Microbial functional gene diversity with a shift of subsurface redox conditions during in situ uranium reduction

Applied and Environmental Microbiology

Volumn 78, Issue 8, 2012, Pages 2966-2972

  Liang, Yuting ^a,b,c   Van Nostrand, Joy D ^c   N'Guessan, Lucie A ^e,g   Peacock, Aaron D ^d   Deng, Ye ^c   Long, Philip E ^e   Tom Resch, C ^e   Wu, Liyou ^c   He, Zhili ^c   Li, Guanghe ^a   Hazen, Terry C ^f   Lovley, Derek R ^g   Zhoua, Jizhong ^a,c,f  

^a TSINGHUA UNIVERSITY   (China)

^b CHANGZHOU UNIVERSITY   (China)

^c UNIVERSITY OF OKLAHOMA   (United States)

^d UNIVERSITY OF TENNESSEE   (United States)

^e PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^f LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^g UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOREDUCTIONS; CODING GENES; ELECTRON-ACCEPTING PROCESS; ENVIRONMENTAL PARAMETER; FUNCTIONAL DIVERSITY; FUNCTIONAL GENES; GEOBACTER; GEOCHEMICAL VARIABLES; HIERARCHICAL CLUSTERS; IN-FIELD; IN-SITU; METABOLIC PROCESS; MICROBIAL COMMUNITIES; MICROBIAL COMMUNITY STRUCTURES; MICROBIAL PROCESS; REDOX CONDITION; REDOX POTENTIALS; REMEDIAL ACTIONS; SULFATE-REDUCING CONDITIONS; SULFITE REDUCTASE; URANIUM MILL TAILINGS; URANIUM REDUCTION;

BIODEGRADATION; BIOREMEDIATION; BIOTECHNOLOGY; HIERARCHICAL SYSTEMS; METHANATION; MICROORGANISMS; REDOX REACTIONS; URANIUM; VOLATILE FATTY ACIDS;

GENES;

URANIUM;

BIOREMEDIATION; COMMUNITY STRUCTURE; FUNCTIONAL CHANGE; GENETIC VARIATION; IN SITU MEASUREMENT; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; REDOX CONDITIONS; REDUCTION; TAILINGS; URANIUM;

ARTICLE; BIOREMEDIATION; BIOTA; GENETIC VARIABILITY; METABOLISM; MICROARRAY ANALYSIS; MICROBIOLOGY; OXIDATION REDUCTION REACTION; POLLUTANT;

BIODEGRADATION, ENVIRONMENTAL; BIOTA; ENVIRONMENTAL MICROBIOLOGY; ENVIRONMENTAL POLLUTANTS; GENETIC VARIATION; MICROARRAY ANALYSIS; OXIDATION-REDUCTION; URANIUM;

GEOBACTER SP.;

EID: 84861148674     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.06528-11     Document Type: Article

References (36)

