A comparison of operational eDNA sampling methods for effective marine fish biodiversity monitoring: a controlled study in aquarium conditions

Understanding ecosystem changes and implementing effective management require comprehensive environmental monitoring, including biodiversity assessment and the tracking of alien, endangered and indicator species. Environmental DNA (eDNA) has emerged as a powerful non-invasive tool for monitoring marine habitats, particularly for detecting rare and elusive megafauna. Within the framework of a national biomonitoring project for Mediterranean elasmobranchs we conceived and performed a methodological investigation to test the efficacy of various eDNA water sampling methods in a controlled environment and establish benchmarks for interpreting metabarcoding data from diverse sampling methods. Five types of eDNA samplers, including both active and passive filtering instruments, were evaluated in four tanks at the Genoa Aquarium, containing different species assemblages, including both cartilaginous and bony fishes. DNA extraction from the collected samples was performed using modified protocols for higher volumes. PCR amplification was performed targeting a short 12S ribosomal fragment using an elasmobranch specific marker (Elas02) and samples were sequenced on an Illumina iSeq™ 100 platform. Bioinformatic processing will be performed following the OBITools metabarcoding pipeline, with customized modifications at the taxonomic assignment step based on a custom-made reference database of the species in the tanks. Preliminary results showed that the active filtration device accumulated and, consequently, allowed the extraction of, a higher quantity of DNA. Expected outcomes include a comparative analysis of eDNA samplers focusing on species richness and the correlation between taxa abundance in each tank and obtained reads per samples, towards an informed, calibrated interpretation of marine eDNA surveys conducted using different collection methods.