Ghent, 18 August 2026 — Beneath the soil, tomato roots are not passive anchors but dynamic biological interfaces where plants and fungi negotiate an exchange of resources. Now, scientists at the VIB-UGent Center for Plant Systems Biology and Ghent University have produced the most detailed molecular map yet of that partnership, tracing how individual root cells change as they are colonized by arbuscular mycorrhizal fungi. The study, published in Current Biology, follows the interaction from the first signs of fungal arrival to the development of mature nutrient-exchange structures. Its findings reveal that symbiosis is not a single switch that turns on inside the root, but a carefully choreographed progression involving distinct cellular states, signaling pathways, metabolic adjustments, and previously unknown genetic regulators. The work could ultimately help scientists develop crops that obtain nutrients more efficiently while relying less heavily on synthetic fertilizers.

Arbuscular mycorrhizal fungi are among the oldest and most widespread partners of land plants. Fossil and molecular evidence suggests that this relationship began more than 400 million years ago, around the time plants were establishing themselves on land. Today, these fungi associate with the roots of most terrestrial plant species. The fungus extends a network of microscopic filaments, known as hyphae, through the surrounding soil, greatly expanding the plant’s reach beyond the physical limits of its roots. In return, the plant supplies the fungus with carbon-rich sugars and lipids produced through photosynthesis. The fungal network can improve the plant’s access to phosphate, nitrogen, and trace nutrients, while also influencing water uptake and stress tolerance. Yet the molecular details that allow a living fungus to enter root tissue without triggering a destructive immune response have remained difficult to resolve.

A major obstacle has been that colonization is spatially and temporally mixed. A single root may contain surface cells that have only just detected fungal signals, deeper cells preparing for invasion, cells actively building arbuscules, and cells already hosting mature exchange structures. Conventional genetic and biochemical methods generally average molecular signals across thousands or millions of cells, blurring these different stages together. “Despite decades of research, the molecular details of how plants accommodate fungal structures called arbuscules remained poorly understood,” said Prof. Sofie Goormachtig of VIB-UGent. Arbuscules are highly branched fungal structures formed inside root cells. They dramatically increase the membrane surface available for exchange, allowing nutrients to move from the fungus to the plant while carbon compounds move in the opposite direction.

To separate these overlapping stages, Goormachtig’s team worked with the VIB Single Cell Core to apply single-nucleus transcriptomics to tomato roots colonized by Rhizophagus irregularis, one of the best-studied arbuscular mycorrhizal fungi. Rather than measuring gene activity from a whole root, the technique profiles RNA molecules inside individual nuclei. Because messenger RNA reflects which genes are actively being transcribed, these profiles provide a molecular snapshot of each cell’s identity and condition. The researchers also used a fluorescent marker to identify root regions in which the fungus was actively present. This enrichment step allowed them to focus their sequencing effort on the most informative tissue instead of treating colonized and uncolonized regions as a single biological sample. In total, the dataset contained gene-activity profiles from nearly 66,000 individual root cells.

The resulting map revealed a sequence of four major cellular stages. The first involved root surface cells detecting the approaching fungus and initiating the earliest symbiotic responses. The second occurred in inner root cells that began preparing the tissue for fungal entry, changing their gene activity before mature fungal structures appeared. The third stage was characterized by cells constructing arbuscules, with extensive remodeling of cellular architecture and metabolism. The final stage involved cells containing fully developed arbuscules capable of sustained nutrient exchange. These stages were not merely anatomical categories. Each displayed a distinctive transcriptional signature, indicating that the plant progressively rewires its cells as the partnership develops. “Each stage has its own characteristic molecular signature,” said Dr. Naomi Stuer, first author of the study. “This helps us understand how the plant gradually rewires its cells as the partnership develops.”

The researchers next asked which molecular regulators coordinate these changes. They used MINI-EX, a computational framework designed to infer relationships between transcription factors and the genes they may control. Transcription factors are proteins that bind specific DNA sequences and influence whether target genes are activated or suppressed. By integrating the single-cell expression patterns with regulatory predictions, the team identified candidate transcription factors associated with each stage of colonization. The analysis recovered several regulators already known to participate in mycorrhizal symbiosis, providing an internal validation of the approach. It also identified new candidates whose roles had not previously been connected to the interaction. Three of these candidates were tested directly in living tomato roots, where they displayed the predicted stage-specific activity. This agreement between computational inference and experimental observation suggests that the candidates may function as genuine regulators rather than being passive markers of colonized cells.

