Abstract
Microcystis is one of the most common bloom-forming cyanobacteria colonizing freshwater ecosystems worldwide. This genus remarkably produces numerous bio-active accessory metabolites, which are believed to be potentially involved in different ecological and/or physiological processes. However, their genuine contribution to the evolutionary success of Microcystis blooms remains undetermined. To better depict the potential relationship between the local genetic diversity of blooming Microcystis populations and their respective associated chemical diversity, we conducted a joint genomic and metabolomic analysis of 65 Microcystis strains collected from various lakes in France and surrounding Western European countries. Interestingly, both core and pan-gene phylogenetic analysis place 57 of these strains in 11 distinct genotypes with at least 2 genomes, being widely distributed along the entire Microcystis phylogeny and presenting specific signatures of accessory metabolite biosynthesis. The direct chemical analysis of metabolite diversity produced by these strains, cultured under laboratory conditions, reveals the production of stable metabolite cocktails, with minimal variations over replication, growth phases and culture conditions. Remarkably, these strains belonging to 11 different genotypes correspond to 13 distinct chemotypes according to an accurate one-chemotype-for-one-genotype rule. Furthermore, these genotypes also appear distinguishable regarding their respective ecotoxicological traits and might be considered as specific toxico-ecotypes. Overall, our investigations reveal that the production of accessory metabolites constitute well conserved chemical traits across the different Microcystis genotypes, suggesting these molecules may be involved in key adaptive and selective processes, that still remain under-explored.
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Data availability
The raw data of new Microcystis genomes reported in this study (58 and 13 from PMC and PCC, respectively) have been deposited in the ENA database and are available under the accession numbers PRJEB101697 and PRJEB105414, respectively. The accession numbers of the assembled genomes corresponding to these individual strains are listed in Supplementary Data S1. Figure 4 combines AntiSmash and metabolomic data that are available on Supplementary Data S2, the data used for Fig. 7B are available on Supplementary Data S4. Whole metabolomics dataset can be found on Mendeley (DOI: 10.17632/2rnz75jpzr.1). Raw data are available upon request.
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Acknowledgements
This work was supported by the ANR MC-Tox project, grant ANR CE34-SJ 11008-22 of the French Agence Nationale de la Recherche. The Paris Muséum Collection (PMC) and the Pasteur Cultures of Cyanobacteria (PCC) collection are funded by the MNHN and the Institut Pasteur, respectively. The mass spectrometry analyses were acquired at the Plateau technique de spectrométrie de masse bio-organique, Muséum National d’Histoire Naturelle, Paris, France. The authors thank the anonymous referees for providing valuable suggestions that significantly improved the quality of the manuscript.
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S.H., M.G., and B.M. conceived and designed the experiments; C.D. isolated all new strains of the PMC; A.H., M.L.M., C.D., S.H., M.Q., and M.B. performed the analysis; A.H., J.B.P., L.M., M.D., S.H., M.D., and B.M. treated the data. All authors wrote and reviewed the manuscript.
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Huré, A., Le Meur, M., Duval, C. et al. Metabolite diversity of Microcystis strains shows tight correspondence to genotype and may contribute to ecotype specificities. Commun Biol (2026). https://doi.org/10.1038/s42003-026-09599-7
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DOI: https://doi.org/10.1038/s42003-026-09599-7
