Monitoring Atlantic salmon (Salmo salar) smolt migration in a large river system using environmental DNA

Effective monitoring strategies are key for aquatic species conservation,
but traditional methods often require significant resources, especially in
large aquatic systems. The emergence of quantitative environmental DNA
(eDNA) is a promising alternative. Yet, few studies have evaluated the
possibility of quantifying Atlantic salmon abundance with eDNA when
individuals are at low abundance and occur in large river systems. In this
study, we tested the efficacy of eDNA to monitor and quantify daily
variation in smolts counts during their downstream migration in a large
river system with low abundance of smolts. During the 2021 and 2022
downstream migrations, trap nets were used to conduct a daily census of
smolts in the Romaine and Puyjalon rivers (Québec, Canada) while eDNA
samples were collected daily over a transect perpendicular to the
riverbank. Using quantitative real-time qPCR, we showed that
discharge-corrected eDNA concentrations were positively correlated with
daily smolt counts for both years. In addition, we found that controlling
for temperature and precipitation improved model transferability between
years, showing the importance of considering environmental correlates when
using eDNA for abundance quantification. Finally, smolt counts were
correlated with eDNA concentrations on the same day, but not with eDNA
concentrations one or two days prior, highlighting the capacity of the
model to track daily fluctuations in smolt abundance. Our results
underscore the potential of using eDNA to monitor Atlantic salmon in large
river systems with low smolt abundance when the river hydrology and
environmental conditions are documented.