Higher trophic status leads to more diverse and divergent microeukaryote communities over time in urban lakes from the Greater Paris (France)

Effects of trophic status on lake microeukaryote community dynamics remain underexplored. Spanning oligotrophic to hypereutrophic conditions, peri-urban lakes located in the Greater Paris region (France) offer unique opportunities to compare these dynamics along a eutrophication gradient. Here, community composition was characterized using 18S rRNA gene metabarcoding, and analyzed in the context of environmental parameters and chlorophyll a-derived trophic status throughout an 18-month sampling period. Microeukaryote assemblages were dominated by Cryptophyceae, Spirotrichea, Chrysophyceae, and Chlorophyceae, with mixotrophic and heterotrophic taxa dominating across all lakes. Taxa richness peaked at intermediate trophic levels, consistent with the intermediate disturbance hypothesis. Beta-diversity and network analyses revealed increasing community modularity, reduced connectivity, and enhanced temporal variability with higher trophic status. In lakes reaching the hypereutrophic status, communities diverged progressively over time, suggesting the onset of regime shifts. Conversely, oligo-to mesotrophic lakes maintained more connected and stable assemblages. These findings demonstrate that eutrophication fosters more diverse and increasingly divergent microeukaryote communities, underscoring its role as a central driver of microbial community restructuring in urban freshwater systems.