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

marine-biology
molecular-biology
environmental-impacts

Abstract

Environmental DNA (eDNA) offers unprecedented potential for monitoring high-risk coastal environments impacted by anthropogenic activities and is increasingly used for marine biosecurity applications. Yet, optimal temporal-spatial sampling strategies remain unresolved for dynamic coastal settings. Recent advances in automated eDNA sampling have allowed practitioners to improve temporal resolution, enabling simplified sampling methods and more adaptive sampling strategies. In this study, we evaluated whether higher temporal resolution improves biodiversity assessment and marine non-indigenous species (NIS) detection in a marina in Ōpua (Te Pēwhairangi (Bay of Islands), Aotearoa-New Zealand) using the recently introduced Smith-Root automated eDNA sampler. For this purpose, daily samples were collected over four weeks between 12:00–18:00 to assess eukaryotic and metazoan biodiversity using metabarcoding of the small ribosomal subunit RNA (18S rRNA) and mitochondrial Cytochrome C Oxidase subunit I (COI) genes. The results revealed that alpha diversity remained similar among weeks, but beta diversity shifted significantly, indicating that weekly replication captures meaningful ecological change in this setting. In parallel, NIS detections by screening the data with the Pest Alert Tool (PAT) comprised a mix of consistently present bivalves (e.g., Arcuatula senhousia) and sporadically detected other fouling taxa (e.g., Botrylloides spp.), illustrating how short-term (daily) temporal resolution modulates detection probability for intermittent targets. These patterns align with expectations for dynamic estuarine-coastal systems where behaviour, reproduction, and transport processes drive short-term variability. Comparison with prior single-day sampling at the same site suggests that a multi-week temporal design better resolves biodiversity compositional change. Operational refinements to the autosampler device (e.g. optimized maintenance and temperature management) would further stabilize performance. Overall, automated high-frequency or repeated weekly eDNA sampling enhances biodiversity monitoring and biosecurity surveillance in coastal marinas by resolving temporal variability that governs detectability of rare taxa. Because these systems are low-infrastructure and portable, they are also suited for remote deployments and structured citizen-science use.
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