Mechanisms and dynamics underlying host preference of commensal root-associated bacteria

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Different plant species host root microbiota that differ in prevalence and relative abundance of bacterial species. Previously, I grew Lotus japonicus and Arabidopsis thaliana in gnotobiotic microbiota reconstitution systems to investigate the assembly of such plant species-specific bacterial communities, and whether commensals (not harmful bacteria) derived from a given plant species inherit a preference for their host. Synthetic bacterial communities (SynComs) designed from Lotus and Arabidopsis root culture collections were used as inoculum. I showed that, in a competition context within a mixed community of Lotus- and Arabidopsis-derived bacteria, strains accumulated to higher relative abundances on roots of their original host (“native” strains) than on the other plant species, indicating patterns of host preference among commensal bacteria. Further experiments revealed that host preference requires active host participation, and that it is linked to the ability to invade into established root communities. In this project, I aim to decipher the mechanisms and spatiotemporal dynamics of commensal host preference. My objectives are to (i) identify the impact on the plant of hosting native bacterial communities, (ii) explore colonization patterns and mechanisms of bacterial community assembly and host preference, and (iii) investigate the role of root exudates in community establishment and regulation of bacterial traits. To achieve this, I will apply transcriptomic, metabolic, genetic, and microscopy techniques with the comparative reconstitution system, in addition to state-of-the-art community profiling methods. RNA seq analysis of the two hosts co-cultivated with native and non-native SynComs and targeted downstream experiments will identify host genetic factors involved in bacterial host preference. Evaluating plant performance under biotic and abiotic stresses in the presence of SynComs will reveal potential benefits of hosting specific communities. Using spatiotemporal observation of root colonization by fluorescently tagged commensals alone and in a community context, I will address if native strains display host-specific colonization patterns, and if these are disturbed by non-native communities and vice versa. By coupling community profiling of bacterial SynComs after in vitro incubation in plant species-specific exudates with the exudates’ metabolomic profiling, I aim to identify compounds triggering host-specific microbiota assembly and host preference. Furthermore, the characterization of bacterial metatranscriptomes after incubation of native and non-native SynComs in different root exudates will identify both common and specific commensal traits induced by the two hosts. Overall, with this research programme, I will advance our understanding of plant microbiota establishment and commensal host preference, which has implications for eco-friendly and sustainable agricultural practices.