Environmental DNA sequences from aquatic insects indicate freshwater ecosystem state

Ecosystem state assessments based on indicator taxa are paramount to inform effective conservation measures and address the ongoing biodiversity crisis. Environmental DNA (eDNA) can offer a scalable biomonitoring approach, especially when using analysis methods, such as CRISPR-Dx, which do not rely on sequencing. Here, we investigated to which extent eDNA with metabarcoding or CRISPR-Dx assays can be used to assess ecosystem state similar to traditional kick-sampling for aquatic insects. We compared ecosystem state classifications from eDNA metabarcoding to kick-sampling from 36 catchments. We show that eDNA metabarcoding, based on a 16S insect primer, detects Ephemeroptera sequences effectively and provides ecosystem state classifications corresponding with those measured with traditional surveys. In contrast, some of the designed indicator CRISPR-Dx assays showed non-specific detections which reduced performance when indicating ecosystem state. Low ecosystem state classifications were mainly associated with a high proportion of built environment at the catchment scale. Our results highlight the suitability of eDNA metabarcoding to classify ecosystem state and identify the main associated environmental variables. As more CRISPR-Dx assays are developed and validated, this technology is poised to greatly simplify eDNA analysis, unlocking biomonitoring at unprecedented spatial and temporal scales to support effective conservation efforts. • Indicator eDNA metabarcoding sequences can reliably classify ecosystem state. • Environmental variables at large spatial scales affect ecosystem state the most. • Higher proportion of built environment is associated with lower ecosystem state. • eDNA metabarcoding is an appropriate method to scale up biomonitoring. • Indicators based on CRISPR-Dx show reduced predictability and accuracy.