Thiocyanate and organic carbon inputs drive convergent selection for specific autotrophic<i>Afipia</i>and<i>Thiobacillus</i>strains within complex microbiomes

<jats:title>Abstract</jats:title><jats:p>Thiocyanate (SCN<jats:sup>-</jats:sup>) contamination threatens aquatic ecosystems and pollutes vital fresh water supplies. SCN<jats:sup>-</jats:sup>degrading microbial consortia are commercially deployed for remediation, but the impact of organic amendments on selection within SCN<jats:sup>-</jats:sup>degrading microbial communities has not been investigated. Here, we tested whether specific strains capable of degrading SCN<jats:sup>-</jats:sup>could be reproducibly selected for based on SCN<jats:sup>-</jats:sup>loading and the presence or absence of added organic carbon. Complex microbial communities derived from those used to treat SCN<jats:sup>-</jats:sup>contaminated water were exposed to systematically increased input SCN concentrations in molasses-amended and -unamended reactors and in reactors switched to unamended conditions after establishing the active SCN<jats:sup>-</jats:sup>degrading consortium. Five experiments were conducted over 790 days and genome-resolved metagenomics was used to resolve community composition at the strain level. A single<jats:italic>Thiobacillus</jats:italic>strain proliferated in all reactors at high loadings. Despite the presence of many<jats:italic>Rhizobiales</jats:italic>strains, a single<jats:italic>Afipia</jats:italic>variant dominated the molasses-free reactor at moderately high loadings. This strain is predicted to breakdown SCN<jats:sup>-</jats:sup>using a novel thiocyanate dehydrogenase, oxidize resulting reduced sulfur, degrade product cyanate (OCN<jats:sup>−</jats:sup>) to ammonia and CO<jats:sub>2</jats:sub>via cyanase, and fix CO<jats:sub>2</jats:sub>via the Calvin-Benson-Bassham cycle. Removal of molasses from input feed solutions reproducibly led to dominance of this strain. Neither this<jats:italic>Afipia</jats:italic>strain nor the thiobacilli have the capacity to produce cobalamin, a function detected in low abundance community members. Although sustained by autotrophy, reactors without molasses did not stably degrade SCN<jats:sup>-</jats:sup>at high loading rates, perhaps due to loss of biofilm-associated niche diversity. Overall, convergence in environmental conditions led to convergence in the strain composition, although reactor history also impacted the trajectory of community compositional change.</jats:p>