Candidatus Accumulibacter: a refined phylogeny reveals the existence of novel species, their potential function, and their global distribution.

Candidatus Accumulibacter is the first microorganism identified as polyphosphate-accumulating organism (PAO), essential for phosphorus (P) removal from wastewater. However, the current taxonomic of this lineage is flawed, with the majority of the publicly available genomes or 16S rRNA gene sequences classified as “Candidatus Accumulibacter phosphatis”, despite notable phylogenetic divergence. The use of the ppk1 marker gene for fine-scale differentiation into “clades” has further increased the confusion in taxonomic assignment. Here, we provide a reassessment of the phylogeny of Ca. Accumulibacter, using a comparison between genome-, ppk1, and 16S rRNA gene-based phylogenies from a comprehensive dataset. With this approach, several novel species were identified and some were targeted by new species-specific FISH probes. The MiDAS4 global survey, containing samples from 667 wastewater treatment plants (WWTPs) located in 33 different countries, was used to investigate their geographical distribution and factors that may influence their abundance. Ca. Accumulibacter had a higher relative abundance in WWTPs with P removal and was globally distributed, indicating the process design as a major driver for their presence. Metabolic annotation and FISH-Raman microspectroscopy confirmed the potential for the PAO metabolism in all Ca. Accumulibacter species, with detection in situ of the typical PAO storage polymers. The annotation revealed fine-scale differences in the nitrate/nitrate reduction pathways, giving some insights into niche differentiation, and explaining to some extent how they could contribute to overall nutrient removal.