Chlorinated Electron Acceptor Abundance Drives Selection of Dehalococcoides mccartyi (D. mccartyi) Strains in Dechlorinating Enrichment Cultures and Groundwater Environments

Abstract

Dehalococcoides mccartyi (D. mccartyi) strains differ primarily from one another by the number and identity of the reductive dehalogenase homologous catalytic subunit A (rdhA) genes within their respective genomes. While multiple rdhA genes have been sequenced, the activity of the corresponding proteins has been identified in only a few cases. Examples include the enzymes whose substrates are groundwater contaminants such as trichloroethene (TCE), cis-dichloroethene (cDCE) and vinyl chloride (VC). The associated rdhA genes, namely tceA, bvcA, and vcrA, along with the D. mccartyi 16S rRNA gene are often used as biomarkers of growth in field samples. In this study, we monitored an additional 12 uncharacterized rdhA sequences identified in the metagenome in the mixed D. mccartyi-containing culture KB-1 to monitor population shifts in more detail. Quantitative PCR (qPCR) assays were developed for 15 D. mccartyi rdhA genes and used to measure population diversity in 11 different sub-cultures of KB-1, each enriched on different chlorinated ethenes and ethanes. The proportion of rdhA gene copies relative to D. mccartyi 16S rRNA gene copies revealed the presence of multiple distinct D. mccartyi strains in each culture, many more than the two strains inferred from 16S rRNA analysis. The specific electron acceptor amended to each culture had a major influence on the distribution of D. mccartyi strains and their associated rdhA genes. We also surveyed the abundance of rdhA genes in samples from two bioaugmented field sites (Canada and United Kingdom). Growth of the dominant D. mccartyi strain in KB-1 was detected at the United Kingdom site. At both field sites, the measurement of relative rdhA abundances revealed D. mccartyi population shifts over time as dechlorination progressed from TCE through cDCE to VC and ethene. These shifts indicate a selective pressure of the most abundant chlorinated electron acceptor, as was also observed in lab cultures. These results also suggest that reductive dechlorination at contaminated sites is brought about by multiple strains of D. mccartyi whether or not the site is bioaugmented. Understanding the driving forces behind D. mccartyi population selection and activity is improving predictability of remediation performance at chlorinated solvent contaminated sites.

Insights into origins and function of the unexplored majority of the reductive dehalogenase gene family as a result of genome assembly and ortholog group classification

“…Hug et al (2013) 19 developed a classication system for reductive dehalogenases where sequences were assigned to Ortholog Groups (OGs) in an attempt to cluster rdhA sequences into groups with similar activity on specic halogenated electron acceptors. 35 Previous studies identied 32 distinct rdhA genes in the KB-1/ TCE-MeOH culture, 38,69,70 with two being identical to genes found previously in D. mccartyi CBDB1. Although 104 RdhA were found in this study, only three new OGs could be described, and the remaining RdhA sequences fell into previously identied groupings (Table S2 †).…”

“…We had previously noted that different electron acceptors enriched for different strains of D. mccartyi. 38 From three cultures, 8 new D. mccartyi genomes were closed, increasing the total number of publicly available D. mccartyi genomes to 24. As well, one new Dehalobacter restrictus genome was closed increasing the number publicly available to 4 (as of December 2019).…”

Mechanistic Dichotomy in Bacterial Trichloroethene Dechlorination Revealed by Carbon and Chlorine Isotope Effects

“…Before 33 and after the TCE dechlorination experiment with KB-1/VC, vcrA was the most abundant RDase gene analyzed. The information obtained from the qPCR data therefore suggests that the maintenance on one specific precultivation substrate has a significant influence on the microbial community and the prevalence of RDase genes 35 .…”

Reductive dechlorination of 1,2-dichloroethane in the presence of chloroethenes and 1,2-dichloropropane as co-contaminants

“…Our results indicate that the type of chlorinated substrate drives the selection of OHRB. Likewise, a recent study showed that a Dehalococcoides population shift was driven by different chlorinated electron acceptors in enrichment cultures containing Dehalococcoides and at a contaminated site (Pérez-de-Mora et al 2018).…”