Environmental DNA Metabarcoding Details the Spatial Structure of a Diverse Tropical Fish Assemblage in a Major East African River System

Management and conservation of species-rich tropical freshwater systems require reliable information on the diversity and distribution of species present. Here, we used environmental DNA metabarcoding to reveal the diversity of the fishes in the Rufiji River catchment of central Tanzania. Across 174 samples from 49 sites, and using a newly developed reference library, we mapped the presence of 66 fish species from an estimated 91 that we are confident are present in the system. We found clear evidence of community structuring of the assemblage linked to key environmental gradients—elevation, temperature, and turbidity. We also identified core distributions of rare or threatened taxa, including migratory species such as the anguillid eels. With a focused analysis of 50 samples collected over a small spatial scale (<2 km) from the Kilombero River, we showed that each single sample can capture an average of 23.1 species, while three samples can capture 39.4 species, from a total of 56 species encountered in the 50 samples. Collectively the results help to identify species vulnerable to ongoing change in the catchment, including dam construction and agricultural intensification. The results clearly demonstrate how eDNA-based metabarcoding can reliably describe the diversity and distributions of riverine fish species across a catchment, providing standardized information that will be valuable for environmental management.