellow M. . New York:: Wiley;.
     [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. [View Article] [PubMed]
    [Google Scholar]
  19. Maidak B. L., Cole J. R., Lilburn T. G., Parker C. T. Jr, Saxman P. R., Farris R. J., Garrity G. M., Olsen G. J., Schmidt T. M., Tiedje J. M. ( 2001 ). The RDP-II (Ribosomal Database Project). . Nucleic Acids Res 29, 173–174. [View Article] [PubMed]
    [Google Scholar]
  20. Margesin R., Shivaji S. ( 2011 ). Genus II. Pedobacter Steyn, Segers, Vancanneyt, Sandra, Kersters and Joubert 1998, 171VP . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 4, pp. 339–347. Edited by Krieg N. R., Staley J. T., Brown D. R., Hedlund B. P., Paster B. J., Ward N. L., Ludwig W., Whitman W. B. . New York:: Springer;.
     [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. 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]
  24. Nohynek L. J., Nurmiaho-Lassila E. L., Suhonen E. L., Busse H.-J., Mohammadi M., Hantula J., Rainey F., Salkinoja-Salonen M. S. ( 1996 ). Description of chlorophenol-degrading Pseudomonas sp. strains KF1T, KF3, and NKF1 as a new species of the genus Sphingomonas, Sphingomonas subarctica sp. nov.. Int J Syst Bacteriol 46, 1042–1055. [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. et al. ( 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. Sambrook J., Russell D. W. ( 2001 ). Molecular Cloning: a Laboratory Manual, , 3rd edn.. New York:: Cold Spring Harbor Laboratory;.
     [Google Scholar]
  28. Sasser, M. (2001). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  29. 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. [View Article] [PubMed]
    [Google Scholar]
  30. Stackebrandt E., Goebel B. M. ( 1994 ). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44, 846–849. [View Article]
    [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. 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]
  33. Ten L. N., Im W. T., Kim M. K., Kang M. S., Lee S. T. ( 2004 ). Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. . J Microbiol Methods 56, 375–382. [View Article] [PubMed]
    [Google Scholar]
  34. Ten L. N., Baek S. H., Im W. T., Lee M., Oh H. W., Lee S. T. ( 2006 ). Paenibacillus panacisoli sp. nov., a xylanolytic bacterium isolated from soil in a ginseng field in South Korea. . Int J Syst Evol Microbiol 56, 2677–2681. [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. Yoon J. H., Kang S. J., Park S., Oh T. K. ( 2007a ). 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]
  39. Yoon J. H., Kang S. J., Oh T. K. ( 2007b ). Pedobacter terrae sp. nov., isolated from soil. . Int J Syst Evol Microbiol 57, 2462–2466. [View Article] [PubMed]
    [Google Scholar]
  40. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.033134-0
Loading
Pedobacter luteus sp. nov., isolated from soil
Int J Syst Evol Microbiol 63, 1304 (2013); https://doi.org/10.1099/ijs.0.033134-0
/content/journal/ijsem/10.1099/ijs.0.033134-0
/content/journal/ijsem/10.1099/ijs.0.033134-0
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