Abstract
Aluminium (Al) toxicity impedes crop growth in acidic soils and is considered the second largest abiotic stress after drought for crops worldwide. Despite remarkable progress in understanding Al resistance in plants, it is still unknown whether and how the soil microbiota confers Al resistance to crops. Here we found that a synthetic community composed of highly Al-resistant bacterial strains isolated from the rice rhizosphere increased rice yield by 26.36% in acidic fields. The synthetic community harvested rhizodeposited carbon for successful proliferation and mitigated soil acidification and Al toxicity through extracellular protonation. The functional coordination between plants and microbes offers a promising way to increase the usage of legacy phosphorus in topsoil. These findings highlight the potential of microbial tools for advancing sustainable agriculture in acidic soils.
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Data availability
The raw sequence data reported in this paper have been deposited (PRJCA011216) in the Genome Sequence Archive in the BIG Data Center62, Chinese Academy of Sciences under accession code CRA007891 for Rhodococcus erythropolis transcriptome sequencing, CRA007889 for Pseudomonas aeruginosa transcriptome sequencing, CRA008623 for bacterial 16S rRNA gene sequencing data in the 13C isotope labelling experiment, CRA007869 for phoD gene sequencing, CAR007871 for rice leaf transcriptome sequencing, and CAR008056 for rice root transcriptome sequencing in the pot experiment and are publicly accessible at http://bigd.big.ac.cn/gsa. All pure strains were deposited in the CNGB Sequence Archive (CNSA)63 of the China National GeneBank DataBase (CNGBdb)64 at https://db.cngb.org/ with accession number CNP0003393. Source data are provided with this paper.
Code availability
The code used for this work is available from the corresponding author on request.
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Acknowledgements
We thank J. E. Shaff and E. J. Craft (Robert W. Holley Center of Agriculture and health, USDA-ARS, Cornell University) for providing the helpful tool Geochem-EZ software. We thank C. Huang (Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences) and G. Huang (School of Life Sciences and Biotechnology, Shanghai Jiao Tong University) for critical discussion and feedback on the paper. We thank J. Fan, M. Liu, X. Liu and L. Chen from the Yingtan Agroecosystem Field Experiment Station of the Chinese Academy of Sciences for field experiment management and sampling assistance. We received fundings from Strategic Priority Research Program of the Chinese Academy of Sciences (XDA24020104 to Y.L.), National Key R&D Program of China (2021YFD1900400 to Y.L.), National Natural Science Foundation of China (42377121 to Y.L.), Innovation Program of Institute of Soil Science (ISSASIP2201 to Y.L.) and Youth Innovation Promotion Association of Chinese Academy of Sciences (2016284 to Y.L.). The funders had roles in study design and data collection and analysis.
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Conceptualization: Y.L., Y.B., T.W.C., R.S. and J. Zhang. Methodology: Y.L., C.L., M.J., M.M.Y., Z.M., Y.B., L.Z., Y.W., J.D., W.L. and J. Zhou. Investigation: Y.L., C.L., M.J. and M.M.Y. Data curation: C.L., M.J., M.M.Y., Z.M., L.Z. and J.D. Formal analysis: Y.L., C.L., M.J., M.M.Y., Z.M. and L.Z. Supervision: Y.L., E.W., R.S. and J. Zhang. Writing—original draft: Y.L., C.L., M.J. and M.M.Y. Writing—review and editing: C.L., M.J., M.M.Y., Y.L., E.W., Y.B., T.W.C., J. Zhou, Z.M., L.Z., Y.W., J.D., W.L., B.S., R.S. and J. Zhang.
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Nature Food thanks Hongwei Liu, Miguel Pineros and Qing Yao for their contribution to the peer review of this work.
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Supplementary Figs. 1–25, text and methods.
Supplementary Table
Supplementary Table 1. Strain information. Supplementary Table 2. Parameters of the logistic models of Rhodococcus erythropolis and Pseudomonas aeruginosa growing under different Al3+ conditions. Supplementary Table 3. Intensity of differential metabolites in rice roots with and without SynCom. Supplementary Table 4. Ionic interactions predicted by Geochem-EZ. Supplementary Table 5. Physicochemical properties of experimental soils collected from the field.
Supplementary Data
Source data of Supplementary Figs. 2–10, 12–14, 16, 19–23 and 25.
Supplementary Video 1
3D video of rice root under Al3+ stress.
Supplementary Video 2
3D video of rice root under Al3+ stress with SynCom inoculation.
Supplementary Video 3
3D video of rice root under limed condition.
Supplementary Video 4
3D video of rice root under limed condition with SynCom inoculation.
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Liu, C., Jiang, M., Yuan, M.M. et al. Root microbiota confers rice resistance to aluminium toxicity and phosphorus deficiency in acidic soils. Nat Food 4, 912–924 (2023). https://doi.org/10.1038/s43016-023-00848-0
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DOI: https://doi.org/10.1038/s43016-023-00848-0
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