The genetic basis for anaerobic metabolism of dichloromethane

Dichloromethane (DCM) is both an ozone-depleting agent and greenhouse gas in addition to being a pervasive groundwater contaminant. DCM is emitted naturally from marine systems and wetlands, during biomass combustion, and has been detected in volcanic emissions. DCM was likely present on early Earth and has even been detected on Mars. Atmospheric concentrations of DCM have risen by ~8% per year over the last two decades, presumably due to anthropogenic activities. To date, anaerobic catabolism of DCM has been reported in three taxa, all grouping with the bacterial family Peptococcaceae. DCM is metabolized via the Wood-Ljungdahl pathway; however, the initial dechlorination steps have yet to be characterized. Comparative genomics revealed that each of the three described DCM-degrading organisms, Dehalobacterium formicoaceticum, Ca. Dichloromethanomonas elyunquensis, and Peptococcaceae bacterium DCMF, contains a highly homologous cluster comprising eight to ten genes. Functional annotation of this gene cassette revealed a two-component regulatory system, a corrinoid methyl-carrier protein, four methyltransferases, a corrinoid protein regeneration system, and a cation exchange membrane protein. Shotgun proteomics analyses performed with two DCM degraders revealed that the proteins encoded on this gene cluster were highly expressed during growth with DCM. A scan of ~15,000 metagenomes available in the JGI IMG system revealed the presence of homologous gene clusters in diverse environments including peat bogs, the deep subsurface, and several low oxygen marine systems such as the Eastern Pacific Oxygen Minimum Zone (OMZ). In addition, qPCR assays were developed, which allowed for sensitive detection and enumeration of the gene cluster in peat bog and OMZ samples. Identification of this putative DCM catabolic gene cluster in peat bogs, the deep subsurface and OMZs implies unrecognized sources of DCM, suggesting a relevant role for DCM as an energy source supporting microbial growth in critical zone environments. The results presented here also offer new tools for bioremediation monitoring and provide insight into a metabolism that may have existed on early Earth.