Evaluation of qPCR-Based Environmental Messenger RNA (emRNA) in Aquatic Weed Biosecurity: A Case Study of Amazon Frogbit

Abstract

Environmental DNA (eDNA) is a highly sensitive tool widely used in biodiversity studies and for detecting organisms of biosecurity or conservation importance. However, the persistence of eDNA, even after the removal of an organism, can complicate interpretation and lead to false indications of ongoing presence. In contrast, environmental RNA (eRNA) is short-lived and may offer improved spatiotemporal precision for detecting living organisms. In this study, we evaluated the viability of environmental messenger RNA (emRNA) for targeted detection of aquatic weeds, using Amazon frogbit (Hydrocharis laevigata) as a model species. A highly sensitive qPCR assay, targeting the chloroplast rpoB transcript, was used alongside positive and negative controls to ensure workflow reliability. Our results showed that emRNA was undetectable at low density (0.56 plants per litre) and was consistently detectable at very high abundance (over eight plants per litre), although copy numbers were very low. These findings suggest that the effective detection threshold for emRNA may exceed densities typically encountered during early invasion. Consequently, the qPCR-based emRNA approaches evaluated in this study showed limited applicability for biosecurity surveillance, where reliable detection at low abundance is essential. Future research should focus on improving detection sensitivity, including eRNA enrichment.