Ecological forensics: Using eDNA to detect diverse taxonomic groups in aquatic ecosystems

Background/Question/Methods

Invasive species cause large environmental changes in the Great Lakes, with consequently large economic damages to the regional economy. Through a variety of anthropogenic pathways, potentially harmful species are allowed into the states and provinces of the Great Lakes region. Self-sustaining populations are, therefore, often established by the time a harmful species has even been detected. Resource limitations can then prevent effective management responses even as established species spread throughout one lake and ultimately to all connected lakes. One increasingly utilized method for detecting novel species in aquatic systems is environmental DNA (eDNA). We have developed and applied novel genetic markers for eDNA detection of high risk invasive vertebrates, invertebrates, and plants in the Great Lakes region. In addition to these species-specific assays, which inform presence/absence detections of the organisms of interest, we have designed experiments and field surveys to examine the general effectiveness of eDNA across taxonomic boundaries and under varying environmental conditions. We hypothesize that eDNA detectability may differ systematically among major taxonomic groups because of taxa-specific differences in morphology (including the presence-absence of an exoskeleton), physiology, and habitat (e.g., benthic vs. pelagic, littoral vs. off-shore).

Results/Conclusions

We developed novel genetic markers for environmental DNA (eDNA) detection of 11 species in the Great Lakes region. These markers have been validated at either the mesocosm scale, in the field, or in some cases, both. Detection capabilities have been shown for a variety of taxa, including planktonic crustaceans (spiny water flea and native water flea), benthic decapods (signal and rusty crayfish), malacostracans (Bloody red shrimp and Hyalella), bivalve mollusks (asian pea clam), benthic fishes (Eurasian ruffe), and plants (Hydrilla, parrot’s feather and pondweed). For some species, we found differences in presence/absence detection or abundance based upon differences in depth sampling on a gradient or location of sampling in a lotic system (e.g., up or downstream). We measured eDNA longevity under varying environmental conditions in mesocosms for four taxa and found differences ranging from 26-32 days. All taxonomic groups produced eDNA within the first 24 hours in the experimental setting. Overall, our results indicate that most aquatic organisms can be detected with eDNA. Tailoring sampling methods to specific taxonomic groups may be necessary. Use of eDNA will continue to improve early detection surveillance efforts in the Great Lakes region, reducing future environmental and economic damages.