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

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. XX:XXX–XXX. 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.