1. Anderson R, et al. 2003. Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uraniumcontaminated aquifer. Appl. Environ. Microbiol. 69:5884-5891.
2. Boonchayaanant B, Nayak D, Xin D, Criddle C. 2009. Uranium reduction and resistance to reoxidation under iron-reducing and sulfatereducing conditions. Water Res. 43:4652-4664.
3. Chang Y, et al. 2005. Microbial incorporation of C-13-labeled acetate atthe field scale: detection of microbes responsible for reduction of U(VI). Environ. Sci. Technol. 39:9039-9048.
4. Clarke KR, Ainsworth M. 1993. A method of linking multivariate community structure to environmental variables. Mar. Ecol. Prog. Ser. 92: 205-219.
5. Druhan J, et al. 2008. Sulfur isotopes as indicators of amended bacterial sulfate reduction processes influencing field scale uranium bioremediation. Environ. Sci. Technol. 42:7842-7849.
6. Eisen M, Spellman P, Brown P, Botstein D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U. S. A. 95:14863-14868.
7. Elias D, Suflita J, McInerney M, Krumholz L. 2004. Periplasmic cytochrome c3 of Desulfovibrio vulgaris is directly involved in H2-mediated metal but not sulfate reduction. Appl. Environ. Microbiol. 70:413-420.
8. Finneran KT, Housewright M, Lovley DR. 2002. Multiple influences of nitrate on uranium solubility during bioremediation of uranium contaminated subsurface sediments. Environ. Microbiol. 4:510-516.
9. Gao W, Francis AJ. 2008. Reduction of uranium(VI) to uranium(IV) by clostridia. Appl. Environ. Microbiol. 74:4580-4584.
10. He Z, et al. 2007. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J. 1:67-77.
11. Holmes D, et al. 2007. Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments. ISME J. 1:663-677.
12. Hwang C, et al. 2009. Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths. ISME J. 3:47-64.
13. Istok J, et al. 2004. In situ bioreduction of technetium and uranium in a nitrate-contaminated aquifer. Environ. Sci. Technol. 38:468-475.
14. Ivanova I, et al. 2000. A survey of 16S rRNA and amoA genes related to autotrophic ammonia-oxidizing bacteria of the beta-subdivision of the class Proteobacteria in contaminated groundwater. Can. J. Microbiol. 46: 1012-1020.
15. Komlos J, Moon HS, Jaffe PR. 2008. Effect of sulfate on the simultaneous bioreduction of iron and uranium. J. Environ. Qual. 37:2058-2062.
16. Liang Y, et al. 2011. Functional gene diversity of soil microbial communities from five oil-contaminated fields in China. ISME J. 5:403-413.
17. Lovley D, Phillips E, Gorby Y, Landa E. 1991. Microbial reduction of uranium. Nature 350:413-416.
18. 3 of Desulfovibrio vulgaris. Appl. Environ. Microbiol. 59:3572-3576.
19. Marshall M, et al. 2006. c-type cytochrome-dependent formation of U(IV) nanoparticles by Shewanella oneidensis. PLoS Biol. 4:1324-1333.
20. N'Guessan A, Vrionis H, Resch C, Long P, Lovley D. 2008. Sustained removal of uranium from contaminated groundwater following stimulation of dissimilatory metal reduction. Environ. Sci. Technol. 42:2999- 3004.
21. N'Guessan AL, et al. 2010. Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer. ISME J. 4:253-266.
22. North N, et al. 2004. Change in bacterial community structure during in situ biostimulation of subsurface sediment cocontaminated with uranium and nitrate. Appl. Environ. Microbiol. 70:4911-4920.
23. Shelobolina E, et al. 2007. Importance of c-type cytochromes for U(VI) reduction by Geobacter sulfurreducens. BMC Microbiol. 7:16.
24. Tebo B, Obraztsova A. 1998. Sulfate-reducing bacterium grows with Cr(VI), U(VI), Mn(IV), and Fe(III) as electron acceptors. FEMS Microbiol. Lett. 162:193-198.
25. ter Braak CJF, Smilauer P. 1998. CANOCO reference manual and user';s guide to CANOCO for windows: software for canonical community ordination, version 4ed. Microcomputer Power, New York, NY.
26. Van Nostrand JD, et al. 2011. Dynamics of microbial community composition and function during in situ bioremediation of a uraniumcontaminated aquifer. Appl. Environ. Microbiol. 77:3860-3869.
27. Van Nostrand JD, et al. 2009. GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uraniumcontaminated aquifer. Environ. Microbiol. 11:2611-2626.
28. Vrionis H, et al. 2005. Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl. Environ. Microbiol. 71:6308-6318.
29. Wang F, et al. 2009. GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proc. Natl. Acad. Sci. U. S. A. 106:4840-4845.
30. Wilkins MJ, et al. 2009. Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Appl. Environ. Microbiol. 75:6591-6599.
31. Wu L, Kellogg L, Devol A, Tiedje J, Zhou J. 2008. Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico. Appl. Environ. Microbiol. 74:4516-4529.
32. Wu LY, Liu X, Schadt CW, Zhou JZ. 2006. Microarray-based analysis of subnanogram quantities of microbial community DNAs by using wholecommunity genome amplification. Appl. Environ. Microbiol. 72:4931- 4941.
33. Xu M, et al. 2010. Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation. ISME J. 4:1060-1070.
34. Yabusaki SB, et al. 2007. Uranium removal from groundwater via in situ biostimulation: field-scale modeling of transport and biological processes. J. Contam. Hydrol. 93:216-235.
35. Zhou J, Bruns M, Tiedje J. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316-322.
36. Zhou J, Kang S, Schadt C, Garten C. 2008. Spatial scaling of functional gene diversity across various microbial taxa. Proc. Natl. Acad. Sci. U. S. A. 105:7768-7773.