24 June 2026
Min-Yao Jhu, Jo Heffer, Chongjing Xia, Thiago Alexandre Moraes, Claire M. Mulvey, Dario Bressan, Chen Liu, Jin-Peng Gao, Philip Poole, Katharina Schiessl, Giles E. D. Oldroyd - 2026
Legume root nodules enable symbiotic nitrogen fixation through the development of specialized cells that accommodate nitrogen-fixing bacteria intracellularly and support bacterial nitrogenase activity. Here, we present a 4D (3D space and time) spatial transcriptomic atlas of Medicago truncatula nodules and lateral roots, revealing specialized symbiotic cell types that develop alongside a conserved lateral-root-derived program that underpins vascularization. Spatial profiling of both plant and bacterial transcripts resolves distinct transcriptional states and previously unrecognized cell states. Spatial analysis of developmental regulator mutants uncovers a cascading series of cell-type-specific programs during nodule maturation. LSH1/LSH2 are central regulators of these programs, and lsh1/lsh2 mutants exhibit collapse of hormonal gradients and nodule identity. Strikingly, loss of nodule identity collapses to a primary-root identity rather than lateral-root fate. This work reveals how tissue complexity emerges through stacked developmental programs sustained in distinct cellular compartments, allowing the emergence of cell types specialized for harboring nitrogen-fixing bacteria.
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