Uncovering the genomic basis of symbiotic interactions and niche adaptations in freshwater picocyanobacteria

Picocyanobacteria from the genera Prochlorococcus, Synechococcus, and Cyanobium are the most widespread photosynthetic organisms in aquatic ecosystems. However, their freshwater populations remain poorly explored, due to the insufficient sampling across diverse inland waterbodies. In this study, we present 170 high-quality genomes of freshwater picocyanobacteria and 33 genomes of potential symbiotic partners from non-axenic cultures collected across Central Europe. The genomic basis of symbiotic interactions involved heterotrophs benefiting from picocyanobacteria-derived nutrients, while providing detoxification of ROS. The global abundance patterns of picocyanobacterial genomes revealed ecologically significant ecotypes, associated with trophic status, temperature, and pH as key environmental factors. The adaptation of picocyanobacteria in (hyper-)eutrophic waterbodies could be attributed to their colonial lifestyles and CRISPR-Cas systems. The prevailing CRISPR-Cas subtypes in picocyanobacteria were I-G and I-E, which appear to have been acquired through horizontal gene transfer from other bacterial phyla.