Evaluation of primer pairs for eDNA‐based assessment of Ephemeroptera, Plecoptera, and Trichoptera across a biogeographically diverse region

Macroinvertebrates serve as key indicators in ecological assessments of aquatic ecosystems, where the composition and richness of their communities is indicative of environmental and anthropogenic drivers. Established monitoring of macroinvertebrates is expensive, time-consuming, and relies on expert taxonomic knowledge. In contrast, biomonitoring based on molecular tools can support faster characterization of aquatic communities but needs validation for the target taxonomic groups and the study region. Here, we used data from a biomonitoring program covering a large biogeographic gradient to compare the routine kick-net method with eDNA metabarcoding. We used two primer pairs targeting COI, one targeting a broad metazoan spectrum (miCOIintF/jgHCO2198) and another more recently developed primer pair optimized for the detection of freshwater invertebrates (fwhF2/EPTDr2n). We used the data of the macroinvertebrate monitoring with a focus on the orders of Ephemeroptera, Plecoptera, and Tri..., In the federal water quality assessment in Switzerland, rivers are routinely surveyed and in spring 2019, 92 sites were sampled for eDNA. The eDNA was then extracted in a cleanroom. From these extracts, we generated 2 MiSeq libraries targeting the CO1 barcode focused on the detection of macroinvertebrates. One of the libraries, using the primer jgHCO2198/miCOIintF (Leray et al., 2013, Geller et al., 2013) was already analyzed and published in the context of biotic indices based on eDNA data: (https://doi.org/10.1371/journal.pone.0257510). The second library that used the primer EPTDr2n/fwhF2 (Leese et al., 2021, Vamos et al., 2017) was targeted more specifically at aquatic invertebrates. The libraries were prepared in-house and at the GDC at ETH Zurich, then bioinformatically processed by J.C.W.
, The folder contains two eDNA metabarcoding amplicon paired-end sequenced raw data sets (one using the jgHCO2198/miCOIintF primers (Leray et al., 2013, Geller et al., 2013), the other using the EPTDr2n/fwhF2 primers (Leese et al., 2021, Vamos et al., 2017) in two separate zip folders. Once unzipped, all raw sequencing files are available as fasta files and can be opened with a text editor.