Molecular characterization of polychlorinated biphenyl-dechlorinating populations in contaminated sediments

  • Kyoung-Hee Oh
  • Ellen B. Ostrofsky
  • Young-Cheol ChoEmail author


Polychlorinated biphenyl (PCB)-dechlorinating microorganisms were characterized in PCB-contaminated sediments using amplified ribosomal DNA restriction analysis (ARDRA). The sediments were prepared by spiking Aroclor 1248 into PCB-free sediments, and were inoculated with microorganisms eluted from St. Lawrence River sediments. PCB-free sediments inoculated with the same inoculum served as the control. Four restriction fragment length polymorphism (RFLP) groups in the eubacterial and two in the archaeal domain were found exclusively in PCB-spiked sediment clone libraries. Sequence analysis of the four eubacterial clones showed homology to Escherichia coli, Lactosphaera pasteurii, Clostridium thermocellum, and Dehalobacter restrictus. The predominant archaeal sequence in the PCB-spiked sediment clone library was closely related to Methanosarcina barkeri, which appear to support earlier findings that methanogens are involved in PCB dechlorination. When the dot-blot hybridization was performed between the sediment DNA extract and the probes designed with eubacterial RFLP groups, the intensity of two of eubacterial RFLP groups, which showed high sequence homology to C. pascui and D. restrictus, was highly correlated with the number of dechlorinating microorganisms suggesting these two members intend to contribute to PCB dechlorination.


polychlorinated biphenyls reductive dechlorination dechlorinating bacteria amplified ribosomal DNA restriction analysis restriction fragment length polymorphism 


