Geobacter lovleyi sp. nov. strain SZ, a novel metal-reducing and tetrachloroethene-dechlorinating bacterium

Applied and Environmental Microbiology

Volumn 72, Issue 4, 2006, Pages 2775-2782

  Sung, Youlboong ^a,g   Fletcher, Kelly E ^a   Ritalahti, Kirsti M ^a   Apkarian, Robert P ^f   Ramos Hernández, Natalia ^c   Sanford, Robert A ^d   Mesbah, Noha M ^e   Löffler, Frank E ^a,b  

^a Georgia Institute of Technology   (United States)

^b GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^c UNIVERSITY OF PUERTO RICO   (Puerto Rico)

^d UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^e UNIVERSITY OF GEORGIA   (United States)

^f EMORY UNIVERSITY   (United States)

^g UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOREMEDIATION; CONCENTRATION (PROCESS); CONTAMINATION; DECHLORINATION; OXIDATION; SEDIMENTS;

CREEK SEDIMENT MICROCOSMS; ELECTRON ACCEPTORS; ELECTRON DONORS; THRESHOLD CONCENTRATIONS;

BACTERIA;

ACETIC ACID; AMMONIA; FERRIC CITRATE; FERRIC ION; FERROUS ION; FRESH WATER; FUMARIC ACID; GENOMIC DNA; HYDROGEN; MALIC ACID; MANGANESE; METAL; NITRATE; PYRUVIC ACID; RNA 16S; SOLVENT; SUCCINIC ACID; SULFIDE; SULFUR; TETRACHLOROETHYLENE; TRICHLOROETHYLENE; URANIUM;

BACTERIOLOGY; BACTERIUM; BIOREMEDIATION; CONCENTRATION (COMPOSITION); MICROCOSM; OXIDATION; PROTEIN; SEDIMENT;

ARTICLE; BIOREMEDIATION; DECHLORINATION; DNA HYBRIDIZATION; ECOSYSTEM; GENE SEQUENCE; GEOBACTER; GEOBACTER LOVLEYI; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLLUTANT; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEDIMENT; SOIL POLLUTION; STRAIN IDENTIFICATION; WATER CONTAMINATION;

ACETATES; CHLORINE; ENVIRONMENTAL POLLUTANTS; FRESH WATER; GEOBACTER; GEOLOGIC SEDIMENTS; METALS; MOLECULAR SEQUENCE DATA; NITRATES; OXIDATION-REDUCTION; SEQUENCE ANALYSIS, DNA; TETRACHLOROETHYLENE; URANIUM;

BACTERIA (MICROORGANISMS); GEOBACTER; TRICHLOROBACTER;

EID: 33646110083     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.72.4.2775-2782.2006     Document Type: Article

References (53)

