Spatiotemporal Dynamics of Microbial and Fish Communities in the Thracian Sea Revealed by eDNA Metabarcoding

The Thracian Sea, a semi-enclosed coastal basin in the northeastern Aegean Sea, represents a dynamic marine environment influenced by freshwater inputs, stratification, and seasonal variability. Here, we investigated the spatiotemporal dynamics of microbial and ichthyofaunal communities using environmental DNA (eDNA) and high-throughput sequencing across various stations in the vicinity of the Thracian Sea, in consecutive months (through spring and summer). Seawater samples were collected from the surface and thermocline layers, and environmental parameters were recorded to examine their influence on biodiversity patterns. Microbial communities exhibited strong seasonal and depth-related structuring. Alpha diversity was highest in spring and declined during summer, while beta diversity analyses revealed clear clustering by month and depth. Dominant taxa included Alphaproteobacteria (SAR11), Cyanobacteria (<i>Synechococcus</i>, <i>Prochlorococcus</i>), with distinct core microbiomes. Fish communities, identified via <i>CytB</i> metabarcoding, displayed marked temporal turnover but limited spatial segregation. While alpha diversity metrics did not differ significantly, beta diversity analyses showed seasonal shifts with dominant taxa such as <i>Raja</i> spp., <i>Engraulis</i> spp., and <i>Diplodus sargus</i>. Multivariate and co-structure analyses (Mantel, Procrustes) revealed moderate but significant concordance between microbial and fish communities and support the existence of similar biodiversity responses to environmental parameters across temporal and spatial variability. Co-occurrence networks further present depth-specific associations, with surface communities being more cooperative and phototrophic, while thermocline networks showed modularity and potential ecological specialization. This study highlights the value of integrated eDNA-based monitoring in revealing seasonal biodiversity dynamics and ecological interactions in coastal marine ecosystems, supporting future spatial planning and conservation strategies in the Thracian Sea.