Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns

Highlights•Crop root bacterial (CRBC) and viral (CRVC) genome categories were established•We found 1,817 undefined bacterial species and 1,572 unreported viral genera•Despite varied taxa, root microbiome functions remain conserved across plants and soils•A total of 27% of abundant bacteria in crop root microbiomes are linked to phagesSummaryReference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of crop root microbiomes. By combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (68.9% from isolates) and 1,817 undefined species, expanding crop root bacterial diversity by 290.6%. The crop root viral genome collection (CRVC) contains 9,736 non-redundant viral genomes, with 1,572 previously unreported genus-level clusters in crop root microbiomes. From these, we identified conserved bacterial functions enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria-virus connections in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture.Graphical abstract