Group-Specific Monitoring of Phenol Hydroxylase Genes for a Functional Assessment of Phenol-Stimulated Trichloroethylene Bioremediation

Applied and Environmental Microbiology

Volumn 67, Issue 10, 2001, Pages 4671-4677

  Futamata, Hiroyuki ^a   Harayama, Shigeaki ^a   Watanabe, Kazuya ^a  

^a MARINE BIOTECHNOLOGY INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

MIXED FUNCTION OXIDASE; PHENOL; PHENOL 2-MONOOXYGENASE; PHENOL HYDROXYLASE; TRICHLOROETHYLENE;

ARTICLE; BETAPROTEOBACTERIA; BIOREMEDIATION; CLASSIFICATION; DNA SEQUENCE; ENZYMOLOGY; GENETICS; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; POLYMERASE CHAIN REACTION; PSEUDOMONAS; WATER POLLUTION;

BETAPROTEOBACTERIA; BIODEGRADATION, ENVIRONMENTAL; MIXED FUNCTION OXYGENASES; MOLECULAR SEQUENCE DATA; PHENOL; PHYLOGENY; POLYMERASE CHAIN REACTION; PSEUDOMONAS; SEQUENCE ANALYSIS, DNA; TRICHLOROETHYLENE; WATER MICROBIOLOGY; WATER POLLUTION, CHEMICAL;

EID: 0035491632     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.67.10.4671-4677.2001     Document Type: Article

References (42)

