Dehalococcoides strains respire a wide variety of chloro-organic compounds and are important for the bioremediation of toxic, persistent, carcinogenic, and ubiquitous ground water pollutants. In order to better understand metabolism and optimize their application, we have developed a pan-genome-scale metabolic network and constraint-based metabolic model of Dehalococcoides. The pan-genome was constructed from publicly available complete genome sequences of Dehalococcoides sp. strain CBDB1, strain 195, strain BAV1, and strain VS. We found that Dehalococcoides pan-genome consisted of 1118 core genes (shared by all), 457 dispensable genes (shared by some), and 486 unique genes (found in only one genome). The model included 549 metabolic genes that encoded 356 proteins catalyzing 497 gene-associated model reactions. Of these 497 reactions, 477 were associated with core metabolic genes, 18 with dispensable genes, and 2 with unique genes. This study, in addition to analyzing the metabolism of an environmentally important phylogenetic group on a pan-genome scale, provides valuable insights into Dehalococcoides metabolic limitations, low growth yields, and energy conservation. The model also provides a framework to anchor and compare disparate experimental data, as well as to give insights on the physiological impact of “incomplete” pathways, such as the TCA-cycle, CO2 fixation, and cobalamin biosynthesis pathways. The model, referred to as iAI549, highlights the specialized and highly conserved nature of Dehalococcoides metabolism, and suggests that evolution of Dehalococcoides species is driven by the electron acceptor availability.
Dehalococcoides are strictly anaerobic bacteria capable of detoxifying widespread and harmful ground water pollutants — chlorinated ethenes, chlorinated benzenes, polychlorinated biphenyls and dioxins — largely originated from industry and agriculture sectors. However, how this unique niche has been acquired by these microbes is not well understood, specifically at the level of metabolism. In addition, these bacteria harness energy from the pollutant detoxification process — reductive dechlorination — for their growth; but they grow very slowly. Their slow growth rate, as well as their low growth yield, can hamper bioremediation processes. Thus, in order to obtain an improved understanding of Dehalococcoides' metabolism and the factors limiting their growth, we developed a constraint-based metabolic model of Dehalococcoides from publicly accessible genome sequences of 4 strains. This model, in addition to creating a valuable knowledgebase on Dehalococcoides, offers researchers in the bioremediation community a valuable tool for generating experimentally testable hypothesis for improving the efficacy of bioremediation by Dehalococcoides.