Effect of activated carbon amendment on bacterial community structure and functions in a PAH impacted urban soil

Environmental Science and Technology

Volumn 46, Issue 9, 2012, Pages 5057-5066

  Meynet, Paola ^a   Hale, Sarah E ^b   Davenport, Russell J ^a   Cornelissen, Gerard ^b,c,d   Breedveld, Gijs D ^b,e   Werner, David ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b NORWEGIAN GEOTECHNICAL INSTITUTE   (Norway)

^c STOCKHOLM UNIVERSITY   (Sweden)

^d NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^e UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

AMENDED SOIL; AVAILABILITY ASSESSMENT; BACTERIAL COMMUNITY STRUCTURE; BATCH TESTS; DENATURING GRADIENT GEL ELECTROPHORESES (DGGE); DETRIMENTAL EFFECTS; DIOXYGENASES; FIELD TRIAL; GENE COPY NUMBER; MICROBIAL CELLS; PAH DEGRADERS; POLYCYCLIC AROMATIC HYDROCARBONS(PAHS); REAL-TIME POLYMERASE CHAIN REACTION; RESPIRATION RATE; RHODOCOCCUS; RHODOCOCCUS ERYTHROPOLIS; SIDE EFFECT; SOIL MICROBIOLOGY; URBAN SOILS;

ACTIVATED CARBON; BIODEGRADATION; ELECTROPHORESIS; GENES; MICROBIOLOGY; POLLUTION; POLYCYCLIC AROMATIC HYDROCARBONS; POLYMERASE CHAIN REACTION; SOCIAL SCIENCES; SORPTION;

SOILS;

ACTIVATED CARBON; BIOCIDE; DIOXYGENASE; POLYCYCLIC AROMATIC HYDROCARBON;

BACTERIUM; BIODEGRADATION; COMMUNITY STRUCTURE; MICROBIAL COMMUNITY; PAH; SOIL AMENDMENT; SOIL MICROORGANISM; SOIL POLLUTION; SOIL REMEDIATION; SUBLETHAL EFFECT; URBAN SITE;

ARTICLE; BIODEGRADATION; BREATHING RATE; CELL COUNT; COMMUNITY STRUCTURE; CONTROLLED STUDY; DENATURING GRADIENT GEL ELECTROPHORESIS; ECOSYSTEM RESTORATION; GENE DOSAGE; MICROBIAL COMMUNITY; MICROBIAL RESPIRATION; NONHUMAN; REAL TIME POLYMERASE CHAIN REACTION; RHODOCOCCUS; RHODOCOCCUS ERYTHROPOLIS; RHODOCOCCUS JOSTII; SOIL AMENDMENT; SOIL POLLUTANT; SOIL QUALITY;

ADSORPTION; BIODEGRADATION, ENVIRONMENTAL; CHARCOAL; DENATURING GRADIENT GEL ELECTROPHORESIS; MICROBIAL CONSORTIA; POLYCYCLIC HYDROCARBONS, AROMATIC; POLYMERASE CHAIN REACTION; SOIL MICROBIOLOGY; SOIL POLLUTANTS;

BACTERIA (MICROORGANISMS); RHODOCOCCUS ERYTHROPOLIS; RHODOCOCCUS JOSTII;

EID: 84860495991     PISSN: 0013936X     EISSN: 15205851     Source Type: Journal    
DOI: 10.1021/es2043905     Document Type: Article

References (51)

