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Abstract

The bacterial genera Pseudomonas and Sphingomonas dominate the phyllosphere of wild Arabidopsis thaliana. Many Pseudomonas isolates from A. thaliana are pathogenic, reaching high titers in wild plants, while Sphingomonas do not reach such loads but are more consistent in

abundance. Prior work showed that some can protect against pathogens. Many members of both genera seem to be commensals. We compare the genomes of hundreds of endophytic Sphingomonas isolates collected from a wild population of A. thaliana to investigate intra- and inter-plant strain diversity, and contrast this with Pseudomonas diversity in the same plants, which previous research has shown are colonized primarily by a putatively pathogenic lineage. To help understand the persistence of strain-level diversity, we surveyed the local plant host range of these strains. We used a new approach, culturing both genera in bulk from A. thaliana and other plant families, in spring and also in summer before the germination of the next cohort of A. thaliana. We sequenced the bulk cultures as metagenomes and mapped reads to local reference genomes. These data, together with 16S rDNA amplicon data of the plants and genomes of bacteria isolated from the other plant species, reveal that common bacterial strains on A. thaliana thrive on other local hosts. This suggests that other hosts may be equally or more important for the evolution of these bacteria, despite the great success of these strains on A. thaliana.