Unveiling soil microbial diversity through ultra-deep short-read metagenomic sequencing and co-assembly

By combining ultra-deep short-read shotgun metagenomic sequencing with 5-sample co-assembly across 600 agricultural soil samples, we significantly enhanced the representation and recovery of microbial communities in both clay and sandy soils. Despite an average of 107 Gb clean reads per sample, projections indicated that 1-4 Tb per sample would be required to capture 95% of the microbial community. Co-assembly of five biological replicates markedly improved metagenomic recovery, yielding up to 3.7× more metagenome-assembled genomes, up to 95% more unique genes, and broader recovery of prokaryotic phyla compared to single-sample assemblies.