A non-invasive eDNA tool for detecting sea lamprey larvae in river sediments: analytical validation and field testing in a low abundance ecosystem

Anthropogenic activities are increasingly threatening aquatic biodiversity, especially anadromous species. Monitoring and conservation measures are thus required to protect, maintain, and restore imperilled populations. While many species can be surveyed using traditional capture and visual census techniques, species that use riverine habitats in a less conspicuous manner, such as sea lamprey Petromyzon marinus, can be more challenging to monitor. Sea lamprey larvae (ammocoetes) can spend several years in freshwater burrowed within soft sediments, inhibiting their detection and assessment. Here we present an environmental DNA (eDNA) assay to detect ammocoetes burrowed in the sediment. We performed a battery of tests that ensured both species-specificity of the assay as well as the capacity to detect ammocoetes when abundances are low. Experiments on burrowing activity suggested that most of the DNA released into the sediment occurs during burrowing. Overall, we demonstrated this new molecular-based tool is an efficient and effective complement to traditional monitoring activities targeting larval stages of sea lampreys.