Gene Probes pp 193-209 | Cite as

Detection of Polychlorinated Biphenyl-Degrading Organisms in Soil

  • John Sanseverino
  • Alice C. Layton
  • Gary S. Sayler
Part of the Methods in Molecular Biology book series (MIMB, volume 179)


Polychlorinated biphenyls (PCBs) are a group of 209 congeners consisting of a biphenyl ring with 1–10 chlorines. In the United States, PCBs, manufactured under the trade name Aroclor, are ubiquitous and recalcitrant pollutants in the environment. PCBs have been shown to biomagnify in the food chain and are associated with chronic health effects (1,2).


  1. 1.
    Hooper, S. W., Pettigrew, C. A. and Sayler, G. S. (1990) Ecological fate, effects, and prospects for the elimination of environmental polychlorinated biphenyls (PCBs). Environ. Toxicol. Chem. 9, 655–667.CrossRefGoogle Scholar
  2. 2.
    Cogliano, V. J. (1998) Assessing the cancer risk from environmental PCBs. Environ. Health Perspect. 106, 317–323.PubMedCrossRefGoogle Scholar
  3. 3.
    Ahmed, M. and Focht, D. D. (1973) Degradation of polychlorinated biphenyls by two species of Achromobacter. Can. J. Microbiol. 19, 47–52.PubMedCrossRefGoogle Scholar
  4. 4.
    Harkness, M. R., McDermott, J. B., Abramowicz, D. A., Salvo, J. J., Flanagan, W. P., Stephens, M. L., et al. (1993) In situ stimulation of aerobic PCB biodegradation in Hudson River sediments. Science 259, 503–507.PubMedCrossRefGoogle Scholar
  5. 5.
    Bedard, D. L. and Quensen, J. F., III. (1995) Microbial reductive dechlorination of polychlorinated biphenyls. In Microbial Transformation and Degradation of Toxic Organic Chemicals (Young, L, and Cerniglia, C., eds.), Wiley-Liss, Inc., New York, pp. 127–216.Google Scholar
  6. 6.
    Sayler, G. S., Sherrill, T. W., Perkins, R. E., Mallory, L. M., Shiaris, M. P., and Pedersen, D. (1982) Impact of coal-coking effluent on sediment microbial communities: a multivariate approach. Appl. Environ. Microbiol. 44, 1118–1129.PubMedGoogle Scholar
  7. 7.
    Sayler, G. S., Perkins, R. E., Sherrill, T. W., Perkins, B. K. Reid, M. C., Shields, M. S., et al. (1983) Microcosm and experimental pond evaluation of microbial community response to synthetic oil contamination in freshwater sediments. Appl. Environ. Microbiol. 46, 211–219.PubMedGoogle Scholar
  8. 8.
    Mallory, L. M. and Sayler, G. S. (1983) Heterotrophic bacterial guild structure: relationship to biodegradative populations. Microbial Ecol. 9, 41–55.CrossRefGoogle Scholar
  9. 9.
    Furukawa, K. (1994) Molecular genetics and evolutionary relationship of PCB-degrading bacteria. Biodegradation 5, 289–300.PubMedCrossRefGoogle Scholar
  10. 10.
    Bartels, F., Backhaus, S., Moore, E. R., Timmis, K. N., and Hofer, B. (1999) Occurrence and expression of glutathione-S-transferase-encoding bphK genes in Burkholderia sp. strain LB400 and other biphenyl-utilizing bacteria. Microbiology 145, 2821–2834.PubMedGoogle Scholar
  11. 11.
    Hofer, B. Backhaus, S., and Timmis, K. N. (1994) The biphenyl/polychlorinated biphenyl-degradation locus (bph) of Pseudomonas sp. LB400 encodes four additional metabolic enzymes. Gene 144, 9–16.PubMedCrossRefGoogle Scholar
  12. 12.
    Erickson, B. D. and Mondello, F. J. (1992) Nucleotide sequencing and transcriptional mapping of genes encoding biphenyl dioxygenase, a multicomponent PCB-degrading enzyme in Pseudomonas strain LB400. J. Bacteriol. 174, 2903–2912.PubMedGoogle Scholar
  13. 13.
    Hofer, B., Eltis, L. D., Dowling, D. N., and Timmis, K. N. (1993) Genetic analysis of a Pseudomonas locus encoding a pathway for biphenyl/polychlorinated biphenyl degradation. Gene 130, 47–55.PubMedCrossRefGoogle Scholar
  14. 14.
