Evaluation of eDNA qPCR monitoring as an early detection tool for a non-native mysid in Great Lakes Waters

Abstract

Early detection of aquatic invasive species (AIS) is vital to cost-effective prevention of their spread in the Great Lakes. Unfortunately, AIS surveillance has been generally too slow and geographically limited to support this purpose. Environmental DNA (eDNA) detection using quantitative polymerase chain reaction (qPCR) offers more rapid and affordable detection of likely AIS presence, but it does not directly discern live/dead status. Vital status verification using conventional surveys following positive eDNA qPCR detections could resolve this barrier, but only if the latter are adequately reliable and sensitive. Here we explore the reliability and sensitivity of eDNA qPCR monitoring for the bloody red shrimp (Hemimysis anomala), an AIS established in the southern Great Lakes but not yet widely distributed in Lake Superior, against conventional microscopy-based methods. We conducted this comparison using 1) harbor water from Muskegon Lake, MI where H. anomala is established, and 2) raw ballast water from ships transporting ballast from lower Lake Michigan to western Lake Superior. Our studies showed positive eDNA qPCR detections of H. anomala in all harbor and ballast samples for which conventional detection results were positive, and in some samples for which conventional results were negative. These results suggest that qPCR assays with adequate specificity could be an important tool in support of more effective and affordable early detection of target species in Great Lakes water, especially when combined with confirmatory conventional monitoring.