Emerging applications of single cell and spatial transcriptomics under abiotic soil stress conditions

Single-cell and spatial transcriptomics are transforming our ability to understand how crop roots respond to soil stress by resolving gene expression at cellular resolution within intact tissues. This is particularly important because roots grow in heterogeneous soil environments, where physical structure, mechanical impedance, water availability, and nutrient distribution vary at fine spatial and temporal scales. Such complexity generates dynamic and localized stress signals that cannot be captured by bulk transcriptomics. The logic of applying these approaches lies in linking soil structure and stress gradients to cell-specific transcriptional responses that ultimately regulate root growth. While recent advances have enabled single-cell atlases in several crop species and emerging spatial transcriptomic datasets, most studies have been conducted under simplified conditions (e.g. gels, hydroponics, artificial chemical treatments), only few studies are adopting soil stresses. Despite this progress, major gaps remain, including the need for true in-situ spatial maps in intact agriculture soil systems, integration with temporal dynamics of root growth, and coupling transcriptional data with local measurements of water status, mechanical stress, gaseous diffusion, microbial assembly and nutrient gradients. Addressing these challenges will be essential to capture the full complexity of root responses and to translate cell-level transcriptional dynamics under realistic soil stress conditions.