Strain-level dissection of complex rhizosphere bacterial communities using single-cell genomics and metagenomics

We demonstrated that SAGs, with higher sequence resolution, greater gene content, and broader taxonomic coverage of medium- to high-quality genomes, are better suited than MAGs for expanding the microbial tree of life in complex soil and biofilm-forming rhizoplane environments. In highly diverse soil microbiomes, metagenomes lacked sufficient coverage, with substantial information loss during MAG reconstruction. Combining SAGs with metagenomic reads revealed strain-level microbial dynamics in the rhizoplane. Additionally, SAGs provided insights into plasmid-host associations and dynamics in the rhizoplane, whereas MAGs failed to capture them.