Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the -Containing Consortium SDC-9.

At groundwater sites contaminated with chlorinated ethenes, fermentable substrates are often added to promote reductive dehalogenation by indigenous or augmented microorganisms. Contemporary bioremediation performance monitoring relies on nucleic acid biomarkers of key organohalide-respiring bacteria, such as (). Metagenome sequencing of the commercial, -containing consortium, SDC-9, identified 12 reductive dehalogenase (RDase) genes, including (two copies), , and , and allowed for specific detection and quantification of RDase peptides using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Shotgun (i.e., untargeted) proteomics applied to the SDC-9 consortium grown with tetrachloroethene (PCE) and lactate identified 143 RDase peptides, and 36 distinct peptides that covered greater than 99% of the protein-coding sequences of the PceA, TceA, and VcrA RDases. Quantification of RDase peptides using multiple reaction monitoring (MRM) assays with C-/N-labeled peptides determined 1.8 × 10 TceA and 1.2 × 10 VcrA RDase molecules per cell. The MRM mass spectrometry approach allowed for sensitive detection and accurate quantification of relevant RDases and has potential utility in bioremediation monitoring regimes.