Advances in single-cell and spatial omics for studying symbiotic nitrogen fixation: comparative cellular and evolutionary perspectives

Single-cell and spatial transcriptomics have revolutionized studies of symbiotic nitrogen fixation by resolving cellular heterogeneity, spatial gene-expression, and regulatory dynamics within root nodules. Recent investigations in model legumes have revealed conserved and species-specific programs controlling immune recognition, nodule development, and nitrogen-fixation metabolism. Integrating these datasets with single-cell epigenomic profiles, such as chromatin accessibility and three-dimensional genome architecture, provides new insight into epigenetic mechanisms that regulate key symbiotic genes. Comparative single-cell analyses across legumes and non-legumes elucidate phenotypic diversity and core regulatory networks of symbiotic nitrogen fixation at the cellular level, offering critical frameworks for engineering this process in non-legume crops.