Environmental DNA for assessing impact and recovery of aquatic communities in an invaded mountain lake

Abstract

Beaulieu J, Yates MC, Astorg L, Trépanier-Leroux D, Jeon H, Rudko SP, Humphries S, Fraser DJ, Cristescu ME, Derry AM. 2024. Environmental DNA for assessing impact and recovery of aquatic communities in an invaded mountain lake. Lake Reserv Manage. 40:111–131. The eradication of invasive species and associated side effects that influence the reestablishment of biological communities is a major challenge for conservation management of invaded ecosystems. We present a before-and-after-disturbance whole lake manipulation study from a high-elevation mountain lake in which we applied a 2-pronged approach to environmental DNA (eDNA) for assessing (1) impact and recovery of aquatic communities to the chemical eradication of invasive brook trout (Salvelinus fontinalis) and (2) the success of chemical eradication of the invasive fish. Using 18S and cytochrome oxidase I (COI) eDNA metabarcoding, we contribute to a paucity of literature that has comprehensively addressed nontarget effects of rotenone for invasive fish eradication on aquatic communities. We found that key trophic groups (phytoplankton, fungi, zooplankton, and macroinvertebrates) changed in community composition in response to rotenone applications. Fungi and macroinvertebrates, but not zooplankton and phytoplankton, reverted back toward pre-rotenone communities over the time scale of 2 yr. However, COI failed to detect several key species for food web reestablishment that were detected using physical specimen collection, likely due to low primer efficiency. We also found that quantitative polymerase chain reaction (qPCR), using species-specific primers, was effective for detecting brook trout presence/absence, although strong eDNA signals likely produced from carcasses in the ecosystem limited the utility of eDNA immediately following rotenone treatment. We provide specific recommendations for lake managers for the future application of eDNA approaches to monitor invasive fish eradication efforts and nontarget community effects for lake ecosystem restoration.

Keywords:

• Environmental DNA (eDNA)
• invasive species eradication
• invasive trout
• metabarcoding
• nontarget impacts
• qPCR
• rotenone

Acknowledgments

The author JB received scholarship support from the Groupe inter-universitaire en limnologie (GRIL), a limnology excellence cluster funded by the FRQNT in Québec, through a collaborative partnership with Parks Canada, Banff, Kootenay, and Yoho Division. MCY was supported by a FRQNT postdoctoral excellence fellowship. Data provided by Aquality were paid for by Parks Canada (SH). We thank M. Salamon, S. Urschel and A. Yaghi for their help in the field.

Disclosure statement

The authors report there are no competing interests to declare.

Data accessibility statement

Data are available in the Environmental Data Initiative (Environmental Data Initiative—Create. Package. Archive. Discover. Reuse) for qPCR data, https://doi.org/10.6073/pasta/c1deed4b686c49e813117e262c661a96, and metabarcoding data, https://doi.org/10.6073/pasta/963a004e94689bde81adb38e1b792615.

Additional information

Funding

This research was funded by a Fonds de Recherche du Québec—Nature et Technologie (FRQNT) team grant to AMD, MEC, and DJF, and a grant from the Natural Sciences and Engineering Research Council of Canada (NSERC Strategic Project grant, AMD, DJF).