Highly sensitive environmental DNA detection of topmouth gudgeon, Pseudorasbora parva: a comparison of qPCR and microfluidic qdPCR

Topmouth gudgeon is a freshwater fish species native to East Asia. Nowadays, P. parva is spread throughout Europe which is of concern because besides being considered one of the worst aquatic Invasive Alien Species (IAS) in Europe it is also a known vector of Spherotecum destruens, the rosette-like parasite lethal to other fish species. The present study describes the development and validation of a new species-specific assay based on hydrolysis probe chemistry to detect P. parva environmental DNA (eDNA) in water samples collected in a northern region of Italy (Friuli Venezia Giulia). Water samples were collected from 55 sites in an area where partial information on the occurrence of the species is available. eDNA was isolated from all samples and the presence of P. parva eDNA was tested by means of qPCR (quantitative PCR) and microfluidic qdPCR (quantitative digital PCR) techniques. Field results for both qPCR and qdPCR were largely in agreement in terms of detection (presence/absence). Thus, we judged the presence/absence by combining the results from the two methods and found that nine sites showed “strong positive” signal of P. parva eDNA (at least 2 positive replicates), 3 showed “suspected” (only 1 positive replicate), and 42 showed “absent”. The current study shows the strong potential of the newly developed eDNA approach to be a valuable addition to the monitoring of the highly invasive topmouth gudgeon in freshwater ecosystems.