Can eDNA Present in Aquatic Environments of Rural Areas Help Identify Species Diversity in the Order Anura?

Paddy fields are classified as wetland environments, and they comprise freshwater ecosystems. They are ecologically important habitats and breeding grounds for many aquatic insects, amphibians, and reptiles. However, paddy field ecosystems are constantly threatened by climate change and the indiscriminate use of pesticides. The metabarcode analysis of eDNA (environmental DNA) method is highly effective at accumulating information on many organisms that inhabit paddy field ecosystems. It can indirectly identify the existence of taxa that are no longer found in the target ecosystem due to behavioral characteristics, such as those exhibited by amphibians. In the metabarcoding results of this study, genes of five species of frogs were found, but it was impossible to confirm all of the frogs’ taxa, morphological pictures, and croak sounds. On the other hand, some frog taxa were only found in the metabarcoding analysis. The eDNA of the frogs found only in the metabarcoding analysis is estimated to have been introduced from nearby areas inhabited by frogs rather than the target region. Due to the powerful analytical resolution of eDNA metabarcoding, this eDNA-based paddy field search is expected to help investigate the biodiversity in agricultural ecosystems.