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Aims <p>Root exudates critically regulate the rhizosphere microenvironment to control soil-borne diseases, yet how their differential abundances modulate the microbiome remains unclear. This study distinguishes between abundant root exudates (AREs) and rare root exudates (RREs) to investigate their regulatory mechanisms on rhizosphere bacterial communities under healthy and disease-stressed conditions.</p> Methods <p>We integrated 16S rRNA gene sequencing and LC–MS-based non-targeted metabolomics to analyze rhizosphere bacterial composition and root exudate profiles. Key microbial taxa and exudate components were identified, and their interactions explored through correlation analysis.</p> Results <p>Depending on root exudate abundance and soil conditions, AREs and RREs exhibited distinct regulatory mechanisms on bacterial communities. In healthy soil, H-AREs maintained community stability through a nutrient-driven mechanism. H-RREs mainly regulated microbial functions through signaling. LEfSe and interaction network analyses revealed that H-RREs promoted rhizosphere colonization of soybean roots through quorum sensing (QS), enhanced biofilm formation, and increased microbial resistance to environmental stress. Consequently, these microbial communities stimulated soybean plants to produce more H-AREs, thereby supporting microbial survival. Under soil-borne disease stress, quorum quenching disrupted rhizobacterial QS. The diversity of S-AREs and S-RREs was associated with increased functional redundancy in the microbial community, contributing to enhanced soybean resilience under environmental stress.</p> Conclusions <p>The findings reveal that soybean plants regulate rhizosphere bacterial communities through functionally differentiated yet cooperative AREs and RREs under different soil conditions, thereby enhancing adaptation to both healthy and stressed environments. This study advances the understanding of root exudate-microbiome interactions and offers novel insights for developing sustainable agricultural strategies against soil-borne diseases.</p>

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Functional differences between healthy and stressed soils: Rare and abundant root exudates as a regulatory switch for quorum sensing in rhizosphere microbiota

  • 期刊论文

  • 发表日期：

    2026年7月30日

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  • Yueyi Liu,
  • Zhenchao Wu,
  • Zeming Ye,
  • Liangyang Mao,
  • Xiujun Tu,
  • Yuhao Guo,
  • Weige Yao,
  • Ying Yang,
  • Shuo Li,
  • Jie Kang,
  • Baiyan Cai,
  • Jingping Ge

摘要

Aims

Root exudates critically regulate the rhizosphere microenvironment to control soil-borne diseases, yet how their differential abundances modulate the microbiome remains unclear. This study distinguishes between abundant root exudates (AREs) and rare root exudates (RREs) to investigate their regulatory mechanisms on rhizosphere bacterial communities under healthy and disease-stressed conditions.

Methods

We integrated 16S rRNA gene sequencing and LC–MS-based non-targeted metabolomics to analyze rhizosphere bacterial composition and root exudate profiles. Key microbial taxa and exudate components were identified, and their interactions explored through correlation analysis.

Results

Depending on root exudate abundance and soil conditions, AREs and RREs exhibited distinct regulatory mechanisms on bacterial communities. In healthy soil, H-AREs maintained community stability through a nutrient-driven mechanism. H-RREs mainly regulated microbial functions through signaling. LEfSe and interaction network analyses revealed that H-RREs promoted rhizosphere colonization of soybean roots through quorum sensing (QS), enhanced biofilm formation, and increased microbial resistance to environmental stress. Consequently, these microbial communities stimulated soybean plants to produce more H-AREs, thereby supporting microbial survival. Under soil-borne disease stress, quorum quenching disrupted rhizobacterial QS. The diversity of S-AREs and S-RREs was associated with increased functional redundancy in the microbial community, contributing to enhanced soybean resilience under environmental stress.

Conclusions

The findings reveal that soybean plants regulate rhizosphere bacterial communities through functionally differentiated yet cooperative AREs and RREs under different soil conditions, thereby enhancing adaptation to both healthy and stressed environments. This study advances the understanding of root exudate-microbiome interactions and offers novel insights for developing sustainable agricultural strategies against soil-borne diseases.