Thiocyanate and organic carbon inputs drive convergent selection for specific autotrophicAfipiaandThiobacillusstrains within complex microbiomes

Thiocyanate (SCN - ) contamination threatens aquatic ecosystems and pollutes vital fresh water supplies. SCN - degrading microbial consortia are commercially deployed for remediation, but the impact of organic amendments on selection within SCN - degrading microbial communities has not been investigated. Here, we tested whether specific strains capable of degrading SCN - could be reproducibly selected for based on SCN - loading and the presence or absence of added organic carbon. Complex microbial communities derived from those used to treat SCN - 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 - 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 Thiobacillus strain proliferated in all reactors at high loadings. Despite the presence of many Rhizobiales strains, a single Afipia variant dominated the molasses-free reactor at moderately high loadings. This strain is predicted to breakdown SCN - using a novel thiocyanate dehydrogenase, oxidize resulting reduced sulfur, degrade product cyanate (OCN − ) to ammonia and CO 2 via cyanase, and fix CO 2 via the Calvin-Benson-Bassham cycle. Removal of molasses from input feed solutions reproducibly led to dominance of this strain. Neither this Afipia 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 - 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.