1. Ghosh, U.; Luthy, R. G.; Cornelissen, G.; Werner, D.; Menzie, C. A. In-situ Sorbent Amendments: A New Direction in Contaminated Sediment Management Environ. Sci. Technol. 2011, 45, 1163-1168
2. Brandli, R. C.; Hartnik, T.; Henriksen, T.; Cornelissen, G. Sorption of native polyaromatic hydrocarbons (PAH) to black carbon and amended activated carbon in soil Chemosphere 2008, 73, 1805-1810
3. Fagervold, S. K.; Chai, Y. Z.; Davis, J. W.; Wilken, M.; Cornelissen, G.; Ghosh, U. Bioaccumulation of Polychlorinated Dibenzo-p-Dioxins/Dibenzofurans in E. fetida from Floodplain Soils and the Effect of Activated Carbon Amendment Environ. Sci. Technol. 2010, 44, 5546-5552
4. Langlois, V.; Rutter, A.; Zeeb, B. Activated carbon immobilizes residual polychlorinated biphenyls in weathered contaminated soil J. Environ. Qual. 2011, 40, 1130-1134
5. Baker, J.; Chang, C. W.; Ghosh, U.; Paul, P.; Kjellerup, B. Application of Tools to Measure Pcb Microbial Dechlorination and Flux into Water during in-Situ Treatment of Sediments; SERDP, 2011; p 138.
6. Hilber, I.; Wyss, G. S.; Mäder, P.; Bucheli, T. D.; Meier, I.; Vogt, L.; Schulin, R. Influence of activated charcoal amendment to contaminated soil on dieldrin and nutrient uptake by cucumbers Environ. Pollut. 2009, 157, 2224-2230
7. Vasilyeva, G. K.; Strijakova, E. R.; Nikolaeva, S. N.; Lebedev, A. T.; Shea, P. J. Dynamics of PCB removal and detoxification in historically contaminated soils amended with activated carbon Environ. Pollut. 2010, 158, 770-777
8. Hale, S. E.; Elmquist, M.; Brändli, R.; Hartnik, T.; Jakob, L.; Henriksen, T.; Werner, D.; Cornelissen, G. Activated carbon amendment to sequester PAHs in contaminated soil: A lysimeter field trial Chemosphere 2012, 87, 177-184
9. Rhodes, A. H.; Carlin, A.; Semple, K. T. Impact of Black Carbon in the Extraction and Mineralization of Phenanthrene in Soil Environ. Sci. Technol. 2008, 42, 740-745
10. Karapanagioti, H. K.; Gossard, C. M.; Strevett, K. A.; Kolar, R. L.; Sabatini, D. A. Model coupling intraparticle diffusion/sorption, nonlinear sorption, and biodegradation processes J. Contam. Hydrol. 2001, 48, 1-21
11. Payne, R. B.; May, H. D.; Sowers, K. R. Enhanced Reductive Dechlorination of Polychlorinated Biphenyl Impacted Sediment by Bioaugmentation with a Dehalorespiring Bacterium Environ. Sci. Technol. 2011, 45 (20) 8772-8779
12. Bushnaf, K. M.; Puricelli, S.; Saponaro, S.; Werner, D. Effect of biochar on the fate of volatile petroleum hydrocarbons in an aerobic sandy soil J. Contam. Hydrol. 2011, 126, 208-215
13. Hale, S. E.; Meynet, P.; Davenport, R. J.; Jones, M. D.; Werner, D. Changes in polycyclic aromatic hydrocarbon availability in River Tyne sediment following bioremediation treatments or activated carbon amendment Water Res. 2010, 44, 4529-4536
14. Davenport, R.; Curtis, T.; Goodfellow, M.; Stainsby, F.; Bingley, M. Quantitative use of fluorescent in situ hybridization to examine relationships between mycolic acid-containing actinomycetes and foaming in activated sludge plants Microbiology 2000, 66, 1158-1166
15. Griffiths, R. I.; Whiteley, A. S.; O'Donnell, A. G.; Bailey, M. J. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition Appl. Environ. Microbiol. 2000, 66, 5488-5491
16. Muyzer, G.; de Waal, 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 rRNA Appl. Environ. Microbiol. 1993, 59, 695-700
