Spatiotemporal dynamics and potential pathogen fate of microeukaryotic communities in a full-scale waste stabilization pond system

Abstract Waste stabilization ponds (WSPs) represent a sustainable, low-cost wastewater treatment option, yet the ecological dynamics of microeukaryotic communities and their pathogenic potential remain underexplored. Here, we investigate how treatment stage and season shape microeukaryotic communities—and the fate of potentially pathogenic taxa—in a full-scale WSP, interpreting patterns with ecological assembly models to inform safe wastewater reuse. Over one year, 48 samples were collected from four stages (inlet, anaerobic, facultative, and outlet) and analyzed for physicochemical parameters and microeukaryotic communities via high-throughput 18S rRNA gene sequencing. Water quality improved markedly along the treatment train, with ≥ 75% removal of biochemical oxygen demand, chemical oxygen demand, and ammonium nitrogen. Microeukaryotic community composition was significantly structured by treatment stage and season (PERMANOVA, p < 0.001), with the highest diversity observed at the inlet. Opisthokonta, mainly heterotrophic fungi and protists, dominated all stages, while biomarker analysis revealed functional compartmentalization—Ascomycota fungi in the inlet and phototrophic taxa such as Eustigmatophyceae and Scenedesmus in later stages. Ecological modeling showed a shift from stochastic assembly (ecological drift) upstream to deterministic processes (heterogeneous selection) downstream. Notably, 150 potentially pathogenic genera were identified, including Candida , Aspergillus , Acanthamoeba , and Entamoeba , with incomplete removal of some taxa. Persistence of Candida and Saccharomyces in effluent, despite moderate removal (~ 65–81%), highlights potential public health risks. These findings provide novel insights into the ecological functioning of WSPs and underscore the need for improved pathogen monitoring using molecular approaches to ensure safe wastewater reuse.