Eukaryote diversity and interactions with bacterial communities within laboratory granular activated carbon biofilter treating surface water.

Top-down ecological processes in engineered drinking water biofilters remain poorly understood despite their importance for biofilter stability and performance. Here, we tracked eukaryotic community assembly over six-months and across depth in a laboratory-scale granular activated carbon biofilter from start-up. Despite consistently low richness (60-80 ASVs), eukaryotes spanned over 25 phyla and formed communities distinct from influent and effluent assemblages, indicating strong environmental selection within the biofilter. Neutral modelling identified deterministically selected taxa, including Vermamoeba, enriched beyond neutral expectations. Generalised Linear Latent Variable Models identified 24 eukaryotes and 75 bacteria with significant positive or negative correlations, including a weak positive association between Vermamoeba and Legionella. Network analysis highlighted three peripheral eukaryotes (Chaetonotida, Pterocystis, Rigifilida) exhibiting predominantly negative associations with bacteria, consistent with top-down ecological control. These findings challenge bacteria-centric models of engineered biofilms, demonstrating that low-diversity, deterministically selected eukaryotes regulate bacterial network organisation with implications for microbiome stability, biofilter function, and drinking water quality.