Application of digital PCR in the detection of low-abundance Pomacea canaliculata eDNA

Environmental DNA (eDNA) methods have been increasingly applied in the detection of invasive alien species (IAS). Pomacea canaliculata, a top 100 worldwide IAS native to South America, poses a significant threat to food production and ecosystems. Its invasion severely disrupts ecological balance and biodiversity, making precise detection and scientific management essential. The aim of this study was to establish and validate a dPCR-eDNA assay and the feasibility of monitoring the invasion of P. canaliculata in the water column by applying it in the field and in the laboratory, especially the accuracy and sensitivity of the assay in low-abundance samples.

The results of digital PCR (dPCR) are closely related to those of conventional real-time quantitative PCR (qPCR) in laboratory and environmental samples. Differences between methods were observed at low gene copies (10⁰-10⁴cell L^-1) by laboratory standard systems, with dPCR having higher accuracy at low cell concentrations compared to qPCR. Furthermore, dPCR showed the highest detection rate of 92% across 75 environmental samples, followed by high-throughput sequencing (HTS) and qPCR with detection rates of 80% and 56%, respectively. The visual method had the lowest detection rate at only 52%.

These findings demonstrate that the dPCR-eDNA assay can be used as a sensitive and accurate detection method for early monitoring and invasion control of P. canaliculata. © 2026 Society of Chemical Industry.