Integrating eDNA Metabarcoding and Functional Trait Analysis to Uncover Fish Community Structure and Assembly Mechanism in the Taiwan Strait

Marine fish communities in coastal systems are increasingly shaped by environmental gradients associated with anthropogenic pressures and climate variability, yet how these factors influence community assembly and functional traits remain poorly understood. In this study, environmental DNA (eDNA) metabarcoding using the 12S MiFish primer with 33 water samples was integrated with taxonomic and functional diversity analyses, co-occurrence network analysis, the neutral community model, hierarchical modeling of species communities, and single-trait-based community-weighted means to investigate fish communities in the Taiwan Strait (TWS).  This interdisciplinary approach provides both a unique perspective and a comprehensive framework for fish biodiversity assessment. fish communities exhibited high modularity and weak interspecific interactions, with an uneven distribution of species within functional space, indicating elevated ecological vulnerability. Community assembly was jointly governed by stochastic and deterministic processes, with NO₂⁻ identified as a significant environmental driver shaping fish community assembly. Notably, fish communities in the inshore and principal axis regions exhibited higher clustering coefficient but lower network modularity compared to other regions. Hierarchical modeling of species communities and community-weighted means further indicated clear distributional and trait differences among fish from the estuarine to offshore areas, consistent with species-specific responses to environmental gradients from inshore to offshore areas. Overall, TWS fish communities are dominated by species with very small and small body-length traits, while reef-associated fishes are mainly concentrated in inshore and midshore regions. Fish community assembly and functional traits in TWS exhibited systematic variation along the offshore distance gradient and were jointly modulated by key environmental factors.