Projects

Agricultural crops perform well below their maximum potential and improving their performance is a key step toward ensuring food security andsustainability. To accomplish this, we must expand our understanding of plant ecosystems, which comprise communities of microorganisms, suchas bacteria and fungi. As there is a clear functional connection between microbes and plant performance, an important strategy is to engineersynthetic microbial communities to augment the microbial functions of natural plant ecosystems. Our research objective is thus to study the potatophytobiome and improve our understanding of how microbes affect potato growth and stress response. We will develop and apply advancedmathematical modelling approaches to model the potato plant and its phytobiome, taking advantage of large-scale omics data. Based on thesemodels and newly-acquired knowledge, we will design synthetic communities and experimentally validate their performance and stability in acircular design-build-test-learn fashion.

Plants and microbes interact via cellular metabolism, a set of enzyme-catalysed reactions that allow organisms to grow, reproduce and respond totheir environments. Plants also exhibit interplay between growth and defence via complex signalling and regulatory networks, and microbes producecompounds that either positively or negatively affect plant growth and stress resilience. For instance, beneficial endophytes that colonize internalplant tissues were shown to be useful as alternatives to chemical pesticides and fertilisers under field conditions. The engineering of microbialsynthetic communities is thus an increasingly popular approach to understand the function and composition of minimal functional communitiesaffecting plant performance. However, field applications have demonstrated that present designs perform only under a narrow range of conditions,with low robustness across different environmental settings. To improve the situation, we hypothesise that by learning from beneficial symbioticinteractions of potato with endophytes, we can improve community design toward increased stability and performance. By finding host- andmicrobe-promoting mechanisms, we can increase the likelihood of designing robust communities due to increased support for and from the plant,resulting in the development of reliable plant protection products.

The proposed project is organised into five work packages (WP). The first WP involves resource and project management, and in WP2, we willacquire, process and analyse plant and microbiome data required for modelling. To accurately capture potato growth and defence characteristics, inWP3 we will integrate multiple modelling paradigms including metabolism, signalling and gene regulation into a multi-domain model across keytissues, constructing a 'virtual plant'. In WP4, we will expand the developed framework to multi-species community modelling, a 'virtual phytobiome',that can accurately simulate and characterise plant-microbe interactions. In WP5, we will prototype a procedure based on the models to designimproved synthetic communities.

The proposed interdisciplinary systems approach can help us understand the interactions within phytobiomes, and the principles of plant-associated microbial community composition and function. Our focus on crop species enables the direct translation of new-found knowledge to theagronomically important goals of improving crop yield, quality and environmental stress tolerance under field conditions. By identifying microbeswith major effects on metabolic and phenotypic outcomes, we have a high possibility of developing breakthrough crop protection strategies withimproved field-specific responses, contributing towards sustainable agriculture and healthier soils. The project thus promotes national, EU andglobal directives on food security and sustainability, and is of exceptional scientific, societal and economic importance.

SICRIS