    Furukawa, K. and Miyazaki, T. (1986) Cloning of a gene cluster encoding biphenyl and chlorobiphenyl degradation in Pseudomonas pseudoalcaligenes. J. Bacteriol. 166, 392–398.PubMedGoogle Scholar
  15. 15.
    Taira, K., Hirose, J., Hayashida, S., and Furukawa, K. (1992) Analysis of bph operon from the polychlorinated biphenyl-degrading strain of Pseudomonas pseudoalcaligenes KF707. J. Biol. Chem. 267, 4844–4853.PubMedGoogle Scholar
  16. 16.
    Kahn, A. and Walia, S. (1989) Cloning of bacterial genes specifying degradation of 4-chlorobiphenyl from Pseudomonas putida OU83. Appl. Environ. Microbiol. 55, 798–805.Google Scholar
  17. 17.
    Walia, S., Khan, A., and Rosenthal, N. (1990) Construction and applications of DNA probes for detection of polychlorinated biphenyl-degrading genotypes in toxic organic-contaminated soil environments. Appl. Environ. Microbiol. 56, 254–259.PubMedGoogle Scholar
  18. 18.
    Kahn, A. A., Wang, R. F., Nawaz, M. S., and Cerniglia, C. E. (1997) Nucleotide sequence of the genes encoding cis-biphenyl dihydrodiol dehydrogenase (bphB) and the expression of an active recombinant His-tagged bphB gene product from PCB degrading bacterium, Pseudomonas putida OU83. FEMS Microbiol. Lett. 154, 317–324.CrossRefGoogle Scholar
  19. 19.
    Ahmad, D., Masse, R., and Sylvestre, M. (1990) Cloning and expression of genes involved in 4-chlorobiphenyl transformation by Pseudomonas testosteroni: homology to polychlorobiphenyl-degrading genes in other bacteria. Gene 86, 53–61.PubMedCrossRefGoogle Scholar
  20. 20.
    Ahmad, D., Sylvestre, M., and Sondossi, M. (1991) Subcloning of bph genes from Pseudomonas testosteroni B-356 in Pseudomonas putida and Escherichia coli: evidence for dehalogenation during initial attack on chlorobiphenyls. Appl. Environ. Microbiol. 57, 2880–2887.PubMedGoogle Scholar
  21. 21.
    Sylvestre, M., Sirois, M., Hurtubise, Y., Bergeron, J., Ahmad, D., Shareck, F., et al. (1996) Sequencing of Comamonas testosteroni strain B-356 biphenyl/chlorobiphenyl dioxygenase genes: Evolutionary relationships among Gram-negative bacterial biphenyl dioxygenases. Gene 174, 195–205.PubMedCrossRefGoogle Scholar
  22. 22.
    Sharma, A., Chunn, C. D., Rothmel, R. K., and Unterman, R. (1991) Studies on bacterial degradation of polychlorinated biphenyls: optimization of parameters for in vivo enzyme activity. Poster Q48. 91st Gen. Meet Am. Soc. Microbiol., May 5–9, Dallas, TX.Google Scholar
  23. 23.
    Asturias, J. A., Diaz, E., and Timmis, K. N. (1995) The evolutionary relationship of biphenyl dioxygenase from gram-positive Rhodococcus globerulus P6 to multicomponent dioxygenease from Gram-negative bacteria. Gene 156, 11–18.PubMedCrossRefGoogle Scholar
  24. 24.
    Yamada, A., Kishi, H., Sugiyama, K., Hatta, T., Nakamura, K. Masai, E., and Fukuda, M. (1998) Two nearly identical aromatic compound hydrolase genes in a strong polychlorinated biphenyl degrader, Rhodococcus sp. strain RHA1. Appl. Environ. Microbiol. 64, 2006–2012.PubMedGoogle Scholar
  25. 25.
    Masai, E., Yamada, A., Healy, J. M., Hatta, T., Kimbara, K., Fukuda, M., and Yano, K. (1995) Characterization of biphenyl catabolic genes of Gram-positive polychlorinated biphenyl degrader Rhodococcus sp. strain RHA1. Appl. Environ. Microbiol. 61, 2079–2085.PubMedGoogle Scholar
  26. 26.
    Masai, E., Sugiyama, K., Iwashita, N., Shimizu, S., Hauschild, J. E., Hatta, T., et al. (1997) The bphDEF meta-cleavage pathway genes involved in biphenyl/polychlorinated biphenyl degradation are located on a linear plasmid and separated from the initial bphACB genes in Rhodococcus sp. strain RHA1. Gene 187, 141–149.PubMedCrossRefGoogle Scholar
  27. 27.
