Functional capacities drive recruitment of bacteria into plant root microbiota.

Root-associated microbiomes are shaped by the plant, yet vary across environments and hosts, challenging prediction and engineering. Here, to uncover principles of bacterial selection at the root-soil interface, we applied a systems-level approach using reconstitution studies with communities of isolates from Arabidopsis, barley and Lotus grown in soil. Functional divergence among the microbiota of the host plants reflected distinct strategies: in Arabidopsis and barley, recruitment was primarily shaped by inoculum, while Lotus root environment favoured fewer, functionally diverse isolates, akin to a 'Swiss army knife' strategy. Despite taxonomic variability, root microbiomes encoded overlapping functions. Across major taxa, isolates with broad but distinct functional repertoires within their families were consistently more abundant. Using a genome-to-function framework that is function centric, taxonomically inclusive and host-context aware, we identified 266 functions enriched across all root microbiomes. This functional backbone emerged as a core signature of plant-associated bacteria, providing a solid foundation for microbiome engineering in agriculture.