A system for rapid eDNA detection of aquatic invasive species

Abstract

Environmental DNA (eDNA) detection of aquatic invasive species using quantitative polymerase chain reaction (qPCR) is a powerful tool for resource managers, but qPCR has traditionally been confined to laboratory analysis. Laboratory results often take days or weeks to be produced, limiting options for rapid management response. To circumvent laboratory delay, we combined a purpose‐built eDNA filtration system (Smith‐Root eDNA‐Sampler) with a field DNA extraction and qPCR analysis platform (Biomeme) to form a complete field eDNA sampling and detection process. A controlled laboratory study involving serial dilutions of New Zealand mudsnail (Potamopyrgus antipodarum; Gray, 1843) eDNA was conducted to compare the detection capabilities of the field system with traditional bench qPCR. Additionally, field validation studies were conducted to determine whether field eDNA analysis can be used to map mudsnail eDNA distribution and quantify temporal fluctuations. In the laboratory experiment, both qPCR platforms (Biomeme, bench qPCR) lost the ability to reliably detect mudsnail eDNA at the same dilution level, with starting quantity values as low as 21 DNA copies/reaction. A strong linear relationship was observed between the average quantification cycle values of the two platforms (slope = 1.101, intercept = −1.816, R2 = 0.997, p < 0.001). Of the 80 field samples collected, 44 (55%) tested positive for mudsnail eDNA with Biomeme, and results identified both spatial and temporal fluctuations in mudsnail eDNA/L. However, the average qPCR inhibition rate with Biomeme was 28% for field samples, and up to 39% in the temporal dataset. With additional optimization to reduce inhibition, the eDNA‐Sampler/Biomeme system has potential to be a rapid and highly effective detection/quantification tool for aquatic invasive species.

In-situnon-lethal rapid test to accurately detect the presence of the nematode parasite,Anguillicoloides crassus, in European eel,Anguilla anguilla

“…DNA-based molecular diagnostics for helminth parasite detection are gaining in popularity (O'Connell & Nutman, 2016). However, as has been observed for the detection for many pathogens of medical and veterinary interest, qPCR is preferred over standard PCR to deliver the sensitivity required (Thomas et al, 2019). Point-of-care qPCR for viral pathogens can now deliver a result in less than 20 minutes (Melchers et al, 2017).…”

Optimizing an eDNA protocol for estuarine environments: Balancing sensitivity, cost and time

“…The typical protocol used to isolate eDNA from water samples can be described in four steps: filtration, DNA extraction, inhibitor removal and DNA amplification in order to estimate the initial concentration of eDNA [6]. In the filtration step, the water samples, with preferred volumes of 1 liter [7][8][9], are pressure-pumped through a membrane filter which captures the free DNA as well as tissue and cells suspended in the water. One problem that arises is filter clogging, which leads to under-sampling and irregular sampling volumes.…”

Molecular Detection Mapping and Analysis Platform for R (MDMAPR) facilitating the standardization, analysis, visualization, and sharing of qPCR data and metadata

“…The volume of qPCR data is increasing, along with the urgent need for qPCR data integration and centralized documentation. In the past decade, qPCR has been utilized as a tool to support numerous biological fields of inquiry, including natural resource management ( Thomas et al, 2019 ; Fritts et al, 2019 ), food safety ( Amaral et al, 2016 ), conservation planning ( Franklin et al, 2019 ), and disease vector/infectious disease monitoring ( Qurollo et al, 2017 ; Ikten et al, 2016 ). Research using qPCR methodologies extends beyond the detection and quantification of target gene expression.…”