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Background <p>The structure of endophytic microbial communities and metabolic functions differ significantly among plant varieties with different resistance levels. Currently, there is a lack of research articles that combine microbiomics and metabolomics to explore the mechanism of resistance to wilt disease in watermelon. To seek out the antagonistic microorganisms and metabolites against watermelon wilt from different watermelon varieties, we investigated the characteristics of endophytic microbial communities, metabolic features and functions in the roots of wilt–resistant (RW) and susceptible (SW) watermelon varieties.</p> Results <p>The results suggested that significant differences of endophytic microbial communities and metabolites could be found in the roots between RW and SW. Meanwhile, the endophytic bacterial genera such as <i>Chryseobacterium</i>, <i>Pseudomonas</i>, <i>Delftia</i>, <i>Lechevalieria</i>, <i>unclassified_f__Methylophilaceae</i>, <i>Tahibacter</i>, and the endophytic fungal genera, <i>unclassified_p__Basidiomycota</i>, <i>Neocosmospora</i>, <i>unclassified_f__Lasiosphaeriaceae</i>, <i>Edenia</i> were the unique dominant bacterial and fungal genera in the roots of RW, respectively. Additionally, the differential metabolites, including Galactinol, Sucrose, Stachyose, Coniferyl Aldehyde, Coniferin, 5–Hydroxyconiferyl alcohol, 4–Coumaryl alcohol, 3–Hydroxybenzoic Acid, and the metabolic pathways including Galactose metabolism, Phenylpropanoid biosynthesis, Phenylalanine, tyrosine and tryptophan biosynthesis significantly upregulated in wilt resistant watermelon varieties.</p> Conclusion <p>This study systematically reveals, for the first time, the synergistic defense mechanisms between root endophytic microbiome and metabolome during <i>Fusarium</i> wilt resistance formation in watermelon. Significantly, we have identified potential functional microorganisms, key metabolites, and critical pathways that actively contribute to these defense mechanisms. However, the specific functions of these potential antagonistic microorganisms and metabolites still need further validation. These findings provide a novel perspective for crop disease resistance research, transcending the limitations of traditional single-factor analytical paradigms, while establishing a methodological foundation for developing multi-omics integrated approaches in crop disease resistance regulation strategies.</p>

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The distinct characteristics of the endophytic microbiome and metabolome within the root system result in varying abilities of watermelon resistance against Fusarium wilt

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年10月29日

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  • Xinyan Zhou,
  • Jinyan Huang,
  • Yu Zhu,
  • Yufei Wei,
  • Liyuan Liao,
  • Jiaoming Li,
  • Yi He,
  • Shangdong Yang

摘要

Background

The structure of endophytic microbial communities and metabolic functions differ significantly among plant varieties with different resistance levels. Currently, there is a lack of research articles that combine microbiomics and metabolomics to explore the mechanism of resistance to wilt disease in watermelon. To seek out the antagonistic microorganisms and metabolites against watermelon wilt from different watermelon varieties, we investigated the characteristics of endophytic microbial communities, metabolic features and functions in the roots of wilt–resistant (RW) and susceptible (SW) watermelon varieties.

Results

The results suggested that significant differences of endophytic microbial communities and metabolites could be found in the roots between RW and SW. Meanwhile, the endophytic bacterial genera such as Chryseobacterium, Pseudomonas, Delftia, Lechevalieria, unclassified_f__Methylophilaceae, Tahibacter, and the endophytic fungal genera, unclassified_p__Basidiomycota, Neocosmospora, unclassified_f__Lasiosphaeriaceae, Edenia were the unique dominant bacterial and fungal genera in the roots of RW, respectively. Additionally, the differential metabolites, including Galactinol, Sucrose, Stachyose, Coniferyl Aldehyde, Coniferin, 5–Hydroxyconiferyl alcohol, 4–Coumaryl alcohol, 3–Hydroxybenzoic Acid, and the metabolic pathways including Galactose metabolism, Phenylpropanoid biosynthesis, Phenylalanine, tyrosine and tryptophan biosynthesis significantly upregulated in wilt resistant watermelon varieties.

Conclusion

This study systematically reveals, for the first time, the synergistic defense mechanisms between root endophytic microbiome and metabolome during Fusarium wilt resistance formation in watermelon. Significantly, we have identified potential functional microorganisms, key metabolites, and critical pathways that actively contribute to these defense mechanisms. However, the specific functions of these potential antagonistic microorganisms and metabolites still need further validation. These findings provide a novel perspective for crop disease resistance research, transcending the limitations of traditional single-factor analytical paradigms, while establishing a methodological foundation for developing multi-omics integrated approaches in crop disease resistance regulation strategies.