Hidden in plain sight: The invasive macroalga Caulerpa prolifera evades detection by environmental DNA methods

Abstract

Environmental managers need a rapid and cost‐effective monitoring tool for tracking the spread of invasive species, particularly at the onset of introduction. The macroalgae Caulerpa prolifera is considered an invasive species outside its native range, colonizing large patches of seafloor, reducing native species, and altering ecosystem functioning. Here, we developed a droplet digital PCR assay for detection of C. prolifera from environmental DNA seawater samples using the internal transcribed spacer (ITS) region. While the assay itself was confirmed to be highly efficient, we discovered concentrations of C. prolifera eDNA were present below detectable levels in the water column surrounding an outbreak. To understand why, we conducted tank‐based experiments for two California invasive algae species, Caulerpa prolifera and Sargassum horneri. The steady‐state eDNA concentration (eDNA copies/ gram of biomass detected) of C. prolifera was found to be two orders of magnitude lower than S. horneri. A meta‐analysis of steady‐state concentrations reported in the literature showed a remarkable range from ~104–1011 (copies/g), revealing C. prolifera to have the lowest recorded steady‐state concentrations of eDNA of any known species. We attribute C. prolifera's low steady‐state eDNA concentration to its unique biology as a unicellular macroscopic algae which reduces the possible modes of eDNA release compared to similarly sized multicellular organisms. Critically our results demonstrate the potential limits of eDNA approaches, the influence of shedding rates in the reliability of species detections, and the vital importance of benchmarking and validating eDNA assays in both field and laboratory settings.