Crop root bacterial and viral genome resources unveil novel species and conserved patterns of root microbiomes
Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of crop root microbiomes. Combining high-throughput bacterial cultivation with metagenomic sequencing, we systematically constructed crop root bacterial and viral genome collections from wheat, rice, maize and alfalfa. The crop root bacterial genome collection, CRBC, dramatically expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes. From these data, we identified conserved bacterial functions enriched in root microbiomes across multiple crops and soil sources, and found unexplored bacteria and virus interactions in crop root ecosystems.