Intralineage Diversity and Global Biogeography of Ca . Phosphoribacter

In wastewater treatment plants (WWTPs), the newly defined polyphosphate-accumulating organism (PAO) “ Candidatus Phosphoribacter” demonstrated important contributions to phosphorus removal. However, their phylogenetic and metabolic diversity, as well as ecological distributions, remain largely uncharacterized. By sequencing 81 activated sludge samples from 34 provinces in China and integrating 747 WWTP metagenomes from six continents, we recovered 166 metagenome-assembled genomes (MAGs) of this genus, expanding the number of Ca . Phosphoribacter MAGs by 17 times and identifying 12 novel species. Biogeographical analysis demonstrated their distinct intercontinental distribution. The coexistence of cosmopolitan species and regionally dominant ones was observed globally as a result of metabolic differentiation. Ancestral gene family reconstruction indicated that this genus underwent a streamlining process dominated by gene loss. Vertically inherited ppk2 and horizontally acquired phoU jointly underpinned the genetic basis of a PhoU-dysregulation-driven polyphosphate phenotype. Comparative genomics revealed broad metabolic potential, including versatile carbon utilization, α-glucan metabolism, and three complementary denitrifying phenotypes. Metatranscriptomic analyses further supported glucose uptake and potential α-glucan cycling as a carbon storage polymer. Overall, this study establishes the most comprehensive genomic framework of Ca . Phosphoribacter, elucidates their functional metabolisms, ecological roles, and global distributions, providing new insights into Ca . Phosphoribacter-mediated enhanced biological phosphorus removal (EBPR) for improved engineering implementation and system sustainability.