Design and Validation of a Single-Species Environmental DNA qPCR Assay for the Detection of the Invasive Chinese Mitten Crab Eriocheir sinensis

Abstract

Biological invasions are a leading driver of biodiversity loss and generate significant economic costs, either through direct impact on native ecosystems or through repairs and remediation. Reducing the impact of invasive species is a key aspect of environmental management targets, necessitating early detection and comprehensive distribution data for effective management. Environmental DNA (eDNA) has been demonstrated to enable sensitive monitoring, able to infer the presence of a target organism without physical observations and is particularly advantageous in aquatic environments where invasive species detection is challenging. The Chinese mitten crab (Eriocheir sinensis) is amongst the world's top 100 invasive species and is considered amongst the most damaging invasive species globally, causing significant detriment to riverbanks, fishing practices, and native populations, for example, through generalist predation and as a carrier of crayfish plague. In the UK, its distribution remains poorly understood, with current management relying on reporting of ad hoc sightings. This study developed and validated a species-specific qPCR assay for detecting E. sinensis eDNA against a standardized scale. Primer design utilized genome skimming of E. sinensis and related species collected in the UK, with the final assay achieving a detection limit of 15.6 copies/μL. Field tests in the UK detected target species eDNA at three sites with historical sightings, despite no recent visual records. Overall, the assay shows potential as a tool to support environmental monitoring and offer insights into the distribution, population dynamics, and invasion pathways, to support informed management of E. sinensis.