Isolation of Dehalococcoides mccartyi strain (NIT-OBY) and identification of a reductive dehalogenase dechlorinating cis-1,3-dichloropropene but not trans-1,3-dichloropropene to non-toxic propene

The popular soil fumigant 1,3-dichloropropene (1,3-D) is widely used worldwide and one of the top five most-used pesticides in the United States. However, 1,3-D is classified as a Group 2B carcinogen and understanding its environmental fate is important. The aerobic degradation pathway of 1,3-D, along with the involved microorganisms and enzymes have been comprehensively described, whereas anaerobic transformation and the associated functional players remain incompletely understood. Therefore, this study aimed to investigate the ability of Dehalococcoides mccartyi strain NIT-OBY, a new isolate from a trichloroethene-dechlorinating consortium, to dechlorinate 1,3-D. Strain NIT-OBY dechlorinated cis-1,3-D but not trans-1,3-D to non-toxic propene via 3-chloropropene and cis-1-chloropropene, a previously unreported intermediate. The preference to cis-1,3-D contrasts with that of the reductive dehalogenase of Sulfurospirillum multivorans, which preferentially dechlorinates trans-1,3-D. However, dechlorination of cis-1,3-D did not support growth of strain NIT-OBY due to its rapid abiotic hydrolysis to 3-chloroallyl alcohol. Genome analysis revealed that strain NIT-OBY possesses 27 genes coding for the active subunit of reductive dehalogenase homologous proteins (RdhAs) including three for which the encoded proteins have more than 93% amino acid sequence similarity with RdhA proteins functionally characterized previously: RdhA11 (TceA), RdhA12 (VcrA), and RdhA21 (PceA), respectively. Activity tests and protein mass spectrometry from native gels indicate that RdhA11 (TceA) dechlorinates cis-1,3-D to propene. The results specifically differentiate the dehalogenation pathways catalyzed within the Dehalococcoidia class and add to the development of informed guidelines for bioaugmentation approaches.