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. Brosius, J., T. J. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148:107-127.
3. de Bruijn, F. J. 1992. Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl. Environ. Microbiol. 58:2180-2187.
4. Edwards, U., T. Rogall, H. Blöcker, M. Emde, and E. C. Böttger. 1989. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res. 17:7843-7853.
5. Ehrt, S., F. Schirmer, and W. Hillen. 1995. Genetic organization, nucleotide sequence and regulation of expression of genes encoding phenol hydroxylase and catechol 1:2-dioxygenase in Acinetobacter calcoaceticus NCIB8250. Mol. Microbiol. 18:13-20.
6. Ensley, B. D. 1991. Biochemical diversity of trichloroethylene metabolism. Annu. Rev. Microbiol. 45:283-299.
7. 9 desaturase from Ricinus communis is a diiron-oxo protein. Proc. Natl. Acad. Sci. USA 90:2486-2490.
8. Futamata, H., K. Watanabe, and S. Harayama. 1998. Relationships between the trichloroethylene-degrading activities and the amino acid sequences of phenol hydroxylases in phenol-degrading bacteria, p. 99-104. In The First International Conference on Remediation of Chlorinated and Recalcitrant Compounds. Battelle Press, Columbus, Ohio.
9. Futamata, H., S. Harayama, and K. Watanabe. 2001. Diversity in kinetics of trichloroethylene-degrading activities exhibited by phenol-degrading bacteria. Appl. Microbiol. Biotechnol. 55:248-253.
10. Hanada, S., T. Shigematsu, K. Shibuya, M. Eguchi, T. Hasegawa, F. Suda, Y. Kamagata, T. Kanagawa, and R. Kurane. 1998. Phylogenetic analysis of trichloroethylene-degrading bacteria newly isolated from soil polluted with this contaminant. J. Ferment. Bioeng. 86:539-544.
11. Harayama, S., M. Kok, and E. L. Neidle. 1992. Functional and evolutionary relationships among diverse oxygenases. Annu. Rev. Microbiol. 46:565-601.
12. 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.
13. Henckel, T., U. Jakel, S. Schnell, and R. Conrad. 2000. Molecular analyses of novel methanotrophic communities in forest soil that oxidize atmospheric methane. Appl. Environ. Microbiol. 66:1801-1808.
14. Herrmann, H., C. Múller, I. Schmidt, J. Mahnke, L. Petruschka, and K. Hahnke. 1995. Localization and organization of phenol degradation genes of Pseudomonas putida strain H. Mol. Gen. Genet. 247:240-246.
15. Hino, H., K. Watanabe, and N. Takahashi. 1998. Phenol hydroxylase cloned from Ralstonia eutropha strain E2 exhibits novel kinetic properties. Microbiology 144:1765-1772.
16. Hopkins, G. D., and P. L. McCarty. 1995. Field evaluation of in situ aerobic cometabolism of trichloroethylene and three dichloroethylene isomers using phenol and toluene as the primary substrates. Environ. Sci. Technol. 29: 1628-1637.
17. Krumme, M. L., K. N. Timmis, and D. F. Dwyer. 1993. Degradation of trichloroethylene by Pseudomonas cepacia G4 and the constitutive mutant strain G4 5223 PR1 in aquifer microcosms. Appl. Environ. Microbiol. 59: 2746-2749.
18. McDonald, I. R., E. M. Kenna, and J. C. Murrell. 1995. Detection of methanotrophic bacteria in environmental samples with the PCR. Appl. Environ. Microbiol. 61:116-121.
19. Ng, L. C., V. Shingler, C. C. Sze, and C. L. Poh. 1994. Cloning and sequencing of the first eight genes of the chromosomally encoded (methyl) phenol degradation pathway from Pseudomonas putida P35X. Gene 151:29-36.
20. Nordlund, I., J. Powlowski, and V. Shingler. 1990. Complete nucleotide sequence and polypeptide analysis of multicomponent phenol hydroxylase from Pseudomonas sp. strain CF600. J. Bacteriol. 172:6826-6833.
21. Okuta, A., K. Ohnishi, and S. Harayama. 1998. PCR isolation of catechol 2:3-dioxygenase gene fragments from environmental samples and their assembly into functional genes. Gene 212:221-228.
22. Olsen, G. J., D. L. Lane, S. J. Giovannoni, and N. R. Pace. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40:337-365.
23. Pace, N. R., D. A. Stahl, D. L. Lane, and G. J. Olsen. 1986. The analysis of natural microbial populations by rRNA sequences. Adv. Microbiol. Ecol. 9:1-55.
24. Peters, M., E. Heinaru, E. Talpsep, H. Ward, U. Stottmeister, A. Heinaru, and A. Nurk. 1997. Acquisition of a deliberately introduced phenol degradation operon, pheAB, by different indigenous Pseudomonas species. Appl. Environ. Microbiol. 63:4899-4906.
25. Rotthauwe, J. H., K. P. Witzel, and W. Liesack. 1997. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63:4704-4712.
26. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
27. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
28. Semprini, L., P. V. Roberts, G. D. Hopkins, and P. L. McCarty. 1990. A field evaluation of in-situ biodegradation of chlorinated ethenes: part 2: results of biostimulation and biotransformation. Ground Water 29:239-250.
29. Semprini, L. 1997. Strategies for the aerobic cometabolism of chlorinated solvents. Curr. Opin. Biotechnol. 8:296-308.
30. Shih, C. C., M. E. Davey, J. Zhou, J. M. Tiedje, and C. S. Criddle. 1996. Effects of phenol feeding pattern on microbial community structure and cometabolism of trichloroethylene. Appl. Environ. Microbiol. 62:2953-2960.
31. Sinigalliano, C. D., D. N. Kuhn, and R. D. Jones. 1995. Amplification of the amoA gene from diverse species of ammonium-oxidizing bacteria and from an indigenous bacterial population from seawater. Appl. Environ. Microbiol. 61:2702-2706.
32. Speitel, G. E., Jr., R. C. Thompson, and D. Weissman. 1993. Biodegradation kinetics of Methylosinus trichosporium OB3b at low concentrations of chloroform in the presence and absence of enzyme competition by methane. Water Res. 27:15-24.
33. Sprott, G. D., S. F. Koval, and C. A. Schnaitman. 1994. Cell fractionation, p. 72-103. In P. Gerhardt, R.G. E. Murray, W. A. Wood, and N. R. Krieg (ed.), Methods for general and molecular bacteriology. American Society for Microbiology, Washington, D.C.
34. Stams, A. J. M., and S. O. Elferink. 1998. Understanding and advancing wastewater treatment. Curr. Opin. Microbiol. 1:328-334.
35. Takeo, M., Y. Maeda, H. Okada, K. Miyama, K. Mori, Y. Ike, and M. Fujita. 1995. Molecular cloning and sequencing of phenol hydroxylase gene from Pseudomonas putida BH. J. Ferment. Bioeng. 79:485-488.
36. 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.
37. Watanabe, K., S. Hino, K. Onodera, S. Kajie, and N. Takahashi. 1996. Diversity in kinetics of bacterial phenol-oxygenating activity. J. Ferment. Bioeng. 81:562-565.
38. 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.
39. Watanabe, K., M. Teramoto, and S. Harayama. 1999. An outbreak of non-flocculating catabolic populations caused the breakdown of a phenol-digesting activated-sludge process. Appl. Environ. Microbiol. 65:2813-2819.
40. Watanabe, K., and P. W. Baker. 2000. Environmentally relevant microorganisms. J. Biosci. Bioeng. 89:1-11.
41. Watanabe, K. 2000. Microorganisms relevant to bioremediation. Curr. Opin. Biotechnol. 12:237-241.
42. Zhou, J., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316-322.