This study recovered 1083 high-quality metagenome-assembled genomes (MAGs) from activated sludge, including a novel genus involved in phosphate removal. These MAGs, combined with long-term amplicon sequencing data, reveal insights into the structure and function of complex microbial communities crucial for wastewater treatment and resource recovery.

R.H.K., M.A., S.M.K., and P.H.N. own DNASense ApS. The remaining authors declare no competing interests.

This study provides significant advancements in our understanding of activated sludge microbiomes. The methodology used, including the combination of long- and short-read sequencing, has enabled the high-throughput production of 1083 high-quality metagenome-assembled genomes (MAGs), which account for ~30% of the community based on relative abundance. The MAGs meet the stringent MIMAG high-quality draft requirements and provide crucial links between 16S rRNA gene-based studies and gene repertoires, including the characterization of the novel genus Ca. Methylophosphatis, which plays a significant role in phosphate recovery in the activated sludge system. The generation of an HQ MAG database, combined with the linkage to the MiDAS3 amplicon sequencing data, offers significant value for targeting specific functional groups and improving resource recovery and wastewater treatment strategies, which is highly important in the face of growing human population demands and sustainability needs. Overall, the research is well-executed, with high-quality data, a sound methodology, and clear impact.