Behavior and season affect crayfish detection and density inference using environmental DNA

Abstract

Although the presence/absence of aquatic invertebrates using environmental DNA (eDNA) has been established for several species, inferring population densities has remained problematic. The invasive American signal crayfish, Pacifastacus leniusculus (Dana), is the leading cause of decline in the UK's only native crayfish species, Austropotamobius pallipes (Lereboullet). Methods to detect species at low abundances offer the opportunity for the early detection, and potential eradication, of P. leniusculus before population densities reach threatening levels in areas occupied by A. pallipes. Using a factorial experimental design with aquaria, we investigated the impacts of biomass, sex ratio, and fighting behavior on the amount of eDNA released by P. leniusculus, with the aim to infer density per aquarium depending on treatments. The amount of target eDNA in water samples from each aquarium was measured using the quantitative Polymerase Chain Reaction. We show that the presence of eggs significantly increases the concentration of crayfish eDNA per unit of mass, and that there is a significant relationship between eDNA concentration and biomass when females are egg‐bearing. However, the relationship between crayfish biomass and eDNA concentration is lost in aquaria without ovigerous females. Female‐specific tanks had significantly higher eDNA concentrations than male‐specific tanks, and the prevention of fighting did not impact the amount of eDNA in the water. These results indicate that detection and estimate of crayfish abundance using eDNA may be more effective while females are ovigerous. This information should guide further research for an accurate estimation of crayfish biomass in the field depending on the season. Our results indicate that detection and quantification of egg‐laying aquatic invertebrate species using eDNA could be most successful during periods when eggs are developing in the water. We recommend that practitioners consider the reproductive cycle of target species when attempting to study or detect aquatic species using eDNA in the field.

Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds

“…However, substantial variation exists in design, validation, and application of species-specific assays, even for the same target species, e.g. invasive signal crayfish P. leniusculus (Agersnap et al, 2017;Dunn et al, 2017;Larson et al, 2017;Harper et al 2018a;Mauvisseau et al, 2018;Robinson et al, 2018). False positives and negatives remain pertinent issues in eDNA monitoring and intuitive counter-strategies are required for their mitigation.…”

Detection and Control of Invasive Freshwater Crayfish: From Traditional to Innovative Methods

“…eDNA analysis allows early detection even when target species are not directly observed. A few studies have estimated the transport distance of eDNA from the source to about 10 km, depending on population size [64,65], and the permanence of genetic material within the environment at about 10 days, indicating that DNA traces are near contemporary with presence of the species [66,67]. Compared to traditional survey methods (e.g., trapping and visual surveys), eDNA seems to have higher start-up costs for developing and testing the whole assay (eDNA extraction, PCR condition, primers tests, amplicon sequencing), but a few studies suggest that eDNA can reduce total survey costs [68,69].…”

“…Accurate abundance estimation through eDNA is still challenging and depends on multiple factors such as the number of DNA copies released into the water from an individual, the transport rate of the stream and the stability of eDNA over time [65,78]. Moreover, behaviour and season affect crayfish detection and abundance inference using eDNA, as, for example, it has been shown that ovigerous females release higher DNA levels than males do [67]. Therefore, before the application of quantitative eDNA methods, researchers need to quantify the errors generated in order to estimate abundance, depending on many factors, linked both to the target species and to the specific environment studied (i.e., lotic, lentic and ocean waters).…”

Minimizing polymerase biases in metabarcoding

“…Biological differences include organism size, seasonal presence and senescence, preservation and dispersal strategy, among others. Larger taxa, taxa that are present year‐round or taxa whose DNA is readily transported across long distances by wind or water, may be more likely to be observed in environmental samples than smaller, seasonal and sedentary taxa (Andersen et al., ; Barnes & Turner, ; Buxton, Groombridge, Zakaria, & Griffiths, ; Dunn, Priestley, Herraiz, Arnold, & Savolainen, ; Hemery, Politano, & Henkel, ; Rees et al., ). Even when the same number of cells is present in an environmental sample, the starting copy number of target loci may vary between taxa and tissue type.…”