Modeling reveals a metabolic basis of competition among Dehalobacter strains during tandem chloroform and dichloromethane metabolism

SC05-UT is an anaerobic, heterogenous microbial enrichment culture that reduces chloroform to dichloromethane through reductive dechlorination, which it further mineralizes to carbon dioxide. This dichloromethane mineralization yields electron equivalents that are used to reduce chloroform without the addition of exogenous electron donor. By studying this self-feeding chloroform-amended culture and a dichloromethane-amended enrichment subculture (named DCME), we previously found the genomic potential to perform both biodegradation steps in two distinct Dehalobacter strains: Dehalobacter restrictus SAD and Candidatus Dehalobacter alkaniphilus DAD. Though present in each enrichment culture, strain SAD is more abundant in the chloroform-fed subculture SC05-UT, while strain DAD is more prominent in the dichloromethane-fed subculture DCME. To understand if genomic differences between strains impact their metabolic mechanisms, the genome of each strain was curated to reconstruct genome-scale metabolic models of each strain, which were then constrained based on thermodynamic and experimental conditions. We demonstrate that metabolic differences between the two strains may allow Dehalobacter strain DAD to outcompete strain SAD in the absence of chloroform, while strain SAD exhibits an advantage in the presence of chloroform. Additionally, we predict electron cycling methods to reconcile cellular redox imbalances during tandem chloroform and dichloromethane dechlorination. This work highlights the importance of hydrogen and amino acid exchange in these microbial communities and contributes to the growing body of work surrounding organohalide syntrophy. IMPORTANCE Chloroform and dichloromethane contaminate groundwater around the world but can be remediated by microbes capable of metabolizing these toxic compounds. Here, we study two distinct strains of Dehalobacter and show that while both strains can degrade both chloroform and dichloromethane, differences in their genetic makeup allow each strain to thrive under different environmental conditions. This has implications for understanding the fate of halogenated methanes in the environment and the application of Dehalobacter for bioremediation of chlorinated compounds.