Molecular detection, isolation, and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge

Applied and Environmental Microbiology

Volumn 64, Issue 11, 1998, Pages 4396-4402

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

^a MARINE BIOTECHNOLOGY INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

PHENOL;

ACTIVATED SLUDGE; ARTICLE; BACTERIUM; BACTERIUM CULTURE; BACTERIUM DETECTION; BACTERIUM ISOLATION; CHEMOSTAT; DNA DETERMINATION; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; VANOVORAX PARADOXUS;

BACTERIA (MICROORGANISMS); PROKARYOTA; VALIVORAX; VALIVORAX PARADOXUS;

EID: 0031734089     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.64.11.4396-4402.1998     Document Type: Article

References (47)

1. American Petroleum Institute. 1969. Manual on the disposal of refinery wastes. Volume on liquid waste. American Petroleum Institute, Washington, D.C.
2. Bond, P. L., P. Hugenholtz, J. Keller, and L. L. Blackall. 1995. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludge from sequencing batch reactors. Appl. Environ. Microbiol. 61:19111-1916.
3. Borneman, J., and E. W. Triplett. 1997. Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl. Environ. Microbiol. 63:2647-2653.
4. Bowman, J. P., S. A. McCammon, J. L. Brown, P. D. Nichols, and T. A. McMeekin. 1997. Psychroserpens burtonensis gen. nov., sp. nov., and Gelidibacter algens gen. nov., sp. nov., psychrophilic bacteria isolated from antarctic lacustrine and sea ice habitats. Int. J. Syst. Bacteriol. 47:670-677.
5. Cardy, D. L., V. Laidler, G. P. Salmond, and J. C. Murrell. 1991. Molecular analysis of the methane monooxygenase (MMO) gene cluster of Methylosinus trichosporium OB3b. Mol. Microbiol. 5:335-342.
6. 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.
7. Delong, E. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89:5685-5689.
8. Dunbar, J., D. C. L. Wong, M. J. Yarus, and L. J. Forney. 1996. Autoradiographic method for isolation of diverse microbial species with unique catabolic traits. Appl. Environ. Microbiol. 62:4180-4185.
9. Dunbar, J., S. White, and L. J. Forney. 1997. Genetic diversity through the looking glass: effect of enrichment bias. Appl. Environ. Microbiol. 63:1326-1331.
10. 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.
11. a desaturase from Ricinus communis is a diiron-oxo protein. Proc. Natl. Acad. Sci. USA 90:2486-2490.
12. Frey, J., M. Bagdasarian, D. Feiss, F. C. H. Franklin, and J. Deshusses. 1983. Stable cosmid vectors that enable the introduction of cloned fragments into a wide range of Gram-negative bacteria. Gene 24:299-308.
13. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature (London) 345: 60-63.
14. Hashimoto, S., and M. Fujita. 1987. Identification of three phenol-degrading microorganisms isolated from activated sludges and their characteristics. J. Jpn. Sewage Works 9:655-660.
15. Herrmann, H., C. Müller, 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.
16. Hino, H., K. Watanabe, and N. Takahashi. 1998. Phenol hydroxylase cloned from Ralstonia eutropha strain E2 exhibits novel kinetic properties. Microbiology 144:1765-1772.
17. Hiraishi, A., Y. Shin, and J. Sugiyama. 1995. Brachymonas denitrificans gen. nov., sp. nov., an aerobic chemoorganotrophic bacterium which contains rhodoquinones and evolutionary relationships of rhodoquinone producers to bacterial species with various quinone classes. J. Gen. Appl. Microbiol. 41: 99-117.
18. Hopper, D. J., P. J. Chapman, and S. Dagley. 1970. Metabolism of L-malate and D-malate by a species of Pseudomonas. J. Bacteriol. 104:1197-1202.
19. Janke, D., R. Pohl, and W. Fritsche. 1981. Regulation of phenol degradation in Pseudonomas putida. Z. Allg. Mikrobiol. 21:295-303.
20. Japanese Industrial Standard Committee. 1986. Testing methods for industrial wastewater. Publication JIS K0102. Japanese Standards Association. Tokyo, Japan.
