Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation

Journal Article · Thu Jan 01 04:00:00 EST 2009 · Applied and Environmental Microbiology

DOI:https://doi.org/10.1128/AEM.01064-09· OSTI ID:1081632

Wilkins, Mike ^[1]; Verberkmoes, Nathan C ^[2]; Williams, Ken ^[3]; Callister, Stephen J ^[4]; Mouser, Paula J ^[5]; Elifantz, Hila ^[5]; N'Guessan, A. Lucie ^[5]; Thomas, Brian ^[1]; Nicora, Carrie D. ^[4]; Shah, Manesh B ^[2]; Abraham, Paul E ^[2]; Lipton, Mary S ^[4]; Lovley, Derek ^[5]; Long, Phil ^[4]; Banfield, Jillian F. ^[1]

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1. University of California, Berkeley
2. ORNL
3. Lawrence Berkeley National Laboratory (LBNL)
4. Pacific Northwest National Laboratory (PNNL)
5. University of Massachusetts, Amherst

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.

• Research Organization: Oak Ridge National Laboratory (ORNL)
• Sponsoring Organization: ORNL work for others
• DOE Contract Number: AC05-00OR22725
• OSTI ID: 1081632
• Journal Information: Applied and Environmental Microbiology, Journal Name: Applied and Environmental Microbiology Journal Issue: 20 Vol. 75; ISSN 0099-2240
• Country of Publication: United States
• Language: English