Universal plant and animal eDNA metabarcoding using Nanopore sequencing v1

Environmental DNA (eDNA) is a powerful, non-invasive tool for biodiversity monitoring, but traditional approaches face challenges including limited sensitivity, taxonomic restrictions, lengthy processing times, and reliance on specialized lab equipment and computational resources. To address these limitations, we present an integrated eDNA workflow from extraction to real-time analysis. Our approach combines the Tagsteady protocol for multiplexed eDNA metabarcoding with Oxford Nanopore library preparation and sequencing, enabling simultaneous detection of animals (Metazoa) and plants (Viridiplantae) using universal markers (COI and ITS2). By integrating metabarcoding and barcoding in a single protocol, this workflow can assess species presence in environmental samples and barcode individual specimens to expand reference databases, providing a streamlined solution for broad, field-based biodiversity assessment.