Assessing ecosystem state with environmental DNA of aquatic insects

Data associated to the publication "Environmental DNA sequences from aquatic insects indicate freshwater ecosystem state" Authors: Flurin Leugger, Martina Lüthi, Meret Jucker, Virginie Marques, Sarah Thurnheer, Zacharias Kontarakis and Loïc Pellissier Contact: [email protected] [email protected] Project description: In this project, we aimed to compare kick-sampling-derived taxa lists and ecosystem state classifications (IBCH: Indece biologique Suisse) with eDNA metabarcoding and CRISPR-Dx. Additionally, we calculated the association with environmental variables and ecosystem state. We retrieved the kick-sampling-derived data from Haberthür et al. (2021) and Keck et al. (2023). We collected eDNA samples in 36 sites in the Rhine catchment in Switzerland (lowland) which are used for the national monitoring of freshwater in Summer 2024. We extracted the samples in the clean lab at ETH using the protocol described in Leugger et al. (2025). We used the 16S Ins primer (Elbrecht et al. 2016) for metabarcoding and for CRISPR analysis. To select indicator eDNA metabarcoding sequences, we applied a machine learning approach combining LASSO and rpart decision trees. For CR