A PCR-based specific assay reveals a population of bacteria within the Chloroflexi associated with the reductive dehalogenation of polychlorinated biphenyls

Microbiology

Volumn 151, Issue 6, 2005, Pages 2039-2046

  Watts, Joy E M ^a,c   Fagervold, Sonja K ^a   May, Harold D ^b   Sowers, Kevin R ^a  

^a UNIVERSITY OF MARYLAND   (United States)

^b MEDICAL UNIVERSITY OF SOUTH CAROLINA   (United States)

^c TOWSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEXACHLOROBIPHENYL; POLYCHLORINATED BIPHENYL; RIBOSOME RNA; RNA 16S;

ARTICLE; BACTERIUM DETECTION; CHLOROFLEXI; DECHLORINATION; DEHALOGENATION; ENVIRONMENT; GENE SEQUENCE; GENETIC VARIABILITY; MICROCOSM; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RIVER; SEDIMENT; UNITED STATES;

BASE SEQUENCE; BIODEGRADATION, ENVIRONMENTAL; CHLOROFLEXI; DNA, BACTERIAL; DNA, RIBOSOMAL; GENES, RRNA; GEOLOGIC SEDIMENTS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYCHLORINATED BIPHENYLS; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; WATER MICROBIOLOGY;

CHLOROFLEXI; CHLOROFLEXI (CLASS); DEHALOCOCCOIDES;

EID: 21344471699     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.27819-0     Document Type: Article

References (35)

