Seasonal variation of eukaryotic communities in tertiary wastewater photobioreactors: associations with treatment performance

Microalgae-based photobioreactors offer promising alternatives for sustainable tertiary treatment of urban wastewater. While bacterial communities in these systems have been extensively studied, diversity and ecological roles of eukaryotic communities remain poorly understood. We used 18S rRNA gene metabarcoding to characterize eukaryotic diversity in outdoor photobioreactors treating secondary effluent under two hydraulic retention times (HRT) across seasons with contrasting environmental conditions. Seasonal variation strongly structured eukaryotic communities, whereas HRT effects could not be demonstrated due to unbalanced sampling design. Summer conditions, including higher temperatures and irradiance, were associated with increased relative abundance of thermotolerant chlorophytes, particularly Chlorella, and reduced representation of predator-associated taxa. This period also showed higher phosphate removal rates although the relative contributions of microalgal uptake, bacterial assimilation and physicochemical processes could not be resolved. In contrast, spring communities were characterized by a peak in rotifer-associated ASVs and a lower relative abundance of microalgae, coinciding with enhanced ammonium removal and higher biogas production from harvested biomass. Autumn and winter conditions were associated with more balanced communities comprising chlorophytes (Tetradesmus and Desmodesmus), rotifers and amoebae, together with reduced nutrient removal efficiency. Exploratory co-occurrence network analysis suggested season-specific associations among taxa, reflecting changes in community organization. Overall, results demonstrate consistent associations between seasonal variation in eukaryotic community composition and photobioreactor performance under real outdoor conditions. However, because bacterial and archaeal communities were not characterized, relative contributions of eukaryotic, prokaryotic and physicochemical processes could not be disentangled. Future studies integrating eukaryotic and prokaryotic communities are needed to elucidate mechanisms underlying these associations.