Abstract
Implementation of uranium bioremediation requires methods to monitor the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here we report a proteomics-based approach to simultaneously document strain membership and microbial physiology of the dominant Geobacter community members during in situ acetate amendment of the U-contaminated Rifle, CO aquifer. Three planktonic Geobacter-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching LC MS/MS spectra to peptides predicted from 7 isolate Geobacter genomes. Genome-specific peptides indicate early proliferation of multiple M21 and G. bemidjiensis–like strains and later possible emergence of M21 and G. bemidjiensis–like strains more closely related to G. lovleyi. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-CoA and pyruvate for central metabolism while abundant peptides matching TCA cycle proteins and ATP synthase subunits were also detected, indicating the importance of energy generation during the period of rapid growth following the start of biostimulation. Evolving Geobacter strain composition may be linked to changes in protein abundance over the course of biostimulation and may reflect changes in metabolic functioning. Thus, metagenomics
independent community proteogenomics can be used to diagnose the status of the subsurface consortia upon which remediation biotechnology relies.