21. Johnson, G. R., and R. H. Olsen. 1995. Nucleotide sequence analysis of genes encoding a toluene/benzene-2-monooxygenase from Pseudomonas sp. strain JS150. Appl. Environ. Microbiol. 61:3336-3346.
22. Kamagata, Y., R. R. Fulthorpe, K. Tamura, H. Takami, L. J. Forney, and J. M. Tiedje. 1997. Pristine environments harbor a new group of oligotrophic 2,4-dichlorophenoxyacetic acid-degrading bacteria. Appl. Environ. Microbiol. 63:2266-2272.
23. Karlin, S., and S. F. Altschul. 1990. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA 87:2264-2268.
24. Machado, R. J., and L. Grady, Jr. 1989. Dual substrate removal by an anexic bacterial culture. Biotechnol. Bioeng. 33:327-337.
25. 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.
26. 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 Pseudomonus putida P35X. Gene 151:29-36.
27. 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.
28. Nordlund, I., J. Powlowski, A. Hagström, and V. Shingler. 1993. Conservation of regulatory and structural genes for a multi-component phenol hydroxylase within phenol-catabolizing bacteria that utilize a meta-cleavage pathway. J. Gen. Microbiol. 139:2695-2703.
29. 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.
30. 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.
31. 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.
32. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-125.
33. 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.
34. Shingler, V. 1996. Molecular and regulatory check points in phenol degradation by Pseudomonas sp. CF600, p. 153-164. In T. Nakazawa, K. Furukawa, D. Haas, and S. Silver (ed.), Molecular biology of pseudomonads. American Society for Microbiology, Washington, D.C.
35. Shmidt, T. M., E. H. Delong, and N. R. Pace. 1991. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173:4371-4378.
36. Snaidr, J., R. Amann, I. Huber, W. Ludwig, and K. H. Schleifer. 1997. Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl. Environ. Microbiol. 63:2884-2896.
37. 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.
38. 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.
39. Wagner, M., R. Amann, H. Lemme, and K. Schleife. 1993. Probing activated sludge with oligonucleotides specific for proteobacteria: inadequacy of culture-dependent methods for describing microbial community structure. Appl. Environ. Microbiol. 59:1520-1525.
40. Ward, D. M., R. Weller, and M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature (London) 345:63-65.
41. 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.
42. Watanabe, K., and S. Hino. 1996. Identification of a functionally important population in phenol-digesting activated sludge with antisera raised against isolated bacterial strains. Appl. Environ. Microbiol. 62:3901-3904.
43. Watanabe, K., S. Hino, and N. Takahashi. 1996. Responses of activated sludge to an increase in phenol loading. J. Ferment. Bioeng. 82:522-524.
44. Watanabe, K., S. Yamamoto, S. Hino, and S. Harayama. 1998. Population dynamics of phenol-degrading bacteria in activated sludge determined by gyrB-targeted quantitative PCR. Appl. Environ. Microbiol. 64:1203-1209.
45. Watanabe, K., and S. Harayama. Rapid estimation of population densities of uncultured bacteria in the environment. Microbes Environ., in press.
46. Yang, R. D., and A. E. Humphrey. 1975. Dynamics and steady state studies of phenol degradation in pure and mixed cultures. Biotechnol. Bioeng. 17: 1211-1235.
47. Yen, K. M., M. R. Karl, L. M. Blatt, M. J. Simon, R. B. Winter, P. R. Fausset, H. S. Lu, A. A. Harcourt, and K. Chen. 1991. Cloning and characterization of a Pseudomonas medocina KR1 gene cluster encoding toluene-4-monooxygenase. J. Bacteriol. 173:5315-5327.