Ecophysiology and niche differentiation of three genera of polyphosphate-accumulating bacteria in a full-scale wastewater treatment plant

Polyphosphate-accumulating organisms (PAOs) are the main bacteria responsible for phosphorus removal and recovery in full-scale wastewater treatment plants (WWTPs). They encompass members of the genera <i>Candidatus</i> Accumulibacter, <i>Azonexus</i> (formerly <i>Dechloromonas</i>), and <i>Candidatus</i> Phosphoribacter (formerly <i>Tetrasphaera</i>), with most studies focusing on <i>Ca</i>. Accumulibacter, primarily using lab-scale enrichment cultures. Although members from the three genera often co-exist in full-scale WWTPs, the metabolic capabilities and traits that determine the niche differentiation of the specific species are still unknown. We retrieved 214 high-quality metagenome-assembled genomes from a full-scale plant with phosphorus removal and examined the polyphosphate-related metabolic pathways using genome-resolved metatranscriptomics in the different process tanks <i>in situ</i> and by using short-term incubations <i>ex situ</i>. We observed the co-existence of nine uncultured PAO species from the three genera with clear niche differentiation in the utilization of different carbon sources and involvement in the denitrification process. Additionally, we observed several physiological differences among species of the same genus, indicating variations in niche specialization. This suggests that biological P removal and other processes in full-scale WWTPs are carried out by a complex and diverse PAO community that together ensures stable plant performance.IMPORTANCEThe current understanding of the ecology and physiology of polyphosphate-accumulating organisms (PAOs) is mostly based on <i>Candidatus</i> Accumulibacter, primarily studied in enriched lab-scale studies. Recent taxonomic reclassification revealed that the most studied <i>Ca</i>. Accumulibacter species are either not present or present in low abundance in full-scale wastewater treatment plants (WWTPs). This raises concerns that knowledge from lab-scale studies may not apply to species in full-scale plants. Additionally, the indication of a distinct PAO physiology in <i>Candidatus</i> Phosphoribacter compared to <i>Ca</i>. Accumulibacter and the other abundant PAO <i>Ca</i>. Azonexus poses further questions about the accuracy of the current PAO model. Here, we show that in full-scale plant species from <i>Ca</i>. Accumulibacter, <i>Ca</i>. Azonexus, and <i>Ca</i>. Phosphoribacter always co-exist, and they have distinct niche separations in terms of carbon source utilization and the use of electron acceptors. This co-existence and metabolic diversity indicate that a complex microbial community is crucial for efficient phosphorus removal in full-scale WWTPs.