PROTEOGENOMICS: UNDERSTANDING MICROBIAL COMMUNITY FUNCTION DURING URANIUM BIOREMEDIATION

While it is known that indigenous microbial communities can be stimulated to transform and remediate a range of environmental contaminants through carbon substrate amendment, community response can be complex. Recent advancements in genomic sequencing technologies make it possible to couple community genomics (metagenomics) with proteomics to assess whole community function and better inform bioremediation strategies. Current research at the Rifle IFRC site aims to highlight this point. Proteogenomic analyses of groundwater and sediment communities during acetate stimulated Fe(III), sulfate and uranium reduction, has yielded new insights into biogeochemical cycling, and the function of multiple novel taxa. Near-complete and partial bacterial genomes were reconstructed from metagenomic data generated using 454 and Illumina platforms. Proteomes were analyzed using liquid chromatography-mass spectrometry, and spectra were searched against peptides predicted from genomic sequences. Communities enriched during Fe(III) reduction contained Geobacter spp., uncultivated candidate divisions (e.g. BD1-5, OD1, OP11), Proteoboacteria, Bacteriodetes, Chloroflexi and Spirochaetes. While Geobacter are well characterized Fe(III) and U(VI) reducers, genomics suggest the other novel bacteria are capable of acetate utilization, glycolysis, anaerobic fermentation, and sulfite and nitrate reduction. Peptides also revealed use of an alternate genetic code by candidate division BD1-5. In comparison, analysis of Desulfobacter- (FC09-1), Sulfurovum- (FC09-2) and Sulfurimonas-like (FC09-3) organisms that dominate the sulfate-reducing community, revealed the expression of proteins used in sulfate reduction (Dsr and APS) and nitrogen-fixation (Nif) by FC09-1, and nitrate, nitrite, and nitrous oxide reduction (Nap, Nir, and Nos) and the sulfur oxidation (Sox proteins) by FC09-2 and FC09-3. These results indicate a feedback loop between sulfate reduction and nitrate-dependent sulfur oxidation. As such, including geochemical characterizations of these processes in future experimental designs at the site would likely improve geochemical models. Sulfur oxidation may also have implications for uranium mobility post-reduction owing to spatial association of U(IV) with sulfide minerals.