17. Johnsen, A.; Schmidt, S.; T.K., H.; Henriksen, S.; Jacobsen, C. J.; Andersen, O. Strong impact on the polycyclic aromatic hydrocarbon (PAH)-degrading community of a PAH-polluted soil but marginal effect on PAH degradation when priming with bioremediated soil dominated by Mycobacteria Appl. Environ. Microbiol. 2007, 73, 1474-1480
18. Rogers, S. W.; Ong, S. K.; Moorman, T. B. Mineralization of PAHs in coal-tar impacted aquifer sediments and associated microbial community structure investigated with FISH Chemosphere 2007, 69, 1563-1573
19. Bloem, J.; Veninga, M.; Shepherd, J. Fully automatic determination of soil bacterium numbers, cell volumes, and frequencies of dividing cells by confocal laser scanning microscopy and image analysis Appl. Environ. Microbiol. 1995, 61, 1488-1493
20. Whitman, W.; Coleman, D.; Wiebe, W. Prokaryotes: The unseen majority Proc. Natl. Acad. Sci., U.S.A. 1998, 95, 6578-6583
21. Jakob, L.; Hartnik, T.; Henriksen, T.; Elmquist, M.; Brandli, R.; Hale, S. E.; Cornelissen, G. PAH-sequestration capacity of granular and powdered activated carbon amendments in soil, and their effects on earthworms and plants. Chemosphere 2011, not supplied.
22. Dawson, J. J. C.; Godsiffe, E. J.; Thompson, I. P.; Ralebitso-Senior, T. K.; Killhama, K. S.; Patona, G. I. Application of biological indicators to assess recovery of hydrocarbon impacted soils Soil Biol. Biochem. 2007, 39, 164-177
23. Cho, Y. M.; Ghosh, U.; Kennedy, A. J.; Grossman, A.; Ray, G.; Tomaszewski, J. E.; Smithenry, D. W.; Bridges, T. S.; Luthy, R. G. Field Application of Activated Carbon Amendment for In-Situ Stabilization of Polychlorinated Biphenyls in Marine Sediment Environ. Sci. Technol. 2009, 43, 3815-3823
24. Cornelissen, G.; Krusa, M. E.; Breedveld, G. D.; Eek, E.; Oen, A. M. P.; Arp, H. P. H.; Raymond, C.; Samuelsson, G.; Hedman, J. E.; Stokland, O.; Gunnarsson, J. S. Remediation of Contaminated Marine Sediment Using Thin-Layer Capping with Activated Carbon-A Field Experiment in Trondheim Harbor, Norway Environ. Sci. Technol. 2011, 45, 6110-6116
25. Kitagawa, W.; Suzuki, A.; Hoaki, T.; Masai, E.; Fukuda, M. Multiplicity of aromatic ring hydroxylation dioxygenase genes in a strong PCB degrader, Rhodococcus sp. strain RHA1 demonstrated by denaturing gradient gel electrophoresis Biosci., Biotechnol. Biochem. 2001, 65, 1907-1911
26. Kanaly, R. A.; Harayama, S. Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by bacteria J. Bacteriol. 2000, 182, 2059-2067
27. Kazuya, W. Microorganisms relevant to bioremediation Curr. Opin. Biotechnol. 2001, 12, 237-241
28. Head, I. M.; Jones, D. M.; Roling, W. F. M. Marine microorganisms make a meal of oil Nat. Rev. Microbiol. 2006, 4, 173-182
29. Pérez-Pantoja, D.; Donoso, R.; Junca, H.; González, B.; Pieper, D. H., Phylogenomics of aerobic bacterial degradation of aromatics. In Handbook of Hydrocarbon and Lipid Microbiology; Timmis, K. N., Ed.; Springer Verlag: Heidelberg, 2010.
30. Heitkamp, M.; Franklin, W.; Cerniglia, C. Microbial metabolism of polycyclic aromatic hydrocarbons: Isolation and characterization of a pyrene-degrading bacterium Appl. Environ. Microbiol. 1988, 54, 2549-2555
31. Stingley, R. L.; Khan, A. A.; Cerniglia, C. E. Molecular characterization of a phenanthrene degradation pathway in Mycobacterium vanbaalenii PYR-1 Biochem. Biophys. Res. 2004, 322, 136-146
32. Shimodaira, J.; Miyauchi, K.; Takeda, H.; Kasai, D.; Masai, E.; Fukuda, M. Regulatory mechanism of biphenyl/PCB-degradation gene transcription in Rhodococcus jostii RHA1 J. Biotechnol. 2010, 150, S246-S246
