Seasonal drivers of picoeukaryotic community structure and assembly in complex aquatic systems: A case study of the Changjiang (Yangtze) River Estuary and East China Sea.

This study investigates the seasonal dynamics, environmental drivers, and assembly mechanisms of picoeukaryotic communities in the hydrographically complex Changjiang River Estuary and adjacent East China Sea. Using 18S rRNA gene high-throughput sequencing and concurrent environmental profiling, we found pronounced differences in picoeukaryotic assemblages between the winter and summer surveys that were associated with contrasting hydrodynamic conditions. During winter, strong vertical mixing weakened environmental differentiation among water masses, and geographical distance was identified as the strongest correlate of picoeukaryotic community variation. Community assembly was predominantly associated with stochastic processes, particularly dispersal limitation and ecological drift, together with broader ecological niche breadths. In contrast, summer stratification strengthened environmental differentiation among water masses and increased the contribution of heterogeneous selection to community assembly. Taxonomic and network analyses revealed that communities were predominantly composed of Syndiniales-affiliated sequences. Co-occurrence networks demonstrated that parasitic Syndiniales and other potential parasitic groups acted as crucial keystone taxa (hubs and connectors) across seasons, suggesting significant host-parasite co-adaptation and their potential role in carbon transfer within the microbial loop. Notably, these keystone taxa transitioned from widespread, cosmopolitan distributions during winter mixing to highly compartmentalized, water-mass-specific niches during summer stratification. Collectively, our observations suggest that the contrast between winter mixing and summer stratification can alter the selective pressures and spatial gradients governing picoeukaryotic communities. This study underscores the critical importance of seasonal sampling to evaluate microbial interactions and assembly mechanisms in highly dynamic estuary-sea systems.