The effects of individual PCB congeners on the soil bacterial community structure and the abundance of biphenyl dioxygenase genes

Environment International

Volumn 36, Issue 8, 2010, Pages 901-906

  Correa, Paola A ^a   Lin, LianShin ^a   Just, Craig L ^b   Hu, Dingfei ^b   Hornbuckle, Keri C ^b   Schnoor, Jerald L ^b   Van Aken, Benoit ^c  

^a WEST VIRGINIA UNIVERSITY   (United States)

^b UNIVERSITY OF IOWA   (United States)

^c TEMPLE UNIVERSITY   (United States)

Author keywords

Aerobic biodegradation; Bacterial community; Biphenyl dioxygenase; Polychlorinated biphenyl (PCB); Soil microcosm

Indexed keywords

AEROBIC BACTERIA; BACTERIA; BIODEGRADATION; CHEMICAL ANALYSIS; CHLORINATION; CHROMATOGRAPHIC ANALYSIS; CHROMATOGRAPHY; GAS CHROMATOGRAPHY; GENE EXPRESSION; GENES; MIXTURES; ORGANIC POLLUTANTS; POLYMERASE CHAIN REACTION; SOILS;

AEROBIC BIODEGRADATION; BACTERIAL COMMUNITY; BIPHENYL DIOXYGENASE; POLYCHLORINATED BIPHENYLS (PCB); SOIL MICROCOSMS;

POLYCHLORINATED BIPHENYLS;

2,4,4' TRICHLORINATED BIPHENYL; 3,3',4,4' TRICHLORINATED BIPHENYL; 4 MONOCHLORINATED BIPHENYL; 4,4' DICHLORINATED BIPHENYL; AROCLOR 1242; BACTERIAL DNA; BIPHENYLDIOXYGENASE; DIOXYGENASE; DNA 16S; POLYCHLORINATED BIPHENYL DERIVATIVE; UNCLASSIFIED DRUG;

ABUNDANCE; BIODEGRADATION; CHLORINATION; COMMUNITY STRUCTURE; GENE EXPRESSION; MICROBIAL COMMUNITY; MICROCOSM; PCB; POLLUTION EFFECT; POLLUTION EXPOSURE; SOIL BIOTA; TAXONOMY; TOXIC MATERIAL;

ACTINOBACTERIA; ANAEROBIC METABOLISM; ARTICLE; BACTERIAL COUNT; BETAPROTEOBACTERIA; BIOREMEDIATION; CHEMICAL MODIFICATION; CHLORINATION; CONTROLLED STUDY; INCUBATION TIME; MASS FRAGMENTOGRAPHY; MICROBIAL COMMUNITY; MICROCOSM; NONHUMAN; POPULATION ABUNDANCE; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; SOIL ANALYSIS; SOIL MICROFLORA; SOIL POLLUTION; SOIL STRUCTURE;

ACIDOBACTERIA; ACTINOBACTERIA; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA;

EID: 77957222557     PISSN: 01604120     EISSN: 18736750     Source Type: Journal    
DOI: 10.1016/j.envint.2009.07.015     Document Type: Article

References (43)

