Using eDNA metabarcoding to complement traditional aquatic invertebrate biodiversity surveys in the Sierra Nevada of California

Benthic macroinvertebrate (BMI) communities play a crucial role in maintaining ecosystem function and health, and represent a rich tapestry of biodiversity in freshwater habitats of the Sierra Nevada of California. However, the patchiness of BMI surveys completed to date limits our ability to make baselines and measure changes across the Sierra Nevada ecosystems. Environmental DNA (eDNA) metabarcoding can complement traditional stream biodiversity surveys and can provide leads for where there are critical knowledge gaps about BMI diversity, but eDNA methods that produce useful BMI data need development before they can be utilized for BMI surveys. Here, we develop, test, and evaluate non-destructive molecular methods aimed to capture invertebrate community profiles in riverine ecosystems. We used BMI samples from two sites in the Yuba watershed to compare DNA extraction methods to obtain the partial CO1 locus from the ethanol fixative of these collections, which is a non-destructive method of sampling collections. We also collected filtered water from these sites and metabarcoded CO1. We compared community profiles from these eDNA results to aquatic kicknet morphologically-based taxon lists. Our results show morphological identifications capture highest species richness and delineate community profiles more reliably than metabarcoding. However, metabarcoding improves taxonomic resolution of many groups and detects taxa that appeared absent in kicknet surveys. In conclusion, the complementarity of these approaches is appealing for use in future BMI biodiversity surveys.