Divergent responses of prokaryotic and eukaryotic microbiomes drive assembly, stability, and functional dynamics in...

Coastal oceans, critical for biodiversity and biogeochemistry, are increasingly altered by anthropogenic pressures that interact with natural spatiotemporal variability. However, the relative influence of spatial versus temporal drivers on microbiomes assembly, association, and function remains unclear. To resolve this, we integrated multi-kingdom amplicon and metagenomic sequencing to analyze microbial communities across spatial (Laizhou Bay vs. open Bohai Sea) and temporal (seasonal to interannual) gradients in the Bohai Sea, a semi-enclosed coastal system heavily influenced by recurrent human activities. Our results demonstrate that temporal variation exerts relatively stronger influences than spatial heterogeneity on the structure and dynamics of microbial communities in the Bohai Sea. Microeukaryotes exhibited the greatest responsiveness to spatiotemporal change, followed by archaea, with bacteria showing the highest stability. Archaeal and microeukaryotic communities were primarily governed by stochastic processes, whereas bacterial assembly transitioned from deterministic to stochastic control along spatiotemporal gradients. Microbiome co-occurrence networks were increasingly complex but less stable under spatiotemporal variability, dominated by competitive interactions and demonstrating a clear complexity-stability trade-off. Metagenomic analysis revealed a scale-dependent hierarchy of environmental drivers regulating metabolic pathways, with temperature predominant at the regional scale, DO in summer, and DON within homogeneous sub-regions. Two parallel microbial strategies for coping with anthropogenic pressure were identified, including enhanced catabolic pathways for xenobiotic degradation and a seasonally dynamic, mobile antibiotic resistome. This study provides a multidimensional and systematic perspective by demonstrating that temporal dynamics are the principal regulator of coastal microbiomes structure, stability, and function, with critical implications for predicting the responses of anthropogenically stressed coastal ecosystems under continuous environmental change.