1. Anderson, R. T., and D. R. Lovley. 2002. Microbial redox interactions with uranium: an environmental perspective, p. 205-223. In M. J. Keith-Roach and F. R. Livens (ed.), Interactions of microorganisms with radionuclides. Elsevier Science Limited, Amsterdam, The Netherlands.
2. Anderson, R. T., H. A. Vrionis, I. Ortiz-Bernad, C. T. Resch, P. E. Long, R. Dayvault, K. Karp, S. Marutzky, D. R. Metzler, A. Peacock, D. C. White, M. Lowe, and D. R. Lovley. 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.
3. Beliaev, A. S., D. K. Thompson, T. Khare, H. Lim, C. C. Brandt, G. Li, A. E. Murray, J. F. Heidelberg, C. S. Giometti, J. Yates III, K. H. Nealson, J. M. Tiedje, and J. Zhou. 2002. Gene and protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors. OMICS J. Integr. Biol. 6:39-60.
4. Burnes, B. S., M. J. Mulberry, and T. J. DiChristina. 1998. Design and application of two rapid screening techniques for isolation of Mn(IV) reduction-deficient mutants of Shewanella putrefaciens. Appl. Environ. Microbiol. 64:2716-2720.
5. Cashion, P., M. A. Hodler-Franklin, J. McCully, and M. Franklin. 1977. A rapid method for base ratio determination of bacterial DNA. Anal. Biochem. 81:461-466.
6. Childers, S. E., S. Ciufo, and D. R. Lovley. 2002. Geobacter metallireducens accesses insoluble Fe(III) oxide by chemotaxis. Nature 416:767-769.
7. Cline, J. D. 1969. Spectrophotometric determination of hydrogen sulfide in natural waters. Limnol. Oceanogr. 14:454-458.
8. De Ley, J., H. Cattoir, and A. Reynaerts. 1970. The quantitative measurement of DNA hybridization from renaturation rates. Eur. J. Biochem. 12:133-142.
9. Dennis, P. C., B. E. Sleep, R. R. Fulthorpe, and S. N. Liss. 2003. Phylogenetic analysis of bacterial populations in an anaerobic microbial consortium capable of degrading saturation concentrations of tetrachloroethylene. Can. J. Microbiol. 49:15-27.
10. De Wever, H., J. R. Cole, M. R. Fettig, D. A. Hogan, and J. R. Tiedje. 2000. Reductive dehalogenation of trichloroacetic acid by Trichlorobacter thiogenes gen. nov., sp. nov. Appl. Environ. Microbiol. 66:2297-2301.
11. Dolfing, J., and J. E. M. Beurskens. 1995. The microbial logic and environmental significance of reductive dehalogenation, p. 143-206. In J. G. Jones (ed.), Advances in microbial ecology, vol. 14. Plenum Press, New York, N.Y.
12. Duhamel, M., K. Mo, and E. A. Edwards. 2004. Chracterization of a highly enriched Dehalococcoides-containing culture that grows on vinyl chloride and trichloroethene. Appl. Environ. Microbiol. 70:5538-5545.
13. Ellis, D. E., E. J. Lutz, J. M. Odom, J. Ronald, J. Buchanan, C. L. Bartlett, M. D. Lee, M. R. Harkness, and K. A. Deweerd. 2000. Bioaugmentation for accelerated in situ anaerobic bioremediation. Environ. Sci. Technol. 34:2254-2260.
14. Fennell, D. E., J. M. Gossett, and S. H. Zinder. 1997. Comparison of butyric acid, ethanol, lactic acid, and propionic acid as hydrogen donors for the reductive dechlorination of tetrachloroethene. Environ. Sci. Technol. 31:918-926.
15. Finneran, K. T., R. T. Anderson, K. P. Nevin, and D. R. Lovley. 2002. Potential for bioremediation of uranium-contaminated aquifers with microbial U(VI) reduction. Soil Sediment. Contam. 11:339-357.
16. Finneran, K. T., M. E. Housewright, and D. R. Lovley. 2002. Multiple influences of nitrate on uranium solubility during bioremediation of uranium-contaminated subsurface sediments. Environ. Microbiol. 4:510-519.
17. Gorby, Y. A., and D. R. Lovley. 1992. Enzymatic uranium precipitation. Environ. Sci. Technol. 26:205-207.
18. He, J., K. M. Ritalahti, K.-L. Yang, S. S. Koenigsberg, and F. E. Löffler. 2003. Detoxification of vinyl chloride to ethene coupled to growth of an anaerobic bacterium. Nature 424:62-65.
19. He, J., Y. Sung, M. E. Dollhopf, B. Z. Fathepure, J. M. Tiedje, and F. E. Löffler. 2002. Acetate versus hydrogen as direct electron donors to stimulate the microbial reductive dechlorination process at chloroethene- contaminated sites. Environ. Sci. Technol. 36:2945-3952.
20. He, Q., and R. A. Sanford. 2004. Acetate threshold concentrations suggest varying energy requirements during anaerobic respiration by Anaeromyxobacter dehalogenans. Appl. Environ. Microbiol. 70:6940-6943.
21. Holmes, D. E., K. T. Finneran, R. A. O'Neil, and D. R. Lovley. 2002. Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments. Appl. Environ. Microbiol. 68:2300-2306.
22. Holmes, D. E., K. Nevin, and D. R. Lovley. 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.
23. Huss, V. A. R., H. Festl, and K. H. Schleifer. 1983. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst. Appl. Microbiol. 4:184-192.
24. Ingvorsen, K., A. J. B. Zehnder, and B. B. Jørgensen. 1984. Kinetics of sulfate and acetate uptake by Desulfobacter postgatei. Appl. Environ. Microbiol. 47:403-408.
25. Johnson, D. A., and T. M. Florence. 1971. Spectrophotometric determination of uranium(VI) with 2-(5-bromo-2-pyridylazo)-5-diethylaminophenol. Anal. Chim. Acta 53:73-79.
26. Krumholz, L. R., R. Sharp, and S. Fishbain. 1996. A freshwater anaerobe coupling acetate oxidation to tetrachloroethene dehalogenation. Appl. Environ. Microbiol. 62:4108-4113.
27. Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17:1244-1245.
28. Langmuir, D. 1997. Aqueous environmental geochemistry. Prentice Hall, Upper Saddle River, N.J.
29. Lendvay, J. M., F. E. Löffler, M. Dollhopf, M. R. Aiello, G. Daniels, B. Z. Fathepure, M. Gebhard, R. Heine, R. Helton, J. Shi, R. Krajmalnik-Brown, C. L. Major, Jr., M. J. Barcelona, E. Petrovskis, J. M. Tiedje, and P. Adriaens. 2002. Bioreactive barriers: bioaugmentation and biostimulation for chlorinated solvent remediation. Environ. Sci. Technol. 37:1422-1431.
30. Löffler, F. E., and R. A. Sanford. 2005. Analysis of trace hydrogen metabolism. Methods Enzymol. 397:222-237.
31. Löffler, F. E., Q. Sun, J. Li, and J. M. Tiedje. 2000. 16S rRNA gene-based detection of tetrachloroethene-dechlorinating Desulfuromonas and Dehalococcoides species. Appl. Environ. Microbiol. 66:1369-1374.
32. Löffler, F. E., J. M. Tiedje, and R. A. Sanford. 1999. Fraction of electrons consumed in electron acceptor reduction and hydrogen thresholds as indicators of halorespiratory physiology. Appl. Environ. Microbiol. 65:4049-4056.
33. Lonergan, D. J., H. L. Jenter, J. D. Coates, E. J. P. Phillips, T. M. Schmidt, and D. R. Lovley. 1996. Phylogenetic analysis of dissimilatory Fe(III)-reducing bacteria. J. Bacteriol. 178:2402-2408.
34. Lovley, D. R., D. E. Holmes, and K. P. Nevin. 2004. Dissimilatory Fe(III) and Mn(IV) reduction. Adv. Microb. Physiol. 49:119-286.
35. Lovley, D. R., and E. J. P. Phillips. 1987. Competitive mechanisms for inhibition of sulfate reduction and methane production in the zone of ferric iron reduction in sediments. Appl. Environ. Microbiol. 53:2636-2641.
36. Lovley, D. R., and E. J. P. Phillips. 1988. Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese. Appl. Environ. Microbiol. 54:1472-1480.
37. Lovley, D. R., and E. J. P. Phillips. 1986. Organic matter mineralization with reduction of ferric iron in anaerobic sediments. Appl. Environ. Microbiol. 51:683-689.
38. Macbeth, T. W., D. E. Cummings, S. Spring, L. M. Petzke, and K. S. Sorenson. 2004. Molecular characterization of a dechlorinating community resulting from in situ biostimulation in a trichloroethene-contaminated deep, fractured basalt aquifer and comparison to a derivative laboratory culture. Appl. Environ. Microbiol. 70:7329-7341.
39. Major, D. W., M. L. McMaster, E. E. Cox, E. A. Edwards, S. M. Dworatzek, E. R. Hendrickson, M. G. Starr, J. A. Payne, and L. W. Buonamici. 2002. Field demonstration of successful bioaugmentation to achieve dechlorination of tetrachloroethene to ethene. Environ. Sci. Technol. 36:5106-5116.
40. Mazur, C. S., and W. J. Jones. 2001. Hydrogen concentrations in sulfate-reducing estuarine sediments during PCE dehalogenation. Environ. Sci. Technol. 35:4783-4788.
41. Mesbah, M., U. Permachandran, and W. B. Whitman. 1989. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int. J. Syst. Bacteriol. 39:159-167.
42. Rademaker, J. L., B. Hoste, F. J. Louws, K. Kersters, J. Swings, L. Bauterin, P. Vauterin, and F. J. de Bruijn. 2000. Comparison of AFLP and rep-PCR genomic fingerprinting with DNA-DNA homology studies: Xanthomonas as a model system. Int. J. Syst. Evol. Microbiol. 50:665-677.
43. Ritalahti, K. M., and F. E. Löffler. 2004. Populations implicated in anaerobic reductive dechlorination of 1,2-dichloropropane in highly enriched bacterial communities. Appl. Environ. Microbiol. 70:4088-4095.
44. Smatlak, C. R., and J. M. Gossett. 1996. Comparative kinetics of hydrogen utilization for reductive dechlorination of tetrachloroethene and methanogenesis in an anaerobic enrichment culture. Environ. Sci. Technol. 30:2850-2858.
45. Stookey, L. L. 1970. Ferrozine-a new spectrophotometric reagent for iron. Anal. Chem. 42:779-781.
46. Sung, Y., K. M. Ritalahti, R. A. Sanford, J. W. Urbance, S. J. Flynn, J. M. Tiedje, and F. E. Löffler. 2003. Characterization of two tetrachloroethene-reducing, acetate-oxidizing anaerobic bacteria and their description as Desulfuromonas michiganensis sp. nov. Appl. Environ. Microbiol. 69:2964-2974.
47. U.S. Department of Energy. 1999. From cleanup to stewardship. Office of Environmental Management, U.S. Department of Energy, Washington, D.C.
48. Versalovic, J., T. Koeuth, and J. R. Lupski. 1991. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 19:6823-6831.
49. Wan, X.-F., N. C. VerBerkmoes, L. A. McCue, D. Stanek, H. Connelly, L. J. Hauser, L. Wu, X. Liu, T. Yan, A. Leaphart, R. L. Hettich, J. Zhou, and D. K. Thompson. 2004. Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis. J. Bacteriol. 186:8385-8400.
50. Weast, R. C. 1986. CRC handbook of chemistry and physics, 67th ed. CRC Press, Boca Raton, Fla.
51. West, M., N. M. Burdash, and F. Freimuth. 1977. Simplified silver-plating stain for flagella. J. Clin. Microbiol. 6:414-419.
52. Westermann, P., B. K. Ahring, and R. A. Mah. 1989. Threshold acetate concentrations for acetate catabolism by aceticlastic methanogenic bacteria. Appl. Environ. Microbiol. 55:514-515.
53. Yang, Y., and P. L. McCarty. 1998. Competition for hydrogen within a chlorinated solvent dehalogenating anaerobic mixed culture. Environ. Sci. Technol. 32:3591-3597.