The integration of eDNA metabarcoding into monitoring programs provides valuable information about fish community structure. Despite the growing body of evidence supporting the method's effectiveness in distinguishing fine-scale eDNA signatures, there is a limited understanding of eDNA distribution in shallow, well-mixed environments. Furthermore, inferring population abundance and biomass via eDNA remains challenging due to the numerous biotic and abiotic factors affecting eDNA persistence. We analyzed 167 samples from 17 stations collected from the surface and bottom waters of the Belgian Part of the North Sea (BPNS). We utilized degenerated 12S MiFish_U/E primers to target both Actinopterygii and Elasmobranchii. eDNA enhanced taxonomic detection by 54% compared to beam trawling and detected an additional 21 species. Beta diversity analysis successfully revealed horizontal community patterns obtained from long-term monitoring. We did not detect any significant difference in vertical space for diversity measurements. Out of six species tested, only half of them returned a significant correlation between read number and catch-based abundance/biomass. Our results demonstrate the efficacy of eDNA metabarcoding in spatially identifying community patterns, even in highly dynamic environments such as the BPNS. However, we caution that eDNA read count is currently not a robust proxy for quantifying fish populations.
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