Modeling reveals metabolic basis of competition among Dehalobacter strains during tandem CF and DCM metabolism

Abstract

SC05-UT is an anaerobic mixed microbial enrichment culture that reduces chloroform (CF) to dichloromethane (DCM) through reductive dechlorination, which it further mineralizes to carbon dioxide. This DCM mineralization yields electron equivalents that are used to reduce CF without addition of exogenous electron donor. By studying this self-feeding CF-amended culture and a DCM-amended enrichment culture (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 CF-fed subculture SC05-UT, while strain DAD is more prominent in the DCM-fed subculture DCME. To understand if genomic differences between strains and 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 CF, while strain SAD exhibits an advantage in the presence of CF. Additionally, we predict electron cycling methods to reconcile redox imbalances in the cell is required for tandem CF and DCM 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. ImportanceChloroform 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.