Chlorinated electron acceptor availability selects for specific Dehalococcoides populations in dechlorinating enrichment cultures and in groundwater

Individual Dehalococcoides mccartyi (Dhc) strains differ primarily from one another by the number and identity of the reductive dehalogenase homologous catalytic subunit A (rdhA) genes contained within their respective genomes. While thousands of rdhA genes have been sequenced, the activity of the corresponding proteins have been identified in only a handful of cases. Most effort has focused on identifying the enzymes that dechlorinate substrates including trichloroethene (TCE), cis-dichloroethene (cDCE) and vinyl chloride (VC) relevant to groundwater remediation. The associated rdhA genes, namely tceA, bvcA, and vcrA, along with the D. mccartyi 16S rRNA gene are often used to track growth and dechlorinating activity in DNA extracted from field samples. In this study, we augmented the typical suite of three characterized rdhA genes to include an additional 12 uncharacterized rdhA sequences identified in the metagenome in the mixed Dhc-containing culture KB-1 to track population shifts within the culture and at two bioaugmented field sites. Quantitative PCR assays were developed for the 15 selected D. mccartyi rdhA genes and evaluated using 11 different sub-cultures of KB-1, each enriched on different chlorinated ethenes and ethanes. The proportion of rdhA gene copies relative to Dhc 16S gene copies indicated the presence of multiple distinct Dhc populations in each culture. The specific electron acceptor amended to each culture had a major influence on the distribution of D. mccartyi populations and their associated rdhA genes. We also surveyed the abundance of rdhA genes in samples obtained from two bioaugmented field sites. Growth of the dominant D. mccartyi population in the KB-1 inoculum was detected in the UK site samples. At both field sites, the measurement of relative rdhA abundances revaled significant D. mccartyi population shifts over time as dechlorination progressed from TCE through cDCE to VC and ethene, indicating that the selective pressure of the most abundant chlorinated electron acceptor that was observed in lab cultures was also occurring in the populations in the field. Understanding driving forces behind D. mccartyi population selection and activity is improving predictability of remediation performance at chlorinated solvent contaminated sites.