Estimation of “Dehalococcoides” Populations in Lake Sediment Contaminated with Low Levels of Polychlorinated Dioxins

Microbes and Environments

Volumn 20, Issue 4, 2005, Pages 216-226

  Hiraishi, Akira ^a   Sakamaki, Noriko ^a   Miyakoda, Hideki ^b   Maruyama, Tomoko ^c   Kato, Kenji ^c   Futamata, Hiroyuki ^a  

^a TOYOHASHI UNIVERSITY OF TECHNOLOGY   (Japan)

^b Shintokogyo Ltd   (Japan)

^c SHIZUOKA UNIVERSITY   (Japan)

Author keywords

dioxins; real time PCR; sediment; Dehalococcoides

Indexed keywords

EID: 34948869688     PISSN: 13426311     EISSN: 13474405     Source Type: Journal    
DOI: 10.1264/jsme2.20.216     Document Type: Article

References (55)

1. Abraham, W.R., B. Nogales, P.N. Golyshin, D.H. Pieper and K.N. Timmis. 2002. Polychlorinated biphenyl-degrading microbial communities in soils and sediments. Curr. Opin. Microbiol. 5: 246–253.
2. Adriaens, P., Q. Fu and D. Grbic'-Galic' 1995. Bioavailability and transformation of highly chlorinated dibenzo-p-dioxins and dibenzofurans in anaerobic soils and sediments. Environ. Sci. Technol. 29: 2252–2260.
3. Adrian, L., U. Szewzyk, J. Wecke and H. Görisch. 2000. Bacterial dehalorespiration with chlorinated benzenes. Nature 408: 580–583.
4. Altschul, S.F., T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller and D.J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389–3402.
5. Ballerstedt, H., J. Hantke, M. Bunge, B. Werner, J. Gerritse, J.R. Andreesen and U. Lechner. 2004. Properties of a trichlorodiben-zo-p-dioxin-dechlorinating mixed culture with a Dehalococcoides as putative dechlorinating species. FEMS Microbiol. Ecol. 47: 223–234.
6. Ballerstedt, H., A. Kraus and U. Lechner. 1997. Reductive dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin and its products by anaerobic mixed cultures from Saale River sediment. Environ. Sci. Technol. 31: 1749–1753.
7. Barkovskii, A.L. and P. Adriaens. 1996. Microbial dechlorination of historically present and freshly spiked chlorinated dioxins and diversity of dioxin-dechlorinating populations. Appl. Environ. Microbiol. 62: 4556–4562.
8. Beurskens, J.E.M., M. Toussaint, J. de Wolf, J.M.D. van der Steen, P.C. Slot, L.C.M. Commandeur and J.R. Parsons. 1995. Dehalogenation of chlorinated dioxins by an anaerobic microbial consortium from sediment. Environ. Toxicol. Chem. 14: 939–943.
9. Bunge, M., L. Adrian, A. Kraus, M. Opel, W.G. Lorenz, J.R. Andreesen, H. Gorisch and U. Lechner. 2003. Reductive dehalogenation of chlorinated dioxins by an anaerobic bacterium. Nature 421: 357–360.
10. Bunge, M., H. Ballerstedt and U. Lechner. 2001. Regiospecific dechlorination of spiked tetra- and trichlorodibenzo-p-dioxins by anaerobic bacteria from PCDD/F-contaminated Spittelwasser sediments. Chemosphere 43: 675–681.
11. Cutter, L.A., J.E. Watts, K.R. Sowers and H.D. May. 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. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.
13. Fennell, D.E., I. Nijenhuis, S.F. Wilson, S.H. Zinder and M.M. Häggblom. 2004. Dehalococcoides ethenogenes strain 195 reductively dechlorinates diverse chlorinated aromatic pollutants. Environ. Sci. Technol. 38: 2075–2081.
14. Fogel, G.B., C.R. Collins, J. Li and C.F. Brunk. 1999. Prokaryotic genome size and SSU rDNA copy number: estimation of microbial relative abundance from a mixed population. Microb. Ecol. 38: 93–113.
15. Fu, Q.S., A.L. Barkovskii and P. Adriaens. 1999. Reductive transformation of dioxins: an assessment of the contribution of dissolved organic matter to dechlorination reactions. Environ. Sci. Technol. 33: 3837–3842.
16. Futamata, H., T. Uchida, N. Yoshida, Y. Yonemitsu and A. Hiraishi. 2004. Distribution of dibenzofuran-degrading bacteria in soils polluted with different levels of polychlorinated dioxins. Microbes Environ. 19: 172–177.