33. Arai, H.; Kosono, S.; Taguchi, K.; Maeda, M.; Song, E.; Fuji, F.; Chung, S.; Kudo, T. Two sets of biphenyl and PCB degradation genes on a linear plasmid in Rhodococcus erythropolis TA421 J. Ferment. Bioeng. 1998, 86, 595-599
34. Kesseler, M.; Dabbs, E.; Averhoff, B.; Gottschalk, G. Studies on the isopropylbenzene 2,3-dioxygenase and the 3-isopropylcatechol 2,3-dioxygenase genes encoded by the linear plasmid of Rhodococcus erythropolis BD2 Microbiology 1996, 142, 3241-3251
35. HuiJie, L.; CaiYun, Y.; Yun, T.; GuangHui, L.; TianLing, Z. Using population dynamics analysis by DGGE to design the bacterial consortium isolated from mangrove sediments for biodegradation of PAHs Int. Biodeter. Biodegrad. 2010, 65, 269-275
36. Vinas, M.; Sabate, J.; Espuny, M.; Solanas, M. Bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosote-contaminated soil Appl. Environ. Microbiol. 2005, 71, 7008-7018
37. Jones, M.; Crandell, D.; Singleton, D. Stable-isotope probing of the polycyclic aromatic hydrocarbon-degrading bacterial guild in a contaminated soil Environ. Microbiol. 2011, 13, 2623-2632
38. 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
39. α) genes from Gram positive and Gram negative bacteria in soil and sediment samples J. Microbiol. Methods 2008, 148-159
40. Bamforth, S. M.; Singleton, I. Bioremediation of polycyclic aromatic hydrocarbons: current knowledge and future directions J. Chem. Technol. Biotechnol. 2005, 80, 723-736
41. Parales, R. E. The role of active-site residues in naphthalene dioxygenase J. Ind. Microbiol. Biotechnol. 2003, 30, 271-278
42. Laurie, A. D.; Lloyd-Jones, G. Quantification of phnAc and nahAc in contaminated New Zealand soils by competitive PCR Appl. Environ. Microbiol. 2000, 66, 1814-1817
43. Lillis, L.; Clipson, N.; Doyle, E. Quantification of catechol dioxygenase gene expression in soil during degradation of 2,4-dichlorophenol FEMS Microbiol. Ecol. 2010, 73, 363-369
44. Widada, J.; Nojiri, H.; Kasuga, K.; Yoshida, T.; Habe, H.; Omori, T. Quantification of the carbazole 1,9a-dioxygenase gene by real-time competitive PCR combined with co-extraction of internal standards FEMS Microbiol. Lett. 2001, 202, 51-57
45. Van Hamme, J. D.; Singh, A.; Ward, O. P. Recent advances in petroleum microbiology Microbiol. Mol. Biol. Rev. 2003, 67, 503-549
46. Fry, J. C. Direct methods and biomass estimation Methods Microbiol. 1990, 22, 41-85
47. Hawthorne, S. B.; Azzolina, N. A.; Neuhauser, E. F.; Kreitinger, J. P. Predicting Bioavailability of sediment polycyclic aromatic hydrocarbons to Hyalella azteca using equilibrium partitioning, Supercritical fluid extraction, and pore water concentrations Environ. Sci. Technol. 2007, 41, 6297-6304
48. Cho, Y. M.; Werner, D.; Choi, Y.; Luthy, R. G. Long-term monitoring and modeling of the mass transfer of polychlorinated biphenyls in sediment after pilot-scale in-situ amendment with activated carbon J. Contam. Hydrol. 2012, 129-130, 25-37
49. Ahn, S.; Werner, D.; Luthy, R. G. Physicochemical characterization of coke plant soil for the assessment of PAH availability and the feasibility of phytoremediation Environ. Toxicol. Chem. 2005, 24, 2185-2196
50. Hale, S. E.; Werner, D. Modeling the mass transfer of hydrophobic organic pollutants in briefly and continuously mixed sediment after amendment with activated carbon Environ. Sci. Technol. 2010, 44, 3381-3387
51. Wiedemeier, T. H.; Rifai, H. S.; Newell, C. J.; Wilson, J. T. Natural Attenuation of Fuels and Chlorinated Solvents in the Subsurface; Wiley: New York, 1999; p 617.