Comparison of PCR and capture enrichment and bulk and etDNA on freshwater invertebrates mock communities

Metabarcoding has been announced as a miracle identification tool to the taxonomic limitations encountered with the traditional morphological approach. However, this method comes with its own weaknesses and need optimizations to be truly reliable. Limitations encountered in two key metabarcoding steps need particular attention. First, the sorting and destruction of organism for DNA extraction which are time and cost consuming and do not allow organism storage for evaluation. Second, the species qualitative and quantitative biases induced by the widely-used amplicon enrichment method using PCR during the enrichment step. In this study, we first evaluated the capacity of capture enrichment as a replacement to amplicon enrichment to detect species and recover relative biomass in controlled freshwater invertebrate mock communities (MC).Then, we tested if DNA extracted from the fixative ethanol (etDNA) of the same MC can be used as an alternative to DNA extracted from whole organisms (bulk DNA) to facilitate and to enhance metabarcoding.