Compartment-Specific Variation in Bacterial Microbiome and Polyphyllin Profiles in Paris polyphylla

Paris polyphylla (P. polyphylla) is a valuable traditional Chinese medicinal plant, yet the spatial distribution of its compartment-specific bacterial microbiomes and their correlative relationships with bioactive polyphyllins remain poorly characterized. Here, we combined 16S rRNA amplicon sequencing, metabolite analysis, and bioinformatics to investigate the distribution patterns of bacterial communities and polyphyllins across bulk soil (BS), rhizosphere soil (RS), root endospheres (REs), stem endospheres (SEs), and leaf endospheres (LEs) of P. polyphylla. A spot inoculation assay was further used to verify the interactions between the dominant genus Pseudomonas (strain Pseudomonas palleroniana P6) and key polyphyllin I and VII. The results showed that polyphyllin I and II were highly accumulated in aerial SEs and leaves, whereas polyphyllin VI, VII, and diosgenin were predominantly concentrated in REs. Bacterial diversity and richness showed a gradual decline from BS to LE, with ecological niche differentiation identified as the primary driver of bacterial community divergence across compartments, which was further modulated by polyphyllin content. Pseudomonas, the dominant genus in all compartments, displayed a decreasing relative abundance with ascending compartmental niches, and its abundance was significantly negatively correlated with polyphyllin I levels but positively correlated with polyphyllin VII levels-a trend experimentally validated by gradient polyphyllin concentration-based microbial growth assays. Redundancy analysis (RDA) indicated that polyphyllin content (especially VI, VII, and diosgenin) significantly influenced bacterial community composition. Additionally, P. polyphylla exhibited selective enrichment of beneficial microbes, with selection pressure intensifying progressively across compartments. This study clarifies the compartment-specific distribution patterns of bacterial microbiomes and polyphyllins in P. polyphylla and their correlative relationships, deepens the understanding of plant-microbiome interactions in medicinal plants, and provides a theoretical basis for optimizing P. polyphylla cultivation strategies and developing microbial inoculants for sustainable agricultural production.