Microalgae cultivation is proposed as an effective system for pathogens reduction and wastewater depuration, however, a full characterisation of the risks is still needed. Two raceways were inoculated with Scenedesmus, one using wastewater and the other using a fertilizer medium. Microbial community and pathogen presence were explored by next generation sequencing (NGS), commercial qPCR array and plate counts. These methods proved to be complementary for a full characterization of community structure and potential risks. Media and sampling locations contributed to shape communities and pathogenic loads. The main pathogenic genera detected were Arcobacter and Elizabethkingia (mainly in wastewater) with an important presence of Aeromonas (all samples). A lower presence of pathogens was detected in fertilizer samples, while wastewater showed a reduction from inlet to outlet. Raceways showed potential as an effective biotreatment, with most of the retained pathogens released in the outlet and only a minor part settled in the biomass.
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