Low-Effort eDNA Sampling Reveals Fish Community Patterns in a Neotropical River Basin

Environmental DNA (eDNA) metabarcoding offers a powerful tool for rapid species monitoring in diverse river basins. However, the success of eDNA-based species detection is influenced by various biotic and abiotic factors (i.e., eDNA ecology). To overcome challenges posed by funding limitations and remote locations in the Neotropics, deploying affordable, portable sampling kits and low-effort sampling protocols could significantly expand the use of eDNA for monitoring anthropogenic impacts on fish biodiversity. This approach would enable timely and cost-effective assessments of biodiversity changes in these often-overlooked regions. Here, we investigated whether rapid eDNA sampling using a portable on-site kit with syringe filters and a moderate water volume (average of 360 mL/site) could provide a reliable assessment of fish communities and shed light on fish eDNA ecology upstream and downstream of a large hydroelectric reservoir. Water samples were collected from five sites along a 400-km stretch of free-flowing river in the lotic remnant of the Upper Paraná River and one site downstream of Emborcação hydroelectric dam. Using eDNA metabarcoding and the 12S MiFish molecular marker, we detected 68 fish taxa across the six sampling locations. After careful data curation, 28 taxa were confidently assigned to species level, 36 to genus level, and four taxa to family level. eDNA-assessed fish richness displayed a negative correlation with river elevation (R = −0.82, p = 0.001), corroborating the hypothesis that in freshwater river systems, species richness generally increases along the upstream–downstream gradient. The site below the dam exhibited the highest species richness due to its community composition and not to upstream uptake and accumulation of eDNA. In conclusion, our eDNA metabarcoding approach using a portable kit and low water volume per sample site effectively provided a rapid, robust snapshot of fish biodiversity, particularly valuable for rapid decision-making regarding the conservation importance of specific regions.