The design of long‐term effective uranium bioremediation strategy using a community metabolic model

Abstract

Acetate amendment at uranium contaminated sites in Rifle, CO. leads to an initial bloom of Geobacter accompanied by the removal of U(VI) from the groundwater, followed by an increase of sulfate-reducing bacteria (SRBs) which are poor reducers of U(VI). One of the challenges associated with bioremediation is the decay in Geobacter abundance, which has been attributed to the depletion of bio-accessible Fe(III), motivating the investigation of simultaneous amendments of acetate and Fe(III) as an alternative bioremediation strategy. In order to understand the community metabolism of Geobacter and SRBs during artificial substrate amendment, we have created a genome-scale dynamic community model of Geobacter and SRBs using the previously described Dynamic Multi-species Metabolic Modeling framework. Optimization techniques are used to determine the optimal acetate and Fe(III) addition profile. Field-scale simulation of acetate addition accurately predicted the in situ data. The simulations suggest that batch amendment of Fe(III) along with continuous acetate addition is insufficient to promote long-term bioremediation, while continuous amendment of Fe(III) along with continuous acetate addition is sufficient to promote long-term bioremediation. By computationally minimizing the acetate and Fe(III) addition rates as well as the difference between the predicted and target uranium concentration, we showed that it is possible to maintain the uranium concentration below the environmental safety standard while minimizing the cost of chemical additions. 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 environmental biotechnology.

The Family Geobacteraceae

“…Genomescale metabolic models integrated into reactive transport models allowed for in silico evaluation of various strategies to stimulate in situ uranium bioremediation (Scheibe et al 2009). Flux balance analysis based on genome-scale models also contributed to a better understanding on when and why Geobacter species become dominant iron reducers or lose to other iron-reducing microorganisms (Zhuang et al 2011) or microorganisms that employ other electron accepting processes Zhuang et al 2012). These models have contributed to directed rational engineering to accelerate rates of respiration and power output, by creating ATP consuming futile cycles (Izallalen et al 2008).…”

Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico

“…Mechanisms behind a community's behavior can be proposed in silico and subsequently validated experimentally (16). For example, in an in silico bioremediation model, added acetate and Fe(III) were predicted to be major factors influencing competition, which led to the proposal of a long-term bioremediation strategy (21,22). The applications of constraint-based multispecies modeling to the complex ecosystem residing in the human gut are particularly promising (16).…”

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

“…They termed this method as the Dynamic Multispecies Metabolic Modeling (DyMMM) framework. The same method has also been applied to the community of Geobacter and sulfate-reducing bacteria (7SRBs) [134]. Figure 14 shows the procedures of implementing DyMMM.…”