Isolation of marine polycyclic aromatic hydrocarbon (PAH)-degrading Cycloclasticus strains from the Gulf of Mexico and comparison of their PAH degradation ability with that of Puget Sound Cycloclasticus strains

Applied and Environmental Microbiology

Volumn 64, Issue 12, 1998, Pages 4703-4710

  Geiselbrecht, Allison D ^a,b   Hedlund, Brian P ^a   Tichi, Mary A ^a,c   Staley, J T ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b NORTHWEST FISHERIES SCIENCE CENTER   (United States)

^c OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACENAPHTHENE DERIVATIVE; ANTHRACENE DERIVATIVE; BACTERIAL DNA; BIPHENYL DERIVATIVE; FLUORANTHENE; FLUORENE DERIVATIVE; IRON SULFUR PROTEIN; NAPHTHALENE DERIVATIVE; OXYGENASE; PHENANTHRENE DERIVATIVE; POLYCYCLIC AROMATIC HYDROCARBON; PYRENE; RIBOSOME DNA;

BACTERIUM; BIODEGRADATION; COMPARATIVE STUDY; PAH; PHYLOGENY;

AMINO ACID SEQUENCE; ARTICLE; BACTERIUM; BACTERIUM ISOLATION; BIODEGRADATION; CONTROLLED STUDY; CYCLOCLASTICUS; DNA SEQUENCE; MARINE ENVIRONMENT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; POLYMERASE CHAIN REACTION; SEDIMENT;

GULF OF MEXICO; PUGET SOUND; UNITED STATES; WASHINGTON;

BACTERIA (MICROORGANISMS); CYCLOCLASTICUS; CYCLOCLASTICUS PUGETII;

EID: 0031768236     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.64.12.4703-4710.1998     Document Type: Article

References (63)

