Coherence of Microcystis species revealed through population genomics


Microcystis is a genus of freshwater cyanobacteria, which causes harmful blooms in ecosystems worldwide. Some Microcystis strains produce harmful toxins such as microcystin, impacting drinking water quality. Microcystis colony morphology, rather than genetic similarity, is often used to classify Microcystis into 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, Microcystis populations are thought to disperse globally and constitute a homogeneous gene pool. However, this assertion is based on relatively incomplete characterization of Microcystis genomic 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 Microcystis clusters 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. aeruginosa is 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.

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Data availability

The raw reads and the Microcystis genomes contigs are available in GenBank under Bioproject number PRJNA507251 (Table S1).


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We are grateful to David Bird, Naíla Barbosa da Costa, Mylène Boyer, Julie Marleau, and Coralie Deladrière for assistance isolating strains and maintaining cultures. This work was supported by the Genome Québec and Genome Canada-funded ATRAPP Project (Algal blooms, Treatment, Risk Assessment, Prediction, and Prevention). NT was funded by a project from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 656647. Cultures collections (Brazilian and some Canadian strains) were partially obtained and maintained thanks to CNPq and FAPEMIG grants to AG. We also want to acknowledge the financial support of the National Research Council.

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Pérez-Carrascal, O.M., Terrat, Y., Giani, A. et al. Coherence of Microcystis species revealed through population genomics. ISME J 13, 2887–2900 (2019) doi:10.1038/s41396-019-0481-1

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