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Plants harbor abundant and diverse bacterial microbiota.Culture-independent 16S rRNA gene profiling revealed distinctive bacterial communities associated with Arabidopsis roots and leaves.The availability of comprehensive pure cultures of root-and leaf-derived bacteria is critical to deeply understand the colonization ability and organ specificity of Arabidopsis-associated bacteria in a bacterial community context.We established Arabidopsis root-and leaf-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detected by previous 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 illustrated that the isolates form bacterial communities resembling natural microbiotas on their cognate host organs,and root-and leaf-derived bacteria have specific roles in the microbiota establishment of their original niches.The comprehensive bacteria culture collections and high quality genomes together with the remarkable reproducibility of the gnotobiotic reconstitution system enable future studies on bacterial community establishment and functions under laboratory conditions(Bai et al.,2015,Nature).