Response of PAH-degrading genes to PAH bioavailability in the overlying water, suspended sediment, and deposited sediment of the Yangtze River

Chemosphere

Volumn 128, Issue , 2015, Pages 236-244

  Xia, Xinghui ^a   Xia, Na ^a   Lai, Yunjia ^b   Dong, Jianwei ^a   Zhao, Pujun ^a   Zhu, Baotong ^a   Li, Zhihuang ^a   Ye, Wan ^a   Yuan, Yue ^a   Huang, Junxiong ^a  

^a BEIJING NORMAL UNIVERSITY   (China)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Bioavailability; Biodegradation; Freely dissolved concentration; NahAc and nidA gene; PAH ring hydroxylating dioxygenase genes; Suspended sediment

Indexed keywords

BACTERIA; BIODEGRADATION; BIOMARKERS; DISSOLUTION; NAPHTHALENE; PYRENE; SUSPENDED SEDIMENTS; WATER RESOURCES;

BIOAVAILABILITY; DIOXYGENASE GENES; ENVIRONMENTAL PARAMETER; FREELY DISSOLVED CONCENTRATION; GRAM-NEGATIVE BACTERIA; HYDROPHOBIC ORGANIC COMPOUND; POLYCYCLIC AROMATIC HYDROCARBON (PAH); PYRENE-DEGRADING BACTERIA;

GENES;

DIOXYGENASE; NAPHTHALENE DERIVATIVE; POLYCYCLIC AROMATIC HYDROCARBON; PYRENE DERIVATIVE; WATER; BIOLOGICAL MARKER; POLLUTANT; PYRENE;

BIOAVAILABILITY; BIODEGRADATION; BIOMARKER; CONCENTRATION (COMPOSITION); GENE EXPRESSION; GENOTYPE; HYDROPHOBICITY; IN SITU TEST; NAPHTHALENE; ORGANIC COMPOUND; PAH; PHYLOGENETICS; PYRENE; SUSPENDED SEDIMENT;

ARTICLE; BACTERIAL GENE; BIOAVAILABILITY; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; GENE DOSAGE; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE; GRAM NEGATIVE BACTERIUM; NAGAC GENE; NAHAC GENE; NIDA GENE; NONHUMAN; PARTICLE RESUSPENSION; PHYLOGENY; RIVER; ANALYSIS; BIOREMEDIATION; CHEMISTRY; CHINA; GENETIC VARIATION; GENETICS; METABOLISM; POLLUTANT; SEDIMENT;

CHINA; YANGTZE RIVER;

BACTERIA (MICROORGANISMS); NEGIBACTERIA;

BIODEGRADATION, ENVIRONMENTAL; BIOLOGICAL AVAILABILITY; BIOMARKERS; CHINA; DIOXYGENASES; ENVIRONMENTAL POLLUTANTS; GENES, BACTERIAL; GENETIC VARIATION; GEOLOGIC SEDIMENTS; GRAM-NEGATIVE BACTERIA; PHYLOGENY; POLYCYCLIC HYDROCARBONS, AROMATIC; PYRENES; RIVERS;

EID: 84925258730     PISSN: 00456535     EISSN: 18791298     Source Type: Journal    
DOI: 10.1016/j.chemosphere.2015.02.011     Document Type: Article

References (43)

