Monitoring spawning migrations of potamodromous fish species via eDNA

Abstract

Potamodromous fish are considered important indicators of habitat connectivity in freshwater ecosystems, but they are globally threatened by anthropogenic impacts. Hence, non-invasive techniques are necessary for monitoring during spawning migrations. The use of environmental DNA (eDNA) potentially facilitates these efforts, albeit quantitative examinations of spawning migrations remain so far mostly uncharted. Here, we investigated spawning migrations of Danube bleak, Alburnus mento, and Vimba bream, Vimba vimba, and found a strong correlation between daily visual fish counts and downstream eDNA signals obtained from filtered water samples analysed with digital PCR and end-point PCR coupled with capillary electrophoresis. By accounting for daily discharge fluctuations, it was possible to predict eDNA signal strength from the number of migrating fish: first, the whole spawning reach was taken into account. Second, the model was validated using eDNA signals and fish counts obtained from the upper half of the examined river stretch. Consequently, fish counts and their day-to-day changes could be described via an eDNA-based time series model for the whole migration period. Our findings highlight the capability of eDNA beyond delivering simple presence/absence data towards efficient and informative monitoring of highly dynamic aquatic processes such as spawning migrations of potamodromous fish species.

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

“…For example, filtering submitted data by time helps understand the invasion pathway of introduced non-native species and can identify possible routes of species introduction. In epidemiology, this functionality helps evaluate the temporal distribution of disease-causing pathogens ( Arino, 2017 ; Thalinger et al, 2019 ).…”

Endpoint PCR coupled with capillary electrophoresis (celPCR) provides sensitive and quantitative measures of environmental DNA in singleplex and multiplex reactions

“…This disadvantage can be compensated by analysing the endpoint PCR product via capillary electrophoresis (celPCR): in capillary electrophoresis all double-stranded DNA fragments are separated by their size and the amount of each fragment is quantified in a relative manner by measuring the Relative Fluorescence Units (RFU) of each fragment. This is possible as either the primers or the whole fragment is fluorescently labelled [17,18]. In the past, celPCR has been used to determine if the fluorescence of a target amplicon exceeds a predefined threshold and samples can thus be scored “positive” [19,20].…”

“…In the past, celPCR has been used to determine if the fluorescence of a target amplicon exceeds a predefined threshold and samples can thus be scored “positive” [19,20]. However, there has been only rudimentary attempts to assess the general quantification capabilities of celPCR for eDNA analyses [18,21]. This possibility for quantification is especially appealing for target eDNA detection in a large number of samples, as there is a high potential for cost-reduction based on PCR-chemicals alone (Table 1).…”

“…Endpoint PCR is sometimes associated with reduced sensitivity in comparison to qPCR and dPCR [28,29]. However, the LODs determined for invertebrate and vertebrate DNA with celPCR (10 to 30 target DNA copies in the reaction [17,18,27]) are similar to qPCR LODs ranging from five to 50 copies in PCR [28,30,31]. celPCR can therefore be considered sufficiently sensitive for detecting minute eDNA quantities.…”

Identifying spawning activity in aquatic species based on environmental DNA spikes

“…Environmental DNA (eDNA) analysis has been used to estimate species distribution, and recent works have shown a relatively higher eDNA concentration in water during the reproductive season (Spear et al, 2015;Bracken et al, 2018;Tillotson et al, 2018;Takahashi et al, 2018;Thalinger et al, 2019). eDNA is a generic term used to refer to the DNA that has been shed by organisms into the surrounding environment, and it is thought to derive from skin, feces, mucus and reproductive materials (e.g.…”