Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries

Abstract

The extraction and characterization of DNA from aquatic environmental samples offers an alternative, noninvasive approach for the detection of rare species.Environmental DNA, coupled with PCR and next-generation sequencing ("metabarcoding"), has proven to be very sensitive for the detection of rare aquatic species. Our study used a custom-designed group-specific primer set and nextgeneration sequencing for the detection of three species at risk (Eastern Sand Darter, Ammocrypta pellucida; Northern Madtom, Noturus stigmosus; and Silver Shiner, Notropis photogenis), one invasive species (Round Goby, Neogobius melanostomus) and an additional 78 native species from two large Great Lakes tributary rivers in southern Ontario, Canada: the Grand River and the Sydenham River. Of 82 fish species detected in both rivers using capture-based and eDNA methods, our eDNA method detected 86.2% and 72.0% of the fish species in the Grand River and the Sydenham River, respectively, which included our four target species. Our analyses also identified significant positive and negative species co-occurrence patterns between our target species and other identified species. Our results demonstrate that eDNA metabarcoding that targets the fish community as well as individual species of interest provides a better understanding of factors affecting the target species spatial distribution in an ecosystem than possible with only target species data. Additionally, eDNA is easily implemented as an initial survey tool, or alongside capture-based methods, for improved mapping of species distribution patterns.

Environmental DNA metabarcoding as an effective and rapid tool for fish monitoring in canals

“…While many studies have shown the advantages of using eDNA metabarcoding in lotic (flowing streams and rivers; Balasingham et al ., ) and lentic (still lakes and ponds; (Hänfling et al ., ; Harper et al ., ) systems, they also raise concerns about the influence of flow in DNA dispersal in fast running water and the need to sample multiple locations in lentic waters. Canals represent man‐made environments with a semi‐lotic regime and regulated flow, which minimise the risk of detection of species present too far away, while at the same time allowing enough water movement to reduce the need for extra sampling akin to that undertaken in lentic systems.…”

Using occupancy models to assess the effectiveness of underwater cameras to detect rare stream fishes

“…Given that detection probabilities tend to increase when multiple conventional methods are used, they would presumably also increase if multiple non‐harmful methods are employed. Another non‐harmful method that could be used with underwater cameras, and is becoming increasingly popular for detecting rare aquatic species, is environmental DNA (eDNA; Balasingham, Walter, Mandrak, & Heath, ; Boothroyd, Mandrak, Fox, & Wilson, ; Janosik & Johnson, ). This emerging method detects species based on collected genetic material from water samples (Janosik & Johnson, ), but also has some limitations, such as the heterogeneous distribution of eDNA across temporal and spatial scales in a river, reducing the detection of species even at small spatial scales (Macher & Leese, ).…”

Effect of water temperature and fish biomass on environmental DNA shedding, degradation, and size distribution

“…The presence of a target species can be estimated by detecting the eDNA in water samples instead of locating or capturing individuals (Lodge et al, ). These advantages have enabled noninvasive, quick, and wide‐ranging assessments of the presence/absence of species and their biodiversity and abundance in freshwater (Balasingham, Walter, Mandrak, & Heath, ; Bista et al, ; Deiner, Fronhofer, Mächler, Walser, & Altermatt, ; Fukumoto, Ushimaru, & Minamoto, ; Yamanaka & Minamoto, ) and marine environments (Boussarie et al, ; Lacoursière‐Roussel et al, ; Sigsgaard et al, ; Thomsen, Kielgast, Iversen, Møller, et al, ; Thomsen, Kielgast, Iversen, Wiuf, et al, ; Yamamoto et al, ).…”