Neotropical freshwaters and their associated riparian communities are extremely diversified but remain among the most imperilled ecosystems worldwide. Riverine ecosystems are particularly sensitive to anthropisation because hydrologic connectivity transfers disturbances downstream by transporting matters and pollutants over long distances. Hence, catchement-scale disturbances affect local aquatic but also terrestrial biodiversity through the lateral connectivity between rivers and terrestrial habitats resulting from ecological land/water interactions.

Characterizing both aquatic and terrestrial assemblages is thus a prerequisite to understanding how anthropogenic disturbances alter biodiversity. However, biodiversity measurements often rely on selective and destructive methods providing incomplete inventories. This applies especially in tropical freshwater ecosystems, where water turbidity, depth, or current velocity impede exhaustive assessment of biodiversity. Over the last decade, however, eDNA metabarcoding has demonstrated an extensive potential to enhance biodiversity monitoring.

In line with these advances, we present a summary of methodological studies aiming at improving aquatic eDNA-based inventories in Northern Amazonian freshwaters. We first demonstrate the robustness of the eDNA metabarcoding method, which is highly replicable even with two distinct sampling protocols. We then show that eDNA-based inventories provide realistic pictures of the local fish fauna comparable to inventories obtained with traditional capture-based methods, and demonstrate that eDNA travels over short distances in the water. We finally extend the application of aquatic eDNA metabarcoding to tropical mammal inventories and show that the expected spatial distribution of aquatic and terrestrial mammals can be retrieved from aquatic eDNA samples.

Based on these methodological advances, we show how eDNA data can constitute a robust baseline to the design of regional and multi-taxa ecological studies through the case of study of fish and mammal distribution in large rivers of the Guiana Shield. Our results show how human disturbances erode freshwater and terrestrial biodiversity over entire watersheds and call for a closer consideration of the upstream-downstream hydrologic connectivity and the lateral connectivity between rivers and terrestrial habitats in conservation programs.