At the forefront: evidence of the applicability of using environmental DNA to quantify the abundance of fish populations in natural lentic waters with additional sampling considerations

Abstract

Environmental DNA (eDNA) sampling has proven to be a valuable tool for detecting species in aquatic ecosystems. Within this rapidly evolving field, a promising application is the ability to obtain quantitative estimates of relative species abundance based on eDNA concentration rather than traditionally labor-intensive methods. We investigated the relationship between eDNA concentration and Arctic char (Salvelinus alpinus) abundance in five well-studied natural lakes; additionally, we examined the effects of different temporal (e.g., season) and spatial (e.g., depth) scales on eDNA concentration. Concentrations of eDNA were linearly correlated with char population estimates ([Formula: see text] = 0.78) and exponentially correlated with char densities ([Formula: see text] = 0.96 by area; 0.82 by volume). Across lakes, eDNA concentrations were greater and more homogeneous in the water column during mixis; however, when stratified, eDNA concentrations were greater in the hypolimnion. Overall, our findings demonstrate that eDNA techniques can produce effective estimates of relative fish abundance in natural lakes. These findings can guide future studies to improve and expand eDNA methods while informing research and management using rapid and minimally invasive sampling.

Environmental DNA detects a rare large river crayfish but with little relation to local abundance

“…Many studies to date have sought to compare the reliability of eDNA to conventional sampling methods in estimating both occupancy and abundance of target organisms. In general, eDNA has performed well for representing occupancy of species (Dougherty et al., ; Pilliod et al., ; Smart et al., ), and some studies have found strong agreement between abundance or biomass of organisms and abundance of eDNA in the environment (Doi et al., ; Klobucar et al., ). Specific to crayfishes, studies have generally found eDNA to accurately represent occupancy of crayfishes, potentially with more sensitivity than some conventional methods, but eDNA has performed poorly in reflecting crayfish abundance (Agersnap et al., ; Cai et al., ; Dougherty et al., ; Larson et al., ).…”

“…Despite its somewhat recent emergence for macrobiota in freshwater species surveys, eDNA has been successfully applied to a variety of freshwater taxa including amphibians (Goldberg, Pilliod, Arkle, & Waits, ; Pilliod, Goldberg, Arkle, Waits, & Richardson, ), crayfishes (Cai et al., ; Tréguier et al., ), fishes (Minamoto, Yamanaka, Takahara, Honjo, & Kawabata, ; Takahara, Minamoto, & Doi, ), gastropods (Goldberg, Sepulveda, Ray, Baumgardt, & Waits, ), insects (Thomsen et al., ), molluscs (Egan et al., ) and reptiles (Piaggio et al., ). Further, eDNA has shown promising results in both lentic (Klobucar, Rodgers, & Budy, ; Takahara et al., ) and lotic (Doi et al., ; Katano, Harada, Doi, Souma, & Minamoto, ) environments, although its reliability in lotic environments may be challenged by the downstream transport of detectable eDNA.…”

Rapid assessment of coral cover from environmental DNA in Hawai'i

“…As an efficient alternative, the analysis of environmental DNA (eDNA), DNA shed or expelled from organisms into the environment, has been used to assess species diversity, primarily in aquatic environments (Andruszkiewicz, Starks, et al, ; Boussarie et al, ; DiBattista et al, ; Everett & Park, ; Jerde, Mahon, Chadderton, & Lodge, ; Klymus, Marshall, & Stepien, ; Li et al, ; Parsons, Everett, Dahlheim, & Park, ; Port et al, ; Stat et al, ; Thomsen, Kielgast, Iversen, Moller, et al, ; Thomsen, Kielgast, Iversen, Wiuf, et al, ; Ushio et al, ). Despite the growing use of eDNA to catalog the presence and absence of species, the quantitative description of the relative abundance of species (or guilds of functionally similar species) with eDNA remains an open question (Bakker et al, ; Elbrecht & Leese, ; Evans et al, ; Hänfling et al, ; Kelly, Port, Yamahara, & Crowder, ; Kelly, Port, Yamahara, Martone, et al, ; Klobucar, Rodgers, & Budy, ; Lacoursière‐Roussel, Côté, Leclerc, & Bernatchez, ; Piñol, Senar, & Symondson, ; Port et al, ; Sigsgaard et al, ; Stoeckle, Soboleva, & Charlop‐Powers, ; Taberlet, Bonin, Zinger, & Coissac, ).…”

Environmental DNA analysis as a non‐invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers

“…Despite this, degree of correlation between eDNA concentration and abundance demonstrated in the field is variable between studies. A recent study of a stream‐dwelling char demonstrated a high correlation (Wilcox et al, ), but other studies reported marginally significant correlations or secondary contribution of abundance to eDNA amount (Doi et al, ; Erickson et al, ; Lacoursière‐Roussel, Côté, Leclerc, & Bernatchez, ; Klobucar, Rodgers, & Budy, ; Nevers et al, ; Pilliod, Goldberg, Arkle, Waits, & Richardson, ; Thomsen et al, ; Yamamoto et al, ). In some studies, eDNA concentration did not correlate with the biomass of the target animals (Biggs et al, ; Spear, Groves, Williams, & Waits, ).…”