CONCLUSION
DNA metabarcoding is a promising and cost-efficient tool for monitoring benthic communities in the marine environment. In view of the large taxonomic and phylogenetic diversity in marine communities (Appeltans et al., 2012; Mora, Tittensor, Adl, Simpson, & Worm, 2011) and differences in benthic communities between geographic realms, optimisation of the protocol for the taxonomic group and geographic region at hand are necessary. By aiming for the detection of the highest number of known morphological species in a given area, a link with long time series of monitoring data based on morpho-taxonomy can be made. Our results demonstrate the impact of primer choice and DNA source when using the mitochondrial COI gene to assess macrobenthic species diversity. We show that the probability of detecting macrobenthos species is linked to morphological traits and this detection is most robust and most comparable with morphological results when using the Leray primer set and bulkDNA as template for DNA metabarcoding.