1887

Abstract

An Fe(III)- and uranium(VI)-reducing bacterium, designated strain FRC-32, was isolated from a contaminated subsurface of the USA Department of Energy Oak Ridge Field Research Center (ORFRC) in Oak Ridge, Tennessee, where the sediments are exposed to mixed waste contamination of radionuclides and hydrocarbons. Analyses of both 16S rRNA gene and the -specific citrate synthase () mRNA gene sequences retrieved from ORFRC sediments indicated that this strain was abundant and active in ORFRC subsurface sediments undergoing uranium(VI) bioremediation. The organism belonged to the subsurface clade of the genus and shared 92–98 % 16S rRNA gene and 75–81 % gene sequence similarities with other recognized species of the genus. In comparison to its closest relative, Rf4, according to 16S rRNA gene sequence similarity, strain FRC-32 showed a DNA–DNA relatedness value of 21 %. Cells of strain FRC-32 were Gram-negative, non-spore-forming, curved rods, 1.0–1.5 μm long and 0.3–0.5 μm in diameter; the cells formed pink colonies in a semisolid cultivation medium, a characteristic feature of the genus . The isolate was an obligate anaerobe, had temperature and pH optima for growth at 30 °C and pH 6.7–7.3, respectively, and could tolerate up to 0.7 % NaCl although growth was better in the absence of NaCl. Similar to other members of the group, strain FRC-32 conserved energy for growth from the respiration of Fe(III)-oxyhydroxide coupled with the oxidation of acetate. Strain FRC-32 was metabolically versatile and, unlike its closest relative, , was capable of utilizing formate, butyrate and butanol as electron donors and soluble ferric iron (as ferric citrate) and elemental sulfur as electron acceptors. Growth on aromatic compounds including benzoate and toluene was predicted from preliminary genomic analyses and was confirmed through successive transfer with fumarate as the electron acceptor. Thus, based on genotypic, phylogenetic and phenotypic differences, strain FRC-32 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is FRC-32 (=DSM 22248=JCM 15807).

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2010-03-01
2024-03-19
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References

  1. Abdelouas A., Lutze W., Nuttall H. E. 1999; Uranium contamination in the subsurface; characterization and remediation. Rev Mineral Geochem 38:433–473
    [Google Scholar]
  2. Adékambi T., Shinnick T. M., Raoult D., Drancourt M. 2008; Complete rpoB gene sequencing as a suitable supplement to DNA-DNA hybridization for bacterial species and genus delineation. Int J Syst Evol Microbiol 58:1807–1814 [CrossRef]
    [Google Scholar]
  3. Akob D. M., Mills H. J., Gihring T. M., Kerkhof L., Stucki J. W., Anastacio A. S., Chin K. J., Kusel K., Palumbo A. V. other authors 2008; Functional diversity and electron donor dependence of microbial populations capable of U(VI) reduction in radionuclide-contaminated subsurface sediments. Appl Environ Microbiol 74:3159–3170
    [Google Scholar]
  4. Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z., Miller W. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [CrossRef]
    [Google Scholar]
  5. Anderson R. T., Vrionis H. A., Ortiz-Bernad I., Resch C. T., Long P. E., Dayvault R., Karp K., Marutzky S., Metzler D. R. other authors 2003; Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. Appl Environ Microbiol 69:5884–5891 [CrossRef]
    [Google Scholar]
  6. Canfield D. E., Thamdrup B., Kristensen E. 2005; The iron and manganese cycles. In Aquatic Geomicrobiology vol 48 pp 269–312 Edited by Southward A. J., Tyler P. A., Young C. M., Fuiman L. A. CA, USA: Elsevier/Academic Press;
    [Google Scholar]
  7. Cashion P., Holder-Franklin M. A., McCully J., Franklin M. 1977; A rapid method for base ratio determination of bacterial DNA. Anal Biochem 81:461–466 [CrossRef]
