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Global exploration of drought-tolerant bacteria in the wheat rhizosphere reveals microbiota shifts and functional taxa enhancing plant resilience

Nature Food (2025)Cite this article

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Abstract

Drought stress impacts plant–microbe interactions, reshaping microbial community composition and biogeochemical cycling, thereby reducing crop productivity and threatening food security. However, the specific microbial responses and roles of plant-derived metabolites remain underexplored. Here we reveal that drought stress shifts the composition of wheat-associated microbiota across the phyllosphere, rhizosphere and root endosphere by favouring Actinobacteria and Ascomycota while depleting Proteobacteria and Basidiomycota. Targeted single-cell sorting and sequencing identified 21 active drought-tolerant bacteria (DTB) enriched in genes related to plant fitness and nutrient cycling. These DTB showed significant positive correlations with drought-enriched plant phytochemicals such as jasmonic acid and pipecolic acid. Moreover, the inoculation of synthetic community including four identified drought-tolerant taxa significantly stimulates the wheat growth under drought stress. A global exploration confirmed the widespread distribution of DTB, underscoring their promising potential to enhance crop resilience. This study provides new insights into drought-induced microbiome shifts and highlights microbial candidates for improving crop resilience in a changing climate.

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Fig. 1: Responses of wheat physiologies to drought.
Fig. 2: The effect of drought on wheat microbiome.
Fig. 3: Raman-based phenotypic profiling of drought tolerance in the rhizosphere.
Fig. 4: Genomic functions of drought-tolerant bacteria in the rhizosphere.
Fig. 5: Effects of DTB on wheat growth under drought stress.
Fig. 6: Global distribution of soil DTB.
Fig. 7: Proposed model illustrating a potential bacterial solution for enhancing drought resilience in wheat.

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Data availability

All raw sequences were deposited in the National Center for Biotechnology Information Sequence Read Archive under accession number PRJNA1155890. All relevant metabolomic data, Raman data and R scripts, including those for microbial co-occurrence network construction and DTB phenotypic-level visualization, are available via GitHub at https://github.com/Lab-qlchen/Global-exploration-of-drought-tolerant-bacteria-in-wheat-rhizosphere. Source data are provided with this paper.

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Acknowledgements

We acknowledge the funds of the Natural Science Foundation of Fujian Province (grant number 2023J02029 to Q.-L.C), National Natural Science Foundation of China (grant number 42207143 to Q.X.) and the fellowship of China Postdoctoral Science Foundation (grant number BX2021293 to Q.X.).

Author information

Author notes

  1. These authors contributed equally: Qiang Xiang, Kai Yang.

Authors and Affiliations

  1. State Key Laboratory of Regional and Urban Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China

    Qiang Xiang, Kai Yang, Li Cui, An-Qi Sun, Jun-Qi Gao, Yi-Long Hao, Qing-Lin Chen & Yong-Guan Zhu

  2. Zhejiang Key Laboratory of Pollution Control for Port-Petrochemical Industry, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China

    Qiang Xiang, An-Qi Sun & Qing-Lin Chen

  3. Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China

    Cai-Yu Lu & Bin Ma

  4. University of Chinese Academy of Sciences, Beijing, China

    Jun-Qi Gao & Yi-Long Hao

  5. School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia

    Hang-Wei Hu

  6. Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia

    Brajesh K. Singh

  7. Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China

    Yong-Guan Zhu

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Contributions

Q.X., Q.-L.C. and Y.-G.Z. conceived and designed the research. Q.X. and K.Y. performed the experiments and analysed the data with the help of B.M. and C.-Y.L. Q.X. and K.Y. wrote the paper with the assistance of all the co-authors. All authors read and approved the paper.

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Correspondence to Qing-Lin Chen.

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Nature Food thanks Josep Peñuelas and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary results (Texts 1–3), methods (Texts 4–6) and Figs. 1–20.

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Source data

Source Data Fig. 1

Wheat metabolome data and the statistical source data for Fig. 1e,f.

Source Data Fig. 3

Statistical source data for Fig. 3a (normalized C–D ratio, DTB percentage and drought-tolerant level) and Fig. 3b (active DTB with normalized C–D ratios > 1.6).

Source Data Fig. 4

Statistical source data for Fig. 4c, showing the correlations between DTB and upregulated phytochemicals in leaf and root tissues.

Source Data Fig. 5

Statistical source data for Fig. 5a,c, showing the effect of DTB on wheat growth parameters under drought.

Source Data Fig. 6

Statistical source data for Fig. 6a,b, including the data of DTB abundance, Shannon index of DT, standardized precipitation evapotranspiration index, and the latitude and longitude of samples.

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Xiang, Q., Yang, K., Cui, L. et al. Global exploration of drought-tolerant bacteria in the wheat rhizosphere reveals microbiota shifts and functional taxa enhancing plant resilience. Nat Food (2025). https://doi.org/10.1038/s43016-025-01248-2

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