Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
e-mail: schlef@mpipz.mpg.de
We have previously shown that healthy roots of Arabidopsis thaliana, grown in natural soils, are colonized by a bacterial consortium with well-defined taxonomic structure. Members of this root microbiota belong mainly to the phyla Actinobacteria, Bacteroidetes, and Proteobacteria (Bulgarelli et al., Nature 2012). A comparison of the bacterial root microbiota of A. thaliana with A. thaliana relatives, grown under controlled environmental conditions or collected from natural habitats, demonstrated a largely conserved microbiota structure with quantitative, rather than qualitative, species-specific footprints (Schläppi et al., PNAS 2014). Unlike this, the root microbiota of monocotyledonous barley and dicotyledonous A. thaliana, grown in the same soil type, revealed a similar overall structure, but with several bacterial taxa uniquely enriched in the Brassicaceae (Bulgarelli et al., Cell Host&Microbe, in press). This suggests bacterial root microbiota structure is an ancient plant trait that was already present in the last common ancestor of monocotyledonous and dicotyledonous plants. We have isolated ~60% of the A. thaliana root-enriched microbiota members as pure bacterial cultures and have generated whole-genome sequence drafts for all microbiota members, enabling systematic analysis of root microbiota functions under laboratory conditions. Using gnotobiotic plant growth systems we show that single microbiota members or synthetic bacterial communities protect the plants against several tested soil-borne fungal pathogens, suggesting that indirect pathogen protection is a physiological function of the bacterial root microbiota. I will also illustrate how we utilize synthetic communities and gnotobiotic plant systems to better understand principles underlying root microbiota establishment.