Data from: Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring

Current biodiversity assessment and biomonitoring are largely based on morphological identification of selected bioindicator taxa. Recently, several attempts have been made to use eDNA metabarcoding as an alternative tool. However, until now, most of applied metabarcoding studies were based on taxonomic assignment of sequences that refers to morphospecies ecology. Usually, only a small portion of metabarcoding data can be used due to limited reference database and lack of phylogenetic resolution. Here, we investigate the possibility to overcome these limitations by using a taxonomy-free approach that allows the computing of a molecular index directly from eDNA data without any reference to the morphotaxonomy. As a case study, we use the benthic diatoms index, commonly used for monitoring the biological quality of rivers and streams. We analysed 87 epilithic samples from Swiss rivers, which ecological status was established based on microscopic identification of diatom species. We compared the diatom index inferred from eDNA data obtained with or without taxonomic assignment. Our taxonomy-free approach gives promising results by providing a correct assessment in 77% of examined sites. The main advantage of our approach is that almost 95% of OTUs could be used for index calculation, compared to 35% in the case of the taxonomic assignment approach. Its main limitations are the under-sampling and need to calibrate the index on microscopic assessment of diatoms communities. However, once calibrated, the taxonomy-free molecular index can be easily standardized and applied in routine biomonitoring, as a complementary tool allowing fast and cost-effective assessment of the biological quality of watercourses.