title: Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation.
abstract: 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.
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Wilkins
authors.forename: Nathan C
authors.initials: NC
authors.lastname: Verberkmoes
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Williams
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Callister
authors.forename: Paula J
authors.initials: PJ
authors.lastname: Mouser
authors.forename: Hila
authors.initials: H
authors.lastname: Elifantz
authors.forename: A Lucie
authors.initials: AL
authors.lastname: N'guessan
authors.forename: Brian C
authors.initials: BC
authors.lastname: Thomas
authors.forename: Carrie D
authors.initials: CD
authors.lastname: Nicora
authors.forename: Manesh B
authors.initials: MB
authors.lastname: Shah
authors.forename: Paul
authors.initials: P
authors.lastname: Abraham
authors.forename: Mary S
authors.initials: MS
authors.lastname: Lipton
authors.forename: Derek R
authors.initials: DR
authors.lastname: Lovley
authors.forename: Robert L
authors.initials: RL
authors.lastname: Hettich
authors.forename: Philip E
authors.initials: PE
authors.lastname: Long
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001673:Biodegradation, Environmental; D023281:Genomics; D045302:Geobacter / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology*; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D010449:Peptide Mapping; D010933:Plankton / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology; D040901:Proteomics; D014501:Uranium / Q000378:metabolism*; D014871:Water Microbiology; D014875:Water Pollutants, Radioactive / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D014875:Water Pollutants, Radioactive; D014501:Uranium