Using environmental DNA metabarcoding to map invasive and native invertebrates in two Great Lakes tributaries

Abstract

Background Aquatic invasive species (AIS) threaten ecosystems and native species. Methods To determine spatial distributions of at‐risk native taxa and AIS in two biologically diverse Laurentian Great Lakes tributaries, we extracted environmental DNA (eDNA) from water samples and used a universal PCR primer set targeting the CO1 gene for metabarcoding of selected taxa. We sampled 43 sites for eDNA in each of the Grand and Sydenham rivers in southwestern Ontario. Results We assigned sequences to 49 taxa at the species level and four mollusks to genus level. Detected AIS included two oligochaete worms (Branchiura sowerbyi, Potamothrix moldaviensis), a freshwater jellyfish (Craspedacusta sowerbyi), a calanoid copepod (Skistodiaptomus pallidus), and a bivalve dreissenid mussel (Dreissena rostriformis bugensis). All but D. r. bugensis were previously unreported in these tributaries. Detected native mollusks included one globally endangered species the rayed bean (Villosa fabalis), one provincially listed threatened species the maple leaf mussel (Quadrula quadrula), and several other at‐risk and unique mollusk species of special interest in Ontario, Canada, and the United States (e.g., Sphaerium fabale, Pyganodon grandis). At several sampling sites in each river, AIS eDNA overlapped with or was near to sites with detections of at‐risk native mollusks. Most AIS and some native taxa demonstrated clustered detection patterns within each river. However, in some cases, independent detections of individual species occurred at individual sites within each river that were relatively far apart. Our findings should be interpreted with some caution due to the limitations of the aquatic “universal” primer set and the availability of comprehensive reference sequence databases. Conclusion Results from eDNA metabarcoding in our study helped reveal invertebrate AIS and at‐risk species distributions and will help direct approaches for conserving biodiversity in each of these Great Lakes tributaries.

Pathway to Increase Standards and Competency of eDNA Surveys (PISCeS)—Advancing collaboration and standardization efforts in the field of eDNA

“…The presence of AIS could have negative impacts on the native species and ecosystem. The results from this study highlight the analytical power of eDNA metabarcoding and its potential to direct conservation and management strategies (Mychek-Londer et al, 2019). eDNA metabarcoding of marine biodiversity was assessed by Morey et al (2020) through a pilot study at Ripley's Aquarium in Toronto, Canada.…”

Advanced molecular-based surveillance of quagga and zebra mussels: A review of environmental DNA/RNA (eDNA/eRNA) studies and considerations for future directions

“…Metabarcoding HTS methods have been successfully applied to QM-ZM eDNA surveillance efforts, where several surveillance objectives have been met using a variety of primers (Table 3). For example, COI metabarcoding primers, designed to generically target metazoans (Leray et al 2013) and/or marine invertebrates (Geller et al 2013), have been used to specifically detect ZM (Ardura et al 2017) or QM eDNA (Blackman et al 2020a) and to detect QM-ZM eDNA in community-wide surveys (Mychek-Londer et al 2020). Metabarcoding primers targeting 18S and designed to detect crustaceans, molluscs and tunicates (Zhan et al 2013), have also been used alongside HTS to detect AIS at freshwater ports, revealing the presence of QM (Brown et al 2016).…”

Improving quantification of bivalve larvae in mixed plankton samples using qPCR: A case study on Mytilus edulis

“…Environmental DNA (eDNA) studies, which analyse air, soil or water samples for the presence of intracellular or extracellular target DNA, have been used to non-invasively detect a range of species (Prié et al, 2020;Mychek-Londer et al, 2019;Günther et al, 2018;Klymus et al, 2017 or see Ruppert et al, 2019 for review).…”