1. Baas-Becking, L. M. G. 1934. Geobiologie of inleiding tot de milieukunde. W. P. van Stockum and Zoon N. V., The Hague, The Netherlands.
2. Boehm P. D., and A. G. Requejo. 1986. Overview of the recent sediment hydrocarbon geochemistry of Atlantic and Gulf Coast outer continental shelt environments. Estuarine Coastal Shelf Sci. 23:29-38.
3. Boronin, A. M., T. V. Tsoi, I. A. Kosheleva, M. U. Arinbasarov and V. M. Adanin. 1989. Cloning of Pseudomonas putida genes responsible or the primary stages of oxidation of naphthalene in Escherichia coli cells. Genetika 25:226-237.
4. Brosius, J., M. L. Palmer, P. Kennedy, and H. F. Woller. 1978. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Natl. Acad. Sci. USA 75:4801-1805.
5. Button D. K., F. Schut, P. Quang, R. Martin, and B. R. Robertson. 1993. Viability and isolation of marine bacteria by dilution culture: theory, procedures and initial results. Appl. Environ. Microbiol. 59:881-891.
6. Carman, K. R., J. C. Means, and S. C. Pomarico. 1996. Response of sedmentary bacteria in a Louisiana salt marsh to contamination by diesel fuel. Aquat. Microbiol. Ecol. 10:231-241.
7. Carman, K. R., J. W. Fleeger, J. C. Means, S. M. Pomarico, and D. J. McMillan. 1995. Experimental investigation of the effects of polynuclear aromatic hydrocarbons on an estuarine sediment food web. Mar. Environ. Res. 40:289-318.
8. DeLong, E., D. G. Franks, and A. L. Alldredge. 1993. Phylogenetic diversity of aggregate-attached versus free-living marine bacterial assemblages. Limnol. Oceanogr. 38:924-934.
9. de Man, J. C. 1975. The probability of most probable numbers. Eur. J. Appl. Microbiol. 1:67-78.
10. Denome, S. A., and K. D. Young. 1992. Unpublished data.
11. Distel, D. L., and A. P. Wood. 1992. Characterization of the gill symbiont of Thyasira flexuosa (Thyasiridae: Bivalvia) by the use of polymerase chain reaction and 16S rRNA sequence analysis. J. Bacteriol. 174:6319-6320.
12. Distel, D. L., and C. M. Cavanaugh. 1994. Independent phylogenetic origins of methanotrophic and chemoautotrophic bacterial endosymbioses in marine bivalves. J. Bacteriol. 176:1932-1938.
13. Distel, D. L., D. J. Lane, G. J. Olson, S. J. Giovannoni, B. Pace, N. R. Pace, D. A. Stahl, and H. Felbeck. 1988. Sulfur-oxiding bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences. J. Bacteriol. 170:2506-2510
14. Distel, D. L., H. Felbeck, and C. M. Cavanaugh. 1994. Evidence for phylogenetic congruence among sulfur-oxidizing bivalve hosts and their chemoautotrophic bacterial endosymbionts. J. Mol. Evol. 38:533-542.
15. Ducrocq, V., and N. Truffaut. 1997. Unpublished data.
16. Dyksterhouse, S. E., J. P. Gray, R. P. Herwig, J. C. Lara, and J. T. Staley. 1995. Cycloclasticus pugetii gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium from marine sediments. Int. J. Syst. Bacteriol. 45:116-123.
17. Endsley, B. D., and D. T. Gibson. 1983. Naphthalene dioxygenase: purification and properties of a terminal oxygenase component. J. Bacteriol. 155: 505-511.
18. Endsley, B. D., D. T. Gibson, and A. L. Laborde. 1982. Oxidation of naphthalene by a multicomponent enzyme system from Pseudomonas sp. strain NCIB. J. Bacteriol. 149:948-954.
19. Erickson, B. D. and F. J. Mondello. 1992. Nucleotide sequencing and transcriptional mapping of the genes encoding biphenyl dioxygenase, a multi-component polychlorinated-biphenyl-degrading enzyme in Pseudomonas strain LB400. J. Bacteriol. 174:2903-2912.
20. Erickson, B. D., and F. J. Mondello. 1993. Enhanced biodegradation of polychlorinated biphenyls alter site-directed mutagenesis of a biphenyl dioxygenase gene. Appl. Environ. Microbiol. 59:3838-3862.
21. Felsenstein, J. 1995. PHYLIP (phylogeny inference package), version 3.572c. Department of Genetics, University of Washington, Seattle.
22. Fuhrman, J. A., K. McCallum, and A. A. Davis. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific oceans. Appl. Environ. Microbiol. 59:1294-1302.
