Major geochemical cycles are driven by autotrophic microorganisms that are able to capture inorganic carbon to build their cells. We proposed that carbon monoxide (CO) is a “currency” metabolite in anaerobic autotrophic ecosystems, and proteins representing anaerobic CO metabolism are common in deep sea metagenomic databases. Deep sequencing reveals a substantial number of carboxydotrophs in deep sea hydrothermal systems, yet isolated and characterized marine CO utilizing strains are few and the isolates are dominated by terrestrial species. We proposed to develop a specialized CO-utilizing isolate as a model system for autotrophic processes in subseafloor environments, with E. coli as backup. Our strategy includes the identification and recombinant expression of genes and gene transcripts encoding for key enzymes in the anaerobic oxidation of CO and the isolation of novel CO utilizers from marine sediments and hydrothermal vents. Our study provides a link between the ecology of CO utilizers and their potential roles as well as insights into the evolution and horizontal exchange of CO related gene clusters. The proposed research contributes to C-DEBI themes 1 and 3 since CO “currency exchange” activities may be central to carbon transformation and survival in subsurface microbial communities.