Identification of functional genes in a chloroform and dichloromethane-degrading microbial culture

Abstract

AbstractChloroform (CF) and dichloromethane (DCM) are groundwater contaminants of concern due to their high toxicity and inhibition of important biogeochemical processes. Biotransformation of CF and DCM have been well documented but always independent of one another. CF is dechlorinated to DCM by organohalide-respiring bacteria using reductive dehalogenases (RDases), while known DCM-degraders either ferment or mineralize DCM, both of which use themeccassette to facilitate the entry of DCM to the Wood-Ljungdahl pathway. The SC05 culture, used commercially for bioaugmentation, is the first and only known stable enrichment culture to transform CF and DCM simultaneously. Here we use metagenomic and metaproteomic analysis to identify the functional genes involved in each of these transformations. A singleDehalobactermetagenome assembled genome contains the genes for an RDase, namedacdA, and a completemeccassette encoded on a single contig. AcdA and several of the Mec proteins were also highly expressed. Furthermore, AcdA displayed high dechlorination activity on CF and other chloroalkanes but did not show significant dechlorination of DCM. Overall, the high expression of Mec proteins and the activity of AcdA suggest aDehalobactercapable of dechlorination of CF to DCM, and subsequent mineralization of DCM using themeccassette.ImportanceChloroform (CF) and dichloromethane (DCM) are harmful groundwater contaminants. SC05 is the first anaerobic microbial culture that can effectively and simultaneously remove both CF and DCM. Here we identify the key CF and DCM-degrading pathways in the culture, which are both found in aDehalobacterstrain. ThisDehalobactercontains and expresses all the genes necessary for both CF dechlorination and DCM mineralization, which has never been observed. Identifying these functional genes will improve our knowledge of how CF and DCM bioremediation progress and provide means to monitor the process when SC05 is deployed in the field.