Metabarcoding outperforms traditional electrofishing in decapod and fish inventories, paving the way for enhanced biodiversity monitoring in the Caribbean

Environmental DNA (eDNA) metabarcoding revolutionized the biodiversity monitoring in aquatic ecosystems, giving access to taxonomic lists in a non-disruptive way. Although the method has limits, such as reduced taxonomic resolution for certain groups and difficulties in estimating species abundance, it has proven its effectiveness in many contexts. In Martinique, a Caribbean island, traditional methods like electrofishing (TEF) are known to be stressful for organisms, non-selective and disruptive for the ecosystem, and have been progressively abandoned for routine monitoring. The aim of this project was to explore the possibility of using the eDNA-based metabarcoding method for the detection of fish and decapods in Martinique streams, by first validating it with TEF. We selected 14 stations, a representative panel of the river diversity, and performed TEF and eDNA-based monitoring to compare both, based on the species richness. Then, from eDNA taxonomic inventories, we assessed the ecological state of the studied stations, using Simpson index and investigated how stations abiotic characteristics shape assemblages. Here, we confirmed the eDNA metabarcoding method is a reliable tool for monitoring fish and decapods, confirming most of the taxa caught by TEF and revealing the presence of additional (native and/or invasive) species. We faced some issues in discriminating some genetically close species (e.g. Sicydium sp.) potentially leading to under-representation in community assemblages, but not in functional diversity. Additional efforts are needed to raise standardized protocols, but we encourage stakeholders to join such an initiative to shed light on the rich biodiversity in sometimes poorly studied regions and to face invasions.