17. Hendrickson, E.R., J.A. Payne, R.M. Young, M.G. Starr, M.P. Perry, S. Fahnestock, D.E. Ellis and R.C. Ebersole. 2002. Molecular analysis of Dehalococcoides 16S Ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe. Appl. Environ. Microbiol. 68: 485–495.
18. Hiraishi, A. 1999. Isoprenoid quinones as biomarkers of microbial populations in the environment. J. Biosci. Bioeng. 88: 449- 460.
19. Hiraishi, A. 2003. Biodiversity of dioxin-degrading microorganisms and potential utilization in bioremediation. Microbes Environ. 18: 105–125.
20. Hiraishi, A., M. Iwasaki, T. Kawagishi, N. Yoshida, T. Narihiro and K. Kato. 2003. Significance of lipoquinones as quantitative biomarkers of bacterial populations in the environment. Microbes Environ. 18: 89–93.
21. Hiraishi, A. and K. Kato. 1999. Quinone profiles in lake sediments: implications for microbial diversity and community structures. J. Gen. Appl. Microbiol. 45: 221–227.
22. Hiraishi, A., H. Miyakoda, B.R. Lim, H.Y. Hu, K. Fujie and J. Suzuki. 2001. Toward the bioremediation of dioxin-polluted soil: structural and functional analyses of in situ microbial populations by quinone profiling and culture-dependent methods. Appl. Microbiol. Biotechnol. 57: 248–256.
23. Ikenaka, Y., H. Eun, E. Watanabe, F. Kumon and Y. Miyabara. 2005. Estimation of sources and inflow of dioxins and polycyclic aromatic hydrocarbons from the sediment core of Lake Suwa, Japan. Environ. Pollut. 138: 529–537.
24. Isosaari, P., H. Pajunen and T. Vartiainen. 2002. PCDD/F and PCB history in dated sediments of a rural lake. Chemosphere 47: 575–583.
25. Iwasaki, M. and A. Hiraishi. 1998. A new approach to numerical analyses of microbial quinone profiles in the environment. Microbes Environ. 13: 67–76.
26. Kanai, Y., Y. Inouchi, H. Katayama and Y. Saito. 1997. Radioactivity measurements in bottom sediments from Lake Suwa, Nagano Prefecture, using a new low background system to estimate sedimentation rates (in Japanese). Bull. Geol. Surv. Jpn. 48: 277–295.
27. Kao, C.M., S.C. Chen, J.K. Liu and M.J. Wu. 2001. Evaluation of TCDD biodegradability under different redox conditions. Chemosphere 44: 1447–1454.
28. Kassenga, G., J.H. Pardue, W.M. Moe and K.S. Bowman. 2004. Hydrogen thresholds as indicators of dehalorespiration in constructed treatment wetlands. Environ. Sci. Technol. 38: 1024- 1030.
29. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111–120.
30. Kube, M., A. Beck, S.H. Zinder, H. Kuhl, R. Reinhardt and L. Adrian. 2005. Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1. Nat. Biotechnol. 23: 1269–1273.
31. Marmur, J. 1961. A procedure for the isolation of deoxyribonucleic acid from microorganisms. J. Mol. Biol. 3: 208–218.
32. Maruyama, T., N. Futatsuguri, H.D. Park and K. Kato. 2001. Distribution of harmful substance degrading microbes in a core sample of Lake Suwa (in Japanease). Ann. Environ. Sci., Shinshu Univ. 23: 61–66.
33. Masunaga, S., Y. Yao, I. Ogura, S. Nakai, Y. Kanai, M. Yamamuro and J. Nakanishi. 2001. Identifying sources and mass balance of dioxin pollution in Lake Shinji Basin, Japan. Environ. Sci. Technol. 35: 1967–1973.
34. Maymo-Gatell, X., Y.T. Chien, J.M. Gossett and S.H. Zinder. 1997. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276: 1568–1571.
35. Miller, G.S., C.E. Milliken, K.R. Sowers and H.D. May. 2005. Reductive dechlorination of tetrachloroethene to trans-dichloro-ethene and cis-dichloroethene by PCB-dechlorinating bacterium DF-1. Environ. Sci. Technol. 39: 2631–2635.
36. Narihiro, T., Y. Yamanaka and A. Hiraishi. 2003. High culturability of bacteria in commercially available personal composters for fed-batch treatment of household biowaste. Microbes Environ. 18: 94–99.
37. Nealson, K.H. 2003. Harnessing microbial appetites for remediation. Nat. Biotechnol. 21: 243–244.
