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Aims <p>Rhizosphere soil nutrients, particularly nitrogen, are closely associated with variation in plant metabolism and influence the growth, development, and therapeutic quality of medicinal plants such as <i>Codonopsis pilosula</i>. While endophytic bacteria are well recognized to modulate plant metabolism, the mechanisms by which they are associated with the balance between primary and secondary putative metabolites in <i>C. pilosula</i> under different rhizosphere nitrogen forms remain insufficiently understood.</p> Methods <p>Untargeted metabolomics, 16S rRNA gene amplicon sequencing, and structural equation modeling were integrated to investigate six representative <i>C. pilosula</i> cultivars from an authentic production region.</p> Results <p>Total nitrogen in rhizosphere soil was strongly associated with variation in primary putative metabolites of <i>C. pilosula</i>. Nitrate nitrogen was positively associated with secondary putative metabolite accumulation, whereas ammonium nitrogen showed negative associations with secondary putative metabolites. Structural equation modeling indicated that endophytic bacteria occupied a central position within the rhizosphere soil nutrient-putative metabolite network. In particular, <i>Bacillus spp</i>. were associated with ammonium nitrogen and primary putative metabolite variation, suggesting links between nitrogen availability and metabolic balance. Variation in secondary putative metabolites was mainly associated with shifts in primary metabolism rather than individual bacterial taxa. Furthermore, different <i>C. pilosula</i> cultivars exhibited distinct nitrogen utilization patterns, characterized as relatively ammonium-associated or nitrate-associated conditions, which corresponded to differences in endophytic bacterial community composition.</p> Conclusions <p>This study highlights integrated associations among rhizosphere nitrogen forms, endophytic bacteria, and metabolic balance, providing a scientific basis for optimizing the medicinal quality of <i>C. pilosula</i> and supporting sustainable cultivation of high-value medicinal plants.</p> Graphical Abstract <p></p>

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Rhizosphere soil nitrogen forms influence endophytic bacterial communities to balance primary and secondary metabolism in the medicinal plant Codonopsis pilosula

  • 期刊论文

  • 发表日期：

    2026年5月8日

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  • Wen Luo,
  • Wenying Wang,
  • Fengzhong Wang,
  • Fei Zhang,
  • Yali Guo,
  • Li Li,
  • Fusheng Wang,
  • Yuanli Li,
  • Dan Gao,
  • Yonggang Wang

摘要

Aims

Rhizosphere soil nutrients, particularly nitrogen, are closely associated with variation in plant metabolism and influence the growth, development, and therapeutic quality of medicinal plants such as Codonopsis pilosula. While endophytic bacteria are well recognized to modulate plant metabolism, the mechanisms by which they are associated with the balance between primary and secondary putative metabolites in C. pilosula under different rhizosphere nitrogen forms remain insufficiently understood.

Methods

Untargeted metabolomics, 16S rRNA gene amplicon sequencing, and structural equation modeling were integrated to investigate six representative C. pilosula cultivars from an authentic production region.

Results

Total nitrogen in rhizosphere soil was strongly associated with variation in primary putative metabolites of C. pilosula. Nitrate nitrogen was positively associated with secondary putative metabolite accumulation, whereas ammonium nitrogen showed negative associations with secondary putative metabolites. Structural equation modeling indicated that endophytic bacteria occupied a central position within the rhizosphere soil nutrient-putative metabolite network. In particular, Bacillus spp. were associated with ammonium nitrogen and primary putative metabolite variation, suggesting links between nitrogen availability and metabolic balance. Variation in secondary putative metabolites was mainly associated with shifts in primary metabolism rather than individual bacterial taxa. Furthermore, different C. pilosula cultivars exhibited distinct nitrogen utilization patterns, characterized as relatively ammonium-associated or nitrate-associated conditions, which corresponded to differences in endophytic bacterial community composition.

Conclusions

This study highlights integrated associations among rhizosphere nitrogen forms, endophytic bacteria, and metabolic balance, providing a scientific basis for optimizing the medicinal quality of C. pilosula and supporting sustainable cultivation of high-value medicinal plants.

Graphical Abstract