Temporal change in culturable phenanthrene degraders in response to long-term exposure to phenanthrene in a soil column system

Environmental Microbiology

Volumn 5, Issue 10, 2003, Pages 888-895

  Bodour, Adria A ^a,b   Wang, Jiann Ming ^c   Brusseau, Mark L ^a   Maier, Raina M ^a  

^a UNIVERSITY OF ARIZONA   (United States)

^b UNIVERSITY OF TEXAS AT SAN ANTONIO   (United States)

^c NONE

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; BIODEGRADATION, ENVIRONMENTAL; DNA, RIBOSOMAL; MOLECULAR SEQUENCE DATA; OXYGEN; PHENANTHRENES; SOIL; SOIL MICROBIOLOGY; SOIL POLLUTANTS;

AFIPIA; BACTERIA (MICROORGANISMS); JANTHINOBACTERIUM; LEPTOTHRIX; MASSILIA; METHYLOBACTERIUM; RHIZOBIUM; SINORHIZOBIUM; THIOBACILLUS;

EID: 0141564890     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1462-2920.2003.00481.x     Document Type: Article

References (50)

1. Ahn, Y., Sanseverino, J., and Sayler, G.S. (1999) Analyses of polycyclic aromatic hydrocarbon-degrading bacteria isolated from contaminated soils. Biodegradation 10: 149-157.
2. Aitken, M.D., Stringfellow, W.T., Nagel, R.D., Kazunga, C., and Chen, S.-H. (1998) Characteristics of phenanthrene-degrading bacteria isolated from soils contaminated with polycyclic aromatic hydrocarbons. Can J Microbiol 44: 742-752.
3. Alley, J.F., and Brown, L.R. (2000) Use of sublimation to prepare solid microbial media with water-insoluble substrates. Appl Environ Microbiol 66: 439-442.
4. Berardesco, G., Dyhrman, S., Gallagher, E., and Shiaris, M.P. (1998) Spatial and temporal variation of phenanthrene-degrading bacteria in intertidal sediments. Appl Environ Microbiol 64: 2560-2565.
5. Bogardt, A.H., and Hemmingsen, B.B. (1992) Enumeration of phenanthrene-degrading bacteria by an overlayer technique and its use in evaluation of petroleum-contaminated sites. Appl Environ Microbiol 58: 2579-2582.
6. Brusseau, M.L., Hu, M.Q., Wang, J.-M., and Maier, R.M. (1999) Biodegradation during contaminant transport in porous media. 2. The influence of physicochemical factors. Environ Sci Technol 33: 96-103.
7. Cerniglia, C.E. (1992) Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3: 227-244.
8. Colores, G.M., Macur, R.E., Ward, D.M., and Inskeep, W.P. (2000) Molecular analysis of surfactant-driven microbial population shifts in hydrocarbon-contaminated soil. Appl Environ Microbiol 66: 2959-2964.
9. Daane, L.L., Harjono, I., Zylstra, G.J., and Haggblom, M.M. (2001) Isolation and characterization of polycyclic aromatic hydrocarbon-degrading bacteria associated with the rhizosphere of salt marsh plants. Appl Environ Microbiol 67: 2683-2691.
10. Dunn, N.W., and Gunsalus, I.C. (1973) Transmissible plasmid coding early enzymes of naphthalene oxidation in Pseudomonas putida. J Bacteriol 120: 974-979.
11. Engelen, B., Reinken, K., VonWintzingerode, F., Heuer, H., Malkomes, H.-P., and Backhaus, H. (1998) Monitoring impact of a pesticide treatment on bacterial soil communities by metabolic and genetic fingerprinting in addition to conventional testing procedures. Appl Environ Microbiol 64: 2814-2821.
12. Estrella, M.R., Brusseau, M.L., Maier, R.S., Pepper, I.L., Wierenga, P.J., and Miller, R.M. (1993) Biodegradation, sorption, and transport of 2,4-dichlorophenoxyacetic acid in saturated and unsaturated soils. Appl Environ Microbiol 59: 4266-4273.
13. Foght, J.M., and Westlake, D.W.S. (1991) Cross hybridization of plasmid and genomic DNA from aromatic and polycyclic aromatic hydrocarbon degrading bacteria. Can J Microbiol 37: 924-932.
