TY - JOUR
T1 - Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation
AU - Wilkins, Michael J.
AU - VerBerkmoes, Nathan C.
AU - Williams, Kenneth H.
AU - Callister, Stephen J.
AU - Mouser, Paula J.
AU - Elifantz, Hila
AU - N'Guessan, A. Lucie
AU - Thomas, Brian C.
AU - Nicora, Carrie D.
AU - Shah, Manesh B.
AU - Abraham, Paul
AU - Lipton, Mary S.
AU - Lovley, Derek R.
AU - Hettich, Robert L.
AU - Long, Philip E.
AU - Banfield, Jillian F.
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=70349932972&partnerID=8YFLogxK
U2 - 10.1128/AEM.01064-09
DO - 10.1128/AEM.01064-09
M3 - Article
C2 - 19717633
AN - SCOPUS:70349932972
SN - 0099-2240
VL - 75
SP - 6591
EP - 6599
JO - Applied and Environmental Microbiology
JF - Applied and Environmental Microbiology
IS - 20
ER -