Development of a European Sea Bass eDNA Assay for Remote Ocean Observation

ABSTRACT The European Sea Bass ( Dicentrarchus labrax ) is a commercially and recreationally significant species across European waters. Despite its value, wild populations have suffered due to overfishing and environmental change, increasing reliance on aquaculture and heightening the need for effective conservation tools. This study reports the first development of a species‐specific environmental DNA (eDNA) assay for D. labrax using recombinase polymerase amplification (RPA) coupled with CRISPR‐Cas detection. The assay is designed for autonomous sensing applications and is both highly sensitive (limit of detection: < 1 pg) and specific, showing no cross‐reactivity with closely related species (as assessed on a qPCR instrument) such as sea bream and other species likely to be found in its marine environment. To optimize field deployment, we validated the assay on lyophilized reagents preserved with trehalose, enabling storage and function on polymethyl methacrylate (PMMA) microfluidic platforms. We further demonstrated successful integration of the assay onto a Lab‐on‐Chip (LOC) system, with simplified fluidics allowing the full RPA reaction volume to rehydrate CRISPR reagents, eliminating the need for intermediate handling. The assay maintained performance when tested with both tissue‐extracted and environmental DNA, including samples from the Wexford Estuary, Ireland. Fluorescence‐based detection on a portable fluorometer was achieved through extended incubation times and reagent optimization. The results confirm that this RPA‐CRISPR‐Cas assay is suitable for non‐laboratory settings that will support real‐time, in situ monitoring of European sea bass populations. This work represents a significant step toward scalable, autonomous eDNA monitoring solutions for marine biodiversity and fisheries management.