  1. Balch, W.E., G.E. Fox, L.J. Magrum, C.R. Woese, and R.S. Wolfe. 1979. Methanogens: reevaluation of a unique biological group. Microbiol. Rev. 43, 260–296.PubMedGoogle Scholar
  2. Bedard, D.L. and J.F. Quensen, 3rd. 1995. Microbial reductive dechlorination of polychlorinated biphenyls, p. 127–216. In L.Y. Young and C.E. Cerniglia (eds.), Microbial transformation and degradation of toxic organic chemicals. Wiley-Liss, Inc., New York, N.Y., USA.Google Scholar
  3. Briones, Jr., A.M. and W. Reicharst. 1999. Estimating microbial population counts by ‘most probable number’ using Microsoft Excel. J. Microbiol. Methods 35, 157–161.PubMedCrossRefGoogle Scholar
  4. Chang, B.V., S.W. Chou, and S.Y. Yuan. 1994. Dechlorination of polychlorinated biphenyls by an anaerobic mixed culture. J. Environ. Sci. Health A. 34, 1299–1316.CrossRefGoogle Scholar
  5. Cho, Y.-C., J. Kim, R.C. Sokol, and G.-Y. Rhee. 2000. Biotransformation of PCBs in St. Lawrence River sediments: reductive dechlorination and dechlorinating microbial populations. Can. J. Fish. Aquat. Sci. 57, 95–100.CrossRefGoogle Scholar
  6. DeLong, E.F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89, 5685–5689.PubMedCrossRefGoogle Scholar
  7. Dojka, M.A., P. Hugenholtz, S.K. Haack, and N.R. Pace. 1998. Microbial diversity in a hydrocarbon-and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64, 3869–3877.PubMedGoogle Scholar
  8. Harris, J.K., S.T. Kelley, and N.R. Pace. 2004. New perspective on uncultured bacterial phylogenetic division OP11. Appl. Environ. Microbiol. 70, 845–849.PubMedCrossRefGoogle Scholar
  9. Holoman, T.R.P., M.A. Elberson, L.A. Cutter, H.D. May, and K.R. Sowers. 1998. Characterization of a defined 2,3,5,6-tetrachlorobiphenyl-ortho-dechlorinating microbial community by comparative sequence analysis of genes coding for 16S rRNA. Appl. Environ. Microbiol. 64, 3359–3367.PubMedGoogle Scholar
  10. Hou, L.H. and S.K. Dutta. 2000. Phylogenetic characterization of several para-and meta-PCB dechlorinating Clostridium species: 16S rDNA sequence analyses. Lett. Appl. Microbiol. 30, 238–243.PubMedCrossRefGoogle Scholar
  11. Janssen, P.H., A. Schuhmann, F. Bak, and W. Liesack. 1996. Disproportionation of inorganic sulfur compounds by the sulfate-reducing bacterium Desulfocapsa thiozymogenes gen. nov., sp. nov. Arch. Microbiol. 166, 184–192.CrossRefGoogle Scholar
  12. Kim, J. and G.-Y. Rhee. 1997. Population dynamics of polychlorinated biphenyl-dechlorinating microorganisms in contaminated sediments. Appl. Environ. Microbiol. 63, 1771–1776.PubMedGoogle Scholar
  13. Kim, J. and G.-Y. Rhee. 1999. Reductive dechlorination of polychlorinated biphenyls: Interactions of dechlorinating microorganisms with methanogens and sulfate reducers. Environ. Toxicol. Chem. 18, 2696–2702.CrossRefGoogle Scholar
  14. Lamontagne, M.G., G.J. Davenport, L.H. Hou, and S.K. Dutta. 1998. Identification and analysis of PCB dechlorinating anaerobic enrichments by amplification-accuracy of community structure based on restriction analysis and partial sequencing of 16S rRNA genes. J. Appl. Microbiol. 84, 1156–1162.PubMedCrossRefGoogle Scholar
  15. Lane, D.J., B. Pace, G.J. Olsen, D.A. Stahl, M.L. Sogin, and N.R. Pace. 1985. Rapid determination of 16S ribosomal sequences for phylogenetic analysis. Proc. Natl. Acad. Sci. USA 82, 6955–6959.PubMedCrossRefGoogle Scholar
  16. Lee, D.-H., Y.-G. Zo, and S.-J. Kim. 1996. Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism. Appl. Environ. Microbiol. 62, 3112–3120.PubMedGoogle Scholar
  17. Maidak, B.L., J.R. Cole, T.G. Lilburn, C.T. Parker, Jr., P.R. Saxman, R.J. Farris, G.M. Garrity, G.J. Olsen, T.M. Schmidt, and J.M. Tiedje. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29, 173–174.PubMedCrossRefGoogle Scholar
  18. Margesin, R., D. Labbe, F. Schinner, C.W. Greer, and L.G. Whyte. 2003. Characterization of hydrocarbon-degrading microbial populations in contaminated and pristine alpine soils. Appl. Environ. Microbiol. 69, 3085–3092.PubMedCrossRefGoogle Scholar
  19. Rhee, G.-Y., B. Bush, C.M. Bethoney, A. DeNucci, H.-M. Oh, and R.C. Sokol. 1993. Reductive dechlorination of Aroclor 1242 in anaerobic sediments: pattern, rate and concentration dependence. Environ. Toxicol. Chem. 12, 1025–1032.CrossRefGoogle Scholar
  20. Rhee, G.-Y., R.C. Sokol, C.M. Bethoney, Y.-C. Cho, R.C. Frohnhoefer, and T. Erkkila. 2001. Kinetics of polychlorinated biphenyl dechlorination and growth of dechlorinating microorganisms. Environ. Toxicol. Chem. 20, 721–726.PubMedCrossRefGoogle Scholar
  21. Sokol, R.C., O.-S. Kwon, C.B. Bethoney, and G.-Y. Rhee. 1994. Reductive dechlorination of polychlorinated biphenyls (PCBs) in St. Lawrence River sediments and variations in dechlorination characteristics. Environ. Sci. Technol. 28, 2054–2064.CrossRefGoogle Scholar
  22. Sokol, R.C., C.B. Bethoney, and G.-Y. Rhee. 1998. Effect of Aroclor 1248 concentration on the rate and extent of polychlorinated biphenyl dechlorination. Environ. Toxicol. Chem. 17, 1922–1926.CrossRefGoogle Scholar
  23. Watts, J.E.M., Q. Wu, S.B. Schreier, H.D. May, and K.R. Sowers. 2001. Comparative analysis of polychlorinated biphenyl-dechlorinating communities in enrichment cultures using three different molecular screening techniques. Environ. Microbiol. 3, 710–719.PubMedCrossRefGoogle Scholar
  24. Wiegel, J. and Q. Wu. 2000. Microbial reductive dehalogenation of polychlorinated biphenyls. FEMS Microbiol. Ecol. 32, 1–15.PubMedCrossRefGoogle Scholar
  25. Wild, A., R. Hermann, and T. Leisinger. 1996. Isolation of an anaerobic bacterium which reductively dechlorinates tetrachloroethene and trichloroethene. Biodegradation 7, 507–511.PubMedCrossRefGoogle Scholar
  26. Williams, W.A. 1994. Microbial reductive dechlorination of polychlorinated biphenyls in heat treated and bromoethanesulfonate treated anaerobic sediment slurries. Chemosphere 28, 2269–2284.CrossRefGoogle Scholar
  27. Ye, D., J.F. Quensen, 3rd, J.M. Tiedje, and S.A. Boyd. 1992. Anaerobic dechlorination of polychlorobiphenyls (Aroclor 1242) by pasteurized and ethanol-treated microorganisms from sediments. Appl. Environ. Microbiol. 58, 1110–1114.PubMedGoogle Scholar
  28. Ye, D., J.F. Quensen, 3rd, J.M. Tiedje, and S.A. Boyd. 1995. Evidence for para dechlorination of polychlorobiphenyls by methanogenic bacteria. Appl. Environ. Microbiol. 61, 2166–2171.PubMedGoogle Scholar
  29. Ye, D., J.F. Quensen, 3rd, J.M. Tiedje, and S.A. Boyd. 1999. 2-Bromoethanesulfonate, sulfate, molybdate, and ethanesulfonate inhibit anaerobic dechlorination of polychlorobiphenyls by pasteurized microorganisms. Appl. Environ. Microbiol. 65, 327–329.PubMedGoogle Scholar
  30. Young, C.C., R.L. Burghoff, L.G. Keim, V. Minak-Bernero, J.R. Lute, and S.M. Hinton. 1993. Polyvinylpyrrolidone-agarose gel electrophoresis purification of polymerase chain reaction-amplifiable DNA from soils. Appl. Environ. Microbiol. 59, 1972–1974.PubMedGoogle Scholar

Copyright information

© The Microbiological Society of Korea and Springer-Verlag Berlin Heidelber GmbH 2008

Authors and Affiliations

  • Kyoung-Hee Oh
    • 1
    • 2
  • Ellen B. Ostrofsky
    • 3
  • Young-Cheol Cho
    • 4
    Email author
  1. 1.School of Biological SciencesSeoul National UniversitySeoulRepublic of Korea
  2. 2.Institute of Construction TechnologyChungbuk National UniversityCheongjuRepublic of Korea
  3. 3.School of Public HealthState University of New York at AlbanyAlbanyUSA
  4. 4.Department of Environmental EngineeringChungbuk National UniversityCheongjuRepublic of Korea

Personalised recommendations