Molecular characterization of a toluene-degrading methanogenic consortium

Applied and Environmental Microbiology

Volumn 65, Issue 12, 1999, Pages 5576-5585

  Ficker, Monica ^a   Krastel, Kirsten ^b   Orlicky, Stephen ^b   Edwards, Elizabeth ^b  

^a MCMASTER UNIVERSITY   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CREOSOTE; DNA; RNA 16S; TOLUENE;

AQUIFER; ARCHAEBACTERIUM; ARTICLE; DEGRADATION; DNA HYBRIDIZATION; EUBACTERIUM; GENOME; IN SITU HYBRIDIZATION; METHANOGENESIS; NONHUMAN; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEQUENCE ANALYSIS;

EID: 0032708969     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.12.5576-5585.1999     Document Type: Article

References (43)

1. Altenschmidt, U., B. Oswald, and G. Fuchs. 1992. Anaerobic toluene oxidation to benzyl alcohol and benzaldehyde in a denitrifying Pseudomonas strain. J. Bacteriol. 174:4860-4862.
2. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. Amann, R. I. 1995. Fluorescently labeled, ribosomal-RNA-targeted oligonucleotide probes in the study of microbial ecology. Mol. Ecol. 4:543-553.
4. Amann, R. I., B. J. Binder, R. J. Olson, S. W. Chisholm, and R. Devereux. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
5. 2-producing syntrophic bacteria, p. 67-83. In A. A. Antonopoulos (ed.), Biotechnological advances in processing municipal wastes for fuels and chemicals. Argonne National Laboratory, Chicago, Ill.
6. Belaich, J.-P., P. Heitz, M. Rousset, and J. L. Garcia. 1990. Energetics of the growth of a new syntrophic benzoate degrading bacterium, p. 269-280. In J.-P. Belaich (ed.), Microbiology and biochemistry of strict anaerobes involved in interspecies transfer. Plenum Press, New York, N.Y.
7. Beller, H. R., A. M. Spormann, P. K. Sharma, J. R. Cole, and M. Reinhard. 1996. Isolation and characterization of a novel toluene-degrading, sulfate-reducing bacterium. Appl. Environ. Microbiol. 62:1188-1196.
8. Boivin-Jahns, V., R. Ruimy, A. Bianchi, A. Daumas, and R. Christen. 1996. Bacterial diversity in a deep-subsurface clay environment. Appl. Environ. Microbiol. 62:3405-3412.
9. Bond, P. L., P. Hugenholtz, J. Keller, and L. L. Blackall. 1995. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing hatch reactors. Appl. Environ. Microbiol. 61:1910-1916.
10. Boone, D. R., W. B. Whitman, and P. Rouviere. 1990. Diversity and taxonomy of methanogens, p. 35-80. In J. G. Ferry (ed.), Methanogenesis: ecology, physiology, biochemistry and genetics. Chapman & Hall, New York, N.Y.
11. Borneman, J., P. W. Skroch, K. M. Osullivan, and J. A. Palus. 1996. Molecular microbial diversity of an agricultural soil in Wisconsin. Appl. Environ. Microbiol. 62:1935-1943.
12. Brunk, C. F., E. Avaniss-Aghajani, and C. A. Brunk. 1996. A computer analysis of primer and probe hybridization potential with bacterial small-subunit rRNA sequences. Appl. Environ. Microbiol. 62:872-879.
13. DeLong, E. F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89:5685-5689.
14. Devereux, R., and G. W. Mundfrom. 1994. A phylogenetic tree of 16S rRNA sequences from sulfate-reducing bacteria in a sandy marine sediment. Appl. Environ. Microbiol. 60:3437-3439.
15. Duetz, W. A., C. Dejong, P. A. Williams, and J. G. Vanandel. 1994. Competition in chemostat culture between Pseudomonas strains that use different pathways for the degradation of toluene. Appl. Environ. Microbiol. 60:2858-2863.
16. Edwards, E. A., A. M. Edwards, and D. Grbic-Galic. 1994. A method for the detection of metabolites at very low concentration: application to the detection of metabolites of anaerobic toluene degradation. Appl. Environ. Microbiol. 60:323-327.
17. Edwards, E. A., and D. Grbic-Galic. 1994. Anaerobic degradation of toluene and o-xylene by a methanogenic consortium. Appl. Environ. Microbiol. 60: 313-322.
18. Edwards, E. A., L. E. Wills, M. Reinhard, and D. Grbic-Galic. 1992. Anaerobic degradation of toluene and xylene by aquifer microorganisms under sulfate-reducing conditions. Appl. Environ. Microbiol. 58:794-800.
