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Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation.

Scheibe TD, Mahadevan R, Fang Y, Garg S, Long PE, Lovley DR - Microb Biotechnol (2009)

Bottom Line: Previous studies of the in situ bioremediation of uranium-contaminated groundwater have demonstrated that Geobacter species are often the dominant members of the groundwater community during active bioremediation and the primary organisms catalysing U(VI) reduction.Therefore, a genome-scale, constraint-based model of the metabolism of Geobacter sulfurreducens was coupled with the reactive transport model HYDROGEOCHEM in an attempt to model in situ uranium bioremediation.In order to simplify the modelling, the influence of only three growth factors was considered: acetate, the electron donor added to stimulate U(VI) reduction; Fe(III), the electron acceptor primarily supporting growth of Geobacter; and ammonium, a key nutrient.

View Article: PubMed Central - PubMed

Affiliation: Pacific Northwest National Laboratory, PO Box 999, MS K9-36, Richland, WA, USA. tim.scheibe@pnl.gov

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Diagram showing the well layout at the Rifle, CO bioremediation research site. Well numbers are referenced in Fig. 6. Black closed circles represent wells in the injection gallery; labelled wells are monitoring locations. Modified from fig. 1 of Yabusaki and colleagues (2007).
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f5: Diagram showing the well layout at the Rifle, CO bioremediation research site. Well numbers are referenced in Fig. 6. Black closed circles represent wells in the injection gallery; labelled wells are monitoring locations. Modified from fig. 1 of Yabusaki and colleagues (2007).

Mentions: Next, the ability of the coupled hybrid constraint‐based and reactive transport models to predict the fate of uranium in an in situ uranium bioremediation field experiment was evaluated. In 2002 a field experiment was conducted at the uranium bioremediation study site in Rifle, CO (Anderson et al., 2003). Acetate was introduced into the groundwater through a series of injection wells and downgradient geochemical changes were monitored in a series of monitoring wells (Fig. 5). As detailed in the Experimental procedures section a pre‐existing reactive transport model (Yabusaki et al., 2007; Y. Fang, S.B. Yabusaki, S.J. Morrison, J.P. Amonette and P.E. Long, in preparation) was coupled with the hybrid constraint‐based model using the look‐up table approach. The time frame of the simulation was limited to the period when Fe(III) reduction was the predominant terminal electron‐accepting process and U(VI) was being actively removed from the groundwater; at longer time intervals accessible Fe(III) became depleted, sulfate reduction became the predominant terminal electron accepting process, and U(VI) was no longer effectively reduced (Anderson et al., 2003). Modelling the sulfate reduction phase with a genome‐based model is not yet feasible because of the lack of genome sequence for an appropriate acetate‐oxidizing sulfate reducer.


Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation.

Scheibe TD, Mahadevan R, Fang Y, Garg S, Long PE, Lovley DR - Microb Biotechnol (2009)

Diagram showing the well layout at the Rifle, CO bioremediation research site. Well numbers are referenced in Fig. 6. Black closed circles represent wells in the injection gallery; labelled wells are monitoring locations. Modified from fig. 1 of Yabusaki and colleagues (2007).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815847&req=5

f5: Diagram showing the well layout at the Rifle, CO bioremediation research site. Well numbers are referenced in Fig. 6. Black closed circles represent wells in the injection gallery; labelled wells are monitoring locations. Modified from fig. 1 of Yabusaki and colleagues (2007).
Mentions: Next, the ability of the coupled hybrid constraint‐based and reactive transport models to predict the fate of uranium in an in situ uranium bioremediation field experiment was evaluated. In 2002 a field experiment was conducted at the uranium bioremediation study site in Rifle, CO (Anderson et al., 2003). Acetate was introduced into the groundwater through a series of injection wells and downgradient geochemical changes were monitored in a series of monitoring wells (Fig. 5). As detailed in the Experimental procedures section a pre‐existing reactive transport model (Yabusaki et al., 2007; Y. Fang, S.B. Yabusaki, S.J. Morrison, J.P. Amonette and P.E. Long, in preparation) was coupled with the hybrid constraint‐based model using the look‐up table approach. The time frame of the simulation was limited to the period when Fe(III) reduction was the predominant terminal electron‐accepting process and U(VI) was being actively removed from the groundwater; at longer time intervals accessible Fe(III) became depleted, sulfate reduction became the predominant terminal electron accepting process, and U(VI) was no longer effectively reduced (Anderson et al., 2003). Modelling the sulfate reduction phase with a genome‐based model is not yet feasible because of the lack of genome sequence for an appropriate acetate‐oxidizing sulfate reducer.

Bottom Line: Previous studies of the in situ bioremediation of uranium-contaminated groundwater have demonstrated that Geobacter species are often the dominant members of the groundwater community during active bioremediation and the primary organisms catalysing U(VI) reduction.Therefore, a genome-scale, constraint-based model of the metabolism of Geobacter sulfurreducens was coupled with the reactive transport model HYDROGEOCHEM in an attempt to model in situ uranium bioremediation.In order to simplify the modelling, the influence of only three growth factors was considered: acetate, the electron donor added to stimulate U(VI) reduction; Fe(III), the electron acceptor primarily supporting growth of Geobacter; and ammonium, a key nutrient.

View Article: PubMed Central - PubMed

Affiliation: Pacific Northwest National Laboratory, PO Box 999, MS K9-36, Richland, WA, USA. tim.scheibe@pnl.gov

Show MeSH