Abstract
The dominant bacteria enriched in the Fusarium wilt plants’ rhizosphere are of increasing interest, as they adapt well to the diseased rhizosphere. However, general information about these bacteria is still lacking. Here, we perform a meta-analysis of Fusarium wilt plants rhizosphere and comprehensive studies to obtain information about the robust variation in the rhizosphere microbiome of Fusarium wilt plants. We demonstrate that Fusarium infection reproducibly changes the rhizosphere bacterial community composition. The rhizosphere microbiomes of Fusarium wilt plants are characterized by the enrichment of Flavobacterium, gene cassettes involved in antioxidant functions related to sulfur metabolism and the root secreted tocopherol acetate. We further isolate …
Abstract
The dominant bacteria enriched in the Fusarium wilt plants’ rhizosphere are of increasing interest, as they adapt well to the diseased rhizosphere. However, general information about these bacteria is still lacking. Here, we perform a meta-analysis of Fusarium wilt plants rhizosphere and comprehensive studies to obtain information about the robust variation in the rhizosphere microbiome of Fusarium wilt plants. We demonstrate that Fusarium infection reproducibly changes the rhizosphere bacterial community composition. The rhizosphere microbiomes of Fusarium wilt plants are characterized by the enrichment of Flavobacterium, gene cassettes involved in antioxidant functions related to sulfur metabolism and the root secreted tocopherol acetate. We further isolate antagonistic Flavobacterium anhuiense from the diseased tomato rhizosphere, and reveal that the growth of F. anhuiense and the expression of genes related to carbohydrate metabolism in this strain are significantly stimulated by tocopherol acetate. Furthermore, the inhibitory effect of F. anhuiense against F. oxysporum and F. anhuiense population enhancement by tocopherol acetate are confirmed in planta. The robust variation in the rhizosphere microbiome elucidates key principles governing the general assembly mechanism of the microbiome in the Fusarium wilt plants’ rhizosphere.
Data availability
The meta-analysis in this study utilized publicly available sequence data from the NCBI SRA (accession numbers are provided in the Supplementary Information). The newly generated experimental data (transcriptome, amplicon, and whole-genome shotgun sequencing) have been deposited in the NCBI SRA under BioProject IDs: PRJNA1138414, PRJNA1138403, PRJNA1240447, PRJNA1240449, and PRJNA1138398. The raw metabolomics data have been deposited in the National Genomics Data Center (NGDC) OMIX repository under BioProject accession PRJCA052462 and are publicly available via: https://ngdc.cncb.ac.cn/omix/release/OMIX013393. Source data are provided with this paper.
Code availability
The scripts for analysis are available on https://zenodo.org/records/16676212.
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Acknowledgements
We thank Jun Zhao (Nanjing Normal University) and Shaozhou Yang (Wenshan Sanqi Science and Technology Demonstration Park) for providing the rhizosphere soil of Panax notoginseng, as well as Xiang Li (Yangzhou University) for his help with DNA extraction from the in planta experiment samples. This work was supported by the National Natural Science Foundation of China (42207359 to L.S., 32270125 to H.-C.F., 32172661 to R.-F.Z. and 32270067 to Y.-L.Y.), Agricultural Science and Technology Innovation Program to Y.-L.Y. and the China Postdoctoral Science Foundation (2021M693448 to L.S.).
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Author notes
These authors contributed equally: Lv Su, Haichao Feng.
Authors and Affiliations
College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, The People’s Republic of China
Lv Su, Kesu Wang, Qirong Shen & Ruifu Zhang 1.
Biotechnology Research Institute/National Key Laboratory of Agricultural Microbiology, Chinese Academy of Agricultural Sciences, Beijing, China
Lv Su, Xiaoqian Yan, Xudong Wang, Pengcheng Li & Yongliang Yan 1.
College of Agriculture, Henan University, Kaifeng, Henan, China
Haichao Feng & Xiaoqian Yan 1.
State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
Huatai Li, Fu Yang, Xia Shu & Yunpeng Liu 1.
College of Life Sciences, Yangzhou University, Yangzhou, Jiangsu, China
Xudong Wang
Authors
- Lv Su
- Haichao Feng
- Huatai Li
- Fu Yang
- Xiaoqian Yan
- Xudong Wang
- Pengcheng Li
- Kesu Wang
- Xia Shu
- Yunpeng Liu
- Qirong Shen
- Yongliang Yan
- Ruifu Zhang
Contributions
L.S. analyzed the metadata and wrote the main manuscript text. H.F. designed and conducted the greenhouse experiments and root exudate analyses. H.L., F.Y., X.Y., X.W. and P.L. performed the experimental studies. K.W., X.S., Y.L. and Q.S. provided critical suggestions and revisions to the manuscript. Y.Y. and R.Z. conceived, organized, and supervised the overall project.
Corresponding authors
Correspondence to Yongliang Yan or Ruifu Zhang.
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Su, L., Feng, H., Li, H. et al. General variation in the Fusarium wilt rhizosphere microbiome. Nat Commun (2025). https://doi.org/10.1038/s41467-025-67760-y
Received: 08 August 2024
Accepted: 08 December 2025
Published: 27 December 2025
DOI: https://doi.org/10.1038/s41467-025-67760-y