Nature, 2012 August 2; 488(7409): 86–90. This study defines the core Arabidopsis thaliana root microbiome. Researchers sequenced the bacterial 16S ribosomal RNA gene of over 600 Arabidopsis thaliana plants to investigate the microbiota in the rhizosphere (root surrounding) and endophytic compartment (within the root). They found that these microbiota are significantly influenced by soil type and host genotype, with distinct bacterial communities in different soils and compartments. The endophytic compartment showed overlapping, low-complexity communities enriched in Actinobacteria and specific families from other phyla. Some bacteria varied quantitatively between developmental stages and genotypes. The study provides a rigorous definition of the endophytic microbiome, facilitating controlled dissection of plant-microbe interactions. Roots influence the rhizosphere by altering soil pH, structure, oxygen availability, antimicrobial concentration, and quorum-sensing mimicry, and by providing an energy source of dead root material and carbon-rich exudates. The microbiota in this niche can benefit or harm plant health. Mutualistic microbes may provide nutrients, suppress pathogens, or help plants withstand environmental stresses. The rhizosphere community is a subset of soil microbes that become endophytic after interacting with the host. Arabidopsis and other Brassicaceae are not well colonized by arbuscular mycorrhizal fungi, implying other microorganisms may fill this niche. Microbial community structure varies across plant species, and host-genotype-dependent differences in microbial associations have been reported. However, previous studies used small sample sizes and low-resolution techniques, potentially confounded by off-target sequences. The study developed a robust experimental system using high-throughput sequencing to sample the root microbiome. Results confirmed earlier conclusions and provided insights into the functional capacity of the microbiome and host genes contributing to microbial associations. The study sequenced 16S rRNA gene amplicons from eight Arabidopsis accessions, revealing distinct bacterial communities in different soils and compartments. The endophytic compartment showed a shared set of OTUs and a set specific to each soil. The microbiome was dominated by Actinobacteria, Proteobacteria, and Firmicutes, and depleted of Acidobacteria, Gemmatimonadetes, and Verrucomicrobia. The study identified specific OTUs enriched in the endophytic compartment, suggesting a core microbiome. The findings highlight the importance of host-genotype and soil type in shaping the root microbiome, with implications for plant health and agriculture. The study also demonstrated the robustness of the endophytic microbiome and its potential for plant probiotics. The results suggest that the Arabidopsis root microbiome assembles based on core ecological principles, similar to the mammalian microbiome. The study provides a frameworkNature, 2012 August 2; 488(7409): 86–90. This study defines the core Arabidopsis thaliana root microbiome. Researchers sequenced the bacterial 16S ribosomal RNA gene of over 600 Arabidopsis thaliana plants to investigate the microbiota in the rhizosphere (root surrounding) and endophytic compartment (within the root). They found that these microbiota are significantly influenced by soil type and host genotype, with distinct bacterial communities in different soils and compartments. The endophytic compartment showed overlapping, low-complexity communities enriched in Actinobacteria and specific families from other phyla. Some bacteria varied quantitatively between developmental stages and genotypes. The study provides a rigorous definition of the endophytic microbiome, facilitating controlled dissection of plant-microbe interactions. Roots influence the rhizosphere by altering soil pH, structure, oxygen availability, antimicrobial concentration, and quorum-sensing mimicry, and by providing an energy source of dead root material and carbon-rich exudates. The microbiota in this niche can benefit or harm plant health. Mutualistic microbes may provide nutrients, suppress pathogens, or help plants withstand environmental stresses. The rhizosphere community is a subset of soil microbes that become endophytic after interacting with the host. Arabidopsis and other Brassicaceae are not well colonized by arbuscular mycorrhizal fungi, implying other microorganisms may fill this niche. Microbial community structure varies across plant species, and host-genotype-dependent differences in microbial associations have been reported. However, previous studies used small sample sizes and low-resolution techniques, potentially confounded by off-target sequences. The study developed a robust experimental system using high-throughput sequencing to sample the root microbiome. Results confirmed earlier conclusions and provided insights into the functional capacity of the microbiome and host genes contributing to microbial associations. The study sequenced 16S rRNA gene amplicons from eight Arabidopsis accessions, revealing distinct bacterial communities in different soils and compartments. The endophytic compartment showed a shared set of OTUs and a set specific to each soil. The microbiome was dominated by Actinobacteria, Proteobacteria, and Firmicutes, and depleted of Acidobacteria, Gemmatimonadetes, and Verrucomicrobia. The study identified specific OTUs enriched in the endophytic compartment, suggesting a core microbiome. The findings highlight the importance of host-genotype and soil type in shaping the root microbiome, with implications for plant health and agriculture. The study also demonstrated the robustness of the endophytic microbiome and its potential for plant probiotics. The results suggest that the Arabidopsis root microbiome assembles based on core ecological principles, similar to the mammalian microbiome. The study provides a framework