Abstract
Environmental DNA (eDNA) analysis is a rapid, cost‐effective, non‐invasive biodiversity monitoring tool which utilises DNA left behind in the environment by organisms for species detection. The method is used as a species‐specific survey tool for rare or invasive species across a broad range of ecosystems. Recently, eDNA and “metabarcoding” have been combined to describe whole communities rather than focusing on single target species. However, whether metabarcoding is as sensitive as targeted approaches for rare species detection remains to be evaluated. The great crested newt Triturus cristatus is a flagship pond species of international conservation concern and the first UK species to be routinely monitored using eDNA. We evaluate whether eDNA metabarcoding has comparable sensitivity to targeted real‐time quantitative PCR (qPCR) for T. cristatus detection. Extracted eDNA samples (N = 532) were screened for T. cristatus by qPCR and analysed for all vertebrate species using high‐throughput sequencing technology. With qPCR and a detection threshold of 1 of 12 positive qPCR replicates, newts were detected in 50% of ponds. Detection decreased to 32% when the threshold was increased to 4 of 12 positive qPCR replicates. With metabarcoding, newts were detected in 34% of ponds without a detection threshold, and in 28% of ponds when a threshold (0.028%) was applied. Therefore, qPCR provided greater detection than metabarcoding but metabarcoding detection with no threshold was equivalent to qPCR with a stringent detection threshold. The proportion of T. cristatus sequences in each sample was positively associated with the number of positive qPCR replicates (qPCR score) suggesting eDNA metabarcoding may be indicative of eDNA concentration. eDNA metabarcoding holds enormous potential for holistic biodiversity assessment and routine freshwater monitoring. We advocate this community approach to freshwater monitoring to guide management and conservation, whereby entire communities can be initially surveyed to best inform use of funding and time for species‐specific surveys.
Highlights
Species monitoring has rapidly evolved with the advent of environmental DNA analysis (Lawson Handley, 2015). eDNA analysis allows highly sensitive detection of rare and invasive species and is increasingly being used for surveys of aquatic species (Biggs et al, 2015; Davy, Kidd, & Wilson, 2015; Evans, Shirey, Wieringa, Mahon, & Lamberti, 2017; Smart et al, 2016; Thomsen et al, 2012)
An identical positive correlation was observed between quantitative PCR (qPCR) score and the average number of T. cristatus reads obtained for samples belonging to each qPCR score, regardless of threshold application to the metabarcoding data
12 independent qPCR replicates were performed for each sample but due to limited resources, metabarcoding was based on three pooled PCR replicates which were sequenced once only
Summary
Species monitoring has rapidly evolved with the advent of environmental DNA (eDNA) analysis (Lawson Handley, 2015). eDNA analysis allows highly sensitive detection of rare and invasive species and is increasingly being used for surveys of aquatic species (Biggs et al, 2015; Davy, Kidd, & Wilson, 2015; Evans, Shirey, Wieringa, Mahon, & Lamberti, 2017; Smart et al, 2016; Thomsen et al, 2012). Passive eDNA monitoring is attractive to ecologists for biodiversity assessment as a means to detect entire species assemblages alongside rare or invasive species (Blackman et al, 2017; Lacoursière-Roussel, Dubois, Normandeau, & Bernatchez, 2016) This gain in community understanding may come at the cost of accuracy and sensitivity. EDNA analysis using targeted qPCR has been repeatedly verified against conventional surveying (bottle trapping, torchlight counts, larval netting, egg searches) for T. cristatus and found to achieve comparable or improved species detection (Biggs et al, 2015; Rees, Bishop, et al, 2014; Thomsen et al, 2012). The targeted eDNA assay is highly effective for T. cristatus detection; should metabarcoding have comparable sensitivity, this approach would allow detection of T. cristatus alongside pond communities and potentially enable more cost-effective monitoring of entire ecosystems and ecological hypothesis testing. We examined cost and investigator effort required by each approach to determine whether a trade-off between cost, time, and amount of data generated exists
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