Continuous monoculture of Panax notoginseng leads to severe replant disease, yet the mechanisms by which root exudates mediate rhizosphere microbiome assembly and pathogen enrichment remain poorly understood. Here, we demonstrate that long-term root exudate accumulation acts as an ecological filter, driving the fungal community toward a phylogenetically impoverished, pathogen-dominated state. Specifically, exudates enriched the soil-borne pathogen Fusarium while reducing the abundance of potentially antagonistic fungi. In contrast, bacterial communities exhibited higher resilience, with exudates selectively enriching oligotrophic taxa such as Terrimonas and MND1, but suppressing nitrifying bacteria (e.g., Nitrospira) and plant-growth-promoting rhizobacteria (PGPR). Microbial functional profiling revealed a shift in nitrogen cycling, characterized by suppressed nitrification and enhanced nitrate reduction. Crucially, co-occurrence network analysis identified bacterial taxa strongly negatively correlated with Fusarium, providing a synthetic community blueprint for biocontrol strategies. Our study establishes a mechanistic link between root exudate accumulation and negative plant–soil feedback in monoculture systems, highlighting microbiome reprogramming as a key driver of replant disease. These insights offer novel avenues for manipulating rhizosphere microbiomes to sustain crop productivity in intensive agricultural systems.

Seed germination of Paris polyphylla var. yunnanensis is intrinsically low, severely restricting its artificial propagation. Despite the known roles of ABA and GAs, the regulatory functions of other phytohormones in this process remain largely unexplored. In this study, we integrated transcriptomic and targeted metabolomic profiling to systematically investigate the dynamics of 34 phytohormones and global gene expression patterns across five germination stages of P. polyphylla seeds. Seven hormones showed significant changes during germination, including auxins, melatonin, cytokinins, and jasmonate, which exhibited distinct accumulation patterns. Integrative correlation analysis further uncovered candidate genes potentially involved in hormone biosynthesis and signaling. Collectively, our findings provide new insights into the hormonal regulation of seed germination in P. polyphylla, establish a foundational framework for understanding its germination mechanisms, and offer candidate molecular targets for improving seed propagation efficiency.