Structure and assembly cues of Arabidopsis root-inhabiting bacterial communities and comparative genomics of selected Rhizobium members

The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on earth. Soil bacteria are able to colonize the root surface and even multiply inside roots as benign endophytes. Some of these bacteria modulate plant growth and development, with implications ranging from enhanced nutrition to resistance against pathogens. \nIn this study a high-resolution methodology based on pyrosequencing of the bacterial 16S rRNA marker gene was adopted to characterize and compare soil and root-inhabiting bacterial communities. Our results show that roots of Arabidopsis 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 of bacteria. Soil type defines the composition of root-inhabiting bacterial communities whereas the host genotype modulates their profiles only to a limited extent. Furthermore, bacterial communities associated to wooden sticks, representing a metabolically inactive lignocellulosic matrix for bacterial colonization, were analyzed to deconvolute actively recruited from opportunistic root microbiota members. This comparison showed that plant cell wall features appear to provide a sufficient cue for the assembly of app. 40% of the Arabidopsis root microbiota. This root- and wood-shared sub-community was mainly composed by Betaproteobacteria. In contrast, specifically recruited members of the root-inhabiting bacteria, mostly Actinobacteria, depended on cues from metabolically active host cells, defining a root-specific sub-community. \nThis culture-independent survey of the Arabidopsis root-associated bacteria was utilized to guide a targeted cultivation-based approach resulting in the isolation of members of both sub-communities of the Arabidopsis root-inhabiting bacterial microbiota. Several Rhizobium spp., which are either members of the shared or specific sub-communities, were isolated from Arabidopsis roots in pure culture and tested for plant growth promotion capabilities. Upon inoculation in a gnotobiotic system, Rhizobium spp. isolated from the specific sub-community increased shoot fresh weight of Arabidopsis, while a Rhizobium strain from the shared sub-community was not able to promote plant growth. Comparative whole-genome analysis of independent exemplars of the isolated Rhizobium spp. revealed differential gene enrichments among members of both sub-communities. Particularly, the amplification and divergence of transcription factor genes might represent a signature of differential habitat adaptation. \nThis culture-based approach backed by a broad scale culture-independent survey sets the stage to advance from descriptive characterization of bacterial communities to testing the functional significance of plant-microbiota interactions.