Influence of distance from source population and seasonality in eDNA detection of white‐clawed crayfish, through qPCR and ddPCR assays

Abstract

The white-clawed crayfish (Austropotamobius pallipes) is an emblematic taxon of European rivers, found mainly in oxygenated streams, known to be an excellent indicator of river quality. Since several decades, the population of A. pallipes declined in relation to anthropogenic pressure, habitat loss, and competition with pests (invasive crayfish, crayfish plague). This endangered species is now submitted to conservation strategies by freshwater managers in order to survey and protect the remaining populations. In France, traditional surveys in freshwater environments were performed by electric fishing, kick-net fishing, or trapping, particularly disruptive for the environment and very time-consuming. However, with the rise of molecular genetic technology, new methods based on the detection of environmental DNA (eDNA) have emerged. We present here the results of an optimized study for the detection of the endangered crayfish Austropotamobius pallipes in France, considering certain environmental co-factors and comparing two PCR methods (qPCR and ddPCR). After improving laboratory procedures, we were able to detect the presence of the crayfish up to 2 km downstream from a known point of presence and unfortunately highlight the disappearance of a historical population, after sampling two consecutive years. Such a level of precision is interesting because it makes it possible to precise the presence of specimens in a relatively restricted area and to orient traditional prospecting, necessary for certain additional studies. During our study, we observed better probabilities of detection during the summer period, but in a growing context of climate change, we advise to adapt the sampling year by year. That said, this methodology is a very useful tool for the detection of rare and/or endemic species and we did not observe any difference between the two PCR methods used.

Marine invasive alien species in Europe: 9 years after the IAS Regulation

“…Different depths harbor different NIS, and the eDNA they release to the water will vary (DiBattista et al, 2019;Canals et al, 2021;Merten et al, 2023). Organism distribution fluctuates throughout the year, resulting in seasonally dependent eDNA release (Sigsgaard et al, 2017;Agersnap et al, 2022;Knudsen et al, 2022;Baudry et al, 2023). Diurnal activity patterns impact eDNA levels (Jensen et al, 2022), necessitating nighttime sampling for monitoring nocturnal NIS.…”

“…In monitoring programs coupling molecular and traditional methods, site occupancy-detection (SOD) modeling holds great promise for converting eDNA-positive detections into robust estimates of species distribution (Darling et al, 2017). Positive correlations have been observed, for example, between eDNA levels and tidewater in SOD for a marine endangered goby on the Californian coast (Schmelzle and Kinziger, 2016) and between oxygen levels and eDNA from an endangered crayfish threatened by the expansion of introduced crayfish (Baudry et al, 2023).…”

Environmental DNA reflects spatial distribution of a rare turtle in a lentic wetland assisted colonization site

“…The concentration and dispersal of eDNA can affect detection rates and interpretability of results. Lotic systems (e.g., streams and rivers) exhibit wide ranges of horizontal eDNA dispersal with detections occurring up to kilometers from the source (Baudry et al., 2023; Deiner & Altermatt, 2014), while lentic systems (e.g., ponds, wetlands, and lakes) are generally associated with lower horizontal dispersal. Lentic freshwater systems differ in size, depth, mixing, aquatic vegetation, abiotic factors, etc., resulting in both homogeneous (Evans et al., 2017; Thomsen et al., 2012) and heterogeneous (Brys et al., 2021; Dunker et al., 2017; Eichmiller et al., 2014; Feng et al., 2019; Harper et al., 2018; Li et al., 2019; Troth et al., 2021) horizontal eDNA distribution.…”