The arbuscular mycorrhizal (AM) symbiosis between plants and beneficial soil fungi provides key benefits to both partners: AM fungi help the host plant to take up mineral nutrients and water from the soil, and in return receive up to 20% of photosynthetically assimilated carbon from the plant. To establish the symbiosis and enable nutrient exchange, fungal hyphae colonize the root and form highly branched fungal structures called arbuscules in the root cortex. This process requires coordination across several different cell layers in the host root and is accompanied by extensive cell-type-specific transcriptional reprogramming. However, the role that each cell type plays in enabling colonization and regulating nutrient exchange is still poorly understood. Using single-nucleus RNA-sequencing of plant roots during fungal colonization, we investigated the transcriptional changes that occur during symbiosis at single-cell resolution. Our approach identified several distinct clusters of root cells that respond to fungal colonization in a transcriptionally unique way, including colonized cortex cells that host different developmental stages of symbiosis such as early-developing, mature, and senescing arbuscules. This high-resolution gene expression atlas now allows us to explore how symbiosis establishment and nutrient exchange are regulated in a cell-type-specific manner during the interaction between plants and AM fungi.
