Résumé
Environmental DNA (eDNA) metabarcoding is increasingly used for biomonitoring of coastal ecosystems, yet its application to aquaculture impact assessment remains limited in understudied tropical environments. Marine aquaculture contributes to global food production but can generate localized organic enrichment, highlighting the need for sensitive and scalable monitoring tools across diverse farming contexts. Here, we investigated eDNA-based indicators to characterize the environmental footprint of a low-input shrimp farm representative of insular socio-ecosystems, where small-scale aquaculture operations dominate. We combined metabarcoding of archaeal, bacterial, and benthic metazoan communities with traditional taxonomy-based indicators to assess ecosystem responses along a distance gradient from the farm, including control sites. Indicators derived from 16S and 18S eDNA metabarcoding effectively captured biological responses to localized, aquaculture-derived organic enrichment, with archaeal and bacterial communities showing the highest sensitivity to spatial gradients. Benthic faunal metabarcoding metrics also provided robust proxies for conventional taxonomy-based indices commonly used in temperate monitoring frameworks. However, their performance highlights the need for continued improvement of reference databases through strengthened collaboration between taxonomists and geneticists. Overall, eDNA metabarcoding provides an integrative multi-compartment approach for effectively assessing tropical low-input aquaculture impacts, and offers practical advantages for routine monitoring in remote and resource-limited systems.