Freshwater and Sediment Host Distinct Yet Overlapping Microeukaryotic Communities, With Sediment Communities Less Impacted by Treated Wastewater.

Freshwater and sediment environments host diverse microeukaryotic communities that differ in structure and composition, yet exhibit taxonomic overlap. Using 18S V9 rRNA gene sequencing, we compared communities from these habitats in controlled 10-day mesocosm experiments, examining diversity, overlap, and responses to treated wastewater (TWW). Habitat type was the strongest determinant of community composition: sediments displayed higher diversity and greater temporal stability than freshwater communities. While many taxa were shared, highly dominant OTUs were mostly rather habitat-specific, whereas taxa occurring evenly across both habitats were generally rare. Distinct trophic structures further distinguished the habitats, with sediments showing relatively balanced assemblages of phototrophs, mixotrophs, consumers, and parasites, while freshwater communities were dominated by consumers. TWW exposure induced pronounced but transient changes in freshwater communities, including an initial increase in richness from allochthonous taxa, followed by partial convergence toward controls, whereas sediment communities remained largely unaffected. We identified 14 taxa associated with TWW, nine of which have not previously been linked to wastewater, highlighting their potential as bioindicators. Our findings reveal contrasting sensitivity and resilience of freshwater microeukaryotic habitats and emphasize the importance of integrating both water column and sediment communities in monitoring and assessing the ecological impacts of treated wastewater.