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.

doi:10.1038/s41586-025-08941-z

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.

Authors

Mingyuan Zhu

Che Wei Hsu

Lucas L. Peralta Ogorek

Isaiah W. Taylor

Salvatore La Cavera

Dyoni M. Oliveira

Lokesh Verma

Poonam Mehra

Medhavinee Mijar

Professor Ari Sadanandom ari.sadanandom@durham.ac.uk
Professor

Fernando Perez-Cota

Wout Boerjan

Trevor M. Nolan

Malcolm J. Bennett

Philip N. Benfey

Bipin K. Pandey

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. (online). 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
Deposit Date	May 20, 2025
Publicly Available Date	May 20, 2025
Journal	Nature
Print ISSN	0028-0836
Electronic ISSN	1476-4687
Publisher	Nature Research
Peer Reviewed	Peer Reviewed
DOI	https://doi.org/10.1038/s41586-025-08941-z
Public URL	https://durham-repository.worktribe.com/output/3956368