38. Rose, N.L. and B. B. Rippey 2002. The historical record of PAH, PCB, trace metal and fly-ash particle deposition at a remote lake in north-west Scotland. Environ. Pollut. 117: 121–132.
39. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425.
40. Sakurai, T. 2003. Dioxins in aquatic sediment and soil in the Kanto region of Japan: major sources and their contributions. Environ. Sci. Technol. 37: 3133–3140.
41. Sakurai, T., N. Suzuki, S. Masunaga and J. Nakanishi. 1998. Origin attribution of polychlorinated dibenzo-p-dioxins and dibenzofurans in sediment and soil from a Japanese freshwater lake area through congener-specific data analysis. Chemosphere 37: 2211- 2224.
42. Sambrook, J., E.F. Fritsch and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
43. Seshadri, R., L. Adrian, D.E. Fouts, J.A. Eisen, A.M. Phillippy, B.A. Methe, N.L. Ward, W.C. Nelson, R.T. Deboy, H.M. Khouri, J.F. Kolonay, R.J. Dodson, S.C. Daugherty, L.M. Brinkac, S.A. Sullivan, R. Madupu, K.E. Nelson, K.H. Kang, M. Impraim, K. Tran, J.M. Robinson, H.A. Forberger, C.M. Fraser, S.H. Zinder and J.F. Heidelberg. 2005. Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science 307: 105–108.
44. Shiang Fu, Q., A.L. Barkovskii and P. Adriaens. 2005. Microbial dechlorination of dioxins in estuarine enrichment cultures: effects of respiratory conditions and priming compound on community structure and dechlorination patterns. Mar. Environ. Res. 59: 177–195.
45. Stern, G.A., E. Braekevelt, P.A. Helm, T.F. Bidleman, P.M. Out-ridge, W.L. Lockhart, R. McNeeley, B. Rosenberg, M.G. Ikonomou, P. Hamilton, G.T. Tomy and P. Wilkinson. 2005. Modern and historical fluxes of halogenated organic contaminants to a lake in the Canadian arctic, as determined from annually laminated sediment cores. Sci. Total Environ. 342: 223–243.
46. Thompson, J.D., D.G. Higgins and T.J. Gibson. 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.
47. van den Berg, M., L. Birnbaum, A.T.C. Bosveld, B. Brunstrom, P. Cook, M. Feeley, J.P. Giesy, A. Hanberg, R. Hasegawa, S.W. Kennedy, T. Kubiak, J.C. Larsen, F.X.R. van Leeuwen, A.K.D. Liem, C. Nolt, R.E. Peterson, L. Poellinger, S. Safe, D. Schrenk, D. Tillitt, M. Tysklind, M. Younes, F. Waern and T. Zacharewski. 1998. Toxic equivalency factors (TEFs) for PCBs, PCDDs, PCDFs for humans and wildlife. Environ. Health Perspect. 106: 775–792.
48. Vargas, C., D.E. Fennell and M.M. Haggblom. 2001. Anaerobic reductive dechlorination of chlorinated dioxins in estuarine sediments. Appl. Microbiol. Biotechnol. 57: 786–790.
49. Watts, J.E., S.K. Fagervold, H.D. May and K.R. Sowers. 2005. A PCR-based specific assay reveals a population of bacteria within the Chloroflexi associated with the reductive dehalogenation of polychlorinated biphenyls. Microbiology 151: 2039–2046.
50. Weisburg, W.G., S.M. Barns, D.A. Pelletier and D.J. Lane. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173: 697–703.
51. Wittich, R.M. 1998. Degradation of dioxin-like compounds by microorganisms. Appl. Microbiol. Biotechnol. 49: 489–499.
52. Wu, Q., C.E. Milliken, G.P. Meier, J.E.M. Watts, K.R. Sowers and H.D. May. 2002. Dechlorination of chlorobenzens by a culture containing bacterium DF-1, a PCB dechlorinating microorganism. Environ. Sci. Technol. 36: 3290–3294.
53. Wu, W.Z., K.W. Schramm, Y. Xu and A. Kettrup. 2001. Mobility and profiles of polychlorinated dibenzo-p-dioxins and dibenzofurans in sediment of Ya-Er Lake, China. Water Res. 35: 3025- 3033.
54. Wu, Q., J.E. Watts, K.R. Sowers and H.D. May. 2002. Identification of a bacterium that specifically catalyzes the reductive dechlorination of polychlorinated biphenyls with doubly flanked chlorines. Appl. Environ. Microbiol. 68: 807–812.
55. Yoshida, N., N. Takahashi and A. Hiraishi. 2005. Phylogenetic characterization of a polychlorinated dioxin-dechlorinating microbial community by use of microcosm studies. Appl. Environ. Microbiol. 71: 4325–4334.