Active versus passive eDNA sampling across depths at a tropical Fish-Aggregating Device (FAD)

2026

Article référencé dans le Web of Science WOS:001770149800001

Martino F., Hartaty H., Crobe V., Hutapea J., Lamy Thomas, Poloni G., Soria Marc, Spiga M., Zane L., Wudianto W., Capello Manuela, Congiu L.

Environmental DNA, 2026, 8 (3), p. e70307 [17 p.] ISSN 2637-4943

Environmental DNA (eDNA) is a valuable tool for monitoring fish biodiversity, particularly in pelagic environments, where conventional methods are difficult to implement. Fish aggregating devices (FADs), floating structures widely used by tropical tuna fishers, are known to attract numerous pelagic fish species, making them ideal sampling locations. In this study, we assessed pelagic fish diversity at a FAD off the coast of Bali, Indonesia, using eDNA metabarcoding. We compared different eDNA sampling strategies with the primary aim of evaluating the effectiveness of eDNA metabarcoding for assessing pelagic fish biodiversity, while testing and refining accessible, low-cost protocols suitable for remote and logistically constrained environments. Sampling was conducted over three consecutive days at four depths (1, 10, 40, and 60 m) using two distinct eDNA collection methods: active filtration and a custom-designed passive system consisting of 3D-printed cylinders filled with sterile gauze, mounted on unit holders that allow the simultaneous deployment of triplicate samples at each depth. A total of 66 samples were collected, and metabarcoding was performed using an available primer pair targeting fish 12S mitochondrial DNA, with sequencing performed on an Illumina NovaSeq platform. Across both sampling methods, a total of 39 fish Operational Taxonomic Units (OTUs) were detected, of which 25 were shared between active and passive approaches, and 31 were assigned to the species level. The two sampling methods yield overlapping assemblages dominated by epipelagic taxa commonly reported at FADs, indicating that both approaches are suitable for characterizing fish communities in this environment. Importantly, the integration of passive and active sampling provided a practical balance between deployment flexibility and taxonomic detection. Beyond technical validation, standardized eDNA protocols can be effectively transferred and applied in contexts where logistical constraints are extremely relevant, thereby supporting the development of biodiversity monitoring programs centered around ecologically relevant features such as FADs.

Sciences fondamentales / Techniques d'analyse et de recherche [020] ; Ecologie, systèmes aquatiques [036]

Fonds IRD [F B010097147]

fdi:010097147