Application of the μAqua microarray for pathogenic organisms across a marine/freshwater interface

•The European Project μAqua (FP7-KBBE-2010-4, 265409) was conceived as a project to make novel tools for the early and sensitive detection of freshwater-borne pathogens and cyanobacterial toxins.•The novel tools developed in μAqua were a phylochip (microarray), which identifies the presence of freshwater pathogenic targets using RNA barcodes and a RT-PCR microarray to amplify the mRNA captured by the barcodes for genes involved in cyanobacterial toxin synthesis.•We present results for three sites in along the Mediterranean coast of south-east France ranging from fresh to brackish to full strength seawater to test the applicability of the probes across the marine/freshwater boundary and infer the distribution of these pathogens across these boundaries.•The results for the cyanobacteria and Protozoa are reported here.•As freshwaters flow into marine systems, these pathogens and their toxins flow into a different environmental habitat.•Nevertheless these pathogens and toxins can still cause health problems in the marine environment and this paper shows the application of a phylochip across these different habitats. Monitoring drinking water quality is an important public health issue and pathogenic organisms present a particularly serious health hazard in freshwater bodies. However, many pathogenic bacteria, including cyanobacteria, and pathogenic protozoa can be swept into coastal lagoons and into near-shore marine environments where they continue to grow and pose a health threat to marine mammals and invertebrates. In this study, we tested the suitability of a phylochip (microarray for species detection) developed for freshwater pathogenic organisms to be applied to samples taken across a marine/freshwater interface at monthly intervals for two years. Toxic cyanobacteria and pathogenic protozoa were more numerous in a coastal lagoon than at the freshwater or marine site, indicating that this microarray can be used to detect the presence of these pathogens across a marine/freshwater interface and thus the potential for toxicity to occur within the entire watershed.