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A large fraction (47%) of the world’s uranium is mined by a technique called “In Situ Recovery”. This mining technique involves the injection of a leaching fluid (acid or alkaline) into a uranium-bearing aquifer and the pumping of the resulting solution through cation exchange columns for the recovery of the dissolved metal. A strategy of rehabilitation of the aquifer is based on the biostimulation of the autochthonous microbial community to remediate the acid plume and immobilize remaining trace metals. Assessment of the biostimulation was carried out using column tests filled with aquifer material. These columns were stimulated with a mixture of molasses, yeast extract and glycerol. Results showed that this mixture efficiently promoted the development of acid-resistant, sulfate-reducing bacterial guild members down to an inlet pH value ~ 4.7, with pH values at the outlet reaching up to 6.5 – 7. The rise of pH values along the columns were attributed to the predominant reduction of nitrate and sulfate. Biostimulation of the microbial community efficiently promoted the complete immobilization of U in the first centimeters of the columns. Synchrotron x-ray analysis and electron microscopy revealed that up to 60% of total U was precipitated as UIV onto bacterial cells. A detailed metagenomic analysis and qPCR data illustrated drastic changes occurring within the community with the reduction of the microbial diversity and the quantitative development of fermentative bacteria. The community was dominated by members of the Phylum Firmicutes (genus “Clostridium”, Pelosinus and Desulfosporosinus), representing up to 89 % of all cells.