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

Mingyuan Zhu, Che-Wei Hsu, Lucas L. Peralta Ogorek, Isaiah W. Taylor, Salvatore La Cavera, Dyoni M. Oliveira (UGent) , Lokesh Verma, Poonam Mehra, Medhavinee Mijar, Ari Sadanandom, et al.
(2025) NATURE. 642(8068). p.721-729
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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.
Keywords
WATER-STRESS, RICE, COMPACTION, ELONGATION, EXPRESSION, RESPONSES, LEAF

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MLA
Zhu, Mingyuan, et al. “Single-Cell Transcriptomics Reveal How Root Tissues Adapt to Soil Stress.” NATURE, vol. 642, no. 8068, 2025, pp. 721–29, doi:10.1038/s41586-025-08941-z.
APA
Zhu, M., Hsu, C.-W., Peralta Ogorek, L. L., Taylor, I. W., La Cavera, S., Oliveira, D. M., … Pandey, B. K. (2025). Single-cell transcriptomics reveal how root tissues adapt to soil stress. NATURE, 642(8068), 721–729. https://doi.org/10.1038/s41586-025-08941-z
Chicago author-date
Zhu, Mingyuan, Che-Wei Hsu, Lucas L. Peralta Ogorek, Isaiah W. Taylor, Salvatore La Cavera, Dyoni M. Oliveira, Lokesh Verma, et al. 2025. “Single-Cell Transcriptomics Reveal How Root Tissues Adapt to Soil Stress.” NATURE 642 (8068): 721–29. https://doi.org/10.1038/s41586-025-08941-z.
Chicago author-date (all authors)
Zhu, Mingyuan, Che-Wei Hsu, Lucas L. Peralta Ogorek, Isaiah W. Taylor, Salvatore La Cavera, Dyoni M. Oliveira, Lokesh Verma, Poonam Mehra, Medhavinee Mijar, Ari Sadanandom, Fernando Perez-Cota, Wout Boerjan, Trevor M. Nolan, Malcolm J. Bennett, Philip N. Benfey, and Bipin K. Pandey. 2025. “Single-Cell Transcriptomics Reveal How Root Tissues Adapt to Soil Stress.” NATURE 642 (8068): 721–729. doi:10.1038/s41586-025-08941-z.
Vancouver
1.
Zhu M, Hsu C-W, Peralta Ogorek LL, Taylor IW, La Cavera S, Oliveira DM, et al. Single-cell transcriptomics reveal how root tissues adapt to soil stress. NATURE. 2025;642(8068):721–9.
IEEE
[1]
M. Zhu et al., “Single-cell transcriptomics reveal how root tissues adapt to soil stress,” NATURE, vol. 642, no. 8068, pp. 721–729, 2025.
@article{01JTFTDSPSTXD7PSHX8DN1MBRQ,
  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.}},
  author       = {{Zhu, Mingyuan and Hsu, Che-Wei and Peralta Ogorek, Lucas L. and Taylor, Isaiah W. and La Cavera, Salvatore and Oliveira, Dyoni M. and Verma, Lokesh and Mehra, Poonam and Mijar, Medhavinee and Sadanandom, Ari and Perez-Cota, Fernando and Boerjan, Wout and Nolan, Trevor M. and Bennett, Malcolm J. and Benfey, Philip N. and Pandey, Bipin K.}},
  issn         = {{0028-0836}},
  journal      = {{NATURE}},
  keywords     = {{WATER-STRESS,RICE,COMPACTION,ELONGATION,EXPRESSION,RESPONSES,LEAF}},
  language     = {{eng}},
  number       = {{8068}},
  pages        = {{721--729}},
  title        = {{Single-cell transcriptomics reveal how root tissues adapt to soil stress}},
  url          = {{http://doi.org/10.1038/s41586-025-08941-z}},
  volume       = {{642}},
  year         = {{2025}},
}
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