Evidence for ecological adaptation of reductive citric acid and reverse oxidative citric acid cycles based on a survey of genomes from autotrophic Bacteria

Abstract The reductive citric acid (rTCA) and reverse oxidative TCA (roTCA) cycles are used by autotrophic Bacteria to fix dissolved inorganic carbon (DIC) at deep-sea and terrestrial hot springs, water treatment facilities, acid rock drainage, sediments and aquatic habitats including lake redoxclines, and more. rTCA and roTCA cycles operating in these contexts likely reflect selective pressures present in them. This genome survey examines the versions of the rTCA and roTCA cycles present in the completed genome sequences of several phyla of Bacteria. The versions of these cycles correlate in part with the phyla to which the organisms belong, as well as with their habitats. There are many potential mechanisms for navigating the carboxylation of C3 compounds, which may diminish its metabolic cost. There are variations in electron donors for reductive steps in these cycles that could push them in a reductive direction. The predicted O2 sensitivity of several enzymes correlates with organisms’ lifestyles. The presence of genes encoding DIC transporters and carbonic anhydrases correlates with habitat pH. Understanding how these cycles have responded to billions of years of selective pressure in a variety of habitats may provide insights into engineering autotrophic biochemistries to function well in a variety of industrial contexts.