Impact of Rainfall on Aquatic and Terrestrial Species Monitoring Using Riverine Environmental DNA

Water-based eDNA has a potential to simultaneously detect aquatic and terrestrial species in watershed-scale eDNA biodiversity monitoring. However, the detection of terrestrial species remains difficult or undetected due to complex environmental effects. This study targeted vertebrate eDNA transported from land to rivers through surface runoff during rainfall in three rivers within the Kiyotake River watershed in Japan. We compared the detection rates of different taxonomic groups under rainfall and non-rainfall conditions and determined how environmental factors (e.g., discharge, rainfall amount) influence sample-level alpha and beta diversity. The vertebrate detection rate after rainfall exceeded that during non-rainfall. Birds, mammals, and amphibians were detected more frequently after rainfall, whereas fish were detected more frequently under non-rainfall conditions. Generalized linear model analyses revealed that river discharge and pH had significant negative effects on the detection number, while filtration volume had a significant positive effect. Furthermore, Permutational Multivariate Analysis of Variance indicated that filtration volume and rainfall occurrence significantly affected beta diversity. Our findings underscore the importance of sampling design after rainfall events, for eDNA-based biomonitoring, offering practical guidance for enhancing biodiversity assessments at the watershed scale.