Spatial heterogeneity driven by pollution shapes distinct microbial community assembly across six coastal bays of the Shandong Peninsula.

Coastal bays are critical land-sea interfaces increasingly threatened by anthropogenic activities, yet how pollution and trophic gradients shape microbial community assembly remains poorly understood. Here, we investigated spatial heterogeneity in environmental conditions and microbial community structure in surface (SW) and subsurface (SSW) waters of six bays along the Shandong Peninsula, China. Notably, diversity patterns did not follow a simple linear response to nutrient enrichment. While the eutrophic Rushan and Jinghai bays supported high microbial diversity, the oligotrophic Rongcheng Bay also exhibited high richness and Shannon diversity. High-throughput sequencing of 18S and 16S rRNA genes revealed that microbial communities in surface and subsurface waters were shaped by distinct environmental drivers. While SW communities were primarily regulated by chemical nutrients (bottom-up), SSW communities were driven by physical factors and trace elements, with Zn emerging as a key determinant for subsurface microeukaryotes. Co-occurrence network analysis further highlighted divergent interaction patterns. Disturbed environment such as TD Bay and DZ Bay were dominated by positive correlations, indicating strong environmental filtering, whereas the stable Rongcheng Bay ecosystem featured a higher proportion of negative interactions. This suggests that niche differentiation and biotic interactions are critical for maintaining biodiversity and preventing competitive exclusion in oligotrophic waters. Our findings provide insights into how multiple pollution sources and environmental heterogeneity drive microbial assembly in coastal bays.