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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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Frequencies of biomass yield levels within the 1000‐element look‐up table generated by the in silico model of G. sulfurreducens for various environmental conditions. In the legend, ‘N2 fix’ denotes nitrogen fixation, and ‘Fe lim’ and ‘Ac lim’ denote iron‐limited and acetate‐limited conditions respectively.
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f2: Frequencies of biomass yield levels within the 1000‐element look‐up table generated by the in silico model of G. sulfurreducens for various environmental conditions. In the legend, ‘N2 fix’ denotes nitrogen fixation, and ‘Fe lim’ and ‘Ac lim’ denote iron‐limited and acetate‐limited conditions respectively.

Mentions: For the remaining 400 out of the 1000 possible combinations of nutrient availability the predicted biomass yield varied over nearly an order of magnitude, from approximately 0.5 to 4.2 g of cell dry weight per mole of acetate consumed (Fig. 2). Note that, because of lumping of values into histogram bins, the range of the individual values is larger than the range of bin midpoints shown in Fig. 2, and that a small number of biomass yield values lower than 1.0 g of cell dry weight per mole of acetate consumed were not included in the histogram plot because they constituted only about 1% of the total number. As indicated in Fig. 2, the same growth yield was possible for different types of nutrient limitation, depending upon the concentration of all three nutrients. These results indicate that, based upon nutrient availability, growth yield can vary substantially and that different physiological states can have similar biomass yields.


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)

Frequencies of biomass yield levels within the 1000‐element look‐up table generated by the in silico model of G. sulfurreducens for various environmental conditions. In the legend, ‘N2 fix’ denotes nitrogen fixation, and ‘Fe lim’ and ‘Ac lim’ denote iron‐limited and acetate‐limited conditions respectively.
© Copyright Policy
Related In: Results  -  Collection

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

f2: Frequencies of biomass yield levels within the 1000‐element look‐up table generated by the in silico model of G. sulfurreducens for various environmental conditions. In the legend, ‘N2 fix’ denotes nitrogen fixation, and ‘Fe lim’ and ‘Ac lim’ denote iron‐limited and acetate‐limited conditions respectively.
Mentions: For the remaining 400 out of the 1000 possible combinations of nutrient availability the predicted biomass yield varied over nearly an order of magnitude, from approximately 0.5 to 4.2 g of cell dry weight per mole of acetate consumed (Fig. 2). Note that, because of lumping of values into histogram bins, the range of the individual values is larger than the range of bin midpoints shown in Fig. 2, and that a small number of biomass yield values lower than 1.0 g of cell dry weight per mole of acetate consumed were not included in the histogram plot because they constituted only about 1% of the total number. As indicated in Fig. 2, the same growth yield was possible for different types of nutrient limitation, depending upon the concentration of all three nutrients. These results indicate that, based upon nutrient availability, growth yield can vary substantially and that different physiological states can have similar biomass yields.

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
Related in: MedlinePlus