eDNA Collected by Custom‐Built Unmanned Surface Vehicles (USVs) Reveals Spatio‐Temporal Shifts in Tropical Coral Reef Faunal Communities

ABSTRACT

High‐frequency environmental DNA (eDNA) sampling offers new opportunities to reveal fine‐scale biodiversity patterns and short‐term ecological dynamics, yet its spatial representativity and capacity to capture diel shifts in communities remain poorly understood. Semi‐autonomous sampling devices can aid high frequency and standardized collection for such assessments, particularly in remote and low‐light conditions, as well as dynamic coastal ecosystems such as tropical coral reefs. Coral reefs are ideal habitats to test such systems, as they support exceptional but rapidly declining biodiversity. We constructed Unmanned Surface Vehicles (USVs) for high‐frequency and cost‐efficient geolocalized sample retrieval around the break between two reef flats (Hermitage Pass) of the La Saline−Hermitage coral complex on Reunion Island. The USVs were deployed to navigate between eight stations, pumping seawater through filters to capture eDNA. Sampling occurred during nighttime and daytime (“sampling events”), across four days, to assess potential shifts in metazoan communities. Samples underwent DNA metabarcoding, applying a Cytochrome Oxidase I (COI) gene marker, to target faunal assemblages. Analyses revealed significant differences between communities surveyed during the nighttime and the daytime on each collection day, and across differing stations. Although eDNA dispersal was largely confined to each reef flat and limited among some stations, some communities towards Hermitage Pass were not statistically distinct in composition, suggesting that localized environmental conditions may influence eDNA distributions in this area. Altogether, these findings reveal a diverse and dynamic seascape within less than 1 km ² , and point to key sites for long‐term monitoring using low‐cost mobile devices for high‐frequency eDNA sampling.