Estuarine Cline in Fish eDNA Composition and Ecotone Between the Inside and Outside of Locally Enclosed Areas

ABSTRACT Estuaries are dynamic environments where monitoring fish biodiversity and detecting ecological change can be logistically difficult and expensive. Environmental DNA metabarcoding offers a cost‐effective alternative for biodiversity assessment. However, recent studies have shown that sharp transitions in fish eDNA composition (ecotones) can occur across boundaries of enclosed areas within estuaries. If these ecotones are strong or occur at unknown locations, they may distort spatial patterns in fish community data. This study investigated the conditions under which such ecotones form and assessed their impact on patterns of fish eDNA distribution in estuarine systems. We compared fish eDNA composition inside and outside six enclosed areas within Tokyo Bay, an estuary with a strong salinity gradient. Our spatially nested sampling design revealed that fish eDNA composition varies along the gradients of salinity and total nitrogen and differs consistently between the inside and outside of localized enclosed areas. These contrasts between inside and outside communities were stronger at high‐salinity sites. Therefore, the choice of sampling location (inside versus outside) can significantly affect estimates of species richness, community structure, and species‐specific DNA concentrations at the bay‐wide scale. We conclude that eDNA ecotones across enclosure boundaries may lead to misinterpretation of fish biodiversity in estuarine systems, and recommend sampling from outside enclosed areas to more accurately capture estuary‐wide patterns of fish biodiversity.