    [Google Scholar]
  8. Clarridge J. E. 2004; Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 17:840–862 [CrossRef]
    [Google Scholar]
  9. Coates J. D., Bhupathiraju V. K., Achenbach L. A., McInerney M. J., Lovley D. R. 2001; Geobacter hydrogenophilus , Geobacter chapellei and Geobacter grbiciae , three new, strictly anaerobic, dissimilatory Fe(III)-reducers. Int J Syst Evol Microbiol 51:581–588
    [Google Scholar]
  10. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142 [CrossRef]
    [Google Scholar]
  11. 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:W394–W399 [CrossRef]
    [Google Scholar]
  12. Gorby Y. A., Lovley D. R. 1992; Enzymatic uranium precipitation. Environ Sci Technol 26:205–207 [CrossRef]
    [Google Scholar]
  13. Goris J., Konstantinidis K. T., Klappenbach J. A., Coenye T., Vandamme P., Tiedje J. M. 2007; DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91 [CrossRef]
    [Google Scholar]
  14. Holmes D. E., Finneran K. T., Lovley D. R. 2002; Enrichment of Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments. Appl Environ Microbiol 68:2300–2306 [CrossRef]
    [Google Scholar]
  15. Holmes D. E., Nevin K. P., Lovely D. R. 2004; Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov. Int J Syst Evol Microbiol 54:1591–1599 [CrossRef]
    [Google Scholar]
  16. Holmes D. E., O'Neil R. A., Vrionis H. A., N'Guessan L. A., Bernad I. O., Larrahondo M. J., Adamas L. A., Ward J. A., Nicoll J. S. other authors 2007; Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments. ISME J 1:663–677 [CrossRef]
    [Google Scholar]
  17. 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 [CrossRef]
    [Google Scholar]
  18. Istok J. D., Senko J. M., Krumholz L. R., Watson D., Bogle M. A., Peacock A., Chang Y. J., White D. C. 2004; In situ bioreduction of technetium and uranium in a nitrate-contaminated aquifer. Environ Sci Technol 38:468–475 [CrossRef]
    [Google Scholar]
  19. Kostka J. E., Thamdrup B., Glud R. N., Canfield D. E. 1999; Rates and pathways of carbon oxidation in permanently cold Arctic sediments. Mar Ecol Prog Ser 180:7–21 [CrossRef]
    [Google Scholar]
  20. Lane D. J. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp 115–175 Edited by Stackebrandt E., Goodfellow M. Chichester: Wiley;
    [Google Scholar]
  21. Lovley D. R. 2006; Dissimilatory Fe(III)- and Mn(IV) reducing prokaryotes. Prokaryotes 2:635–658
    [Google Scholar]
  22. Lovley D. R., Anderson R. T. 2000; The influence of dissimilatory metal reduction on the fate of organic and metal contaminants in the subsurface. Hydrogeol J 8:77–88 [CrossRef]
    [Google Scholar]
  23. Lovley D. R., Phillips E. J. P. 1986; Organic matter mineralization with reduction of ferric iron in anaerobic sediments. Appl Environ Microbiol 51:683–689
    [Google Scholar]
  24. Lovley D. R., Phillips E. J. P., Gorby Y. A., Landa E. R. 1991; Microbial reduction of uranium. Nature 350:413–416 [CrossRef]
    [Google Scholar]
  25. Lovley D. R., Giovannoni S. J., White D. C., Champine J. E., Phillips E. J. P., Gorby Y. A., Goodwin S. 1993; Geobacter metallireducens gen. nov. sp. nov. a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. Arch Microbiol 159:336–344 [CrossRef]
    [Google Scholar]
  26. Lovley D. R., Holmes D. E., Nevin K. P. 2004; Dissimilatory Fe(III) and Mn(IV) reduction. Adv Microb Physiol 49:219–286
    [Google Scholar]
  27. Nevin K. P., Holmes D. E., Woodard T. L., Hinlein E. S., Ostendorf D. W., Lovley D. R. 2005; Geobacter bemidjiensis sp. nov. and Geobacter psychrophilus sp. nov., two novel Fe(III)-reducing subsurface isolates. Int J Syst Evol Microbiol 55:1667–1674 [CrossRef]
    [Google Scholar]
  28. Nevin K. P., Holmes D. E., Woodard T. L., Covalla S. F., Lovley D. R. 2007; Reclassification of Trichlorobacter thiogenes as Geobacter thiogenes comb. nov. Int J Syst Evol Microbiol 57:463–466