    Hauschild, J. E., Masai, E., Sugiyama, K., Hatta, T., Kimbara, K., Fukuda, M., and Yano, K. (1996) Identification of an alternative 2,3-dihydroxybiphenyl 1,2-dioxygenase in Rhodococcus sp. strain RHA1 and cloning of the gene. Appl. Environ. Microbiol. 62, 2940–2946.PubMedGoogle Scholar
  28. 28.
    Kosono, S., Maeda, M., Fuji, F., Arai, H., and Kudo, T. (1997) Three of the seven bphC genes of Rhodococcus erythropolis TA421, isolated from a termite ecosystem, are located on an indigenous plasmid associated with biphenyl degradation. Appl. Environ. Microbiol. 63, 3282–3285.PubMedGoogle Scholar
  29. 29.
    Shimura, M., Mukerjee-Dhar, G., Kimbara, K., Nagato, H., Kiyohara, and Hatta, T. (1999) Isolation and characterization of a thermophilic Bacillus sp. JF8 capable of degrading polychlorinated biphenyls and naphthalenes. FEMS Microbiology Letters 178, 87–93.PubMedCrossRefGoogle Scholar
  30. 30.
    Bedard, D., Untermann, R., Bopp, L. H., Brennan, M. J., Haberl, M. L., and Johnson, C. (1986) Rapid assay for screening and characterizing microorganisms for the ability to degrade polychlorinated biphenyls. Appl. Environ. Microbiol. 51, 761–768.PubMedGoogle Scholar
  31. 31.
    Mondello, F. J., Turcich, M. P., Lobos, J. H., and Erickson, B. D. (1997) Identification and modification of biphenyl dioxygenase sequences that determine the specificity of polychlorinated biphenyl degradation. Appl. Environ.Microbiol. 63, 3096–3103.PubMedGoogle Scholar
  32. 32.
    Seto, M., Kimbara, K., Shimura, M., Hatta, T., Fukuda, M., and Yano, K. (1995) A novel transformation of polychlorinated biphenyls by Rhodococcus sp. strain RHA1. Appl. Environ. Microbiol. 61, 3353–3358.PubMedGoogle Scholar
  33. 33.
    Peng, X., Egashira, T., Hanashiro, K., Masai, E., Nishikawa, S., Katayama, et al. (1998) Cloning of a Sphingomonas paucimobilis SYK-6 gene encoding a novel oxygenase that cleaves lignin-related biphenyl and characterization of the enzyme. Appl. Environ. Microbiol. 64, 2520–2527.PubMedGoogle Scholar
  34. 34.
    Yadav, J. S., Quensen, J. F., III, Tiedje, J. M., and Reddy, C. A. (1995) Degradation of polychlorinated biphenyl mixtures (Aroclors 1242, 1254, and 1260) by the white rot fungus Phanerochaete chyrosporium as evidenced by congener-specific analysis. Appl. Environ. Microbiol. 61, 2560–2565.PubMedGoogle Scholar
  35. 35.
    Erb, R.W. and Wagner-Dobbler, I. (1993) Detection of polychlorinated biphenyl degradation genes in polluted sediments by direct DNA extraction and polymerase chain reaction. Appl. Environ. Microbiol. 59, 4065–4073.PubMedGoogle Scholar
  36. 36.
    Layton, A. C., Lajoie, C. A., Easter, J. P., Jernigan, R., Sanseverino, J., and Sayler, G. S. (1994) Molecular diagnostics and chemical analysis for assessing biodegradation of polychlorinated biphenyls in contaminated soils. J. Industr. Microbiol. 13, 392–401.CrossRefGoogle Scholar
  37. 37.
    Pellizari, V. H., Bezborodnikov, S., Quensen, J. F.,III, and Tiedje, J. M. (1996) Evaluation of strains isolated by growth on naphthalene and biphenyl for hybridization of genes to dioxygnease probes and polychlorinated biphenyl-degrading ability. Appl. Environ. Microbiol. 62, 2053–2058.PubMedGoogle Scholar
  38. 38.
    Van Dyke, M. I., Lee, H., and Trevors, J. T. (1996) Survival of luxAB marked Alcaligenes eutrophus H850 in PCB-contaminated soil and sediment. J. Chem. Tech. Biotech. 65, 115–122.CrossRefGoogle Scholar
  39. 39.
    Kimura, N., Nishi, A., Goto, M., and Furukawa, K. (1997) Functional analyses of a variety of chimeric dioxygenases constructed from two biphenyl dioxygenases that are similar structurally but different functionally. J. Bacteriol. 179, 3936–3943.PubMedGoogle Scholar
  40. 40.
