Abstract
Summary Enhanced biological phosphorus removal ( EBPR ) is an important industrial wastewater treatment process mediated by polyphosphate‐accumulating organisms ( PAOs ). Members of the genus C andidatus A ccumulibacter are one of the most extensively studied PAO as they are commonly enriched in lab‐scale EBPR reactors. Members of different A ccumulibacter clades are often enriched through changes in reactor process conditions; however, the two currently sequenced A ccumulibacter genomes show extensive metabolic similarity. Here, we expand our understanding of A ccumulibacter genomic diversity through recovery of eight population genomes using deep metagenomics, including seven from phylogenetic clades with no previously sequenced representative. Comparative genomic analysis revealed a core of shared genes involved primarily in carbon and phosphorus metabolism; however, each A ccumulibacter genome also encoded a substantial number of unique genes (> 700 genes). A major difference between the A ccumulibacter clades was the type of nitrate reductase encoded and the capacity to perform subsequent steps in denitrification. The A ccumulibacter clade IIF genomes also contained acetaldehyde dehydrogenase that may allow ethanol to be used as carbon source. These differences in metabolism between A ccumulibacter genomes provide a molecular basis for niche differentiation observed in lab‐scale reactors and may offer new opportunities for process optimization.