Data from: The core of the matter – Importance of identification method and biological replication for benthic marine monitoring

Benthic macrofauna are important and widely used biological indicators of
marine ecosystems as they have limited mobility and therefore integrate
the effects of local environmental stressors over time. Recently,
environmental DNA (eDNA) analysis has provided a potentially more
resource-efficient approach for benthic biomonitoring than traditional
morphology-based methods. Several studies have compared eDNA with
morphology-based monitoring, but few have compared the two approaches
using the exact same sediment cores. In addition, the meiofauna and
pelagic organisms obtained as “bycatch” using eDNA have largely been
disregarded from comparisons. Here, we address these shortcomings through
comparative invertebrate analyses from six sediment sample replicates from
each of four stations in Denmark, using eDNA metabarcoding and
morphological identification. Our results revealed large variation between
the six replicates for both methods and little overlap in taxon
compositions between methods. While the morphological dataset was
dominated by molluscs and annelids, the eDNA dataset was dominated by
arthropods and annelids. Using community composition data, we found that
sampling stations could be distinguished both with eDNA and with
morphology. Finally, we evaluated expected total richness inferred from
extrapolated accumulation curves of detected taxa from each method. This
indicated that eDNA metabarcoding requires less replication than
morphology for maximum coverage of diversity to be reached. However, both
methods required high levels of replication, and our results on taxonomic
composition add to the evidence that morphological and eDNA-based methods
should preferably be used as complimentary tools for marine bioassessment.