14. Gauthier, E., Deziel, E., Villemur, R., Juteau, P., Lepine, F., and Beaudet, R. (2003) Initial characterization of new bacteria degrading high-molecular weight polycyclic aromatic hydrocarbons isolated from a 2-year enrichment in a two-liquid-phase culture system. J Appl Microbiol 94: 301-311.
15. Goyal, A.K., and Zylstra, G.J. (1996) Molecular cloning of novel genes for polycyclic aromatic hydrocarbon degradation from Comamonas testosteroni GZ39. Appl Environ Microbiol 62: 230-236.
16. Grosser, R.J., Warshawsky, D., and Vestal, J.R. (1991) Indigenous and enhanced mineralization of pyrene, benzo[a]pyrene and carbazole in soils. Appl Environ Microbiol 57: 3462-3469.
17. Guerin, W.F., and Jones, G.E. (1989) Estuarine ecology of phenanthrene-degrading bacteria. Estuar Coast Shelf Sci 29: 115-130.
18. Hamann, C., Hegermann, J., and Hildebrandt, A. (1999) Detection of polycyclic aromatic hydrocarbon degradation genes in different soil bacteria by polymerase chain reaction and DNA hybridization. FEMS Microbiol Lett 173: 255-263.
19. Hedlund, B.P., Geiselbrecht, A.D., Bair, T.J., and Staley, J.T. (1999) Polycyclic aromatic hydrocarbon degradation by a new marine bacterium, Neptunomonas naphthovorans gen. nov., sp. nov. Appl Environ Microbiol 65: 251-259.
20. Hu, M.Q., and Brusseau, M.L. (1998) Coupled effects of nonlinear, rate-limited sorption and biodegradation on transport of 2,4-dichlorophenoxyacetic acid in soil. Environ Toxicol Chem 17: 1673-1680.
21. Jordan, F.L. (2000) Bacterial transport, distribution and activity in porous media. PhD Dissertation, The University of Arizona, Tucson, AZ.
22. Kaeberlein, T., Lewis, K., and Epstein, S.S. (2002) Isolating 'uncultivable' microorganisms in pure culture in a simulated natural environment. Science 296: 1127-1131.
23. Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics. Stackebrant, E., and Goodfellow, M. (eds). Chichester: John Wiley and Sons, pp. 115-175
24. Laurie, A.D., and Lloyd-Jones, G. (2000) Quantification of phnAc and nahAc in contaminated New Zealand soils by competitive PCR. Appl Environ Microbiol 66: 1814-1817.
25. Lloyd-Jones, G., Laurie, A.D., Hunter, D.W.F., and Fraser, R. (1999) Analysis of catabolic genes for naphthalene and phenanthrene degradation in contaminated New Zealand soils. FEMS Microbiol Ecol 29: 69-79.
26. Madsen, E.L., Winding, A., Malachowsky, K., Thomas, C.T., and Ghiorse, W.C. (1992) Contrasts between subsurface microbial communities and their metabolic adaptation to polycyclic aromatic hydrocarbons at a forested and an urban coal-tar disposal site. Microbiol Ecol 24: 199-213.
27. Medlin, L., Elwood, H.J., Stickel, S., and Sogin, M.L. (1988) The characterization of enzymatically amplified eukaryotic 16-like rRNA-coding regions. Gene 71: 491-499.
28. Menn, F.-M., Applegate, B.M., and Sayler, G.S. (1993) NAH plasmid-mediated catabolism of anthracene and phenanthrene to naphthoic acids. Appl Environ Microbiol 59: 1938-1942.
29. Meyer, S., Moser, R., Neef, A., Stahl, U., and Kampfer, P. (1999) Differential detection of key enzymes of polyaromatic-hydrocarbon-degrading bacteria using PCR and gene probes. Microbiology 145: 1731-1741.
30. Miya, R.K., and Firestone, M.K. (2001) Enhanced phenanthrene biodegradation in soil by slender oat root exudates and root debris. J Environ Qual 30: 1911-1918.
31. Moody, J.D., Freeman, J.P., Doerge, D.R., and Cerniglia, C.E. (2001) Degradation of phenanthrene and anthracene by cell suspensions of Mycobacterium sp. strain PYR-1. Appl Environ Microbiol 67: 1476-1483.
32. Mueller, J.G., Devereux, R., Santavy, D.L., Lantz, S.E., Willis, S.G., and Pritchard, P.H. (1997) Phylogenetic and physiological comparisons of PAH-degrading bacteria from geographically diverse soils. Antonie van Leuwenhoek Int J Gen Mol Microbiol 71: 329-343.
