Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome

Significance The root microbiome composition is largely determined by the soil inoculum, with a distinct contribution from the host. The molecular mechanisms with which the host influences its rhizobiome are only beginning to be discovered. Using a hydroponics-based synthetic community approach, we probe how root-exuded specialized metabolites sculpt the root microbiome. We uncover a role for coumarins in structuring the rhizobiome, particularly by limiting the growth of a Pseudomonas strain, for which we propose a mechanism of action involving reactive oxygen species. Our findings support the possibility that root-exuded coumarins form a part of the plant’s adaptive response to iron deficiency that goes beyond iron mobilization to modulate the rhizobiome, and highlight avenues toward engineering the rhizosphere for plant health.