Is it absent or is it present? Detection of a non-native fish to inform management decisions using a new highly-sensitive eDNA protocol.

Abstract

© 2019, The Author(s). Environmental managers require a sensitive and reliable means to prove, with the highest level of confidence possible, where non-native fish species exist and where they do not. Therefore, a nested PCR (nPCR) protocol was developed to detect the environmental DNA (eDNA) of a case-study species, topmouth gudgeon Pseudorasbora parva, which was recently the subject of a national eradication campaign in the UK. The nPCR protocol was tested in the laboratory and in the field in a series of coordinated surveys (eDNA and conventional sampling with traps) at a commercial angling venue in southern England where an initial eDNA survey, based on conventional PCR (cPCR), found P. parva to be present in one of the seven ponds. In the laboratory, the nPCR protocol was on average 100× more sensitive than cPCR, providing a 100% detection rate at DNA concentrations of 3 × 10 −8  ng/µL (8 DNA copies per µL). In the field, nPCR and conventional trapping both detected P. parva in only one of the seven angling ponds, the same infested pond as in the previous cPCR-based study. Following eradication work on the infested pond, no eDNA of P. parva was detected using nPCR in either the formerly-infested pond or the adjacent pond, which had been used to quarantine large commercially-valuable fishes. In management applications where the veracity of negative results may be of equal importance as confirmation of positive detections, nPCR protocols provide a useful addition to the analytical toolkit available to inform decision makers responsible for non-native species management.