Application of eDNA metabarcoding for high-resolution reconstruction of the trophic web of an Arctic fjord

In a rapidly changing Arctic, the Kongsfjorden marine ecosystem was investigated to explore its community composition and structural dynamics using environmental DNA (eDNA) metabarcoding. Samples were collected with metaprobes , passive eDNA samplers deployed within fish traps in the coastal zone and towed along a transect in the mid-fjord zone. Mitochondrial COI and ribosomal 18 S SSU (V8-V9 region) genes were amplified to characterize metazoan and protist communities, respectively. Community analysis highlighted significant differences between coastal and mid-fjord sites (ANOSIM, R = 0.7, p < 0.05), identifying 23 taxa as indicators of one of the two zones. Taxa identified through metabarcoding were used as nodes in trophic networks, while feeding relationships (producer–consumer and predator–prey) were reconstructed through literature review. Qualitative food webs were obtained for each sampling site and for the coastal and mid-fjord zones. The networks were characterized using key trophic indicators and differences emerged in the apical part of the webs. Overall, eDNA proved to be a sensitive and effective tool for detecting spatial differences in community structure. This approach also shows strong potential for long-term monitoring, offering a rapid, cost-effective, and scalable alternative to traditional methods.