Microarray-Based Analysis of Microbial Community Composition and Dynamics in Uranium Bioremediation

A field-scale system is being used for evaluating in situ biological reduction and immobilization of U(VI) in the DOE ERSP Field Research Center, Oak Ridge, TN. Above-ground treatment of groundwater, including nitrate removal pre-conditions the groundwater for subsurface uranium immobilization. Treated water was then injected into the subsurface with ethanol to stimulate microbial reduction of U(VI) to insoluble U(IV). The microbial community dynamics from one of the 4 frequently sampled monitoring wells (FW 102-3) was intensively analyzed with a functional gene array containing >24,000 probes and covering 10,000 genes in 150 gene categories. The results indicated that during the uranium reduction period, both FeRB and SRB populations reached their highest levels at Day 212, followed by a gradual decrease over 500 days. The uranium concentrations in the groundwater were significantly correlated with the total abundance of c-type cytochrome genes (r=0.73, p<0.05) from Geobacter-type FeRB and Desulfovibrio-type SRB, and with the total abundance of dsrAB (dissimilatory sulfite reductase) genes (r=0.88, p<0.05). The Mantel test of microarray and chemical data also indicated that there was significant correlation between the differences of uranium concentrations and those of total c-cytochrome gene abundance (r=0.75, p <0.001) or dsrAB gene abundance (r=0.72, p<0.01). The changes of more than dozen of individual c-type cytochrome genes from Geobacter sulfurreducens and Desulfovibrio desulfuricans showed significant correlations to the changes of uranium concentrations among different time points. Also the changes of more than 10 dsrAB-containing populations, including both cultured (e.g. D. desulfuricans, D. termitidis, Desulfotomaculum kuznetsovii,) and non-cultured SRB were significantly related to the changes in uranium concentrations, indicating their importance in uranium reduction. Interestingly, as expected, the changes of several dsrAB-containing sulfate-reducing populations previously recovered from this site showed significant correlations to the differences of uranium concentrations