eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants

With an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently been described as biodiversity capsules and suggested as a complementary tool for improving current biodiversity assessments. In this study, using faecal samples from two generalist omnivore species, the Eurasian badger and the red fox, we evaluated the applicability of eDNA metabarcoding in determining dietary composition, compared to macroscopic diet identification techniques. Subsequently, we used the dietary information obtained to assess its contribution to biodiversity assessments. Compared to classic macroscopic techniques, we found that eDNA metabarcoding detected more taxa, at higher taxonomic resolution, and proved to be an important technique to verify the species identification of the predator from field collected faeces. Furthermore, we showed how dietary analyses complemented field observations in describing biodiversity by identifying consumed flora and fauna that went unnoticed during field observations. While diet analysis approaches could not substitute field observations entirely, we suggest that their integration with other methods might overcome intrinsic limitations of single techniques in future biodiversity surveys.

Automated summary

Environmental DNA (eDNA) survey techniques, particularly using eDNA extracted from feces of generalist predators, are increasingly important in biodiversity assessments. eDNA metabarcoding technology can detect more taxa and provide higher taxonomic resolution, serving as a crucial tool for verifying species identification and complementing traditional biodiversity assessments. In addition, dietary analysis using eDNA can help reveal consumed flora and fauna that may have been missed during field observations, enhancing the overall description of biodiversity.