Integrating metagenome-scale metabolic models and metabolomics to explore candidate biochemical interactions in cultivated Microcystis phycospheres.

Favored by global changes, freshwater cyanobacterial harmful blooms generate major ecological, economic, and public health challenges. Microcystis, one of the most widespread cyanobacterial genera, grows within a phycosphere where specialized interactions with its microbiome occur, that are suspected to influence bloom appearance and its potential toxicity. Using a combination of metagenomics, metabolomics, and metabolic modeling, we characterized the culture-associated phycospheres of 12 Microcystis strains isolated from a French pond. The distribution of metabolic reactions within Microcystis was consistent with their genospecies, whereas the metabolic landscape at the community level diverged from cyanobacterial phylogeny, indicating partial functional decoupling between cyanobacteria and their associated microbiomes. Bacteria associated with the simplified phycospheres substantially expanded the metabolic repertoire of the system, while maintaining functional redundancy within and across communities. On the other hand, endometabolomic profiles were largely driven by cyanobacterial metabolic outputs, whereas exometabolomic analysis did not reveal metabolites involved in exchange processes. Metabolic modeling, together with the identification of toxic specialized metabolites produced by specific biosynthetic gene clusters, further highlighted differences in metabolic potential among phycospheres. Together, these findings deepen the understanding of Microcystis' phycosphere functioning and demonstrate the value of multi-omics systems biology approaches, while suggesting that metabolic complementarity between species and across phycospheres could play a role in bloom-associated microbiome structure.