The plant root defines the interface between amulticellular eukaryote and soil, one of the richest microbial ecosystems on Earth(1). Notably, soil bacteria are able to multiply inside roots as benign endophytes and modulate plant growth and development(2), with implications ranging from enhanced crop productivity(3) to phytoremediation(4). Endophytic colonization represents an apparent paradox of plant innate immunity because plant cells can detect an array of microbeassociated molecular patterns (also known as MAMPs) to initiate immune responses to terminate microbial multiplication(5). Several studies attempted to describe the structure of bacterial root endophytes(6); however, different sampling protocols and low-resolution profiling methods make it difficult to infer general principles. Here we describemethodology to characterize and compare soil-and rootinhabiting bacterial communities, which reveals not only a function formetabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization. We showthat the roots ofArabidopsis thaliana, grown in different natural soils under controlled environmental conditions, are preferentially colonized by Proteobacteria, Bacteroidetes and Actinobacteria, and each bacterial phylum is represented by a dominating class or family. Soil type defines the composition of root-inhabiting bacterial communities and host genotype determines their ribotype profiles to a limited extent. The identification of soil-type-specific members within the root-inhabiting assemblies supports our conclusion that these represent soil-derived root endophytes. Surprisingly, plant cell-wall features of other tested plant species seem to provide a sufficient cue for the assembly of approximately 40% of the Arabidopsis bacterial root-inhabitingmicrobiota, with a bias for Betaproteobacteria. Thus, this root sub-community may not beArabidopsis-specific but saprophytic bacteria that would naturally be found on any plant root or plant debris in the tested soils. By contrast, colonization of Arabidopsis roots by members of the Actinobacteria depends on other cues from metabolically active host cells.