We will reconstruct metagenome assembled genomes from more than 1000 publicly available freshwater lake metagenomes. We will then apply a novel pipeline to group these MAGs into species-level pangenomes. For each of this pangenomes we will assess how allelic frequencies and accessory gene content shift across geographic, temporal and environmental gradients. By jointly analyzing intra-species diversity patterns for potentially hundreds of species across thousands of samples, we will attempt to discover general patterns of dispersal, diversification and adaptation in freshwater microorganisms.