Abstract
Rhizosphere microbes benefit plant growth and health. How plant-microbe interactions regulate fruit quality remains poorly understood. Here, we elucidate the multi-level modulation of vitamin accumulation in tomato by flavonoid-mediated crosstalk between host plants and rhizosphere microbes. SlMYB12-overexpressing plants with up-regulated flavonoid biosynthesis accumulate higher levels of vitamins C and B6 in fruits compared to wild-type plants grown in natural soil. Flavonoid-mediated improvement of fruit quality depends on the presence of soil microbiomes and relates to rhizosphere enrichment of key taxa (e.g. Lysobacter). Multi-omics analyses reveal that flavonoids attract Lysobacter soli by stimulating its twitching motility and spermidine biosynthesis, which in turn boosts vitamin accumulation in fruits across tomato cultivars and soil types. RpoN acts as a dual regulator in L. soli that is responsive to flavonoids, controlling bacterial motility and spermidine production. Our study provides insight into flavonoid-mediated rhizosphere signalling and underscores plant-microbiome orchestration for improved tomato fruit quality.
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Data availability
Raw 16S rRNA gene amplicon sequencing and metagenomic data generated in this study have been deposited in the NCBI under BioProject PRJNA1303084 and PRJNA1182265, respectively. The genomic data for strains P18 generated in this study have been deposited in the NCBI under BioProject PRJNA1177803. The transcriptome data have been deposited in NCBI Sequence Read Archive database under BioProject PRJNA1182113 (bacteria) and PRJNA1182117 (tomato fruit). The flavonoid-targeted metabolomic and widely targeted metabolomic data have been deposited in the MetaboLights under MetaboLights accession MTBLS13507 and MTBLS13506, respectively. Source data are provided with a paper. Source data are provided with this paper.
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Acknowledgements
H.L. and Q.G. were supported by grants from the Special Project of Scientific and Technological Innovation of Xinjiang Research Institute of Arid Area Agriculture (XJHQNY-2025-6). Q.G. was supported by grants from the China National Tobacco Corporation Yunnan Branch Major Science and Technology Programme Special Project (2024530000241022) and the “Scientists + Engineers” Team Project of Xianyang (L2024-CXNL-KJRCT-DWJS-0005). H.L. was supported by grants from the Key Research and Development Programme of Shaanxi Province (S2024-YF-ZDXM-NY-0223; S2024-YF-ZDCXL-ZDLNY-0162).
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W.F. and C.S. designed the experiments. P.L. and W.F. collected and analysed the data. W.F. and B.S. performed the experiments. W.F. interpreted the results and draughted the manuscript. D.X. provided experiment materials. H.L., Q.G. and J.Y. revised the manuscript and provided critical suggestions. H.L. and Q.G. obtained funding and conceived the study. All authors edited and approved the manuscript.
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Fu, W., Sun, C., Sun, B. et al. Flavonoid-mediated bacterial spermidine biosynthesis enhances vitamin accumulation in tomato fruits. Nat Commun (2026). https://doi.org/10.1038/s41467-025-68244-9
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DOI: https://doi.org/10.1038/s41467-025-68244-9
