Tomato roots reveal hidden steps in 400-million-year-old fungal partnership

Scientists at VIB and Ghent University have created the first detailed, cell-by-cell map of how tomato roots interact with arbuscular mycorrhizal fungi. These ancient fungal partners assist plants in absorbing nutrients from the soil. The study, published in Current Biology, identifies the precise molecular programs that occur during the symbiosis and reveals potential new genetic regulators for developing more efficient, sustainable crops.

Arbuscular mycorrhizal fungi form symbioses with most land plants, a relationship dating back over 400 million years. They exchange sugars from the plant for nutrients like phosphate, nitrogen, and other essential elements, reducing the need for chemical fertilizers. However, the molecular details of how plants accommodate fungal structures called arbuscules inside their root cells have been poorly understood due to simultaneous colonization stages that are hard to separate with conventional methods.

To overcome this, the researchers used advanced technology to read gene activity in individual cells of tomato roots colonized by the fungus Rhizophagus irregularis, generating gene activity profiles for nearly 66,000 individual cells. The team identified four successive stages of the interaction: root surface cells sensing the fungus, inner cells preparing to receive it, cells building nutrient-exchange structures, and cells housing functional fungal structures ready for nutrient trade.

Each stage has distinct molecular signatures, offering insights into how plants gradually rewire their cells during the partnership. New regulatory candidates were discovered, confirmed through tests in living tomato roots, showing stage-specific activity. The study also found that a key signaling pathway remains active deep inside the root, influencing the development of fungal nutrient-exchange structures.

Moreover, cells housing mature fungal arbuscules appear to adjust the plant's nutrient investment based on its overall status, highlighting the plant's ability to fine-tune the symbiosis. This detailed single-cell profiling provides valuable resources for optimizing mycorrhizal symbiosis in crops, potentially reducing dependence on synthetic fertilizers and enhancing crop resilience under stress conditions.