Dynamic modeling of the microbial community prior to and during uranium-bioremediation

摘要

We have created a dynamic genome-scale metabolic model of Geobacter sulfurreducens and Rhodoferax ferrireducens, the two primary iron-reducers in uranium-contaminated grounds, in order to understand the community competition prior to and during uranium-bioremediation. The simulation results agree with experimental measurements, and suggest that the community competition is modulated by two factors: the ability of G. sulfurreducens to fix nitrogen under ammonium limitation, and a rate vs. yield trade-off between these two organisms. Prior to acetate amendment, if ammonium is limited, G. sulfurreducens dominates due to its ability to fix nitrogen. However, if the system contains abundant ammonium, R. ferrireducens, a yield-strategist, is favoured because the acetate flux is very low. During acetate amendment, the high acetate flux strongly favours G. sulfurreducens, a rate-strategist. The model also predicts the up-regulation of respiration in G. sulfurreducens during nitrogen fixation by sacrificing its biomass yield, leading to an increase in uranium reduction under low ammonium conditions. This model will be an important tool for the designing of effective uranium-bioremediation strategies.