Stimulation of subsurface microbial communities to induce reductive immobilization of metals is a common approach for bioremediation. However, the overall community response is typically poorly understood, hindering optimization. Here we used community proteogenomics to show that excess input of acetate activates syntrophic interactions involving organisms that use the forward tricarboxylic acid (TCA) cycle for energy generation and those that use the reverse TCA cycle for CO2 fixation. A flow-through sediment column was incubated in a groundwater well in an acetate-amended aquifer and recovered during sulfate reduction. Genomic DNA extracted from the community was sequenced, and the sequences were used to reconstruct, de novo, near-complete genomes for relatives of Desulfobacter (Deltaproteobacteria), Sulfurovum and Sulfurimonas (Epsilonproteobacteria), Bacteroidetes, and Clostridiales (Firmicutes). Fragmentary genomic datasets were also obtained for a Desulfuromonadales-like Deltaproteobacterium and other bacteria. Some are related to known metal-reducing bacteria. The majority of proteins identified by mass spectrometry were derived from Desulfobacter-like species, and indicate the role of this organism in sulfate reduction (Dsr and APS), nitrogen-fixation (Nif) and acetate oxidation to CO2. Proteogenomic data indicate that less abundant community members, Desulfuromonadales bacteria and Bacteroidetes, also contribute to the TCA cycle. Interestingly, proteomic data suggest that sulfide was partially re-oxidized by Epsilonproteobacteria through nitrate-dependent sulfur oxidation (using Nap, Nir, Nos, SQR and Sox) and CO2 fixed using the reverse TCA cycle. Thus, high-levels of carbon amendment aimed to stimulate anaerobic heterotrophy led to carbon fixation in co-dependent chemoautotrophs. These results have implications for understanding complex ecosystem behavior, and show that high levels of organic carbon supplementation can expand the range of microbial functionalities accessible for ecosystem manipulation.