Elucidating the role of microbial metabolites in stabilising and protecting the leaf microbiome

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The oomycete pathogen Albugo laibachii plays an important role in structuring the phyllosphere microbiome of Arabidopsis thaliana. Plant-associated microbial communities are known to provide protection against pathogens, at least in part, through the production of specialised metabolites that suppress the activity of pathogen-derived proteases. Thanks to the advances in next-generation sequencing and non-targeted mass spectrometry, we have gained new insights into the community and metabolic dynamics of the plant microbiota. Nevertheless, we are just at the beginning of fully capturing the sheer number and complexity of the community members and the countless, still unknown, metabolites they produce. The molecular mechanisms underlying microbe-microbe and plant-microbe interactions remain thereby mainly elusive. So far, only a few metabolites have been identified as plant-protecting agents but the full protective potential of a microbiome through the synergistic action of multiple microbial compounds remains largely hidden. To shed light on the bioactive potential of the exo-metabolome of the plant microbiome as a whole, I will apply a multi-modal functional metabolomics strategy that provides information on the potential protease inhibitory activity of all the compounds secreted by a predefined synthetic microbial community. Our focus will be on the stabilisation of the microbial community composition mediated by protease inhibition and the related plant-beneficial activities through synergistic interactions with other defence strategies. Connecting those activities to individual metabolites will allow us to better understand the beneficial effects of the community as a whole and how dysbiosis may contribute to pathogenesis. It will also allow for the rational design of next-generation microbiome derived biocontrol agents which are urgently needed for a more sustainable agriculture.