Abstract:

The aerial parts of the plants, which are dominated by leaves, represent one of the largest terrestrial habitats for microorganisms. There is a growing interest to study commensal bacteria to elucidate their interactions with the plants, among each other and to learn how they withstand the hostile conditions of their habitat. A predominance of Proteobacteria, Actinobacteria and Bacteroidetes living in the phyllosphere of numerous plants has been revealed, while metagenomics and metaproteomics approaches gave insights into the general bacterial adaptation strategies to the phyllosphere. We conducted large-scale experiments to isolate Arabidopsis thaliana leaf bacteria as pure cultures. Individual plants as well as individual leaves were sampled at different European sites to determine their core leaf community and to establish a reference strain collection using flow cytometry and dilution series plating. After identifying approximately 3,000 isolates using a high-throughput DNA sequencing-based method we selected more than 200 representative strains belonging to 52 genera of the major phyllosphere phyla covering the majority of the culture-independent taxonomic diversity. Draft genomes of all selected isolates were generated. Recolonization experiments using synthetic communities in a gnotobiotic model system showed reproducible colonization patterns and represents a valuable starting point to identify mechanisms of community formation and function. Examination of plant responses to its microbiota revealed that the plant reacts differently to members of its natural phyllosphere microbiota. A subset of commensals increase expression of defense-related genes and thereby contribute to plant health and performance.

Selected papers (by Johannes):

Bai, Y., Müller, D.B., Srinivas, G., Garrido-Oter, R., Potthoff, E., Rott, M., Dombrowski, N., Münch, P.C., Spaepen, S., Remus-Emsermann, M., et al. (2015). Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528, 364–369.

Delmotte, N., Knief, C., Chaffron, S., Innerebner, G., Roschitzki, B., Schlapbach, R., Mering, von, C., and Vorholt, J.A. (2009). Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. PNAS 106, 16428–16433.

Peyraud, R., Kiefer, P., Christen, P., Massou, S., Portais, J.-C., and Vorholt, J.A. (2009). Demonstration of the ethylmalonyl-CoA pathway by using 13C metabolomics. PNAS 106, 4846–4851.

Publication list:

http://www.micro.biol.ethz.ch/research/vorholt/publications.html