Profiling microalgal cultures growing on municipal wastewater and fertilizer media in raceway photobioreactors

•Both media developed spontaneous microalgae blooms and showed the presence of algal grazers.•Reactors showed sanitizing activity, though some target organisms were found in outlet flow.•Retained pathogens are released in the outlet with only few settled in the biomass.•qPCR and NGS identified additional risks overlooked by standard plate cultivation.•The necessity of posttreatments and protection devices was identified.