Seasonal changes in the structure of river fish communities in temperate Japan depicted using quantitative eDNA metabarcoding

Understanding fish communities contributes to various fields ranging from theoretical ecology to fisheries management. In rivers flowing from mountainous to urban areas and showing seasonal variations in water temperatures, fish community structure may be spatiotemporally affected by natural and anthropogenic factors. We investigated the spatial and seasonal dynamics of fish communities in the Isazu River (17.9 km) and its tributary, Ikeuchi River, in temperate Japan, using eDNA metabarcoding method. We detected 78 fish operational taxonomic units across four seasons at 12 sites along the river length. The fish community differed significantly among different seasons and sites, aligning with the distance from the river mouth. In particular, the eDNA concentrations (copies/L) of major fishery resources and endangered fish species varied among different seasons and sites, which may reflect species migration patterns. The river hosts a spatiotemporally dynamic fish community that provides substantial ecosystem services. Our study provides valuable insights into the complex relationships between fish communities and natural, anthropogenic, temporal, and spatial factors affecting these communities based on changes in eDNA concentrations.