Shared and distinct bacterial genes benefiting colonization of distantly related host plant species

In nature, plants recruit a diverse microbial community, the plant microbiome, which is distinct from the surrounding soil community and is important for plant growth and development. To understand the forces that shape the plant microbiome we first need to characterize the microbial traits and mechanisms that contribute to plant colonization. Here, we used barcoded mutant libraries to identify bacterial genes that contribute to the ability of two plant-associated bacteria to colonize a monocot and a eudicot host, in a long-term, soil-like system. We show that plant colonization was not dominated by a single trait, but rather by dozens of genes and functions contributing to colonization. While many of these colonization traits were shared between the two host plant species, some contributed to the colonization of only one host or of a specific organ, and not the other. We highlight different efflux systems, that specifically contribute to colonization of either above- or below-ground tissues. These efflux systems are prevalent among proteobacteria and enriched among plant colonizers. Overall, our results present a comprehensive characterization of bacterial traits benefiting the colonization of distantly related plant species. Such differentiating genes may help understand the observed variation between microbiomes of different plants and promote the prediction and design of plant-specific microbiota.