Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation
- 15 October 2009
- journal article
- research article
- Published by American Society for Microbiology in Applied and Environmental Microbiology
- Vol. 75 (20), 6591-6599
- https://doi.org/10.1128/aem.01064-09
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.Keywords
This publication has 37 references indexed in Scilit:
- Coupling a genome‐scale metabolic model with a reactive transport model to describe in situ uranium bioremediationMicrobial Biotechnology, 2009
- Computational and Experimental Analysis of Redundancy in the Central Metabolism of Geobacter sulfurreducensPLoS Computational Biology, 2008
- Comparative Bacterial Proteomics: Analysis of the Core Genome ConceptPLOS ONE, 2008
- Flux Analysis of Central Metabolic Pathways in Geobacter metallireducens during Reduction of Soluble Fe(III)-Nitrilotriacetic AcidApplied and Environmental Microbiology, 2007
- Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometryNature Methods, 2007
- Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatilityProceedings of the National Academy of Sciences of the United States of America, 2006
- Application of the Accurate Mass and Time Tag Approach to the Proteome Analysis of Sub-cellular Fractions Obtained from Rhodobacter sphaeroides 2.4.1. Aerobic and Photosynthetic Cell CulturesJournal of Proteome Research, 2006
- PRISM: A data management system for high‐throughput proteomicsProteomics, 2006
- Characterization of Citrate Synthase from Geobacter sulfurreducens and Evidence for a Family of Citrate Synthases Similar to Those of Eukaryotes throughout the GeobacteraceaeApplied and Environmental Microbiology, 2005
- An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein databaseJournal of the American Society for Mass Spectrometry, 1994