eDNA metabarcoding vs. transect walks

Biodiversity monitoring increasingly relies on molecular methods such as eDNA metabarcoding. However, sound applications have so far been only established for a limited number of taxonomic groups. More information on the strengths and weaknesses of eDNA methods, especially for poorly covered groups, is essential for practical applications to produce the highest possible reliability. We compared amphibian and Odonata data from eDNA metabarcoding and traditional transect walks on N=56 plots in 38 water bodies distributed over six extraction sites for building materials in Northwest Germany. The traditional amphibian assessment included visual encounters, dip netting and acoustic detection, while Odonata were assessed using exuviae. In total, both methods detected 8 out of 11 amphibian species, while eDNA detected the remaining species only. We did not find significant differences in amphibian species numbers per plot, but mean detection probabilities were higher with metabarcoding. In contrast, both methods detected 10 out of 29 Odonata species, while the remaining were only detected by exuviae. Species numbers per plot were higher for exuviae, with metabarcoding detecting only 30% of the total species per plot. The species detected by eDNA were significantly more abundant and their detection probabilities were similar to those of the transect walks. The results for amphibians show equal suitability and high complementarity of the methods compared. Metabarcoding detected species more efficiently and therefore offers a suitable protocol for biodiversity monitoring. For Odonata, metabarcoding showed considerable gaps, implying the need for protocol evaluation and improvement in assessment of ecological communities based on eDNA.