Defining the core Arabidopsis thaliana root microbiome

Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root), and the endophytic compartment (within the root), contribute to plant growth, productivity, carbon sequestration, and phytoremediation1,2,3. Colonization of the root occurs despite a sophisticated plant immune system4,5, suggesting finely-tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. We pyrosequenced the bacterial 16S rRNA gene of >600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophyte compartment microbiota of plants grown under controlled conditions in natural soils are (i) sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and (ii) sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils, and in rhizosphere and endophyte compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophyte compartments from either soil feature overlapping low-complexity communities that are markedly enriched for Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stages and genotypes. Our work provides unprecedented rigor to define an endophyte compartment microbiome, facilitating controlled dissection of plant-microbe interactions derived from complex soil communities.