Capture - incubate - release: An animal-friendly approach to assess local aquatic macroinvertebrate species diversity through environmental DNA metabarcoding

Metabarcoding of environmental DNA (eDNA) from water samples has become an important tool for aquatic biodiversity assessment because it is minimally invasive, time-efficient, and generates comprehensive taxa lists. However, species lists obtained through eDNA metabarcoding differ noticeably from those obtained via bulk metabarcoding of the local benthic community because of eDNA traces transported in the water column. But for several assessments, it is important to capture local biodiversity signals, which is challenging with eDNA captured from water samples. Our goal was to test whether we can combine the advantages of both methods, i.e. local sampling of the benthic community followed by incubation of organisms in a water container for eDNA enrichment and analysis, followed by the release of animals back to their habitat. We first quantified eDNA release over time for ten invertebrate species in a laboratory setting using qPCR. Then, we quantified eDNA released by organisms in bulk samples collected at three field sites by incubating these for 0, 20, 40, and 80 min in DNA-free containers. For the individual species, a 5-min incubation was sufficient to successfully detect 50% for six of the ten species, but showed species-specific patterns related to sclerotization and activity. Interestingly, we found a significant increase in eDNA molecules released over time for only three of the species. For the field experiment, we found immediately after sample transfer (0 minutes) a much higher overlap (55-60%) between taxa identified in eDNA collected in the incubation container and bulk samples compared with overlaps reported between bulk and stream water eDNA, which did not change with incubation time. Our study demonstrates that it is possible to detect most locally occurring species via eDNA metabarcoding after shortly incubating them in water. Thus, this approach has great potential for point-sample eDNA analysis of macroinvertebrates without compromising animal welfare.