Analysis of a Bacterial Community in 3-Chlorobenzoate-Contaminated Soil by PCR-DGGE Targeting the 16S rRNA Gene and Benzoate 1,2-Dioxygenase Gene (benA)

Microbes and Environments

Volumn 20, Issue 3, 2005, Pages 151-159

  Morimoto, Sho ^a   Togami, Kazuki ^a   Ogawa, Naoto ^a   Hasebe, Akira ^a   Fujii, Takeshi ^a  

^a NATIONAL INSTITUTE FOR AGRO ENVIRONMENTAL SCIENCES   (Japan)

Author keywords

3 chlorobenzoate degrading bacteria; benA; PCR DGGE; Soil

Indexed keywords

EID: 34547727714     PISSN: 13426311     EISSN: 13474405     Source Type: Journal    
DOI: 10.1264/jsme2.20.151     Document Type: Article

References (41)

1. Amann, R. I., W. Ludwig and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143–169.
2. Bott, T. L. and L. A. Kaplan. 2002. Autecological properties of 3-chlorobenzoate-degrading bacteria and their population dynamics when introduced into sediments. Microb. Ecol. 43: 199–216.
3. Dorn, E., M. Hellwig, W. Reineke and H. J. Knackmuss. 1974. Isolation and characterization of a 3-chlorobenzoate degrading pseudomonad. Arch. Microbiol. 99: 61–70.
4. Duarte, G. F., A. S. Rosado, L. Seldin, W. de Araujo and J. D. van Elsas. 2001. Analysis of bacterial community structure in sulfurous-oil-containing soils and detection of species carrying dibenzothiophene desulfurization (dsz) genes. Appl. Environ. Microbiol. 67: 1052–1062.
5. Fjellbirkeland, A., V. Torsvik and L. Øvreås. 2001. Methan-otrophic diversity in an agricultural soil as evaluated by denaturing gradient gel electrophoresis profiles of pmoA, mxaF and 16S rDNA sequences. Antonie van Leeuwenhoek 79: 209–217.
6. Focht, D. D. and D. Shelton. 1987. Growth kinetics of Pseudomonas alcaligenes C-0 relative to inoculation and 3-chlorobenzoate metabolism in soil. Appl. Environ. Microbiol. 53: 1846–1849.
7. Francisco, P., Jr., N. Ogawa, K. Suzuki and K. Miyashita. 2001. The chlorobenzoate dioxygenase genes of Burkholderia sp. strain NK8 involved in the catabolism of chlorobenzoates. Microbiology 147: 121–133.
8. Fulthorpe, R. R., A. N. Rhodes and J. M. Tiedje. 1996. Pristine soils mineralize 3-chlorobenzoate and 2,4-dichlorophenoxyacetate via different microbial populations. Appl. Environ. Microbiol. 62: 1159–1166.
9. Fulthorpe, R. R., A. N. Rhodes and J. M. Tiedje. 1998. High levels of endemicity of 3-chlorobenzoate-degrading soil bacteria. Appl. Environ. Microbiol. 64: 1620–1627.
10. Gentry, T. J., D. T. Newby, K. L. Josephson and I. L. Pepper. 2001. Soil microbial population dynamics following bioaugmen-tation with a 3-chlorobenzoate-degrading bacterial culture. Bio-augmentation effects on soil microorganisms. Biodegradation 12: 349–357.
11. Gentry, T. J., G. Wang, C. Rensing and I. L. Pepper. 2004. Chlorobenzoate-degrading bacteria in similar pristine soils exhibit different community structures and population dynamics in response to anthropogenic 2-, 3-, and 4-chlorobenzoate levels. Microb. Ecol. 48: 90–102.
12. Haddad, S., D. M. Eby and E. L. Neidle. 2001. Cloning and expression of the benzoate dioxygenase genes from Rhodococcus sp. strain 19070. Appl. Environ. Microbiol. 67: 2507–2514.
13. Harayama, S., M. Rekik, A. Bairoch, E. L. Neidle and L. N. Ornston. 1991. Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWW0 plasmid xylXYZ, genes encoding benzoate dioxygenases. J. Bacteriol. 173: 7540–7548.
14. Henckel, T., M. Friedrich and R. Conrad. 1999. Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Appl. Environ. Microbiol. 65: 1980–1990.
15. Hernandez, B. S., F. K. Higson, R. Kondrat and D. D. Focht. 1991. Metabolism of and inhibition by chlorobenzoates in Pseudomonas putida P111. Appl. Environ. Microbiol. 57: 3361- 3366.
16. Kitagawa, W., K. Miyauchi, E. Masai and M. Fukuda. 2001. Cloning and characterization of benzoate catabolic genes in the gram-positive polychlorinated biphenyl degrader Rhodococcus sp. strain RHA1. J. Bacteriol. 183: 6598–6606.
17. Krooneman, J., A. O. Sliekers, T. M. Pedro Gomes, L. J. Forney and J. C. Gottschal. 2000. Characterization of 3-chlorobenzoate degrading aerobic bacteria isolated under various environmental conditions. FEMS Microbiol. Ecol. 32: 53–59.
18. Krooneman, J., E. B. Wieringa, E. R. Moore, J. Gerritse, R. A. Prins and J. C. Gottschal. 1996. Isolation of Alcaligenes sp. strain L6 at low oxygen concentrations and degradation of 3-chlorobenzoate via a pathway not involving (chloro)catechols. Appl. Environ. Microbiol. 62: 2427–2434.
