The functional ecology of plant microbiome interactions between Pseudomonas bacteria and the fungal wheat pathogen Zymoseptoria tritici

Plants are exposed to a wide range of pathogenic fungi and bacteria. It has been shown that the outcome of individual interactions between pathogen and plant cannot be understood in isolation, as the presence of other microorganisms can act synergistically or antagonistically in the disease progression. Yet, the understanding of complex, i.e. at least tripartite interactions is largely missing. Here, we will establish a new microbiome interaction model using tripartite interactions of bacteria, fungi and plants. For this, we focus on wheat, Zymoseptoria tritici, the major fungal pathogen of wheat, and the bacteria Pseudomonas, a dominant member of the phyllosphere. We will characterize how intra-specific variation in a fungal pathogen determines microbial activities in the phyllosphere using genome-wide association mapping. In addition, we will characterize how differential gene expression of the fungus and the bacteria influences the outcome of bacterial-fungal competition. Our results will provide insights into the mechanism of competitive exclusion in the phyllosphere microbiome. We will generate knowledge of the exact loci that fungi evolved as defenses against Pseudomonas. The identification of such previously unknown loci will likely promote the description of new antimicrobial compounds that could be assessed for agricultural and even human applications.