1887

Abstract

A Gram-negative bacterium, designated TF5-37.2-LB10, was isolated from subsurface water of the Toarcian geological layer of Tournemire, France. Cells were non-motile straight rods that formed cream to light pink colonies on 10-fold diluted LB agar. Strain TF5-37.2-LB10 contained menaquinone 7 and its major fatty acids were iso-C, summed feature 3 (iso-C 2-OH and/or Cω7), iso-C 3-OH and iso-Cω9. The G+C content of the genomic DNA was 46 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain TF5-37.2-LB10 within the genus , family . TR6-06 and DSM 19973 were the closest phylogenetic relatives (93.5 and 93.3 % 16S rRNA gene sequence similarity, respectively). On the basis of 16S rRNA gene sequence comparison and physiological and biochemical characteristics, strain TF5-37.2-LB10 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is TF5-37.2-LB10 ( = DSM 23085 = CIP 110085 = MOLA 820).

Funding
This study was supported by the:
  • , French Institute of Radioprotection and Nuclear Safety (IRSN)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.038968-0
2013-01-01
2020-10-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/1/303.html?itemId=/content/journal/ijsem/10.1099/ijs.0.038968-0&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. ( 1997 ). Gapped blast and psi-blast: a new generation of protein database search programs. . Nucleic Acids Res 25, 33893402. [CrossRef] [PubMed]
    [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, 6972. [CrossRef] [PubMed]
    [Google Scholar]
  3. Basso O., Lascourrèges J. F., Jarry M., Magot M. ( 2005 ). The effect of cleaning and disinfecting the sampling well on the microbial communities of deep subsurface water samples. . Environ Microbiol 7, 1321. [CrossRef] [PubMed]
    [Google Scholar]
  4. Beaucaire C., Michelot J.-L., Savoye S., Cabrera J. ( 2008 ). Groundwater characterisation and modelling of water–rock interaction in an argillaceous formation (Tournemire, France). . Appl Geochem 23, 21822197. [CrossRef]
    [Google Scholar]
  5. 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. [CrossRef] [PubMed]
    [Google Scholar]
  6. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [CrossRef] [PubMed]
    [Google Scholar]
  7. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [CrossRef]
    [Google Scholar]
  8. 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, 24912495. [CrossRef] [PubMed]
    [Google Scholar]
  9. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H., Yi H., Won S, Chun J. ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [CrossRef] [PubMed]
    [Google Scholar]
  10. Lányí B. ( 1987 ). Classical and rapid identification methods for medically important bacteria. . Methods Microbiol 19, 167. [CrossRef]
    [Google Scholar]
  11. 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, 345349. [CrossRef] [PubMed]
    [Google Scholar]
  12. 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, 12911296. [CrossRef] [PubMed]
    [Google Scholar]
  13. 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, 159167. [CrossRef]
    [Google Scholar]
  14. 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, 22212227. [CrossRef] [PubMed]
    [Google Scholar]
  15. Powers E. M. ( 1995 ). Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. . Appl Environ Microbiol 61, 37563758.[PubMed]
    [Google Scholar]
  16. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  17. 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, 10831088. [CrossRef] [PubMed]
    [Google Scholar]
  18. 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, 165177. [CrossRef] [PubMed]
    [Google Scholar]
  19. 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, 25652570. [CrossRef] [PubMed]
    [Google Scholar]
  20. 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, 46734680. [CrossRef] [PubMed]
    [Google Scholar]
  21. Tindall B. J. ( 1990a ). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. . Syst Appl Microbiol 13, 128130. [CrossRef]
    [Google Scholar]
  22. Tindall B. J. ( 1990b ). Lipid composition of Halobacterium lacusprofundi . . FEMS Microbiol Lett 66, 199202. [CrossRef]
    [Google Scholar]
  23. Urios L., Agogué H., Lesongeur F., Stackebrandt E., Lebaron P. ( 2006 ). Balneola vulgaris gen. nov., sp. nov., a new member of the Cytophaga–Flavobacterium–Bacteroides phylum from the NW Mediterranean Sea. . Int J Syst Evol Microbiol 56, 18831887. [CrossRef] [PubMed]
    [Google Scholar]
  24. 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, 12731277. [CrossRef] [PubMed]
    [Google Scholar]
  25. 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, 20892095. [CrossRef] [PubMed]
    [Google Scholar]
  26. Yoon J.-H., Kang S.-J., Oh T.-K. ( 2007b ). Pedobacter terrae sp. nov., isolated from soil. . Int J Syst Evol Microbiol 57, 24622466. [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.038968-0
Loading
/content/journal/ijsem/10.1099/ijs.0.038968-0
Loading

Data & Media loading...

Most cited this month 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