To investigate the effects of different Armillaria mellea (A. mellea) sources on Gastrodia elata (GE) yield, quality, and soil microecology, five A. mellea of difference sources (M1–M5) were co-cultivated with Zhaotong GE at two sites. M5 co-cultivation produced the highest yields (fresh weight) at both Xiaocaoba, Yiliang (XCB) and Wanchang, Zhenxiong (ZXWC), reaching 3239 g/m² and 2550 g/m². For quality, M1 resulted in the highest total gastrodin and parishin content at XCB, while M3 was superior at ZXWC. Post-cultivation, soil pH increased across all treatments. Soil nutrients increased with M1 and M2 at XCB, and with M4 at ZXWC. In GE rhizosphere soil samples, Proteobacteria, Acidobacteria, and Actinobacteria were dominant bacterial phyla, with Proteobacteria abundance decreasing. The dominant fungal phyla were Ascomycota, Basidiomycota, and Mucoromycota; Basidiomycota abundance increased in all soils, while Ascomycota increased only with M1 and M2. M3-treated soils had the highest Gram-negative bacteria abundance, and M1-treated soils were enriched with saprotrophic fungi. This study has several limitations. The conclusions were drawn indirectly with the host (GE) as the focus, and the A. mellea were not identified to clarify potential genetic differences. Future research should integrate fungal omics analyses for a more in-depth investigation.

Armillaria mellea (A. mellea) serves as a crucial nutritional source for Gastrodia elata (GE) growth, and its origin directly influences the GE quality and yield. This study analyzed GE symbiotic with A. mellea from different sources using metabolomics and transcriptomics. Results demonstrated that Group A exhibited significant differences in metabolites and gene expression compared to other groups. Group A showed significantly higher accumulation of active components like gastrodin and p-hydroxybenzyl alcohol than others, but its yield was lower than Group B. Metabolomic analysis identified 2418 metabolites, while transcriptomic sequencing produced 964,110,904 clean reads, with 14,637 annotated transcripts. KEGG analysis revealed that Group A’s DEGs and DEMs were co-enriched in three key pathways, including flavonoid biosynthesis, phenylpropanoid biosynthesis, and plant hormone signal transduction, such as the positive regulatory roles of key genes (CHS, 4CL, MYC2) on metabolites such as hesperetin, ferulate, and jasmonic acid, respectively. The coordinated upregulation of gene–metabolite interactions in Group A GE may be closely related to the accumulation of major active components, indirectly suggesting the influence of the A. mellea source on metabolic and transcriptional response differences in GE. This study, centered on the host GE, indirectly deduces the association between A. mellea and GE, providing a theoretical basis for screening high-quality “fungus-GE” combinations. Further in-depth research and validation experiments will be conducted in conjunction with fungal omics.