Data from: 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 the 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.