(67c) Community Modeling and the Design of Effective Uranium Bioremediation Strategy

During uranium bioremediation at a contaminated site in Rifle, CO, there is an initial bloom of Geobacter accompanied by removal of U(VI) from the groundwater, followed by an increase of sulfate-reducing bacteria (SRBs) which are poor reducers of U(VI). Existing analysis suggests that there is competition between Geobacter and SRB, and when biologically usable and more energy efficient Fe(III) is depleted, the SRB compete more effectively for the substrate and able to grow using the available sulfate. However, the dynamics of the microbial competition at this site is not clearly understood, motivating the need for systems biology tools to understand the associated microbial ecology.

In order to understand the metabolic interactions in microbial communities, we have developed a dynamic genome-scale modeling approach denoted as the Dynamic Multi-species Metabolic Modeling framework. We have previously used this approach to model the community competition among Fe(III) reducers and had shown that the trade-off between growth rate and biomass yield under different environments was the decisive factor controlling the microbial competition at that site. In this work, we have used this framework to create a community model of Geobacter and SRBs. Batch simulations of community dynamics were used to examine the cause of the late onset of sulfate-reduction using different percentages of starting inoculants of Geobacter and SRB. These simulations showed that no matter what the starting conditions, the Geobacter were able to dominate the early period of the experiment with very little change in timing of the onset of sulfate-reduction. The field-scale simulation was able to accurately predict the field data (Figure 1), and suggests that the observed field data are due to growth rate dynamics and not due to thermodynamic competition.

Field-scale simulation of iron addition suggests that Fe(III) addition is a potential strategy for continuous uranium removal. We simulated the simultaneous addition of acetate and Fe(III) in both batch and field conditions using the community model. This showed that the addition of Fe(III) allowed Geobacter species to maintain its dominance over SRB. We then computationally optimized the rate of iron and acetate addition into the subsurface. We show that it is possible to maintain the uranium concentration below the environmental safety standards (Figure 2).

These simulations show that simultaneous addition of acetate and Fe(III) has the potential to be an effective uranium bioremediation strategy. They also show that computational modeling of microbial community is an important tool to design effective strategies for practical applications in biotechnology.

Figure 1. Field-scale simulation of Geobacter and SRB competition during acetate amendment.

Figure 2. Computational Optimization of Acetate and Iron Addition Rates. Red line is the US Environmental Safety Level for Dissolved Uranium (VI)