Automated eDNA sampling for marine monitoring and biosecurity: optimising temporal resolution, remote deployments, and citizen-science participation

Recent advances in automated eDNA sampling have allowed practitioners to improve temporal resolution for marine biosecurity and biodiversity screening, enabling simplified sampling methods and more adaptive strategies. In this study, we evaluated whether higher temporal resolution improves biodiversity assessment and marine non-indigenous species (NIS) detection in a marina in Opua (Bay of Islands, Aotearoa-New Zealand) using a vacuum filtration-based automated eDNA sampler (autosampler, Smith-Root, USA).For this purpose, daily water samples were collected between 12:00 and 18:00 over a 34-day period (2 December 2023 to 4 January 2024) from the pier located at the end of Opua Harbour, Bay of Islands, Aotearoa-New Zealand. The autosampler was programmed via its onboard graphical user interface to autonomously collect eight daily eDNA samples using Smith-Root's self-preserving 47 mm, 5 um polyethersulfone filters (PES; Smith-Root, USA). To assess eukaryotic and metazoan biodiversity and screen for marine NIS, DNA was extracted from the filters and metabarcoding was performed on the small ribosomal subunit RNA (18S rRNA) and mitochondrial Cytochrome C Oxidase subunit I (COI) genes.The results of this study, developed in collaboration with local hapu, provide key recommendations for the operation of autosamplers in marine settings and lay the foundation for their long-term integration. This approach enables flexible, adaptive sampling strategies, which are essential for supporting early detection efforts of marine NIS and other hard-to-detect species.