On-site metabarcoding analysis of environmental DNA samples

Mauvisseau, Q.; Ewer, I.; Blumeris, I.; Iren Bongo, S.; Filipe Brito de Oliveira, L.; Gouvea, B.; Carolina Cei, A.; Ferreira Rodrigues, K.; de Arruda Francisco, J.; Sletteng Garvang, E.; Marena do Rego Henriques, V.; Hurtado Solano, S.; Kvalheim, L.; Kaylynne Lawrence, S.; Ramalho Maciel, B.; Isanda Masaki, H.; Fortunate Mashaphu, M.; Masimula, L.; Prudent Mokgokong, S.; Katrin Onshuus, E.; Lima Paiva, B.; Parker-Allie, F.; Du Plessis, M.; Puzicha, M.; Gabriel Da Silva Solano Reis, O.; Speelman, G.; Moritz Splitthof, W.; Stocco de Lima, A. C.; Strindberg, H.; Smoge Saevik, O.; Tafjord, N. J. D

doi:10.64898/2026.03.27.714757

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bioRxiv · 10.64898/2026.03.27.714757

On-site metabarcoding analysis of environmental DNA samples

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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 resourcelZllimited settings.

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Mauvisseau, Q., Ewer, I., Blumeris, I., Iren Bongo, S., Filipe Brito de Oliveira, L., Gouvea, B., Carolina Cei, A., Ferreira Rodrigues, K., de Arruda Francisco, J., Sletteng Garvang, E., Marena do Rego Henriques, V., Hurtado Solano, S., Kvalheim, L., Kaylynne Lawrence, S., Ramalho Maciel, B., Isanda Masaki, H., Fortunate Mashaphu, M., Masimula, L., Prudent Mokgokong, S., Katrin Onshuus, E., Lima Paiva, B., Parker-Allie, F., Du Plessis, M., Puzicha, M., Gabriel Da Silva Solano Reis, O., Speelman, G., Moritz Splitthof, W., Stocco de Lima, A. C., Strindberg, H., Smoge Saevik, O., Tafjord, N. J. D. 2026-03-30. On-site metabarcoding analysis of environmental DNA samples. https://doi.org/10.64898/2026.03.27.714757

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