Comparative study of traditional and DNA-based methods for environmental impact assessment: a case study of marine aggregate extraction in the North Sea

This project contains the raw sequence reads for a study where DNA-based monitoring was run in parallel with the traditional morphology-based environmental monitoring for sand extraction in the Belgian part of the North Sea (BPNS). Three different sand banks with varying extraction volumes and frequencies were sampled. We investigated whether bulk DNA metabarcoding of macrobenthos samples detected comparable alpha diversity (species richness and Shannon index), beta diversity (assemblage patterns based on Bray-Curtis dissimilarity), and biotic index (BEQI) results as morphology-based analyses. Second, we studied the similarities and differences in detected species by both methods. Third, the effect of a different fixative (ethanol instead of formalin) on morphological species detection was studied and compared with bulk DNA metabarcoding identification. Fourth, we examined whether read abundance of the dominant genera correlated with biomass and density of morphology-based identifications of these genera. Fifth, we tracked the time and costs of processing benthic samples with both bulk DNA metabarcoding and traditional identification to investigate which of both methods was most time and cost-effective. Lastly, we discuss how the strengths of both methods can be combined, and we formulate recommendations for an optimal monitoring programme to assess the impact of sand extraction activities in the BPNS and beyond.