Modeling bacterial communities associated to plant roots
The ecosystem composed by a plant and its rhizosphere (the bacterial community associated to the roots) is determined by complex dynamics still not completely understood. Metabolic interactions play a central role in the definition of these systems, as illustrated by the example of nitrogen fixation by diazotrophs in nodules of plants like legumes. With this project, with strong exchange with experimentalists from RA D, we aim at understanding what drives the assembly of microbial communities associated with plant roots under different environmental conditions. Mathematical and computational models can reveal important information on the regulation of metabolism, on signaling pathways and on environmental effects. Network expansion models are qualitative methods to reconstruct metabolic pathways based on seed and/or target metabolites. Aided by experimental data from different bacterial strains isolated from natural Arabidopsis ecotypes and grown in the laboratory on media with different N and S sources, we aim at pin-pointing critical metabolic functions for root colonization. In a similar way we want to investigate the scope of relevant metabolites identified in plant exudates under different abiotic growth condition. Finally, we will use the model with a community genome to study the metabolic structure and stability.
Keywords expertise: metabolic modeling, synthetic ecology, systems microbiology