1887

Abstract

Bacterial strains 2APBS1 and 116-2 were isolated from the subsurface of a nuclear legacy waste site where the sediments are co-contaminated with large amounts of acids, nitrate, metal radionuclides and other heavy metals. A combination of physiological and genetic assays indicated that these strains represent the first member of the genus shown to be capable of complete denitrification. Cells of strain 2APBS1 and 116-2 were Gram-negative, non-spore-forming rods, 3–5 µm long and 0.25–0.5 µm in diameter. The isolates were facultative anaerobes, and had temperature and pH optima for growth of 30 °C and pH 6.5; they were able to tolerate up to 2.0 % NaCl, although growth improved in its absence. Strains 2APBS1 and 116-2 contained fatty acid and quinone (ubiquinone-8; 100 %) profiles that are characteristic features of the genus . Although strains 2APBS1 and 116-2 shared high 16S rRNA gene sequence similarity with LCS2 (>99 %), levels of DNA–DNA relatedness between these strains were substantially below the 70 % threshold used to designate novel species. Thus, based on genotypic, phylogenetic, chemotaxonomic and physiological differences, strains 2APBS1 and 116-2 are considered to represent a single novel species of the genus , for which the name sp. nov. is proposed. The type strain is 2APBS1 ( = DSM 23569 = JCM 17641).

Funding
This study was supported by the:
  • US Department of Energy, Office of Science, Biological and Environmental Research, Subsurface Biogeochemistry Research Program
  • US Department of Energy (Award DEAC05-00OR22725)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.035840-0
2012-10-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/62/10/2457.html?itemId=/content/journal/ijsem/10.1099/ijs.0.035840-0&mimeType=html&fmt=ahah

References

  1. An D. S., Lee H. G., Lee S. T., Im W. T. 2009; Rhodanobacter ginsenosidimutans sp. nov., isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 59:691–694 [View Article][PubMed]
    [Google Scholar]
  2. Bui T. P., Kim Y. J., Kim H., Yang D. C. 2010; Rhodanobacter soli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 60:2935–2939 [View Article][PubMed]
    [Google Scholar]
  3. Cashion P., Holder-Franklin M. A., McCully J., Franklin M. 1977; A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81:461–466 [View Article][PubMed]
    [Google Scholar]
  4. De Clercq D., Van Trappen S., Cleenwerck I., Ceustermans A., Swings J., Coosemans J., Ryckeboer J. 2006; Rhodanobacter spathiphylli sp. nov., a gammaproteobacterium isolated from the roots of Spathiphyllum plants grown in a compost-amended potting mix. Int J Syst Evol Microbiol 56:1755–1759 [View Article][PubMed]
    [Google Scholar]
  5. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142 [View Article][PubMed]
    [Google Scholar]
  6. DeSantis T. Z. Jr, Hugenholtz P., Keller K., Brodie E. L., Larsen N., Piceno Y. M., Phan R., Andersen G. L. 2006; nast: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34:Web Server issueW394–W399 [View Article][PubMed]
    [Google Scholar]
  7. Green S. J., Prakash O., Gihring T. M., Akob D. M., Jasrotia P., Jardine P. M., Watson D. B., Brown S. D., Palumbo A. V., Kostka J. E. 2010; Denitrifying bacteria isolated from terrestrial subsurface sediments exposed to mixed-waste contamination. Appl Environ Microbiol 76:3244–3254 [View Article][PubMed]
    [Google Scholar]
  8. Huß V. A. R., Festl H., Schleifer K. H. 1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192 [View Article]
    [Google Scholar]
  9. Im W. T., Lee S. T., Yokota A. 2004; Rhodanobacter fulvus sp. nov., a β-galactosidase-producing gammaproteobacterium. J Gen Appl Microbiol 50:143–147 [View Article][PubMed]
    [Google Scholar]
  10. Lee C. S., Kim K. K., Aslam Z., Lee S. T. 2007; Rhodanobacter thiooxydans sp. nov., isolated from a biofilm on sulfur particles used in an autotrophic denitrification process. Int J Syst Evol Microbiol 57:1775–1779 [View Article][PubMed]
    [Google Scholar]
  11. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S. other authors 2004; arb: a software environment for sequence data. Nucleic Acids Res 32:1363–1371 [View Article][PubMed]
    [Google Scholar]
  12. Mahne I., Tiedje J. M. 1995; Criteria and methodology for identifying respiratory denitrifiers. Appl Environ Microbiol 61:1110–1115[PubMed]
    [Google Scholar]
  13. Miller L. T. 1982; Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 16:584–586[PubMed]
    [Google Scholar]
  14. Nalin R., Simonet P., Vogel T. M., Normand P. 1999; Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium. Int J Syst Bacteriol 49:19–23 [View Article][PubMed]
    [Google Scholar]
  15. Ronquist F., Huelsenbeck J. P. 2003; MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574 [View Article][PubMed]
    [Google Scholar]
  16. Sasser M. 1990 Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI, Inc.
  17. Tamura K., Nei M., Kumar S. 2004; Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101:11030–11035 [View Article][PubMed]
    [Google Scholar]
  18. Tamura K., Dudley J., Nei M., Kumar S. 2007; mega4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24:1596–1599 [View Article][PubMed]
    [Google Scholar]
  19. Tindall B. J., Rosselló-Móra R., Busse H. J., Ludwig W., Kämpfer P. 2010; Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266 [View Article][PubMed]
    [Google Scholar]
  20. Van Den Heuvel R. N., van der Biezen E., Jetten M. S., Hefting M. M., Kartal B. 2010; Denitrification at pH 4 by a soil-derived Rhodanobacter-dominated community. Environ Microbiol 12:3264–3271 [View Article][PubMed]
    [Google Scholar]
  21. Wang L., An D. S., Kim S. G., Jin F. X., Lee S. T., Im W. T. 2011; Rhodanobacter panaciterrae sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol 61:3028–3032 [View Article][PubMed]
    [Google Scholar]
  22. Watson D. B., Kostka J. E., Fields M. W., Jardine P. M. 2004 The Oak Ridge Field Research Center Conceptual Model Oak Ridge, TN: NABIR Field Research Center;
    [Google Scholar]
  23. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. other authors 1987; International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [CrossRef]
    [Google Scholar]
  24. Weon H. Y., Kim B. Y., Hong S. B., Jeon Y. A., Kwon S. W., Go S. J., Koo B. S. 2007; Rhodanobacter ginsengisoli sp. nov. and Rhodanobacter terrae sp. nov., isolated from soil cultivated with Korean ginseng. Int J Syst Evol Microbiol 57:2810–2813 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.035840-0
Loading
/content/journal/ijsem/10.1099/ijs.0.035840-0
Loading

Data & Media loading...

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