33. Pellizari, V.H., Bezborodnikov, S., and Quensen, J.F., III, and Tiedje, J.M. (1996) Evaluation of stains isolated by growth on naphthalene and biphenyl for hybridization of genes to dioxygenase probes and polychlorinated biphenyl-degrading ability. Appl Environ Microbiol 62: 2053-2058.
34. Perkiomaki, J., and Fritze, H. (2002) Short- and long-term effects of wood ash on the boreal forest humus microbial community. Soil Biol Biochem 34: 1343-1353.
35. Roslev, P., Iversen, N., and Henriksen, K. (1998) Direct fingerprinting of metabolically active bacteria in environmental samples by substrate specific radiolabelling and lipid analysis. J Microbiol Methods 31: 99-111.
36. Sandrin, S.K., Jordan, F.L., Maier, R.M., and Brusseau, M.L. (2001) Biodegradation during contaminant transport in porous media. 4. Impact of microbial lag and bacterial cell growth. J Contam Hydrol 50: 225-242.
37. Shiaris, M.P., and Cooney, J.J. (1983) Replica plating method for estimating phenanthrene-utilizing and phenanthrene-cometabolizing microorganisms. Appl Environ Microbiol 45: 706-710.
38. Simon, M.J., Osslund, T.D., Saunders, R., Ensley, B.D., Suggs, S., Harcourt, A., et al. (1993) Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4. Gene 127: 31-37.
39. Stapleton, R.D., and Sayler, G.S. (1998) Assessment of the microbiological potential for the natural attenuation of petroleum hydrocarbons in a shallow aquifer system. Microb Ecol 36: 349-361.
40. Takizawa, N., Iida, T., Sawada, T., Yamauchi, K., Wang, Y.-W., Fukuda, M., and Kiyohara, H. (1999) Nucleotide sequences and characterization of genes encoding naphthalene upper pathway of Pseudomonas aeruginosa PaK1 and Pseudomonas putida OUS82. J Biosci Bioeng 87: 721-731.
41. Thompson, J.D., Higgins, D.G., and Gibson, T.J. (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.
42. Weisburg, W.G., Barns, S.M., Pelletier, D.A., and Lane, D.J. (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173: 697-703.
43. Weissenfels, W.D., Beyer, M., and Klein, J. (1990) Degradation of phenanthrene, fluorene and fluoranthene by pure bacterial cultures. Appl Environ Microbiol 32: 479-484.
44. Widada, J., Nojiri, H., Kasuga, K., Yoshida, T., Habe, H., and Omori, T. (2002) Molecular detection and diversity of polycyclic aromatic hydrocarbon-degrading bacteria isolated from geographically diverse sites. Appl Microbiol Biotechnol 58: 202-209.
45. Yang, Y., Chen, R.F., and Shiaris, M.P. (1994) Metabolism of naphthalene, fluorene, and phenanthrene: Preliminary characterization of a cloned gene cluster from Pseudomonas putida NCIB 9816. J Bacteriol 178: 2158-2164.
46. Yen, K.M., and Serdar, C.M. (1988) Genetics of naphthalene catabolism in Pseudomonads. CRC Crit Rev Microbiol 15: 247-267.
47. Yolcubal, I., Pierce, S.A., Maier, R.M., and Brusseau, M.L. (2002) Biodegradation during contaminant transport in porous media. 5. The influence of growth and cell elution on microbial distribution. J Environ Qual 31: 1824-1830.
48. Yuste, L., Corbella, M.E., Turiegano, M.J., Karlson, U., Puyet, A., and Rojo, F. (2000) Characterization of bacterial strains able to grow on high molecular mass residues from crude oil processing. FEMS Microbiol Ecol 32: 69-75.
49. Zylstra, G.J., and Kim, E. (1997) Aromatic hydrocarbon degradation by Sphingomonas yanoikuyae B1. J Ind Microbiol Biotechnol 19: 408-414.
50. Zylstra, G.J., Wang, X.P., Kim, E., and Didolkar, V.A. (1994) Cloning and analysis of the genes for polycyclic aromatic hydrocarbon degradation. Ann NY Acad Sci 721: 386-398.