Estuarine cline in fish eDNA composition and ecotone between the inside and outside of locally enclosed areas

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.