Environmental DNA (eDNA) Monitoring of Noble Crayfish Astacus astacus in Lentic Environments Offers Reliable Presence-Absence Surveillance – But Fails to Predict Population Density

Abstract

Noble crayfish is the most widespread native freshwater crayfish species in Europe. It is threatened in its entire distribution range and listed on the International Union for Concervation Nature- and national red lists. Reliable monitoring data is a prerequisite for implementing conservation measures, and population trends are traditionally obtained from catch per unit effort (CPUE) data. Recently developed environmental DNA (eDNA) tools can potentially improve the effort. In the past decade, eDNA monitoring has emerged as a promising tool for species surveillance, and some studies have established that eDNA methods yield adequate presence-absence data for crayfish. There are also high expectations that eDNA concentrations in the water can predict biomass or relative density. However, eDNA studies for crayfish have not yet been able to establish a convincing relationship between eDNA concentrations and crayfish density. This study compared eDNA and CPUE data obtained the same day and with high sampling effort, and evaluated whether eDNA concentrations can predict relative density of crayfish. We also compared two analytical methods [Quantitative real-time PCR (qPCR) and digital droplet PCR (ddPCR)], and estimated the detection probability for eDNA monitoring compared to trapping using occupancy modeling. In all lakes investigated, we detected eDNA from noble crayfish, even in lakes with very low densities. The eDNA method is reliable for presence-absence monitoring of noble crayfish, and the probability of detecting noble crayfish from eDNA samples increased with increasing relative crayfish densities. However, the crayfish eDNA concentrations were consistently low and mostly below the limit of quantification, even in lakes with very high crayfish densities. The hypothesis that eDNA concentrations can predict relative crayfish density was consequently not supported. Our study underlines the importance of intensified sampling effort for successful detection of very low-density populations, and for substantiating presumed absence, inferred from negative results. Surprisingly, we found a higher likelihood of eDNA detection using qPCR compared to ddPCR. We conclude that eDNA monitoring cannot substitute CPUE data, but is a reliable supplement for rapid presence-absence overviews. Combined with eDNA analyses of alien crayfish species and diseases such as crayfish plague, this is a cost-efficient supplement offering a more holistic monitoring approach for aquatic environments and native crayfish conservation.

The amount of environmental DNA increases with freshwater crayfish density and over time

“…Contrary to most previously published studies (Dougherty et al, 2016; Dunn et al, 2017; Johnsen et al, 2020; Rice et al, 2018), our laboratory experiment showed that crayfish density indeed can be measured by eDNA. This was supported dually by a clear correlation between eDNA concentration and total crayfish biomass, as well as carapace length.…”

“…In fact, so far only a laboratory experiment by Dunn et al (2017) found a weak correlation of eDNA concentration and crayfish densities, but only in egg‐bearing females. From field investigations, there has been little to no correlation between the amount of crayfish eDNA and local population densities in lakes or river systems (Chucholl et al, 2021; Dougherty et al, 2016; Johnsen et al, 2020), where an overall downstream increase of eDNA has so far been observed (Rice et al, 2018).…”

eDNA Detection of Native and Invasive Crayfish Species Allows for Year-Round Monitoring and Large-Scale Screening of Lotic Systems

“…Subsequent validation and fine-scale localization of populations should include conventional monitoring methods, though (c.f. Johnsen et al, 2020). Finally, eDNA might allow for a rough quantification of upstream population size.…”

“…In line with this reasoning, Rice et al (2018) found that the likelihood to detect Faxonius eupunctus in a large lotic system was independent from local crayfish abundance but increased with the upstream length of the populated stretch. In lentic situations, previous studies mostly reported a relationship between eDNA copy number and relative abundance of crayfish, estimated by trapping (Dougherty et al, 2016;Larson et al, 2017) or visual counts (Cai et al, 2017), although a recent study found no correlation between trapping data and eDNA concentration (Johnsen et al, 2020). In our study, manual capture was used as reference method, which is known to have a very high capture probability in streams of the study region (see Chucholl and Schrimpf, 2016), and, which is also known as the least biased conventional sampling method (Peay, 2004;Hilber et al, 2020).…”

Estimation accuracy of species abundance based on environmental DNA with relation to its production source, state, and assay methodology suggested by meta-analyses

“…Fish and jellyfish are likely to constantly produce eDNA as epidermis and/or muco-substances (Merkes et al, 2014;Sassoubre et al, 2016), while crustaceans are characterized by their hard exoskeletons and segmented bodies plans (Hadley, 1986) and are thus unlikely to shed large amounts of eDNA from their body surfaces unless they are molting. Consequently, crustaceans infrequently and irregularly shed eDNA, which may impede sufficient eDNA detection in the field and prevent accurate abundance estimationvia eDNA analysis (Dougherty et al, 2016;Machler et al, 2016;Johnsen et al, 2020). In contrast, estimation accuracy of species abundance was marginally higher for coral and seastars than fish.…”