Targeted detection of Dehalococcoides mccartyi microbial protein biomarkers as indicators of reductive dechlorination activity in contaminated groundwater

Manuel I Villalobos Solis,Cynthia M Swift,Robert L Hettich,Karuna Chourey,Frank E Löffler,Paul E Abraham

doi:10.1038/s41598-019-46901-6

Manuel I Villalobos Solis, Cynthia M Swift + Show 4 more

Open Access

https://doi.org/10.1038/s41598-019-46901-6

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Abstract

Dehalococcoides mccartyi (Dhc) bacterial strains expressing active reductive dehalogenase (RDase) enzymes play key roles in the transformation and detoxification of chlorinated pollutants, including chlorinated ethenes. Site monitoring regimes traditionally rely on qPCR to assess the presence of Dhc biomarker genes; however, this technique alone cannot directly inform about dechlorination activity. To supplement gene-centric approaches and provide a more reliable proxy for dechlorination activity, we sought to demonstrate a targeted proteomics approach that can characterize Dhc mediated dechlorination in groundwater contaminated with chlorinated ethenes. Targeted peptide selection was conducted in axenic cultures of Dhc strains 195, FL2, and BAV1. These experiments yielded 37 peptides from housekeeping and structural proteins (i.e., GroEL, EF-TU, rpL7/L2 and the S-layer), as well as proteins involved in the reductive dechlorination activity (i.e., FdhA, TceA, and BvcA). The application of targeted proteomics to a defined bacterial consortium and contaminated groundwater samples resulted in the detection of FdhA peptides, which revealed active dechlorination with Dhc strain-level resolution, and the detection of RDases peptides indicating specific reductive dechlorination steps. The results presented here show that targeted proteomics can be applied to groundwater samples and provide protein level information about Dhc dechlorination activity.

Highlights

Dehalococcoides mccartyi (Dhc) are key organohalide-respiring bacteria for the bioremediation of groundwater aquifers contaminated with industrial solvents such as tetrachloroethene (PCE) and trichloroethene (TCE)
The global proteomics datasets (Supplementary Table S1) collected from measurements of axenic Dhc cultures including Dhc strains 195, FL2, and BAV1 provided a set of candidate peptide sequences from housekeeping and reductive dechlorination biomarker proteins (Table 1) that were the starting point for the targeted method development (Fig. 1)[7,18,19]
Successful implementation of targeted proteomics for Dhc containing groundwater, in comparison to pure or mixed anaerobic bacterial cultures, requires knowledge of the specificity of the peptides selected from Dhc biomarkers in a broader microbiological context

Summary

Introduction

Dehalococcoides mccartyi (Dhc) are key organohalide-respiring bacteria for the bioremediation of groundwater aquifers contaminated with industrial solvents such as tetrachloroethene (PCE) and trichloroethene (TCE). Specialized Dhc bacteria grow under anoxic conditions by deriving energy from the reductive dechlorination of chlorinated ethenes, including cis-1,2-dichloroethene (cis-DCE) and vinyl chloride (VC), to yield environmentally benign ethene[1,2,3,4,5]. Various Dhc strains have been maintained in axenic cultures or in consortia supplied with a chlorinated ethene as electron acceptor, and several reductive dehalogenase (RDase) genes and their products have been identified as biomarkers of dechlorination activity[4,6,7]. Several studies with mixed cultures have demonstrated the lack of significant correlation between dechlorination activity and the concentration of Dhc 16S rRNA genes[11,12], temporal variation in the expression profiles of RDase transcripts during dechlorination[13,14], as well as different degrees of RDase transcript correlation with dechlorination activity depending on substrate loading rates[13,15,16]

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