On-site metabarcoding analysis of environmental DNA samples

Abstract

Environmental DNA metabarcoding is a powerful monitoring tool for assessing aquatic biodiversity, as well as the sustainability and impacts of fisheries and aquaculture. However, conventional laboratory workflows remain time-consuming and dependent on dedicated infrastructures. Here, we present a field trial of a fully portable, off-grid eDNA metabarcoding pipeline that enables end-to-end analysis within a few days using compact equipment, including a BentoLab workstation and an Oxford Nanopore Technologies (ONT) MinION sequencer. The workflow was implemented during two international training courses in Norway and Brazil, where students and early career researchers collected environmental samples, extracted and amplified DNA, prepared DNA libraries, and sequenced on-site before performing bioinformatics and statistical analyses. In the case study detailed here, seven eDNA samples collected and analysed on-site in the Oslofjord allowed detection of 16 fish and elasmobranch species. Although overall diversity was lower than in earlier studies using Illumina-based sequencing, our protocol reliably detected key species and demonstrates that portable eDNA metabarcoding is feasible for rapid ecological assessment, surveillance of high-risk regions and/or deployment in remote or resource‑limited settings.