Using environmental <scp>DNA</scp> to detect <i>Microseira wollei</i> (Oscillatoriales), a benthic harmful algal bloom, in Lake St. Clair (Michigan, <scp>USA</scp> )

Abstract Microseira wollei is a benthic cyanobacterium that can cause harmful algal blooms (HABs) and often requires management. However, a pervasive challenge for M. wollei management is characterizing the spatial and temporal extent of an impacted area, which can be time and resource intensive. Therefore, the aim of this study was to evaluate environmental DNA (eDNA) as a method for detecting benthic M . wollei using surficial water samples. To meet this objective, this study analyzed water samples collected from areas around Lake St. Clair, Michigan, USA, including regions impacted by M . wollei and secondary rivers (e.g., Clinton River) where no apparent M . wollei biomass was present. Split water samples were analyzed for the presence of M . wollei using traditional light microscopy and compared to eDNA methods using metabarcoding with a universal polymerase chain reaction (PCR) primer. With metabarcoding, we detected Microseira genetic material from the visible onshore biomass up to 93 m into Lake St. Clair and approximately 1–2 m from lakebed biomass. Notably, M. wollei was not discerned using light microscopy of any water samples concurrently collected with eDNA, suggesting greater detection power using the eDNA tool. Our combined datasets provide evidence of the benefits of the eDNA tool in characterizing the spatial extent of M. wollei within large, shallow, HAB‐impacted waterbodies and their connected waterways.