Functional overlap and specialization of the Arabidopsis leaf and root microbiotas

Roots and leaves of healthy plants host taxonomically structured bacterial assemblies, and members of these communities contribute to plant growth and health. We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing. We found an extensive species intersection between the leaf and root microbiotas. Genome drafts of 400 isolates revealed a large overlap of genome-encoded functional capabilities between leaf and root-derived bacteria with few significant differences at the level of individual functional categories. Using defined bacterial communities and a gnotobiotic Arabidopsis plant system we show that the isolates form assemblies resembling natural microbiotas on their cognate host organs, but are also capable of ectopic leaf or root colonization. Whilst this raises the possibility of reciprocal relocation between a subset of root and leaf microbiota members, we also provide evidence for microbiota specialization to their respective niche.