TY - JOUR
T1 - Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles
AU - Callister, Stephen J.
AU - Wilkins, Michael J.
AU - Nicora, Carrie D.
AU - Williams, Kenneth H.
AU - Banfield, Jillian F.
AU - Verberkmoes, Nathan C.
AU - Hettich, Robert L.
AU - N'Guessan, Lucie
AU - Mouser, Paula J.
AU - Elifantz, Hila
AU - Smith, Richard D.
AU - Lovley, Derek R.
AU - Lipton, Mary S.
AU - Long, Philip E.
PY - 2010/12/1
Y1 - 2010/12/1
N2 - Stimulated by an acetate-amendment field experiment conducted in 2007, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this experiment, planktonic biomass was sampled at various time points to quantitatively evaluate proteomes. In 2008, an acetate-amended field experiment was again conducted in a similar manner to the 2007 experiment. As there was no comprehensive metagenome sequence available for use in proteomics analysis, we systematically evaluated 12 different organism genome sequences to generate sets of aggregate genomes, or "pseudo-metagenomes", for supplying relative quantitative peptide and protein identifications. Proteomics results support previous observations of the dominance of Geobacteraceae during biostimulation using acetate as sole electron donor, and revealed a shift from an early stage of iron reduction to a late stage of iron reduction. Additionally, a shift from iron reduction to sulfate reduction was indicated by changes in the contribution of proteome information contributed by different organism genome sequences within the aggregate set. In addition, the comparison of proteome measurements made between the 2007 field experiment and 2008 field experiment revealed differences in proteome profiles. These differences may be the result of alterations in abundance and population structure within the planktonic biomass samples collected for analysis.
AB - Stimulated by an acetate-amendment field experiment conducted in 2007, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this experiment, planktonic biomass was sampled at various time points to quantitatively evaluate proteomes. In 2008, an acetate-amended field experiment was again conducted in a similar manner to the 2007 experiment. As there was no comprehensive metagenome sequence available for use in proteomics analysis, we systematically evaluated 12 different organism genome sequences to generate sets of aggregate genomes, or "pseudo-metagenomes", for supplying relative quantitative peptide and protein identifications. Proteomics results support previous observations of the dominance of Geobacteraceae during biostimulation using acetate as sole electron donor, and revealed a shift from an early stage of iron reduction to a late stage of iron reduction. Additionally, a shift from iron reduction to sulfate reduction was indicated by changes in the contribution of proteome information contributed by different organism genome sequences within the aggregate set. In addition, the comparison of proteome measurements made between the 2007 field experiment and 2008 field experiment revealed differences in proteome profiles. These differences may be the result of alterations in abundance and population structure within the planktonic biomass samples collected for analysis.
UR - http://www.scopus.com/inward/record.url?scp=78650267487&partnerID=8YFLogxK
U2 - 10.1021/es101029f
DO - 10.1021/es101029f
M3 - Article
C2 - 21058662
AN - SCOPUS:78650267487
SN - 0013-936X
VL - 44
SP - 8897
EP - 8903
JO - Environmental Science and Technology
JF - Environmental Science and Technology
IS - 23
ER -