23. Garcia-Pichel, F., L. Prufert-Bebout, and G. Muyzer. 1996. Phenotypic and phylogenetic analyses show Microcoleus chthonoplates to be a cosmopolitan cyanobacterium. Appl. Environ. Microbiol. 62:3284-3291.
24. Gauthier, M. J., B. Lafay, R. Christen, L. Fernandez, M. Acquaviva, P. Bonin, and J. C. Betrand. 1992. Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium. Int. J. Svst. Bacteriol. 42:568-576.
25. Geiselbrecht, A. D., R. P. Herwig, J. W. Deming, and J. T. Staley. 1996. Enumeration and phylogenetic analysis of polycyclic aromatic hydrocarbon-degrading marine bacteria from Puget Sound sediments. Appl. Environ. Microbiol. 62:3344-3349.
26. Genetics Computer Group. 1993. Fragment assembly computer programs. Genetics Computer Group, Madison, Wis.
27. Gilbert, D. G. 1992. SeqApp 1.9a169, a biological sequence editor and analysis program for Macintosh computers. ftp.bio.indiana.edu.
28. Griffiths, R. P., T. M. McNamara, B. A. Caldwell, and R. Y. Morita. 1981. Field observations on the acute effect of crude oil on glucose and glutamate uptake in samples collected from Arctic and subarctic waters. Appl. Environ. Microbiol. 41:1400-1406.
29. Gutell, R. R. 1993. Collection of small subunit (16S- and 16S-like) ribosomal RNA structures. Nucleic Acids Res. 21:3051-3054.
30. Hamann, C. 1997. Unpublished data.
31. Hedlund B. P., A. D. Geiselbrecht, T. J. Bair, and J. T. Staley. Polycyclic aromatic hydrocarbon degradation by a new marine bacterium, Neptunomonas naphthovorans gen. nov., sp. new., Appl. Environ. Microbiol., in press.
32. Herrick, J. B., K. G. Stuart-Keil, W. C. Ghiorse, and E. L. Madsen. 1997. Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native to a coal tar-contaminated field site. Appl. Environ. Microbiol. 63:2330-2337.
33. Hirose, J., A. Suyama, S. Hayashida, and K. Furukawa. 1994. Construction of a hybrid biphenyl (bph) and toluene (tod) genes for functional analysis of aromatic ring dioxygenases. Gene 138:27-33.
34. Kelly, M. T. 1982. Effect of temperature and salinity on Vibrio (Beneckea) vulnificus occurrence in a Gulf Coast environment. Appl. Environ. Microbiol. 44:820-824.
35. Kennicutt, M. C., II (ed.). 1996. Gulf of Mexico offshore operations monitoring experiment, phase I: sublethal responses to contaminant exposure Final Report. OCS study MMS 95-0045. Gulf of Mexico OCS Region, U.S. Department of the Interior Minerals Management Service, New Orleans, La.
36. Kennicutt, M. C., II, R. H. Green, P. Montagna, and P. F. Roscigno. 1996. Gulf of Mexico offshore operations monitoring experiment (GOOMEX), phase 1: sublethal responses to contaminant exposure-introduction and overview. Can. J. Fish. Aquat. Sci. 53:2540-2553.
37. Kimbara, K., T. Hashimoto, M. Fukuda, T. Koana, M. Takagi, M. Oishi, and K. Yano. 1989. Cloning and sequencing of two tandem genes involved in degradation of 2,3-dihydroxybiphenyl to benzoic acid in the polychlorinated biphenyl-degrading soil bacterium Pseudomonas sp. strain KKS102. J. Bacteriol. 171:2740-2747.
38. Kurkela, S., H. Lehvaslaiho, E. T. Palva, and T. H. Teeri. 1988. Cloning, nucleotide sequence and characterization of genes encoding naphthalene dioxygenase of Pseudomonas putida strain NCIB9816. Gene 73:353-362.
39. Larsen, N., G. J. Olsen, B. L. Maidak, M. J. McCaughey, R. Overbeek, T. J. Macke, T. L. Marsh, and C. R. Woese. 1993. The Ribosomal Database Project. Nucleic Acids Res. 21:3021-3023.
40. Lorenz, M. G., and W. Wackernagel. 1994. Bacterial gene transfer by natural genetic transformation in the environment. Microbiol. Rev. 58:563-602.
41. Mackay, D., and W. Y. Shiu. 1981. Aqueous solubility of PAH. J. Chem. Eng. 22:399-402
42. Malins, D. C., M. M. Krahn, D. W. Brown, L. D. Rhodes, M. S. Myers, A. B. McCain, and S. Chan. 1985. Toxic chemicals in marine sediment and biota from Mukilteo, Washington: relationships with hepatic neoplasms and other hepatic lesions in English sole (Parophrys vetulus). J. Natl. Cancer Inst. 74: 487-494.