19. Lane, D. J., B. Pace, G. J. Olsen, D. A. Stahl, M. L. Sogin and N. R. Pace. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. USA 82: 6955–6959.
20. Laurie, A. D. and G. Lloyd-Jones. 1999. The phn genes of Burkholderia sp. strain RP007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism. J. Bacteriol. 181: 531–540.
21. Muyzer, G. 1999. DGGE/TGGE a method for identifying genes from natural ecosystems. Curr. Opin. Microbiol. 2: 317–322.
22. 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.
23. Nakatsu, C. H. and R. C. Wyndham. 1993. Cloning and expression of the transposable chlorobenzoate-3,4-dioxygenase genes of Alcaligenes sp. strain BR60. Appl. Environ. Microbiol. 59: 3625- 3633.
24. Neidle, E. L., C. Hartnett, L. N. Ornston, A. Bairoch, M. Rekik and S. Harayama. 1991. Nucleotide sequences of the Acinetobacter calcoaceticus benABC genes for benzoate 1,2-dioxygenase reveal evolutionary relationships among multicomponent oxy-genases. J. Bacteriol. 173: 5385–5395.
25. Ogawa, N. and K. Miyashita. 1995. Recombination of a 3-chlorobenzoate catabolic plasmid from Alcaligenes eutrophus NH9 mediated by direct repeat elements. Appl. Environ. Microbiol. 61: 3788–3795.
26. Ogawa, N., K. Miyashita and A. M. Chakrabarty. 2003. Microbial genes and enzymes in the degradation of chlorinated compounds. Chem. Rec. 3: 158–171.
27. Oved, T., A. Shaviv, T. Goldrath, R. T. Mandelbaum and D. Minz. 2001. Influence of effluent irrigation on community composition and function of ammonia-oxidizing bacteria in soil. Appl. Environ. Microbiol. 67: 3426–3433.
28. Øvreås, L., L. Forney, F. L. Daae and V. Torsvik. 1997. Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 63: 3367–3373.
29. Pavlu, L., J. Vosahlova, H. Klierova, M. Prouza, K. Demnerova and V. Brenner. 1999. Characterization of chlorobenzoate degraders isolated from polychlorinated biphenyl-contaminated soil and sediment in the Czech Republic. J. Appl. Microbiol. 87: 381- 386.
30. Pepper, I. L., T. J. Gentry, D. T. Newby, T. M. Roane and K. L. Josephson. 2002. The role of cell bioaugmentation and gene bio-augmentation in the remediation of co-contaminated soils. Environ. Health Perspect. 110 Suppl. 6: 943–946.
31. Perriere, G. and M. Gouy. 1996. WWW-query: an on-line retrieval system for biological sequence banks. Biochimie. 78: 364–369.
32. Ramírez-Saad, H. C., A. Sessitsch, W. M. de Vos and A. D. Ak-kermans. 2000. Bacterial community changes and enrichment of Burkholderia-like bacteria induced by chlorinated benzoates in a peat-forest soil-microcosm. Syst. Appl. Microbiol. 23: 591–598.
33. Reineke, W. and H. J. Knackmuss. 1988. Microbial degradation of haloaromatics. Annu. Rev. Microbiol. 42: 263–287.
34. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425.
35. Stover, C. K., X. Q. Pham, A. L. Erwin, S. D. Mizoguchi, P. War-rener, M. J. Hickey, F. S. Brinkman, W. O. Hufnagle, D. J. Kow-alik, M. Lagrou, R. L. Garber, L. Goltry, E. Tolentino, S. West-brock-Wadman, Y. Yuan, L. L. Brody, S. N. Coulter, K. R. Folger, A. Kas, K. Larbig, R. Lim, K. Smith, D. Spencer, G. K. Wong, Z. Wu, I. T. Paulsen, J. Reizer, M. H. Saier, R. E. Hancock, S. Lory and M. V. Olson. 2000. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406: 959–964.
36. Suzuki, K., N. Ogawa and K. Miyashita. 2001. Expression of 2-halobenzoate dioxygenase genes (cbdSABC) involved in the degradation of benzoate and 2-halobenzoate in Burkholderia sp. TH2. Gene 262: 137–145.
37. Torsvik, V., F. L. Daae, R. A. Sandaa and L. Øvreås. 1998. Novel techniques for analysing microbial diversity in natural and perturbed environments. J. Biotechnol. 64: 53–62.
38. Torsvik, V., J. Goksoyr and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56: 782–787.
39. Velicer, G. J., T. M. Schmidt and R. E. Lenski. 1999. Application of traditional and phylogenetically based comparative methods to test for a trade-off in bacterial growth rate at low versus high substrate concentration. Microb. Ecol. 38: 191–200.
40. Watanabe, K., M. Teramoto, H. Futamata and S. Harayama. 1998. Molecular detection, isolation, and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge. Appl. Environ. Microbiol. 64: 4396–4402.
41. Williamson, N., P. Brian and E. M. Wellington. 2000. Molecular detection of bacterial and streptomycete chitinases in the environment. Antonie van Leeuwenhoek 78: 315–321.