Season is the Main Driver of Changes in Biodiversity and Functional Roles of Eukaryotes in Photobioreactors Used in a Wastewater Treatment Plant in Southern Europe

Abstract

The use of microalgae-based photobioreactors (PBRs) offers a promising alternative for the sustainable tertiary treatment of urban wastewater. While the role of bacteria in such systems is well studied, the diversity and ecological function of eukaryotic communities remains poorly understood. Here, we used 18S rRNA gene amplicon sequencing to characterize eukaryotic diversity in outdoor PBRs operated with different hydraulic retention times over four seasons, fed with real wastewater. Our results revealed strong seasonal structuring of the communities, shaped by predator–prey interactions and temperature-dependent selection. Summer was dominated by thermotolerant microalgae such as Chlorella, likely due to reduced grazer pressure, and coincided with the highest phosphate removal which was likely performed by Chlorella under phosphorus depletion conditions. In contrast, spring showed a peak in rotifer abundance and low microalgal biomass, correlating with enhanced biogas and methane production, as well as improved ammonium removal—possibly driven by rotifer-mediated nutrient cycling. Autumn and winter communities were more balanced, with co-occurrence of chlorophytes (Tetradesmus, Desmodesmus) and predators such as rotifers and amoebae. However, nutrient removal efficiency declined during these cooler, rainier seasons, likely due to increased rainfall-driven dilution and reduced phosphorus uptake under suboptimal N:P ratios. Correlation and network analyses highlighted season-specific interactions among taxa, reflecting complex ecological dynamics. These findings demonstrate the critical role of eukaryotic communities in influencing both biomass composition and nutrient removal, offering valuable insights for the seasonal optimization of PBR performance in wastewater treatment.

Keywords: Metagenomics, Eukaryotic communities, Microalgal wastewater treatment, Biodiversity