AUTHOR=Pérez-de-Mora Alfredo , Lacourt Anna , McMaster Michaye L. , Liang Xiaoming , Dworatzek Sandra M. , Edwards Elizabeth A. 

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

JOURNAL=Frontiers in Microbiology

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2018.00812

DOI=10.3389/fmicb.2018.00812

ISSN=1664-302X

ABSTRACT=<p><italic>Dehalococcoides mccartyi</italic> (<italic>D. mccartyi</italic>) strains differ primarily from one another by the number and identity of the reductive dehalogenase homologous catalytic subunit A (<italic>rdhA</italic>) genes within their respective genomes. While multiple <italic>rdhA</italic> 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), <italic>cis</italic>-dichloroethene (cDCE) and vinyl chloride (VC). The associated <italic>rdhA</italic> genes, namely <italic>tceA, bvcA</italic>, and <italic>vcrA</italic>, along with the <italic>D. mccartyi</italic> 16S rRNA gene are often used as biomarkers of growth in field samples. In this study, we monitored an additional 12 uncharacterized <italic>rdhA</italic> sequences identified in the metagenome in the mixed <italic>D. mccartyi</italic>-containing culture KB-1 to monitor population shifts in more detail. Quantitative PCR (qPCR) assays were developed for 15 <italic>D. mccartyi rdhA</italic> 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 <italic>rdhA</italic> gene copies relative to <italic>D. mccartyi</italic> 16S rRNA gene copies revealed the presence of multiple distinct <italic>D. mccartyi</italic> 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 <italic>D. mccartyi</italic> strains and their associated <italic>rdhA</italic> genes. We also surveyed the abundance of <italic>rdhA</italic> genes in samples from two bioaugmented field sites (Canada and United Kingdom). Growth of the dominant <italic>D. mccartyi</italic> strain in KB-1 was detected at the United Kingdom site. At both field sites, the measurement of relative <italic>rdhA</italic> abundances revealed <italic>D. mccartyi</italic> 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 <italic>D. mccartyi</italic> whether or not the site is bioaugmented. Understanding the driving forces behind <italic>D. mccartyi</italic> population selection and activity is improving predictability of remediation performance at chlorinated solvent contaminated sites.</p>