    Anderson, L. M. and Young, B. D. (1985) Quantitative filter hybridization. In Nucleic Acid Hybridization: A Practical Approach (Hames, B. D. and Higgins, S. J., eds.), IRL Press Limited, Oxford, England, Chapter 4, pp. 73–111.Google Scholar
  41. 41.
    Bedard, D., Wagner, R. E., Brennan, M. J., Haberl, M. L., and Brown, J. F., Jr. (1987) Extensive degradation of aroclors and environmentally transformed polychlorinated biphenyls by Alcaligenes eutrophus H850. Appl. Environ. Microbiol. 53, 1094–1102.PubMedGoogle Scholar
  42. 42.
    Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) Clustal W: improving sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680.PubMedCrossRefGoogle Scholar
  43. 43.
    Page, R. D. (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Compu. Appl. Biosci. 12, 357–359.Google Scholar
  44. 44.
    Church, G. M. and Gilbert, W. (1984) Genomic sequencing. Proc. Natl. Acad. Sci. USA 81, 1991–1995.PubMedCrossRefGoogle Scholar
  45. 45.
    Ogram, A., Sayler, G. S., and Barkay, T. (1987) The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 7, 57–66.CrossRefGoogle Scholar
  46. 46.
    Holben, W. E., Jansson, J. K., Chelm, B. K., and Tiedje, J. M. (1988) DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54, 703–711.PubMedGoogle Scholar
  47. 47.
    Tsai, Y.-L. and Olson, B. H. (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57, 1070–1074.PubMedGoogle Scholar
  48. 48.
    Picard, C., Ponsonnet, C., Paget, E., Nesme, X., and Simonet, P. (1992) Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl. Environ. Microbiol. 58, 2717–2722.PubMedGoogle Scholar
  49. 49.
    Jacobsen, C. S. and Rasmussen, O. F. (1992) Development and application of a new method to extract bacterial DNA from soil based on separation of bacteria from soil with cation-exchange resin. Appl. Environ. Microbiol. 58, 2458–2462.PubMedGoogle Scholar
  50. 50.
    Stapleton, R. D., Ripp, S., Jimenez, L. Cheol-Koh, S., Fleming, J. T., Gregory, I. R., and Sayler, G. S. (1998) Nucleic acid analytical approaches in bioremediation: site assessment and characterization. J. Microbiol. Methods. 32, 165–178.CrossRefGoogle Scholar
  51. 51.
    Stapleton, R. D. (1997) Natural attenuation of petroleum hydrocarbons in ground-water. Ph.D. dissertation. University of Tennessee, Knoxville, USA.Google Scholar
  52. 52.
    Promega (1992) Technical Manual 16. Madison, Wisconsin. USA.Google Scholar
  53. 53.
    Applegate, B. M., Matrubutham, U., Sanseverino, J., and Sayler, G. S. (1995) Biodegradation genes as marker genes in microbial ecosystems. Molecular Microbial Ecology Manual 6.1.8, 1–14.Google Scholar
  54. 54.
    Johnston, W. H., Stapleton, R., and Sayler, G. S. (1996) Direct extraction of microbial DNA from soils and sediments. Molecular Microbial Ecology Manual 1.3.2, 1–9.Google Scholar
  55. 55.
    Stahl, D. A., Flesher, B., Mansfield, H. R., and Montgomery, L. (1988) Use of phylogenetically-based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54, 1079–1084.PubMedGoogle Scholar
  56. 56.
    Smith, C. L., Econome, J. G., Schutt, A., Klco, S., and Cantor, C. R. (1987) A physical map of the Escherichia coli K12 genome. Science 236, 1448–1453.PubMedCrossRefGoogle Scholar
  57. 57.
    Klappenbach, J. A., Dunbar, J. M. and Schmidt, T. M. (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 66, 1328–1333.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc. 2002

Authors and Affiliations

  • John Sanseverino
  • Alice C. Layton
    • 1
  • Gary S. Sayler
  1. 1.Center for Environmental Biotechnology and Department of MicrobiologyThe University of TennesseeKnoxville

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