1. Bastiaens L., Springael D., Wattiau P., Harms H., Verachtert H., Diels L. Isolation of adherent polycyclic aromatic hydrocarbon (PAH)-degrading bacteria using PAH-sorbing carriers. Appl. Environ. Microb. 2000, 66:1834-1843.
2. Bengtsson G., Törneman N., De Lipthay J.R., Sørensen S.J. Microbial diversity and PAH catabolic genes tracking spatial heterogeneity of PAH concentrations. Microbial Ecol. 2013, 65:91-100.
3. Bondarenko S., Gan J. Simultaneous measurement of free and total concentrations of hydrophobic compounds. Environ. Sci. Technol. 2009, 43:3772-3777.
4. Cébron A., Norini M.-P., Beguiristain T., Leyval C. Real-time PCR quantification of PAH-ring hydroxylating dioxygenase (PAH-RHD alpha) genes from Gram positive and Gram negative bacteria in soil and sediment samples. J. Microbiol. Meth. 2008, 73:148-159.
5. Cerniglia C.E. Biodegradation of polycyclic aromatic hydrocarbons. Curr. Opin. Biotech. 1993, 4:331-338.
6. Cornelissen G., Gustafsson Ö., Bucheli T.D., Jonker M.T.O., Koelmans A.A., van Noort P.C.M. Extensive sorption of organic compounds to black carbon, coal, and kerogen in sediments and soils: mechanisms and consequences for distribution, bioaccumulation, and biodegradation. Environ. Sci. Technol. 2005, 39:6881-6895.
7. Daane L., Harjono I., Zylstra G., Häggblom M. Isolation and characterization of polycyclic aromatic hydrocarbon-degrading bacteria associated with the rhizosphere of salt marsh plants. Appl. Environ. Microb. 2001, 67:2683-2691.
8. de Menezes A., Clipson N., Doyle E. Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil. Environ. Microbiol. 2012, 14:2577-2588.
9. DeBruyn J.M., Chewning C.S., Sayler G.S. Comparative quantitative prevalence of Mycobacteria and functionally abundant nidA, nahAc, and nagAc dioxygenase genes in coal tar contaminated sediments. Environ. Sci. Technol. 2007, 41:5426-5432.
10. Deyerling D., Wang J., Hu W., Westrich B., Peng C., Bi Y., Henkelmann B., Schramm K.-W. PAH distribution and mass fluxes in the Three Gorges Reservoir after impoundment of the Three Gorges Dam. Sci. Total. Environ. 2014, 491:123-130.
11. Di Gennaro P., Moreno B., Annoni E., Garcia-Rodriguez S., Bestetti G., Benitez E. Dynamic changes in bacterial community structure and in naphthalene dioxygenase expression in vermicompost-amended PAH-contaminated soils. J. Hazard. Mater. 2009, 172:1464-1469.
12. Ding G.-C., Heuer H., Zühlke S., Spiteller M., Pronk G.J., Heister K., Kögel-Knabner I., Smalla K. Soil type-dependent responses to phenanthrene as revealed by determining the diversity and abundance of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase genes by using a novel PCR detection system. Appl. Environ. Microb. 2010, 76:4765-4771.
13. Dong J.W., Xia X.H., Zhai Y.W. Investigating particle concentration effects of polycyclic aromatic hydrocarbon (PAH) sorption on sediment considering the freely dissolved concentrations of PAHs. J. Soil. Sediment. 2013, 13:1469-1477.
14. Feng C.L., Xia X.H., Shen Z.Y., Zhou Z. Distribution and sources of polycyclic aromatic hydrocarbons in Wuhan section of the Yangtze River, China. Environ. Monit. Assess. 2007, 133:447-458.
15. Fuentes S., Mendez V., Aguila P., Seeger M. Bioremediation of petroleum hydrocarbons: catabolic genes, microbial communities, and applications. Appl. Microbiol. Biot. 2014, 98:4781-4794.
16. Haritash A., Kaushik C. Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs): a review. J. Hazard. Mater. 2009, 169:1-15.
17. Isaac P., Sanchez L.A., Bourguignon N., Eugenia Cabral M., Ferrero M.A. Indigenous PAH-degrading bacteria from oil-polluted sediments in Caleta Cordova, Patagonia Argentina. Int. Biodeter. Biodegr. 2013, 82:207-214.
18. Iwai S., Johnson T.A., Chai B., Hashsham S.A., Tiedje J.M. Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples. Appl. Environ. Microbiol. 2011, 77:3551-3557.
19. Jurelevicius D., Alvarez V.M., Peixoto R., Rosado A.S., Seldin L. Bacterial polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases (PAH-RHD) encoding genes in different soils from King George Bay, Antarctic Peninsula. Appl. Soil. Ecol. 2012, 55:1-9.
20. Kile D.E., Chiou C.T., Zhou H., Li H., Xu O. Partition of nonpolar organic pollutants from water to soil and sediment organic matters. Environ. Sci. Technol. 1995, 29:1401-1406.
21. Li G.C., Xia X.H., Yang Z.F., Wang R., Voulvoulis N. Distribution and sources of polycyclic aromatic hydrocarbons in the middle and lower reaches of the Yellow River, China. Environ. Pollut. 2006, 144:985-993.
