Detection of a Bacterial Group within the Phylum Chloroflexi and Reductive-Dehalogenase-Homologous Genes in Pentachlorobenzene-Dechlorinating Estuarine Sediment from the Arakawa River, Japan

Microbes and Environments

Volumn 21, Issue 3, 2006, Pages 154-162

  Santoh, Kyosuke ^a   Kouzuma, Atsushi ^a   Ishizeki, Ryoko ^b   Iwata, Kenichi ^a   Shimura, Minoru ^c   Hayakawa, Toshio ^c   Hoaki, Toshihiro ^d   Nojiri, Hideaki ^a   Omori, Toshio ^b   Yamane, Hisakazu ^a   Habe, Hiroshi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b SHIBAURA INSTITUTE OF TECHNOLOGY   (Japan)

^c RAILWAY TECHNICAL RESEARCH INSTITUTE   (Japan)

^d TAISEI CORPORATION   (Japan)

Author keywords

Chloroflexi; Dehalococcoides; Pentachlorobenzene; Persistent organic pollutants; Reductive dehalogenation

Indexed keywords

EID: 70349950533     PISSN: 13426311     EISSN: 13474405     Source Type: Journal    
DOI: 10.1264/jsme2.21.154     Document Type: Article

References (31)

1. Adrian, L. and H. Görisch. 2002. Microbial transformation of chlorinated benzenes under anaerobic conditions. Res. Microbiol. 153: 131–137.
2. Adrian, L., U. Szewzyk, J. Wecke and H. Görisch. 2000. Bacterial dehalorespiration with chlorinated benzenes. Nature 408: 580–583.
3. 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: 3389–3420.
4. Beurskens, J.E.M., D.G.C. Connie, H. van den Heuvel, M. Swart, J. de Wolf and J. Dolfing. 1994. Dechlorination of chlorinated benzenes by an anaerobic microbial consortium that selectively mediates the thermodynamic most favorable reactions. Environ. Sci. Technol. 28: 701–706.
5. Bruschi, M. and F. Guerlesquin. 1998. Structure, function and evolution of bacterial ferredoxins. FEMS. Microbiol. Rev. 54: 155–174.
6. Chang, B.V., C.J. Su and S.Y. Yuan. 1998. Microbial hexachlo-robenzene dechlorination under three reducing conditions. Chemosphere 36: 2721–2730.
7. Fathepure, B.Z., J.M. Tiedje and S.A. Boyd. 1988. Reductive dechlorination of hexachlorobenzene to tri- and dichlorobenzenes in anaerobic sewage sludge. Appl. Environ. Microbiol. 54: 327- 330.
8. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.
9. Fennell, D.E., I. Nijenhuis, S.F. Wilson, S.H. Zinder and M.M. Häggblom. 2004. Dehalococcoides ethenogens strain 195 reductively dechlorinates diverse chlorinated aromatic pollutants. Environ. Sci. Technol. 38: 2075–2081.
10. Gustafson, D.L., M.E. Long, R.S. Thomas, S.A. Benjamin and R.S.H. Yang. 2002. Comparative heptatocarcinogenicity of hexachlorobenzene, pentachlorobenzene, 1,2,4,5-tetrachlorobenzene, and 1,4-dichlorobenzene: application of a medium-term liver focus bioassay and molecular and cellular indices. Toxicol. Sci. 53: 245–252.
11. Hiraishi, A., S. Kaiya, H. Miyakoda and H. Futamata. 2005. Biotransformation of polychlorinated dioxins and microbial community dynamics in sediment microcosms at different contamination levels. Microbes Environ. 20: 227–242.
12. Hiraishi, A., N. Sakamaki, H. Miyakoda, T. Maruyama, K. Kato and H. Futamata. 2005. Estimation of “Dehalococcoides” populations in lake sediment contaminated with low levels of polychlorinated dioxins. Microbes Environ. 20: 216–226.
13. Hölscher, T., H. Görisch and L. Adrian. 2003. Reductive dehalo-genation of chlorobenzene congeners in cell extracts of Dehalococcoides sp. strain CBDB1. Appl. Environ. Microbiol. 69: 2999–3001.
14. Hölscher, T., R. Krajmalnik-Brown, K.M. Ritalahti, F. von Wintzingerode, H. Görisch, F.E. Löffler and L. Adrian. 2004. Multiple nonidentical reductive-dehalogenase-homologous gene are common in Dehalococcoides. Appl. Environ. Microbiol. 70: 5290–5297.
15. Holliger, C., G. Schraa, A.J.M. Stams and A.J.B. Zehnder. 1992. Enrichment and properties of an anaerobic mixed culture reductively dechlorinating 1,2,3-trichlorobenzene to 1,3-dichloroben-zene. Appl. Environ. Microbiol. 58: 1636–1644.
16. Jayachandran, G., H. Görisch and L. Adrian. 2003. Dehalorespi-ration with hexachlorobenzene and pentachlorobenzene by Dehalococcoides sp. strain CBDB1. Arch. Microbiol. 180: 411–416.
17. 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.
18. Maymó-Gatell, X., Y.T. Chien, J.M. Gosett and S.H. Zinder. 1997. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276: 1568–1571.
19. Muyzer, G., E.C. de Waal and A.G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59: 695–700.
20. Oliver, B.G. and K.D. Nicol. 1982. Chlorobenzenes in sediments, water, and selected fish from lakes Superior, Huron, Erie, and Ontario. Environ. Sci. Technol. 16: 532–536.
21. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425.
22. Sambrook, J., E.F. Fritsch and T. Maniatis. 1989. Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
23. 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-dechlo-rinating bacterium Dehalococcoides ethenogens. Science 307: 105–108.
24. Thompson, J.D., D.G. Higgins and T.J. Gibson. 1994. CLUST-ALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matric choice. Nucleic Acid Res. 22: 4673–4680.
25. United Nations Environmental Programme. 2001. Stockholm Convention on Persistent Organic Pollutants. UNEP/POPS/ CONF/2.
26. van de Pas, B.A., H. Smidt, W.R. Hagen, J. van der Oost, G. Schraa, A.J.M. Stams and W.M. de Vos. 1999. Purification and molecular characterization of ortho-chlorophenol reductive deha-logenase, a key enzyme of halorespiration in Desulfitobacterium dehalogenans. J. Biol. Chem. 274: 20287–20292.
27. 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 dechlorination of polychlorinated biphenyls. Microbiology 151: 2039–2064.
28. Wu, Q., C.E. Milliken, G.P. Meier, J.E.M. Watts, K.R. Sowers and H.D. May. 2002. Dechlorination of chlorobenzenes by a culture containing bacterium DF-1, a PCB dechlorinating microorganism. Environ. Sci. Technol. 36: 3290–3294.
29. Yeh, D.H. and S.G. Pavlostathis. 2001. Development of hexachlorobenzene-dechlorinating mixed cultures using polysor-bate surfactants as a carbon source. Wat. Sci. Technol. 43: 43–50.
30. Yoshida, N., N. Takahashi and A. Hiraishi. 2005. Phylogenetic characterization of a polychlorinated dioxin-dechlorinating microbial community by the use of microcosm studies. Appl. Environ. Microbiol. 71: 4325–4334.
31. Zhou, J., M.A. Buruns and J.M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62: 316–322.