Characterization of a Pure Culture of Dehalogenimonas Dechlorinating 4-Hydroxy-chlorothalonil and Its Putative Reductive Dehalogenase Gene by a Multiomics Approach

4-Hydroxy-chlorothalonil (4-OH-TPN), the main metabolite of the widely used fungicide chlorothalonil, has recently been reported to be reductively dechlorinated by an anaerobic consortium containing Dehalogenimonas. While the pure culture of the Dehalogenimonas has not been isolated and the reductive dehalogenase genes (rdhAs) responsible for the 4-OH-TPN dechlorination remain unclear. The assembled genome of Dehalogenimonas contained a 1,2-dichloroethane (1,2-DCA) reductive dehalogenase gene (dcpA) ortholog. In this study, by alternating the substrate from 4-OH-TPN to 1,2-DCA, a pure culture of Dehalogenimonas, designated as 4OHTPN1, was finally isolated. Strain 4OHTPN1 potentially represents a novel species in the genus Dehalogenimonas and contains 33 rdhA genes and 4 rdhB genes. The novel rdhA26 gene (designated htpnA) was identified as the key gene involved in 4-OH-TPN dechlorination. Its transcriptional and protein expression levels were 25.0-fold and 10.2-fold higher than the average of all rdhA genes when the culture was solely amended with 4-OH-TPN. In contrast, the dcpA ortholog, rdhA25, exhibited 10.1-fold and 9.8-fold higher transcriptional and protein expression levels when only amended with 1,2-DCA, highlighting a substrate-specific regulatory response to a distinct electron acceptor. This study expands our knowledge of the rdhA gene for 4-OH-TPN dechlorination in the pure culture of Dehalogenimonas.