19. Efron, B., and G. Gong. 1983. A leisurely look at the bootstrap, the jackknife and cross-validation. Am. Stat. 37:36-48.
20. Evans, P. J., D. T. Mang, K. S. Kim, and L. Y. Young. 1991. Anaerobic degradation of toluene by a denitrifying bacterium. Appl. Environ. Microbiol. 57:1139-1145.
21. Felsenstein, J. 1989. PHYLIP - phylogeny inference package (version 3.2). Cladistics 5:164-166.
22. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
23. Ficker, M. 1998. M.Eng. thesis. McMaster University, Hamilton, Ontario, Canada.
24. Fries, M. R., J. Zhou, J. Chee-Sandford, and J. M. Tiedje. 1994. Isolation, characterization, and distribution of denitrifying toluene degraders from a variety of habitats. Appl. Environ. Microbiol. 60:2802-2810.
25. Giovannoni, S. J., E. F. DeLong, G. J. Olsen, and N. R. Pace. 1988. Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells. J. Bacteriol. 170:720-726.
26. Higgins, D. G., A. J. Bleasby, and R. Fuchs. 1992. CLUSTAL V: improved software for multiple sequence alignment. Comput. Appl. Biosci. 8:189-191.
27. Hopkins, B. T., M. J. McInerney, and V. Warikoo. 1995. Evidence for an anaerobic syntrophic benzoate degradation threshold and isolation of the syntrophic benzoate degrader. Appl. Environ. Microbiol. 61:526-530.
28. Krumholz, L. R., and M. E. Caldwell. 1996. Biodegradation of "BTEX" hydrocarbons under anaerobic conditions, p. 61-99. In R. L. Crawford and D. L. Crawford (ed.), Bioremediation: principles and applications. Cambridge University Press, Cambridge, United Kingdom.
29. Lovley, D. R., and D. J. Lonergan. 1990. Anaerobic oxidation of toluene, phenol, and p-cresol by the dissimilatory iron-reducing organism GS-15. Appl. Environ. Microbiol. 56:1858-1864.
30. Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1997. The Ribosomal Database Project. Nucleic Acids Res. 25:109-111.
31. Moyer, C. L., J. M. Tiedje, F. C. Dobbs, and D. M. Karl. 1996. A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Appl. Environ. Microbiol. 62:2501-2507.
32. Rabus, R., R. Nordhaus, W. Ludwig, and F. Widdel. 1993. Complete oxidation of toluene under strictly anoxic conditions by a new sulfate-reducing bacterium. Appl. Environ. Microbiol. 59:1444-1451.
33. Raskin, L., L. K. Poulsen, D. R. Noguera, B. E. Rittmann, and D. A. Stahl. 1994. Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization. Appl. Environ. Microbiol. 60: 1241-1248.
34. Raskin, L., J. M. Stromley, B. E. Rittmann, and D. A. Stahl. 1994. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 60:1232-1240.
35. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Press, Cold Spring Harbor, N.Y.
36. Snaidr, J., R. Amann, I. Huber, W. Ludwig, and K. Scheifer. 1997. Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl. Environ. Microbiol. 63:2884-2896.
37. Thiele, J. H., and J. G. Zeikus. 1988. Control of interspecies electron flow during anaerobic digestion: significance of formate transfer versus hydrogen transfer during syntrophic methanogenesis in floes. Appl. Environ. Microbiol. 54:20-29.
38. Weidner, S., W. Arnold, and A. Puhler. 1996. Diversity of uncultured microorganisms associated with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl. Environ. Microbiol. 62:766-771.
39. 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.
40. 39a. Whitehead Institute for Biomedical Research. 1996, 1997, copyright dates. [Online.] Primer 3, old version. http://www.genome.wi.mit.edu/cgi-bin/primer/primer3.cgi. [18 October 1999, last date accessed.]
41. Wilson, B. H., G. B. Smith, and J. F. Rees. 1986. Biotransformations of selected alkylbenzenes and halogenated aliphatic hydrocarbons in methanogenic aquifer material: a microcosm study. Environ. Sci. Technol. 20:997-1002.
42. Zhou, J., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316-322.
43. Zinder, S. H. 1990. Physiological ecology of methanogens, p. 128-206. In J. G. Ferry (ed.), Methanogenesis: ecology, physiology, biochemistry and genetics. Chapman & Hall, New York, N.Y.