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Development of a biomarker for Geobacter activity and strain composition; proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI).

Wilkins MJ, Callister SJ, Miletto M, Williams KH, Nicora CD, Lovley DR, Long PE, Lipton MS - Microb Biotechnol (2011)

Bottom Line: Citrate synthase (gltA) is a key enzyme in Geobacter central metabolism that controls flux into the TCA cycle.Abundances of unique peptides indicated potential differences at the strain level between Fe(III)-reducing populations stimulated during in situ biostimulation experiments conducted a year apart at the Rifle IFRC.These results offer a novel technique for the rapid screening of large numbers of proteomic samples for Geobacter species and will aid monitoring of subsurface bioremediation efforts that rely on metal reduction for desired outcomes.

View Article: PubMed Central - PubMed

Affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99353, USA. michael.wilkins@pnl.gov

ABSTRACT
Monitoring the activity of target microorganisms during stimulated bioremediation is a key problem for the development of effective remediation strategies. At the US Department of Energy's Integrated Field Research Challenge (IFRC) site in Rifle, CO, the stimulation of Geobacter growth and activity via subsurface acetate addition leads to precipitation of U(VI) from groundwater as U(IV). Citrate synthase (gltA) is a key enzyme in Geobacter central metabolism that controls flux into the TCA cycle. Here, we utilize shotgun proteomic methods to demonstrate that the measurement of gltA peptides can be used to track Geobacter activity and strain evolution during in situ biostimulation. Abundances of conserved gltA peptides tracked Fe(III) reduction and changes in U(VI) concentrations during biostimulation, whereas changing patterns of unique peptide abundances between samples suggested sample-specific strain shifts within the Geobacter population. Abundances of unique peptides indicated potential differences at the strain level between Fe(III)-reducing populations stimulated during in situ biostimulation experiments conducted a year apart at the Rifle IFRC. These results offer a novel technique for the rapid screening of large numbers of proteomic samples for Geobacter species and will aid monitoring of subsurface bioremediation efforts that rely on metal reduction for desired outcomes.

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Mentions: While conserved peptides can be used to assess Geobacter abundance within a community, fine‐scale strain‐level shifts between samples can be assessed using unique peptide abundances. Global analysis of unique peptide abundances in 2007 datasets indicated strain shifts and increasing community diversity within the Geobacter population over the duration of the biostimulation period. While this was characterized by an increase in peptides matching G. lovleyi and a decrease in peptides matching G. bemidjiensis and strain M21 as biostimulation progressed, total peptide data revealed that the community was still dominated by strains most closely related to G. bemidjiensis and strain M21, but with increased similarity to G. lovleyi at certain loci (Wilkins et al., 2009). While the abundance of unique peptides matching CS in these global datasets suggested that this protein would be a good candidate for this study, the addition of cloned gltA sequences to the search database for this study increased the strain‐level resolution of the analysis (Fig. 5A and B).


Development of a biomarker for Geobacter activity and strain composition; proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI).

Wilkins MJ, Callister SJ, Miletto M, Williams KH, Nicora CD, Lovley DR, Long PE, Lipton MS - Microb Biotechnol (2011)

© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815795&req=5

Mentions: While conserved peptides can be used to assess Geobacter abundance within a community, fine‐scale strain‐level shifts between samples can be assessed using unique peptide abundances. Global analysis of unique peptide abundances in 2007 datasets indicated strain shifts and increasing community diversity within the Geobacter population over the duration of the biostimulation period. While this was characterized by an increase in peptides matching G. lovleyi and a decrease in peptides matching G. bemidjiensis and strain M21 as biostimulation progressed, total peptide data revealed that the community was still dominated by strains most closely related to G. bemidjiensis and strain M21, but with increased similarity to G. lovleyi at certain loci (Wilkins et al., 2009). While the abundance of unique peptides matching CS in these global datasets suggested that this protein would be a good candidate for this study, the addition of cloned gltA sequences to the search database for this study increased the strain‐level resolution of the analysis (Fig. 5A and B).

Bottom Line: Citrate synthase (gltA) is a key enzyme in Geobacter central metabolism that controls flux into the TCA cycle.Abundances of unique peptides indicated potential differences at the strain level between Fe(III)-reducing populations stimulated during in situ biostimulation experiments conducted a year apart at the Rifle IFRC.These results offer a novel technique for the rapid screening of large numbers of proteomic samples for Geobacter species and will aid monitoring of subsurface bioremediation efforts that rely on metal reduction for desired outcomes.

View Article: PubMed Central - PubMed

Affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99353, USA. michael.wilkins@pnl.gov

ABSTRACT
Monitoring the activity of target microorganisms during stimulated bioremediation is a key problem for the development of effective remediation strategies. At the US Department of Energy's Integrated Field Research Challenge (IFRC) site in Rifle, CO, the stimulation of Geobacter growth and activity via subsurface acetate addition leads to precipitation of U(VI) from groundwater as U(IV). Citrate synthase (gltA) is a key enzyme in Geobacter central metabolism that controls flux into the TCA cycle. Here, we utilize shotgun proteomic methods to demonstrate that the measurement of gltA peptides can be used to track Geobacter activity and strain evolution during in situ biostimulation. Abundances of conserved gltA peptides tracked Fe(III) reduction and changes in U(VI) concentrations during biostimulation, whereas changing patterns of unique peptide abundances between samples suggested sample-specific strain shifts within the Geobacter population. Abundances of unique peptides indicated potential differences at the strain level between Fe(III)-reducing populations stimulated during in situ biostimulation experiments conducted a year apart at the Rifle IFRC. These results offer a novel technique for the rapid screening of large numbers of proteomic samples for Geobacter species and will aid monitoring of subsurface bioremediation efforts that rely on metal reduction for desired outcomes.

Show MeSH
Related in: MedlinePlus