High-frequency sampling unveils biotic and abiotic drivers of rapid phytoplankton morphological changes.

Phytoplankton, as primary producers, play a key role in aquatic ecosystems. Their community turnover is shaped by morphological traits that enable adaptation to diverse abiotic and biotic factors. Yet, the temporal scale of these dynamics remains poorly understood due to limited high-frequency sampling studies. Employing DNA metabarcoding, we assessed the community composition of the phytoplankton lineage Synurales (Chrysophyceae) at 3-d intervals during 70 d at a shallow peat bog lake in the Czech Republic. The selected group possesses a variety of species-specific key morphological traits, such as cell size, coloniality, and bristle formation. Using a custom reference database of cultured species, we assigned 99.93% of eDNA reads to 74 species-level lineages with known morphological traits. Community changes in colonial species were influenced by abiotic drivers such as silica concentration and wind speed. By contrast, shifts in unicellular species communities were mainly driven by Cladocera predators, influencing the occurrence of bristle-bearing species. Changes in species composition and morphological traits occurred within days, mirroring environmental variability. Achieving such fine-scale resolution, especially for small or rare taxa, would be extremely difficult using microscopy alone. eDNA enabled high-resolution community profiling and abundance estimation, demonstrating its key role and the importance of comprehensive reference databases.