General principles for assignments of communities from eDNA: Open versus closed taxonomic databases

Metabarcoding of environmental DNA (eDNA) is a powerful tool for describing biodiversity, such as finding keystone species or detecting invasive species in environmental samples. Continuous improvements in the method and the advances in sequencing platforms over the last decade have meant this approach is now widely used in biodiversity sciences and biomonitoring. For its general use, the method hinges on a correct identification of taxa. However, past studies have shown how this crucially depends on important decisions during sampling, sample processing, and subsequent handling of sequencing data. With no clear consensus as to the best practice, particularly the latter has led to varied bioinformatic approaches and recommendations for data preparation and taxonomic identification. In this study, using a large freshwater fish eDNA sequence dataset, we compared the frequently used zero-radius Operational Taxonomic Unit (zOTUs) approach of our raw reads and assigned it taxonomically i) in..., The data was collected under the framework of the federal water quality assessment in Switzerland. The data is generated from eDNA samples in Swiss rivers that are routinely surveyed. In spring 2019, 92 sites were sampled for eDNA with 4 replicates for each site. The eDNA filters were then extracted in a clean room. From these extracts, we used a nested PCR using the 12S Mifish primers to create an amplicon library, that was paired end sequenced. The 12S barcode is focused on the detection of fish communities. The libraries were prepared in-house and at the Genetic Diversity Center (user labs) at ETH Zurich., The folder contains the eDNA metabarcoded amplicon paired-end sequences as raw data set from the Miseq sequencer. Once unzipped, all raw sequencing files are available as fasta files and can be opened with a text editor or used for further downstream bioinformatic workflow.Â