ROOTMICROBIOTA · Structure, function and evolution of bacterial root microbiota

The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on earth. Roots grow in intimate association with a root microbiota that is distinct from the complex microbial community present in surrounding soil. A subset of soil bacteria is able to multiply inside roots as benign endophytes and modulate plant growth and development, with implications ranging from enhanced crop productivity to phytoremediation. Endophytic colonization represents an apparent paradox of plant innate immunity because plant cells can detect an array of evolutionary conserved microbe-associated molecular patterns to initiate immune responses and terminate microbial multiplication. We have developed an experimental platform to characterize soil, rhizosphere (the zone of soil influenced by roots) and root-inhabiting bacterial communities of Arabidopsis thaliana, grown in contrasting natural soils under controlled environmental conditions. This revealed that A. thaliana roots are preferentially colonized by Proteobacteria, Bacteroidetes, Chloroflexi 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. I propose to apply reductionist approaches to examine microbiota evolution and functions within in a single phylogenetic framework of host species. Towards this objective, we will utilize a combination of genomics, cell biological and microbial transplantation tools.