A coupled hydrologic modeling and multi-omics analysis reveals that inflow magnitude shapes cyanobacterial structure and function

Climate-driven changes to lake inflow regimes are an increasing concern, with many regions expected to experience fewer but more intense storm-driven inflow events interspersed with extended droughts. We assessed how the magnitude of short-period inflows, characterized by hydraulic flushing and associated nitrogen and phosphorus loadings, shape cyanobacterial community composition and functional potential across 20 eutrophic lakes in southcentral USA. Lakes were sampled during the spring and summer of 2021, 2022, and 2023. Integrating hydrologic modeling and nutrient loading estimates with paired metagenomic and metatranscriptomic datasets, we quantified taxon-specific cyanobacterial abundances and functional gene expression in relation to the magnitude of inflows integrated over 7-, 15-, and 30-days. Hierarchical clustering and multivariate ordination (NMDS, PCA) revealed consistent groupings of cyanobacteria and metabolic pathways that tracked variation in flushing, nutrient loading, and season. Our data suggest that projected future inflow regimes characterized by large episodic, nutrient-enriched disturbances will favor Planktothrix , Pseudanabaena , and other Oscillatoriales, while reducing the prevalence of picocyanobacteria and suppressing cyanotoxin biosynthesis genes. In contrast, our data suggest that future regimes characterized by inflows of smaller magnitude may promote picocyanobacteria dominance and increased representation of toxin-associated pathways. Functional gene patterns reinforce these projections in our data, with large inflow events producing short-lived increases in denitrification and nitrite reduction, followed by declines as phytoplankton productivity intensifies, alongside a shift toward organic nitrogen and phosphorus utilization and reduced dependence on high-affinity inorganic nutrient acquisition systems.