Development of a TaqMan qPCR protocol for detecting Acipenser ruthenus in the Volga headwaters from eDNA samples

Abstract

A recent eDNA-metabarcoding study assessing fish diversity in the Upper Volga catchment did not detect sterlet at any of the sampled stretches, despite recent sightings that suggest its presence. We designed a TaqMan qPCR protocol to test for sterlet in selected eDNA samples from that study. In-silico and in-vitro tests confirm the protocol’s high sensitivity and specificity to sturgeon taxa and potentially paddlefishes. Using this assay, sterlet were not detected in 26 eDNA samples from the Volga headwaters, agreeing with the metabarcoding results.