The effect of bivalve filtration on eDNA-based detection of aquatic organisms

Abstract

As the use of environmental-DNA (eDNA) expands as a method to detect the presence and quantity of aquatic taxa, factors potentially impacting the efficacy of this technique must be investigated. Many studies have examined the effects of abiotic parameters on the degradation of environmental-DNA (e.g. UV radiation, pH, temperature, etc.), however, few have focused on biotic effectors. Through high-filtering rates coupled with dense colonization, Asian clams (Corbicula fluminea) are able to drastically alter the quantity of particulate matter through translocation into the sediment, potentially including sources of eDNA in lotic and lentic systems. Using a longitudinal, laboratory experiment, we tested the effect of varying densities of Asian clams on the translocation rate of common goldfish (Carassius auratus) DNA. Target DNA in testing tanks was quantified through quantitative PCR (qPCR) at regular intervals and compared. Tanks housing the highest density of Asian clams produced significantly lower DNA concentrations over time compared to tanks of lower densities. These results show, for the first time, a density-dependent reduction of local eDNA sources by bivalve filtration that may lead to the obstructed detection of target species through the sampling of eDNA. Based on these findings, we recommend highly concentrated bivalve populations be taken into consideration when choosing the time and locality of eDNA sampling efforts.

Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water

“…This contradicts several previous studies that have demonstrated a relationship between biomass or density and DNA copy number (Thomsen et al., 2012; Takahara et al., 2012; Doi et al., 2015). This could in part be due to the physiology and feeding behavior of mussels, since eDNA is being consumed as well as produced (Friebertshauser et al., 2019). The complex pattern of eDNA accumulation and depletion together with the lack of discrimination between different density treatments presents challenges for estimation of quagga mussel abundance.…”

“…(a) qPCR DNA copy number per μl (log 10 ) at all 7 sample sites. (b) Normalized relative read count of taxa assigned to quagga mussel at the three locations sequenced produced (Friebertshauser et al, 2019). The complex pattern of eDNA accumulation and depletion together with the lack of discrimination between different density treatments presents challenges for estimation of quagga mussel abundance.…”

Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels,Dreissena rostriformis bugensisin flowing water

“…This contradicts several previous studies that have demonstrated a relationship between biomass or density and DNA copy number (Thomsen et al, 2012; Takahara., et al 2012; Doi et al, 2015). This could in part be due to the physiology and feeding behaviour of mussels, since eDNA is being consumed as well as produced (Friebertshauser et al, 2019). The complex pattern of eDNA accumulation and depletion together with the lack of discrimination between different density treatments presents challenges for estimation of quagga mussel abundance.…”

Effect of biotic and abiotic factors on the production and degradation of fish environmental DNA: An experimental evaluation

“…Production (associated with origin) and degradation (associated with fate) of eDNA are two of the major processes influencing the amount of eDNA of a given species present in the environment (Barnes & Turner, 2016; Goldberg et al, 2015). Recent studies have shown the effects of abiotic (e.g., pH, temperature, ultraviolet, and salinity; Afzali et al, 2021; Boivin‐Delisle et al, 2021; Collins et al, 2018; Kasai et al, 2020; Mächler et al, 2018; Seymour et al, 2018; Strickler et al, 2015; Tsuji et al, 2017; Zulkefli et al, 2019) or biotic parameters (e.g., microbial activity and bivalve filtering; Friebertshauser et al, 2019; Lance et al, 2017; Mächler et al, 2018; Tsuji et al, 2017; Zulkefli et al, 2019) on eDNA fate, including degradation, but these studies have not taken eDNA production into consideration. On the other hand, production of eDNA has been studied alone as a function of different parameters such as biomass, temperature, diet, or life stage (Doi et al, 2017; Evans et al, 2016; Klymus et al, 2015; Lacoursière‐Roussel et al, 2016; Maruyama et al, 2014; Takahara et al, 2012; Thalinger et al, 2021).…”