1. Abraham W.R., Nogales B., Golyshin P.N., Pieper D.H., Timmis K.N. Polychlorinated biphenyl-degrading microbial communities in soils and sediments. Curr Opin Microbiol 2002, 5:246-253.
2. Abraham W.R., Wenderoth D.F., Glasser W. Diversity of biphenyl degraders in a chlorobenzene polluted aquifer. Chemosphere 2005, 58:529-533.
3. Aguirre de Cárcer D., Martin M., Karlson U., Rivilla R. Changes in bacterial populations and in biphenyl dioxygenase gene diversity in a polychlorinated biphenyl-polluted soil after introduction of willow trees for rhizoremediation. Appl Environ Microbiol 2007, 73:6224-6232.
4. Ausubel F.M., Brent R., Kingston R.E., Moore D.D., Seidman J.G., Smith J.A., et al. Short protocols in molecular biology 1999, John Wiley and Sons.
5. Baker G.C., Smith J.J., Cowan D.A. Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 2003, 55:541-555.
6. Baldwin B.R., Nakatsu C.H., Nies L. Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR. Appl Environ Microbiol 2003, 69:3350-3358.
7. Barns S.M., Takala S.L., Kuske C.R. Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl Environ Microbiol 1999, 65:1731-1737.
8. Bedard D.L., Pohl E.A., Bailey J.J., Murphy A. Characterization of the PCB substrate range of microbial dechlorination process LP. Environ Sci Technol 2005, 39:6831-6838.
9. Blackwood C.B., Oaks A., Buyers J.S. Phylum- and class-specific PCR primers for general microbial community analysis. Appl Environ Microbiol 2005, 71:6193-6198.
10. Borja J., Taleon D.M., Auresenia J., Gallardo S. Polychlorinated biphenyls and their biodegradation. Process Biochem 2005, 40:1999-2013.
11. Callahan M.A., Slimak M.W. Water-related environmental fate of 129 priority pollutants 1979, U.S. Environmental Protection Agency.
12. Cámara B., Herrera C., Gonzalez M., Couve E., Hofer B., Seeger M. From PCBs to highly toxic metabolites by the biphenyl pathway. Environ Microbiol 2004, 6:842-850.
13. Cho Y.C., Sokol R.C., Frohnhoefer R.C., Rhee G.Y. Reductive dechlorination of polychlorinated biphenyls: threshold concentration and dechlorination kinetics of individual congeners in Aroclor 1248. Environ Sci Technol 2003, 37:5651-5656.
14. Chu S., He Y., Xu X. Determination of acute toxicity of polychlorinated biphenyls to Photobacterium phosphoreum. Bull Environ Contam Toxicol 1997, 58:263-267.
15. Field J.A., Sierra-Alvarez R. Microbial transformation and degradation of polychlorinated biphenyls. Environ Pollut 2008, 155:1-12.
16. Fierer N., Jackson J.A., Vilgalys R., Jackson R.B. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl Environ Microbiol 2005, 71:4117-4120.
17. Furukawa K., Fujihara H. Microbial degradation of polychlorinated biphenyls: biochemical and molecular features. J Biosci Bioeng 2008, 105:433-449.
18. Furukawa K., Suenaga H., Goto M. Biphenyl dioxygenases: functional versatilities and directed evolution. J Bacteriol 2004, 186:5189-5196.
19. Giesy J.P., Kannan K. Dioxin-like and non-dioxin-like toxic effects of polychlorinated biphenyls (PCBs): implications for risk assessment. Crit Rev Toxicol 1998, 28:511-569.
20. Gerhardt P., Murray G., Wood W., Krieg N. Methods for general and molecular bacteriology 1993, American Society for Microbiology.
21. Hornbuckle K.C., Smith G.L., Miller S.M., Eadie B.J., Lansing M. Magnitude and origin of PCBs resuspended in open waters of Lake Michigan. Abstr Pap - Am Chem Soc 2004, 228:U544.
22. Hu D, Martinez A, Hornbuckle KC. Discovery of non-Aroclor PCB (3,3'-dichlorobiphenyl) in Chicago air. Environ Sci Technol 2008;42:7873-77.
23. Kohler H.P.E., Kohlerstaub D., Focht D.D. Co-metabolism of polychlorinated-biphenyls - enhanced transformation of Aroclor 1254 by growing bacterial-cells. Appl Environ Microbiol 1988, 54:1940-1945.
