Divergent assembly mechanisms and network stability of microeukaryotes between water column and sediment in a...

Microeukaryotes play a critical role in marine ecosystem functioning, particularly in marginal seas influenced by strong environmental gradients and anthropogenic activities. However, the stability and assembly mechanisms of marine microeukaryotic communities remain poorly understood. Here, we investigated the assembly processes and co-occurrence network stability of microeukaryotic communities in a typical marginal sea, the East China Sea, across vertical gradients (surface, middle, bottom water, and sediment) and along a nearshore to offshore transect. Microeukaryotic diversity was higher in sediments than in seawater, and community composition showed pronounced variation along both vertical and nearshore-offshore gradients. Seawater co-occurrence networks exhibited greater complexity and robustness but lower modularity and vulnerability than sediment networks. Within the water column, the subsurface layer harbored the most complex networks, whereas bottom-water communities displayed higher modularity and slower fragmentation dynamics, indicating a more structured configuration of interaction networks in deep-water environments. Offshore communities exhibited higher network stability than nearshore communities despite comparable niche widths. Rare taxa showed high environmental sensitivity and disproportionately contributed to network structure, with lineages such as Gymnodiniphycidae and Pseudochattonella occupying key network positions. Together, these results suggest that the environmental gradients in marginal seas are associated with distinct community assembly patterns and network organization, which may influence the resilience of microeukaryotic communities to future environmental disturbances.