Round Goby Detection in Lakes Huron and Michigan—An Evaluation of eDNA and Fish Catches

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Abstract

Aquatic surveys for fish in large water bodies (e.g., Laurentian Great Lakes of North America) often require a flexible approach using multiple methods, surveying different depths, and sampling across seasons, especially when the target species is elusive in its natural habitat. The round goby (Neogobius melanostomus) is an invasive, bottom-dwelling fish inhabiting rocky areas of all five Great Lakes. While trawl surveys are typically used for abundance assessments, angling has been demonstrated as a means of supplementing surveys with additional data. Yet, round goby abundance and distribution is still not well described. Recently, with considerable success, scientists have explored sampling environmental DNA (eDNA) to complement traditional monitoring techniques for population abundance estimates, early detection of invasive species, and spawning or migration events. Therefore, we collected eDNA from water samples alongside bottom trawls and hook and line angling in Lakes Huron and Michigan to detect round goby. eDNA samples were analyzed by both droplet digital PCR (ddPCR) and quantitative PCR (qPCR) to maximize the likelihood of detection. Overall, round goby was captured in 23% of the trawls, but the eDNA based methods detected round goby in 74% and 66% of samples by ddPCR and qPCR, respectively, mostly in samples collected at <30 m depths, and mostly in the fall. More studies comparing eDNA based methods to traditional monitoring, especially trawls in large open waters, may contribute to a better understanding of using eDNA in population assessments.

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Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes

Philip Francis Thomsen, Peter Rask Møller, Eva Egelyng Sigsgaard … (2016)

Remote polar and deepwater fish faunas are under pressure from ongoing climate change and increasing fishing effort. However, these fish communities are difficult to monitor for logistic and financial reasons. Currently, monitoring of marine fishes largely relies on invasive techniques such as bottom trawling, and on official reporting of global catches, which can be unreliable. Thus, there is need for alternative and non-invasive techniques for qualitative and quantitative oceanic fish surveys. Here we report environmental DNA (eDNA) metabarcoding of seawater samples from continental slope depths in Southwest Greenland. We collected seawater samples at depths of 188–918 m and compared seawater eDNA to catch data from trawling. We used Illumina sequencing of PCR products to demonstrate that eDNA reads show equivalence to fishing catch data obtained from trawling. Twenty-six families were found with both trawling and eDNA, while three families were found only with eDNA and two families were found only with trawling. Key commercial fish species for Greenland were the most abundant species in both eDNA reads and biomass catch, and interpolation of eDNA abundances between sampling sites showed good correspondence with catch sizes. Environmental DNA sequence reads from the fish assemblages correlated with biomass and abundance data obtained from trawling. Interestingly, the Greenland shark (Somniosus microcephalus) showed high abundance of eDNA reads despite only a single specimen being caught, demonstrating the relevance of the eDNA approach for large species that can probably avoid bottom trawls in most cases. Quantitative detection of marine fish using eDNA remains to be tested further to ascertain whether this technique is able to yield credible results for routine application in fisheries. Nevertheless, our study demonstrates that eDNA reads can be used as a qualitative and quantitative proxy for marine fish assemblages in deepwater oceanic habitats. This relates directly to applied fisheries as well as to monitoring effects of ongoing climate change on marine biodiversity—especially in polar ecosystems.