22. Lozada M., Mercadal J.P.R., Guerrero L.D., Di Marzio W.D., Ferrero M.A., Dionisi H.M. Novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of Patagonia. BMC Microbiol. 2008, 8:50.
23. Lozupone C., Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microb. 2005, 71:8228-8235.
24. Lu X.Y., Zhang T., Herbert Han.-Ping., Fang H., Leung K.M., Zhang G. Biodegradation of naphthalene by enriched marine denitrifying bacteria. Int. Biodeter. Biodegr. 2011, 65:204-211.
25. Marcos M.S., Lozada M., Di Marzio W.D., Dionisi H.M. Abundance, dynamics, and biogeographic distribution of seven polycyclic aromatic hydrocarbon dioxygenase gene variants in coastal sediments of Patagonia. Appl. Environ. Microb. 2012, 78:1589-1592.
26. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microb. 2009, 75:7537-7541.
27. Singleton D.R., Hu J., Aitken M.D. Heterologous expression of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase genes from a novel pyrene-degrading betaproteobacterium. Appl. Environ. Microb. 2012, 78:3552-3559.
28. Stolz A. Molecular characteristics of xenobiotic-degrading sphingomonads. Appl. Microbiol. Biot. 2009, 81:793-811.
29. Wang L.L., Shen Z.Y., Wang H.Y., Niu J.F., Lian G.X., Yang Z.F. Distribution characteristics of phenanthrene in the water, suspended particles and sediments from Yangtze River under hydrodynamic conditions. J. Hazard. Mater. 2009, 165:441-446.
30. Wang F., Bu Q.W., Xia X.H., Shen M.H. Contrasting effects of black carbon amendments on PAH bioaccumulation by Chironomus plumosus larvae in two distinct sediments: role of water absorption and particle ingestion. Environ. Pollut. 2011, 159:1905-1913.
31. Wu P., Wang Y.S., Sun F.L., Wu M.L., Peng Y.L. Bacterial polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases in the sediments from the Pearl River estuary, China. Appl. Microbiol. Biot. 2013, 1-10.
32. Xia X.H., Wang R. Effect of sediment particle size on polycyclic aromatic hydrocarbon biodegradation: Importance of the sediment-water interface. Environ. Toxicol. Chem. 2008, 27:119-125.
33. Xia X.H., Yu H., Chen L. Effect of particles on the biodegradation of PAHs in natural waters-A study for the Yellow River. Acta Scientiae Circumstantiae 2005, 25:1226-1231.
34. Xia X.H., Li Y.R., Zhou Z., Feng C.L. Bioavailability of adsorbed phenanthrene by black carbon and multi-walled carbon nanotubes to Agrobacterium. Chemosphere 2010, 78:1329-1336.
35. Xia X.H., Zhou Z., Zhou C.H., Jiang G.H., Liu T. Effects of Suspended Sediment on the Biodegradation and Mineralization of Phenanthrene in River Water. J. Environ. Qual. 2011, 40:118-125.
36. Xia N., Xia X.H., Zhu B.T., Zheng S.K., Zhuang J. Bacterial diversity and community structure in the sediment of the middle and lower reaches of the Yellow River, the largest turbid river in the world. Aquat. Microb. Ecol. 2013, 71:43-168.
37. Xia X.H., Zhai Y.W., Dong J.W. Contribution ratio of freely to total dissolved concentrations of polycyclic aromatic hydrocarbons in natural river waters. Chemosphere 2013, 90:1785-1793.
38. Xia N., Xia X.H., Liu T., Hu L.J., Zhu B.T., Zhang X.T., Dong J.W. Characteristics of bacterial community in the water and surface sediment of the Yellow River, China, the largest turbid river in the world. J. Soil. Sediment. 2014, 1-11.
39. Yang Z.F., Wang Y., Shen Z.Y., Niu J.F., Tang Z.W. Distribution and speciation of heavy metals in sediments from the mainstream, tributaries, and lakes of the Yangtze River catchment of Wuhan, China. J. Hazard. Mater. 2009, 166:1186-1194.
40. Zhang X.T., Xia X.H., Dong J.W., Bao Y.M., Li H.S. Enhancement of toxic effects of phenanthrene to Daphnia magna due to the presence of suspended sediment. Chemosphere 2014, 104:162-169.
41. Zhang T., Yang W.L., Chen S.J., Shi D.L., Zhao H., Ding Y., Huang Y.R., Li N., Ren Y., Mai B.X. Occurrence, sources, and ecological risks of PBDEs, PCBs, OCPs, and PAHs in surface sediments of the Yangtze River Delta city cluster, China. Environ. Monit. Assess. 2014, 186:5285-5295.
42. Zhou N.Y., Fuenmayor S.L., Williams P.A. Nag genes of Ralstonia (formerly Pseudomonas) sp strain U2 encoding enzymes for gentisate catabolism. J. Bacteriol. 2001, 183:700-708.
43. Zhou H.W., Guo C.L., Wong Y.S., Tam N.F.Y. Genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon-degrading bacteria isolated from mangrove sediments. FEMS. Microbiol. Lett. 2006, 262:148-157.