Monitoring of spatio-temporal occupancy patterns of fish and amphibian species in a lentic aquatic system using environmental DNA

To effectively monitor, manage and protect aquatic species and comprehend their interactions, knowledge on their spatio-temporal distribution is needed. In this study, we used a fine-scale spatio-temporal water sampling design followed by eDNA 12S metabarcoding, to investigate occupancy patterns of a natural community of fish and amphibian species in a lentic system. In the same system, we experimentally estimated the spatial and temporal eDNA dispersion by placing a community of different fish and amphibian species in cages at one side of the pond, creating a controlled point of eDNA emission. Analyses of this cage community revealed a sharp spatial decline in detection rates and relative eDNA quantities at a distance of 5 to 10 m from the source, depending on the species and its abundance. In addition, none of the caged species could be detected anymore one week after removal from the system. This indicates high eDNA decay rates and limited spatial eDNA dispersal, facilitating high local resolution for monitoring spatial occupancy patterns of aquatic species. Remarkably, for seven out of the nine cage species, the presence of one single individual could be detected by pooling water of subsamples taken across the whole water body, illustrating the high sensitivity of the eDNA sampling and detection method applied. Finally, our work demonstrated that a fine-scale sampling design in combination with eDNA metabarcoding, can cover total biodiversity very precisely and allows to construct consistent spatio-temporal patterns of relative abundance and local distribution of free-living fish and amphibian species in a lentic ecosystem.