Coastal bays represent dynamic marine ecosystems where environmental gradients strongly influence microbial biodiversity and ecosystem functioning. Understanding the distribution and assembly of planktonic eukaryotic communities across different coastal systems is essential for predicting ecosystem responses to environmental change.

In this study, environmental DNA (eDNA) metabarcoding was used to investigate the diversity, community structure, and geographic differentiation of planktonic eukaryotic microbial communities across five Chinese coastal bays. Community composition was compared among bays with contrasting environmental conditions, and the relationships between biodiversity patterns and environmental variables were evaluated using multivariate ecological analyses.

The results revealed significant spatial variation in microbial eukaryote communities among bays, indicating strong geographic differentiation. Community turnover was associated with environmental gradients, particularly nutrient concentrations, salinity, and other physicochemical factors. Several taxonomic groups showed distinct distribution patterns, suggesting that environmental filtering plays an important role in shaping community assembly across coastal ecosystems.

These findings demonstrate that Chinese coastal bays harbor diverse and ecologically distinct microbial eukaryote communities and highlight the importance of regional environmental conditions in driving biodiversity patterns. The study provides new insights into microbial biogeography, coastal ecosystem functioning, and biodiversity conservation. Furthermore, the observed community transitions suggest that environmental boundary zones may represent overlooked hotspots of microbial diversity, providing a foundation for future investigations into hidden biodiversity and ecological differentiation in coastal ecosystems.

Keywords: eDNA metabarcoding, microbial eukaryotes, coastal bays, biodiversity, community assembly, environmental gradients, marine ecology.