24. Lane D. 16s/23s rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics 1991, 115-175. John Wiley, West Sussex, UK. E.S.A.M. Goodfellow (Ed.).
25. Leigh M.B., Prouzova P., Mackova M., Macek T., Nagle D.P., Fletcher J.S. Polychlorinated biphenyl (PCB)-degrading bacteria associated with trees in a PCB-contaminated site. Appl Environ Microbiol 2006, 72:2331-2342.
26. Macedo A.J., Kuhlicke U., Neu T.R., Timmis K.N., Abraham W.R. Three stages of a biofilm community developing at the liquid-liquid interface between polychlorinated biphenyls and water. Appl Environ Microbiol 2005, 71:7301-7309.
27. Macedo A.J., Timmis K.N., Abraham W.R. Widespread capacity to metabolize polychlorinated biphenyls by diverse microbial communities in soils with no significant exposure to PCB contamination. Environ Microbiol 2007, 9:1890-1897.
28. Manz W., Amann R., Ludwig W., Vancanneyt M., Schleifer K.H. Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment. Microbiology-UK 1996, 142:1097-1106.
29. Meier H., Amann R., Ludwig W., Schleifer K.H. Specific oligonucleotide probes for in situ detection of a major group of Gram-positive bacteria with low DNA G + C content. Syst Appl Microbiol 1999, 22:186-196.
30. Muyzer G., Dewaal E.C., Uitterlinden A.G. Profiling of complex microbial-populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16s ribosomal-RNA. Appl Environ Microbiol 1993, 59:695-700.
31. Nogales B., Moore E.R.B., Abraham W.R., Timmis K.N. Identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl polluted moorland soil. Environ Microbiol 1999, 1:199-212.
32. Nogales B., Moore E.R.B., Llobet-Brossa E., Rossello-Mora R., Amann R., Timmis K.N. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl Environ Microbiol 2001, 67:1874-1884.
33. Ogram A. Isolation of nucleic acids from environment samples. Techniques in Microbial Ecology 1998, 273-288. Oxford University Press, New York, NY. R.S. Burlage, R. Atlas, D. Stahl, G. Geesey, G. Sayler (Eds.).
34. Ohtsubo Y., Kudo T., Tsuda M., Nagata Y. Strategies for bioremediation of polychlorinated biphenyls. Appl Microbiol Biotechnol 2004, 65:250-258.
35. Olson P., Reardon K., Pilon-Smits E. Ecology of rhizosphere bioremediation. In: Phytoremediation. Transformation and Control of Contaminants 2003, 317-353. John Wiley. S. McCutcheon, J. Schnoor (Eds.).
36. Overmann J., Coolen M.J.L., Tuschak C. Specific detection of different phylogenetic groups of chemocline bacteria based on PCR and denaturing gradient gel electrophoresis of 16S rRNA gene fragments. Arch Microbiol 1999, 172:83-94.
37. Parnell J.J., Park J., Denef V., Tsoi T., Hashsham S., Quensen J., et al. Coping with polychlorinated biphenyl (PCB) toxicity: physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress. Appl Environ Microbiol 2006, 72:6607-6614.
38. Pieper D.H., Seeger M. Bacterial metabolism of polychlorinated biphenyls. J Mol Microbiol Biotechnol 2008, 15:121-138.
39. Safe S. Toxicology, structure-function relationship, and human and environmental-health impacts of polychlorinated-biphenyls - progress and problems. Environ Health Perspect 1993, 100:259-268.
40. Stach J.E.M., Maldonado L.A., Ward A.C., Goodfellow M., Bull A.T. New primers for the class Actinobacteria: application to marine and terrestrial environments. Environ Microbiol 2003, 5:828-841.
41. Tiedje J.M., Boyd S.A. Anaerobic degradation of chlorinated aromatic hydrocarbons. Dev Ind Microbiol Ser 1987, 27:117-127.
42. Tillmann S., Strompl C., Timmis K.N., Abraham W.R. Stable isotope probing reveals the dominant role of Burkholderia species in aerobic degradation of PCBs. FEMS Microbiol Ecol 2005, 52:207-217.
43. Vasilyeva G.K., Strijakova E.R. Bioremediation of soils and sediments contaminated by polychlorinated biphenyls. Microbiology 2007, 76:639-653.