Heavner, G.L.W., C.B. Mansfeldt, M.J. Wilkins, C.D. Nicora, G.E. Debs, E.A. Edwards, et al.
Frontiers in Microbiology 10:1433(2019)

Shotgun proteomics were applied to groundwater samples from a well-characterized, TCE-contaminated industrial site in southern Ontario that was bioaugmented with KB-1™ to measure biomarkers and enzymatic proteins. The relative abundances of specific enzymatic proteins were subsequently compared to corresponding qPCR-derived levels of DNA and RNA biomarkers in the same samples. Samples were obtained from two wells with high hydraulic connectivity to KB-1 and two control wells that showed evidence of low levels of native Dehalococcoides and Geobacter. Enzymes involved in organohalide respiration were detected in the metaproteomes of all four field samples, as were chaperonins of Dehalococcoides mccartyi, chemotaxis proteins, and ATPases. VcrA was the most highly expressed RDase gene in the bioaugmentation culture and bioaugmented groundwater samples. High expression of the Geobacter pceA RDase was found in one background groundwater well. DNA and RNA biomarkers detected using qPCR-based assays were a set of orthologs of Dehalococcoides reductive dehalogenases, and the Ni-Fe uptake hydrogenase, HupL. Within a sample, RNA levels for key enzymes correlated with relative protein abundance. Results indicated that RNA and protein biomarker monitoring is a promising technique to monitor the activity of in situ populations of organohalide-respiring bacteria. This article is Open Access athttps://www.frontiersin.org/articles/10.3389/fmicb.2019.01433/full?report=reader