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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: Although peptide biomarker abundances track Fe(II) production during the initial stages of the 2008 biostimulation experiment, later samples show a disconnect between elevated Fe(II) concentrations that persist in the environment, and low (or absent) biomarker abundances (e.g. D04_day27). As biostimulation progresses towards the transition period, these data suggest that rapid Geobacter growth that characterizes some earlier time points during the most efficient U(VI) removal has ceased. Less active cell growth results in fewer planktonic cells for biomass sampling, and we can infer that any low‐level Fe(III) reduction that occurs during the remainder of biostimulation is likely carried out by mineral‐attached cells (S. Dar, unpublished). There are multiple possible factors responsible for the slowdown of Geobacter cell growth such as the decreasing concentrations of ‘bioavailable’ Fe(III) oxides or other nutrient limitations. The clustering of 2008 samples via non‐metric multidimensional scaling (NMDS) using both conserved ‘biomarker’ and unique CS peptide abundances and the projection of environmental variables onto these axes suggest that acetate concentrations best explain the shifts in Geobacter populations (Fig. 4A). This further confirms the importance of ensuring that the key microbial communities during biostimulation receive excess carbon concentrations wherever possible. This plot additionally shows a negative correlation between U(VI) and the samples containing abundant Geobacter, and the visual correlation between low U(VI) concentrations and high biomarker abundance is clear in Fig. 3A. Thus, these biomarker abundances are useful as indicators of efficient U(VI) removal from groundwater. During the 2008 biostimulation experiment the highest peptide abundances (D04_day7 through D04_day20) are correlated with the lowest U(VI) concentrations (≤ 1 mg l−1) (Fig. 3A), and where peptide abundances begin to decrease (sample D04_day23 onwards), U(VI) concentrations start to rebound within the sampling well. Within the 2007 data, this pattern is repeated with the D07_day21 sample, while the biomass for the D07_day9 sample was sampled just prior to a rapid decrease in U(VI) concentrations (Fig. 2A).


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: Although peptide biomarker abundances track Fe(II) production during the initial stages of the 2008 biostimulation experiment, later samples show a disconnect between elevated Fe(II) concentrations that persist in the environment, and low (or absent) biomarker abundances (e.g. D04_day27). As biostimulation progresses towards the transition period, these data suggest that rapid Geobacter growth that characterizes some earlier time points during the most efficient U(VI) removal has ceased. Less active cell growth results in fewer planktonic cells for biomass sampling, and we can infer that any low‐level Fe(III) reduction that occurs during the remainder of biostimulation is likely carried out by mineral‐attached cells (S. Dar, unpublished). There are multiple possible factors responsible for the slowdown of Geobacter cell growth such as the decreasing concentrations of ‘bioavailable’ Fe(III) oxides or other nutrient limitations. The clustering of 2008 samples via non‐metric multidimensional scaling (NMDS) using both conserved ‘biomarker’ and unique CS peptide abundances and the projection of environmental variables onto these axes suggest that acetate concentrations best explain the shifts in Geobacter populations (Fig. 4A). This further confirms the importance of ensuring that the key microbial communities during biostimulation receive excess carbon concentrations wherever possible. This plot additionally shows a negative correlation between U(VI) and the samples containing abundant Geobacter, and the visual correlation between low U(VI) concentrations and high biomarker abundance is clear in Fig. 3A. Thus, these biomarker abundances are useful as indicators of efficient U(VI) removal from groundwater. During the 2008 biostimulation experiment the highest peptide abundances (D04_day7 through D04_day20) are correlated with the lowest U(VI) concentrations (≤ 1 mg l−1) (Fig. 3A), and where peptide abundances begin to decrease (sample D04_day23 onwards), U(VI) concentrations start to rebound within the sampling well. Within the 2007 data, this pattern is repeated with the D07_day21 sample, while the biomass for the D07_day9 sample was sampled just prior to a rapid decrease in U(VI) concentrations (Fig. 2A).

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