Holistic monitoring of freshwater and terrestrial vertebrates by camera trapping and environmental DNA

Abstract

The anthropogenic impact on the worlds ecosystems is severe and the need for non-invasive, cost-effective tools for monitoring and understanding those impacts are therefore urgent. Here we combine two such methods in a comprehensive multi-year study; camera trapping (CT) and analysis of environmental DNA (eDNA), in river marginal zones of a temperate, wetland Nature Park in Denmark. CT was performed from 2015 to 2019 for a total of 8,778 camera trap days and yielded 24,376 animal observations. The CT observations covered 87 taxa, of which 78 were identified to species level, and 73 were wild native species. For eDNA metabarcoding, a total of 114 freshwater samples were collected from eight sites in all four seasons from 2017 to 2018. The eDNA results yielded a total detection of 80 taxa, of which 74 were identified to species level, and 65 were wild native species. While the number of taxa detected with the two methods were comparable, the species overlap was only 20 %. In combination, CT and eDNA monitoring thus yielded a total of 115 wild species (20 fishes, four amphibians, one snake, 23 mammals and 67 birds), representing half of the species found via conventional surveys over the last ca. 20 years (83% of fishes, 68 % of mammals, 67 % of amphibians, 41 % of birds and 20 % of reptiles). Our study demonstrates that a holistic approach combining two non-invasive methods, CT and eDNA metabarcoding, has great potential as a cost-effective biomonitoring tool for vertebrates.

Airborne environmental DNA captures terrestrial vertebrate diversity in nature

“…Of these, 48 were terrestrial vertebrate taxa naturally occurring in Denmark, that is wildlife (Figure 2). Thereby, in just 3 days of sampling in a limited area, we detected around a fourth of the around 210 terrestrial vertebrate species regularly occurring in and around the study area (compiled by Holm et al, 2022). Airborne eDNA detections had a random spatial distribution between sites, highlighting the spatial movement of airborne eDNA and the sensitivity of detecting trace DNA.…”

“…While air sampling did not catalogue the total vertebrate richness of the area, as seen by the sampling efficiency curves (Figure 4), the 3 days of sampling in the rather limited study site provided a robust species list with identifications of 49 vertebrates known to occur in and around the study area, including one aquatic vertebrate (Figure 2). These represent around a third of the mammal, a sixth of the bird and three fifths of the amphibian species that have been observed in and around the study area (Holm et al, 2022). Importantly, OTUs that could only be identified at a higher taxonomic level were collapsed and collectively assigned to the respective genus, family or order level.…”

“…We verified the known distributions of the detected taxa and assessed the likelihood of them being detected in the overall area at the sampling time by searching for the taxa individually on the Global Biodiversity Information facility (http://gbif.org), arter.dk, dofbasen.dk, a report from the Danish ornithology society (Wejdling & Harding, 2006) (websites accessed between May and September 2022) and a compilation of observation data by Holm et al (2022) from Carl et al (2012), Grell (1998), the Danish Ornithology Society (DOF) and Baagøe and Jensen (2007). The migration pattern and presence in Denmark of detected bird species was verified through the Danish Bird Migration Atlas (Bønløkke et al, 2006).…”