    [Google Scholar]
  29. North N. N., Dollhopf S. L., Petrie L., Istok J. D., Balkwill D. L., Kostka J. E. 2004; Change in bacterial community structure during in situ biostimulation of subsurface sediment cocontaminated with uranium and nitrate. Appl Environ Microbiol 70:4911–4920 [CrossRef]
    [Google Scholar]
  30. Petrie L. N., North N., Dollhopf S. L., Balkwill D. L., Kostka J. E. 2003; Enumeration and characterization of Fe(III)-reducing microbial communities from acidic subsurface sediments contaminated with uranium(VI). Appl Environ Microbiol 69:7467–7479
    [Google Scholar]
  31. Riley R., Zachara J. 1992; Chemical contaminants on DOE lands and selection of contaminants mixture for subsurface science research US Department of Energy . pp 1–92 Washington, DC: Office of Energy Research;
    [Google Scholar]
  32. Roden E. E., Wetzel R. G. 1996; Organic carbon oxidation and suppression of methane production by microbial Fe(III) oxide reduction in vegetated and unvegetated freshwater wetland sediments. Limnol Oceanogr 41:1733–1748 [CrossRef]
    [Google Scholar]
  33. Ronquist F., Huelsenbeck J. P. 2003; MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574 [CrossRef]
    [Google Scholar]
  34. Rooney-Varga J. N., Anderson R. T., Fraga J. L., Ringelberg D., Lovley D. R. 1999; Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer. Appl Environ Microbiol 65:3056–3063
    [Google Scholar]
  35. Shelobolina E. S., Nevin K. P., Blakeney-Hayward J. D., Johnsen C. V., Plaia T. W., Krader P., Woodard T., Holmes D. E., VanPraagh C. W., Lovley D. R. 2007 Geobacter pickeringii sp. nov., Geobacter argillaceus sp. nov. and Pelosinus fermentans gen. nov., sp. nov., isolated from subsurface kaolin lenses. Int J Syst Evol Microbiol 57, 126–135 [CrossRef]
  36. Shelobolina E. S., Vrionis H. A., Findlay R. H., Lovley D. R. 2008; Geobacter uraniireducens sp. nov., isolated from subsurface sediment undergoing uranium bioremediation. Int J Syst Evol Microbiol 58:1075–1078 [CrossRef]
    [Google Scholar]
  37. 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
    [Google Scholar]
  38. Stein L. Y., La Duc M. T., Grundi T. J., Nealson K. H. 2001; Bacterial and archaeal population associated with freshwater ferromanganous micronodules and sediments. Environ Microbiol 3:10–18
    [Google Scholar]
  39. Straub K. L., Buchholz-Cleven B. E. E. 2001; Geobacter bremensis sp. nov. and Geobacter pelophilus sp. nov., two dissimilatory ferric-iron-reducing bacteria. Int J Syst Evol Microbiol 51:1805–1808 [CrossRef]
    [Google Scholar]
  40. Straub K. L., Hanzlik M., Buchholz-Cleven B. E. E. 1998; The use of biologically produced ferrihydrite for the isolation of novel iron-reducing bacteria. Syst Appl Microbiol 21:442–449 [CrossRef]
    [Google Scholar]
  41. 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 [CrossRef]
    [Google Scholar]
  42. Thamdrup B. 2000; Bacterial manganese and iron reduction in aquatic sediments. Adv Microb Ecol 16:41–84
    [Google Scholar]
  43. 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 [CrossRef]
    [Google Scholar]
  44. Vandamme P., Pot B., Gillis M., De Vos P., Kersters K., Swings J. 1996; Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438
    [Google Scholar]
  45. Vrionis H. A., Anderson R. T., Ortiz-Bernad I., O'Neill K. R., Resch C. T., Peacock A. D., Dayvault R., White D. C., Long P. E., Lovley D. R. 2005; Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl Environ Microbiol 71:6308–6318 [CrossRef]
    [Google Scholar]
  46. 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]
  47. Widdel F., Bak F. 1992; Gram-negative mesophilic sulfatereducing bacteria. In The Prokaryotes , 2nd edn. pp 3352–3378 Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K.-H. New York: Springer;
    [Google Scholar]
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