1. Abraham, W. R., Nogales, B., Golyshin, P. N., Pieper, D. H. & Timmis, K. N. (2002). Polychlorinated biphenyl-degrading microbial communities in soils and sediments. Curr Opin Microbiol 5, 246-253.
2. Altschul, S. F., Gish, W., Miller, E., Meyers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. J Mol Biol 215, 403-410.
3. ATSDR (2000). Toxicological Profile for Polychlorinated Biphenyls. Atlanta, GA: Agency for Toxic Substances and Disease Registry.
4. Baker, J., Mason, R., Cornwell, J., Ashley, J., Halka, J. & Hill, J. (1997). Spatial Mapping of Sedimentary Contaminants in the Baltimore Harbor/Patapsco River/Back River System. Final Report to Maryland Department of the Environment. UMCES 97-142.
5. Bedard, D. L. & Quensen, J. F. I. (1995). Microbial reductive dechlorination of polychlorinated biphenyls. In Microbial Transformation and Degradation of Toxic Organic Chemicals, pp. 127-216. Edited by L. Y. Young & C. E. Cerniglia. New York: Wiley.
6. Berkaw, M., Sowers, K. R. & May, H. D. (1996). Anaerobic ortho dechlorination of polychlorinated biphenyls by estuarine sediments from Baltimore Harbor. Appl Environ Microbiol 62, 2534-2539.
7. Brown, J. F., Jr, Bedard, D. L., Brennan, M. J., Carnahan, J. C., Feng, H. & Wagner, R. E. (1987). Polychlorinated biphenyl dechlorination in aquatic sediments. Science 236, 709-712.
8. Chun, J. (1995). Computer-assisted classification and identification of actinomycetes. PhD thesis, University of Newcastle upon Tyne.
9. Cupples, A. M., Spormann, A. M. & Mccarty, P. L. (2003). Growth of a Dehalococcoides-like microorganism on vinyl chloride and cis-dichloroethene as electron acceptors as determined by competitive PCR. Appl Environ Microbiol 69, 953-959.
10. Cutter, L., Sowers, K. R. & May, H. D. (1998). Microbial dechlorination of 2,3,5,6-tetrachlorobiphenyl under anaerobic conditions in the absence of soil or sediment. Appl Environ Microbiol 64, 2966-2969.
11. Cutter, L. A., Watts, J. E., Sowers, K. R. & May, H. D. (2001). Identification of a microorganism that links its growth to the reductive dechlorination of 2,3,5,6-chlorobiphenyl. Environ Microbiol 3, 699-709.
12. Edwards, U., Rogall, T., Blocker, H., Emde, M. & Bottger, E. C. (1989). Isolation and direct complete nucleotide determination of entire genes characterization of a gene coding for 16S-ribosomal RNA. Nucleic Acids Res 19, 7843-7853.
13. Felsenstein, J. (1993). PHYLIP (Phylogeny Inference Package). Seattle: Department of Genetics, University of Washington.
14. Fennell, D. E., Nijenhuis, I., Wilson, S. F., Zinder, S. H. & Häggblom, M. M. (2004). Dehalococcoides ethenogenes strain 195 reductively dechlorinates diverse chlorinated aromatic pollutants. Environ Sci Technol 38, 2075-2081.
15. Fitch, W. M. & Margoliash, E. (1967). Construction of phylogenetic trees: a method based on mutation distances as estimated from cytochrome c sequences is of general applicability. Science 155, 279-284.
16. Hendrickson, E. R., Payne, J. A., Young, R. M., Starr, M. G., Perry, M. P., Fahnestock, S., Ellis, D. E. & Ebersole, R. C. (2002). Molecular analysis of Dehalococcoides 16S ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe. Appl Environ Microbiol 68, 485-495.
17. Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21-132. Edited by H. N. Munro. New York: Academic Press.
18. Kluge, A. G. & Farris, F. S. (1969). Quantitative phletics and the evolution of annurans. Syst Zool 18, 1-32.
19. Lane, D. J., Pace, B., Olsen, G. J., Stahl, D. A., Sogin, M. L. & Pace, N. R. (1985). Rapid determination of 16S ribosomal sequences for phylogenetic analysis. Proc Natl Acad Sci U S A 82, 6955-6959.
20. Loffler, F. E., Sun, Q. & Tiedje, J. M. (2000). 16S rRNA gene-based detection of tetrachloroethene-dechlorinating Desulfuromonas and Dehalococcoides species. Appl Environ Microbiol 66, 1369.
21. Maidak, B. L., Cole, J. R., Lilburn, T. G. & 9 other authors (2000). The RDP (Ribosomal Database Project) continues. Nucleic Acids Res 28, 173-174.
22. Miller, G. S., Milliken, C. E., Sowers, K. R. & May, H. D. (2005). Reductive dechlorination of tetrachloroethene to trans-dichloroethene and cis-dichloroethene by PCB-dechlorinating bacterium DF-1. Environ Sci Technol 39, 2631-2635.
23. Milliken, C. E., Meier, G. P., Watts, J. E., Sowers, K. R. & May, H. D. (2004). Microbial anaerobic demethylation and dechlorination of chlorinated hydroquinone metabolites synthesized by basidiomycete fungi. Appl Environ Microbiol 70, 385-392.
24. Pulliam Holoman, T. R., Elberson, M. A., Cutter, L. A., May, H. D. & Sowers, K. R. (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.
25. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
26. Suzuki, M. T. & Giovannoni, S. J. (1996). Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62, 625-630.
27. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The ClustalX Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876-4882.
28. Von Wintzingerode, F., Gobel, U. B. & Stackebrandt, E. (1997). Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21, 213-229.
29. Watts, J. E., Wu, Q., Schreier, S. B., May, H. D. & Sowers, K. R. (2001). Comparative analysis of polychlorinated biphenyl-dechlorinating communities in enrichment cultures using three different molecular screening techniques. Environ Microbiol 3, 710-719.
30. Watts, J. E. M., Fagervold, S. K., Miller, G. S., Milliken, C. E., May, H. D. & Sowers, K. R. (2004). Microbial reductive dechlorination of organochloride pollutants in the marine environment. Mar Biotechnol 6 (suppl. 1), S378-S386.
31. Wiegel, J. & Wu, Q. (2000). Microbial reductive dehalogenation of polychlorinated biphenyls. FEMS Microbiol Ecol 32, 1-17.
32. Wu, Q. Z., Sowers, K. R. & May, H. D. (1998). Microbial reductive dechlorination of aroclor 1260 in anaerobic slurries of estuarine sediments. Appl Environ Microbiol 64, 1052-1058.
33. Wu, Q., Sowers, K. R. & May, H. D. (2000). Establishment of a polychlorinated biphenyl-dechlorinating microbial consortium, specific for doubly flanked chlorines, in a defined, sediment-free medium. Appl Environ Microbiol 66, 49-53.
34. Wu, Q., Milliken, C. E., Meier, G. P., Watts, J. E., Sowers, K. R. & May, H. D. (2002a). Dechlorination of chlorobenzenes by a culture containing bacterium DF-1, a PCB dechlorinating microorganism. Environ Sci Technol 36, 3290-3294.
35. Wu, Q., Watts, J. E. M., Sowers, K. R. & May, H. D. (2002b). Identification of a bacterium that specifically catalyzes the reductive dechlorination of polychlorinated biphenyls with doubly flanked chlorines. Appl Environ Microbiol 68, 807-812.