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Applied and Environmental Microbiology, October 2009, p. 6591-6599, Vol. 75, No. 20
0099-2240/09/$08.00+0 doi:10.1128/AEM.01064-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation
,
Michael J. Wilkins,1
Nathan C. VerBerkmoes,2
Kenneth H. Williams,3
Stephen J. Callister,4
Paula J. Mouser,5
Hila Elifantz,5
A. Lucie N'Guessan,5
Brian C. Thomas,1
Carrie D. Nicora,4
Manesh B. Shah,2
Paul Abraham,2,6
Mary S. Lipton,4
Derek R. Lovley,5
Robert L. Hettich,2
Philip E. Long,7 and
Jillian F. Banfield1,3*
Department of Earth and Planetary Science and Environmental Science, Policy, and Management, University of California, Berkeley, California 94720,1 Chemical Sciences and Biosciences Divisions, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,2 Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720,3 Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99353,4 Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01002,5 Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37830,6 Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 993537
Received 8 May 2009/ Accepted 20 August 2009
Implementation of uranium bioremediation requires methods for monitoring 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 for simultaneously documenting the 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 liquid chromatography-tandem mass spectrometry spectra to peptides predicted from seven isolate Geobacter genomes. Genome-specific peptides indicate early proliferation of multiple M21 and Geobacter bemidjiensis-like strains and later possible emergence of M21 and G. bemidjiensis-like strains more closely related to Geobacter lovleyi. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-coenzyme A and pyruvate for central metabolism, while abundant peptides matching tricarboxylic acid 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.
* Corresponding author. Mailing address: Hilgard Hall, UC Berkeley, Berkeley, CA 94720. Phone: (510) 643-2155. Fax: (510) 643-9980. E-mail: jbanfield{at}berkeley.edu
Published ahead of print on 28 August 2009.
Supplemental material for this article may be found at http://aem.asm.org/.
Applied and Environmental Microbiology, October 2009, p. 6591-6599, Vol. 75, No. 20
0099-2240/09/$08.00+0 doi:10.1128/AEM.01064-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
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