CRISPR-Dx and metabarcoding enable comparable mammal monitoring with eDNA in high-alpine catchments
Flurin Leugger1,2, Martina Lüthi1,2, Michel Schmidlin1,2, Sarah Marie-Antoine Turnheer1,2, Zacharias Kontarakis2
Loïc Pellissier1,2
1 Eidg. Forschungsanstalt für Wald, Schnee und Landschaft WSL
2 ETH Zürich
Monitoring biodiversity in remote and inaccessible areas, such as rugged mountain ranges, remains challenging and is often lacking. Environmental DNA (eDNA) offers new possibilities for monitoring these areas, as rivers collect and transport genetic material from entire catchments. Recent advances in molecular tools, such as CRISPR-based diagnostic systems (CRISPR-Dx), enable species-specific eDNA detection without the need for fully equipped laboratories. We present an approach that combines multi-species primers with CRISPR-Dx to simultaneously detect multiple terrestrial mammal species from a single eDNA amplification.
We designed species-specific CRISPR-Dx assays for eight terrestrial mammal species native to the European Alps within a short metabarcoding amplicon and tested these assays on eDNA samples collected from high-alpine catchments. We compared CRISPR-Dx results to metabarcoding analyses of the same samples and to species inventories from traditional monitoring.
Our study demonstrates three key findings: 1. Feasibility – Species-specific CRISPR-Dx assays can be successfully designed within a short metabarcoding amplicon for detecting terrestrial mammals in eDNA samples. 2. Sensitivity – CRISPR-Dx performs comparably to metabarcoding in detecting target species. 3. Field Applicability – Catchment-based eDNA sampling combined with CRISPR-Dx enables effective monitoring of terrestrial mammals in remote areas, including high-alpine and strictly protected environments.
This approach bridges the gap between species-specific assays and community-wide analysis, offering a scalable and field-accessible solution for biodiversity monitoring in challenging landscapes.
