This article has been reviewed according to Science X's editorial process and policies. Editors have highlighted the following attributes while ensuring the content's credibility: Scientists at VIB and Ghent University have produced the first high-resolution, cell-by-cell map of how tomato roots respond to colonization by arbuscular mycorrhizal fungi. These ancient fungal partners help plants absorb nutrients from the soil.
The study, published in Current Biology, reveals the precise molecular programs that unfold as the symbiosis progresses through different stages and identifies promising new genetic regulators that could one day be used to engineer more efficient, sustainable crops. Arbuscular mycorrhizal fungi form symbioses with the vast majority of land plants, a relationship that dates back more than 400 million years. In exchange for sugars supplied by the plant, the fungi dramatically improve the plant's access to phosphate, nitrogen and other nutrients, reducing the need for chemical fertilizers.
"Despite decades of research," says Professor Sofie Goormachtig (VIB-UGent Center for Plant Systems Biology), "the molecular details of how plants accommodate fungal structures called arbuscules—the main sites of nutrient exchange—inside their root cells remained poorly understood, largely because different stages of colonization occur simultaneously in the same root, making them difficult to separate using conventional methods." To tackle this challenge, Goormachtig's team, with the help of the VIB Single Cell Core, used a cutting-edge technology that reads the activity of genes in individual cells one by one. Applied to tomato roots colonized by the fungus Rhizophagus irregularis, the approach generated gene activity profiles for nearly 66,000 individual cells. To ensure the team was looking at the right material, researchers used a fluorescent tag to light up root regions where the fungus was actively present, allowing them to zoom in on the most relevant tissue.
Within this dataset, the researchers identified a group of cells that responded specifically to fungal colonization. "We found four successive stages of the interaction: root surface cells sensing the arriving fungus, inner cells gearing up to let it in, cells in the process of building nutrient-exchange structures, and finally cells housing fully functional fungal structures ready for nutrient trade. Each stage has its own characteristic molecular signature, which helps us understand how the plant gradually rewires its cells as the partnership develops," explains Dr.
Naomi Stuer (VIB-UGent), first author of the study. To find out which molecular switches, known as transcription factors, are pulling the strings at each stage, the team used MINI-EX, a computational tool to predict which regulators control which genes. The analysis confirmed many regulators already known to play a role in this symbiosis, but it also uncovered several previously unsuspected candidates.
Three of these new candidates were then tested directly in living tomato roots, where they showed exactly the stage-specific activity the computational tool had predicted. The study also brought several broader insights. First, a key signaling pathway previously thought to act only at the root surface turns out to remain active much deeper inside the root, throughout the formation of the fungal nutrient-exchange structures.
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