One of the study’s most significant findings concerns a signaling pathway previously thought to operate mainly near the root surface. The new data indicate that the pathway remains active farther inside the root and continues functioning during the formation of arbuscules. Its activity may help prepare particular cortical cells for the demanding process of hosting fungal structures. Before an arbuscule can form, a plant cell must alter its metabolism, reorganize its internal membrane system, and establish a specialized interface around the invading fungal branches. These changes require precise coordination between developmental programs, nutrient signaling, and the plant’s immune system. The single-nucleus profiles suggest that some of this preparation begins before the cells show the obvious structural features associated with mature arbuscules. Because these prospective host cells initially look much like neighboring cortical cells, their early molecular state would have been almost impossible to recognize using microscopy alone.

The data also point to a sophisticated feedback system operating in mature arbuscule-containing cells. These cells appear to monitor information about the plant’s broader nutritional condition, including whether the plant is already receiving sufficient nutrients. Such sensing could allow the plant to adjust its investment in the fungus. Maintaining a symbiosis requires carbon and cellular resources, so the relationship must provide enough nutritional benefit to justify its cost. When phosphate or nitrogen is abundant, the plant may reduce colonization or limit the formation and lifespan of arbuscules. When nutrients are scarce, it may support a more extensive fungal network and intensify exchange. The findings suggest that mature host cells are not simply containers for fungal structures; they are active decision-making units that integrate local fungal signals with the plant’s systemic nutrient status.

“What excites me most about this dataset is that it does not just confirm what we suspected; it opens entirely new doors,” said Dr. Judith Van Dingenen of VIB-UGent, co-senior author. The resource gives researchers a way to ask precisely when and where symbiotic genes are activated, how long individual molecular programs persist, and what causes one root cell to become a fungal host while an adjacent cell follows a different developmental path. It may also enable comparisons between plant varieties that form highly efficient fungal partnerships and those that benefit less from colonization. Such comparisons could reveal whether improved symbiosis depends on stronger signaling, more effective nutrient transport, altered immune regulation, or a combination of several traits.

The practical implications extend beyond tomato biology. Modern agriculture often compensates for limited nutrient availability with industrial fertilizers, especially phosphate and nitrogen products whose manufacture, transport, and runoff carry substantial environmental costs. Engineering or breeding crops that make better use of arbuscular mycorrhizal fungi could offer another route to maintaining yields while reducing fertilizer inputs. The newly identified transcription factors provide possible entry points for that effort, although their agricultural value will require further testing in different crops, soils, climates, and microbial communities. The present study does not yet deliver a ready-made “super-symbiotic” crop, but it supplies the cellular atlas and regulatory hypotheses needed to pursue one. By revealing how a root changes cell by cell as it welcomes an ancient fungal partner, the researchers have transformed a hidden underground interaction into a process that can be measured, modeled, and potentially improved.

Article Title: Decoding stage-specific symbiotic programs in the Rhizophagus irregularis-tomato interaction using single-nucleus transcriptomics

News Publication Date: 18 August 2026

Web References: https://doi.org/10.1016/j.cub.2026.05.057

References: Current Biology, published 6 July 2026; DOI: 10.1016/j.cub.2026.05.057

Keywords: arbuscular mycorrhizal fungi, Rhizophagus irregularis, tomato roots, single-nucleus transcriptomics, single-cell biology, arbuscules, plant-fungus symbiosis, transcription factors, nutrient exchange, sustainable agriculture

Tags: arbuscular mycorrhizal fungicrop nutrient efficiencyevolution of plant-microbe relationshipsgenetic regulation of plant-fungi interactionsmolecular mechanisms of symbiosisnutrient exchange in plant rootsplant-fungal signaling pathwaysplant-fungus symbiosisroot cell differentiation during colonizationsingle-cell mapping of root cellssoil microbiome and plant healthsymbiotic development stages