43. Matheson, V. G., L. J. Forney, Y. Suwa, C. H. Nakatsu, A. J. Sexstone, and W. E. Holben. 1996. Evidence for acquisition in nature of a chromosomal 2,4-dicholorphenoxyacetic acid/α-ketoglutarate dioxygenase gene by different Burkholderia spp. Appl. Environ. Microbiol 62:2457-2463.
44. Meador J. P., J. E. Stein, W. L. Reichert, and U. Varanasi. 1995. Bioaccumulation of polycyclic aromatic hydrocarbons by marine organisms. Rev. Environ. Contam. Toxicol. 143:79-165.
45. Menn, F.-M., B. M. Applegate, and G. S. Sayler. 1993. NAH plasmid-mediated catabolism of anthracene and phenanthrene to naphthoic acids. Appl. Environ. Microbiol. 59:1938-1942.
46. Okpokwasili, G. C., C. C. Somerville, D. J. Grimes, and R. R. Colwell. 1984. Plasmid-associated phenanthrene degradation by Chesapeake Bay sediment bacteria. Colloq. Inst. Fr. Rech. Exploit. Mer 3:601-610.
47. Sanseverino, J., B. M. Applegate, J. M. H. King, and G. S. Sayler. 1993. Plasmid-mediated mineralization of naphthalene, phenanthrene, and anthracene. Appl. Environ. Microbiol. 59:1931-1937.
48. Schocken, M. J., and D. T. Gibson. 1984. Bacterial oxidation of the polycyclic aromatic hydrocarbons acenaphthene and acenaphthylene. Appl. Environ. Microbiol. 48:10-16.
49. Shiaris, M. P. 1989. Phenanthrene mineralization along a natural salinity gradient in an urban estuary, Boston Harbor, Massachusetts. Microbiol. Ecol. 18:135-146.
50. Shiaris, M. P. 1989. Seasonal biotransformation of naphthalene, phenanthrene, and benzo(a)pyrene in surficial estuarine sediments. Appl. Environ. Microbiol. 55:1391-1399.
51. Shiaris, M. P., and J. J. Cooney. 1983. Replica plating method for estimating phenanthrene-utilizing and phenanthrene-cometabolizing microorganisms. Appl. Environ. Microbiol. 45:706-710.
52. Sikkema, J., J. A. M. deBont, and B. Poolman. 1995. Mechanisms of membrane toxicity of hydrocarbons. Microbiol. Rev. 59:201-222.
53. Stegeman, J. J. 1981. Polynuclear aromatic hydrocarbons and their metabolism in the marine environment, p. 1-60. In H. V. Gelbom and P. O. P Tso (ed.), Polycyclic hydrocarbons and cancer, vol. 1. Academic Press, Inc., New York, N.Y.
54. Suen, W. C., B. E. Haigler, and J. C. Spain. 1996. 2,4-Dinitrotoluene dioxygenase from Burkholderia sp. strain DNT: similarity to naphthalene dioxygenase. J. Bacteriol. 178:4926-4934.
55. Suen, W. C., and D. T. Gibson. 1993. Isolation and preliminary characterization of the subunits of the terminal component of naphthalene dioxygenase from Pseudomonas putida NCIB 9816-4. J. Bacteriol. 175:5877-5881.
56. Swofford, D. L. 1991. PAUP: phylogenetic analysis using parsimony. Illinois Natural History Survey, Champaign.
57. Sylvestre, M., M. Sirois, Y. Hurtubise, J. Bergeron, D. Ahmad, F. Shareck, D. Barriault, I. Guillemette, and J. M. Juteau. 1996. Sequencing of Comamonas testosteroni strain B-356 biphenyl/chlorobiphenyl dioxygenase genes: evolutionary relationships among Gram-negative bacterial biphenyl dioxygenases. Gene 174:195-202.
58. Tagger, S., N. Truffaunt, and J. Le Petit. 1990. Preliminary study of relationships among strains forming a bacterial community selected on naphthalene from a marine sediment. Can. J. Microbiol. 36:676-681.
59. Takizawa, N., T. Iida, K. Yamauchi, S. Satoh, Y. Wang, M. Fukuda, and H. Kiyohara. 1996. Unpublished data.
60. Taira, K., J. Hirose, S. Hayashida, and K. Furukawa. 1992. Analysis of bph operon from the polychlorinated biphenyl-degrading strain of Pseudomonas pseudoalcaligenes KF707. J. Biol. Chem. 267:4844-4853.
61. Wang, Y., P. C. K. Lau, and D. K. Button. 1996. A marine oligobacterium harboring genes known to be part of aromatic hydrocarbon degradation pathways of soil pseudomonads. Appl. Environ. Microbiol. 62:2169-2172.
62. West, P. A., G. C. Okpokwasili, P. R. Brayton, D. J. Grimes, and R. R. Colwell. 1984. Numerical taxonomy of phenanthrene-degrading bacteria isolated from Chesapeake Bay. Appl. Environ. Microbiol. 48:988-993.
63. Zylstra, G. J., E. Kim, and A. K. Goyal. 1997. Comparative molecular analysis of genes for polycyclic aromatic hydrocarbon degradation. Genet. Eng. 19:257-269.