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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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Geochemical profiles for U(VI) and Fe(II) in well D07 during the 2007 biostimulation experiment. Heat‐map abundances are shown for both the (A) conserved ‘biomarker’ peptides and (B) unique peptides matching CS proteins in all three samples.
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f2: Geochemical profiles for U(VI) and Fe(II) in well D07 during the 2007 biostimulation experiment. Heat‐map abundances are shown for both the (A) conserved ‘biomarker’ peptides and (B) unique peptides matching CS proteins in all three samples.

Mentions: Three proteogenomic datasets were collected during a 13‐day period of the 2007 biostimulation field campaign. As explained in Wilkins and colleagues (2009), all were taken during the period of dominant Fe(III) reduction in the subsurface. The heat map in Fig. 2 illustrates the presence of Geobacter species in all samples, as identified by high abundances of conserved CS peptides (TIPETFEALPK, SLVTDISYLDPQEGIR and QVVPEYVYTAVR). Evidence for enzymatic Fe(III) reduction is present in all three samples in the form of aqueous Fe(II), while a rapid decrease in U(VI) concentrations is observed in the later D07 sample (Fig. 2A). Acetate amendment was stopped in this biostimulation experiment before the Fe(III)‐reducing system transitioned into sulfate‐reducing conditions.


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)

Geochemical profiles for U(VI) and Fe(II) in well D07 during the 2007 biostimulation experiment. Heat‐map abundances are shown for both the (A) conserved ‘biomarker’ peptides and (B) unique peptides matching CS proteins in all three samples.
© Copyright Policy
Related In: Results  -  Collection

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

f2: Geochemical profiles for U(VI) and Fe(II) in well D07 during the 2007 biostimulation experiment. Heat‐map abundances are shown for both the (A) conserved ‘biomarker’ peptides and (B) unique peptides matching CS proteins in all three samples.
Mentions: Three proteogenomic datasets were collected during a 13‐day period of the 2007 biostimulation field campaign. As explained in Wilkins and colleagues (2009), all were taken during the period of dominant Fe(III) reduction in the subsurface. The heat map in Fig. 2 illustrates the presence of Geobacter species in all samples, as identified by high abundances of conserved CS peptides (TIPETFEALPK, SLVTDISYLDPQEGIR and QVVPEYVYTAVR). Evidence for enzymatic Fe(III) reduction is present in all three samples in the form of aqueous Fe(II), while a rapid decrease in U(VI) concentrations is observed in the later D07 sample (Fig. 2A). Acetate amendment was stopped in this biostimulation experiment before the Fe(III)‐reducing system transitioned into sulfate‐reducing conditions.

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