Search

Microcystisis a genus of freshwater cyanobacteria, which causes harmful blooms in ecosystems worldwide. Some Microcystisstrains produce harmful toxins such as microcystin, impacting drinking water quality. Microcystiscolony morphology, rather than genetic similarity, is often used to classify Microcystisinto morphospecies. Yet colony morphology is a plastic trait, which can change depending on environmental and laboratory culture conditions, and is thus an inadequate criterion for species delineation. Furthermore, Microcystispopulations are thought to disperse globally and constitute a homogeneous gene pool. However, this assertion is based on relatively incomplete characterization of Microcystisgenomic diversity. To better understand these issues, we performed a population genomic analysis of 33 newly sequenced genomes mainly from Canada and Brazil. We identified 17 Microcystisclusters of genomic similarity, five of which correspond to monophyletic clades containing at least three newly sequenced genomes. Four out of these five clades match to named morphospecies. Notably, M. aeruginosais paraphyletic, distributed across 12 genomic clusters, suggesting it is not a coherent species. A few clades of closely related isolates are specific to a unique geographic location, suggesting biogeographic structure over relatively short evolutionary time scales. Higher homologous recombination rates within than between clades further suggest that monophyletic groups might adhere to a Biological Species-like concept, in which barriers to gene flow maintain species distinctness. However, certain genes—including some involved in microcystin and micropeptin biosynthesis—are recombined between monophyletic groups in the same geographic location, suggesting local adaptation.