Metabarcoding as a Tool in Characterizing Nordic Deep‐Sea and Arctic Benthic Ecosystems

ABSTRACT Deep‐sea and Arctic soft‐bottom organism communities remain severely underexplored. Sediment environmental DNA (eDNA) metabarcoding can complement existing survey methods, but its ability to discriminate among habitats and to reliably assign taxa must be critically evaluated. Here, we analyzed sediment samples from 10 areas in the Nordic Seas and adjacent Arctic, including the Arctic Mid‐Ocean Ridge (AMOR), continental slope habitats, and abyssal environments. Four genetic markers targeting different organism components were used: prokaryotic 16S and eukaryotic 18S (V1‐V2 and V4 regions) rDNA, and the metazoan cytochrome oxidase subunit I (COI) gene. Our aims were to gain biodiversity insights for these habitats by (1) comparing markers for characterizing and discriminating between samples and habitats, and (2) evaluating the potential for extracting low‐rank (family to species) animal taxa to complement taxonomic inventories. Alpha diversity varied substantially between markers and sampling areas, reflecting ecological variability and methodological differences. In contrast, beta diversity patterns were robust and consistent. Multivariate analyses showed clear separation by area and depth: the included AMOR seamount constituted a distinct community, and Arctic samples showed strong structuring with depth. Depth and geographic position explained significant fractions of community variability across metabarcoding markers. Taxonomic assignment revealed complementary performance of 18S rDNA and COI: 18S rDNA excelled in meio‐ and macrofauna coverage and intermediate‐rank performance. Conversely, COI yielded higher resolution at species rank. In total, 479 unique metazoan taxa were identified at family rank or below, highlighting both current limitations and future potential of metabarcoding for biodiversity inventories in the region. Overall, we find that multi‐marker eDNA metabarcoding can reliably discriminate between soft‐bottom organism communities. When combined with taxonomic validation and standardized workflows, this provides a powerful complement to existing survey methodology for understudied assemblages in the Nordic Seas and on the AMOR and should be integrated with future surveys in the area.