eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants

• Published in: Scientific reports Vol. 11; no. 1; pp. 6820 - 12
• Main Authors: Nørgaard, Louise, Olesen, Carsten Riis, Trøjelsgaard, Kristian, Pertoldi, Cino, Nielsen, Jeppe Lund, Taberlet, Pierre, Ruiz-González, Aritz, De Barba, Marta, Iacolina, Laura
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 25.03.2021; Nature Publishing Group; Nature Research; Nature Portfolio
• Subjects: 631/158; 631/1647; 631/337; Animal Feed - analysis; Animals; Anthropogenic factors; Biodiversity; Biodiversity and Ecology; Denmark; Diet; DNA Barcoding, Taxonomic; DNA, Environmental - analysis; Ecosystem; Ecosystem assessment; Environmental DNA; Environmental Sciences; Feces; Feces - chemistry; Flora; Food Chain; Geography; Humanities and Social Sciences; Matematikk og Naturvitenskap: 400; Mathematics and natural science: 400; multidisciplinary; Predators; Science; Science (multidisciplinary); VDP; Denmark
• DOI: 10.1038/s41598-021-85488-9
• ISSN: 2045-2322

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.