Single-cell transcriptomics reveal how root tissues adapt to soil stress

Zhu, Mingyuan; Hsu, Che-Wei; Peralta Ogorek, Lucas L.; Taylor, Isaiah W.; La Cavera, Salvatore; Oliveira, Dyoni M.; Verma, Lokesh; Mehra, Poonam; Mijar, Medhavinee; Sadanandom, Ari; Perez-Cota, Fernando; Boerjan, Wout; Nolan, Trevor M.; Bennett, Malcolm J.; Benfey, Philip N.; Pandey, Bipin K.

Abstract

Land plants thrive in soils showing vastly different properties and environmental stresses1. Root systems can adapt to contrasting soil conditions and stresses, yet how their responses are programmed at the individual cell scale remains unclear. Using single-cell RNA sequencing and spatial transcriptomic approaches, we showed major expression changes in outer root cell types when comparing the single-cell transcriptomes of rice roots grown in gel versus soil conditions. These tissue-specific transcriptional responses are related to nutrient homeostasis, cell wall integrity and defence in response to heterogeneous soil versus homogeneous gel growth conditions. We also demonstrate how the model soil stress, termed compaction, triggers expression changes in cell wall remodelling and barrier formation in outer and inner root tissues, regulated by abscisic acid released from phloem cells. Our study reveals how root tissues communicate and adapt to contrasting soil conditions at single-cell resolution.

Citation

Zhu, M., Hsu, C.-W., Peralta Ogorek, L. L., Taylor, I. W., La Cavera, S., Oliveira, D. M., Verma, L., Mehra, P., Mijar, M., Sadanandom, A., Perez-Cota, F., Boerjan, W., Nolan, T. M., Bennett, M. J., Benfey, P. N., & Pandey, B. K. (2025). Single-cell transcriptomics reveal how root tissues adapt to soil stress. Nature, https://doi.org/10.1038/s41586-025-08941-z

• Journal Article Type: Article
• Acceptance Date: Mar 26, 2025
• Online Publication Date: Apr 30, 2025
• Publication Date: Apr 30, 2025
• Deposit Date: Apr 14, 2025
• Publicly Available Date: May 1, 2025
• Journal: Nature
• Print ISSN: 0028-0836
• Electronic ISSN: 1476-4687
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• DOI: https://doi.org/10.1038/s41586-025-08941-z
• Public URL: https://nottingham-repository.worktribe.com/output/47820057
• Publisher URL: https://www.nature.com/articles/s41586-025-08941-z
• Additional Information: Received: 5 February 2024; Accepted: 26 March 2025; First Online: 30 April 2025; : P.N.B. was the cofounder and Chair of the Scientific Advisory Board of Hi Fidelity Genetics, Inc., a company that works on crop root growth. The other authors declare no competing interests.