The Gastrodia elata Blume (GE) life cycle is unique, since its successful germination and growth rely on symbiosis with specific fungi (e.g., Armillaria mellea). However, the community succession, tissue specificity and functional potential of endophytic and rhizosphere bacterial communities during the seed formation stage of GE remain unclear. Here, we used high-throughput 16S rRNA gene sequencing to systematically explore the composition, diversity, and dynamic succession of bacterial communities across different stages of seed formation and among various tissues. Our results revealed that the endophytic community remained relatively stable across most developmental stages and tissue types (ANOSIM R = 0.4568, p = 0.001), with significant compositional shifts only occurring at the fruiting stage in specific tissues (stems and seeds). In contrast, the rhizosphere soil bacterial community showed stronger developmental succession (ANOSIM R = 0.7037, p = 0.001), with progressive divergence and the strongest segregation observed between the initial planting and fruiting stages. Alpha diversity peaked at the flowering stage for endophytic bacteria (Shannon index) and at the bud formation stage for rhizosphere soil bacteria, with persistent core taxa (Bacteroides in endophytic bacteria, Pseudarthrobacter in rhizosphere soil bacteria) dominating across stages. Functional predictions revealed stable core metabolic pathways, with stage-specific enrichments of glycolysis or gluconeogenesis at late developmental stages. These results provide novel ecological insights into the spatiotemporal dynamics of bacterial communities across different stages of GE seed formation, highlighting the distinct ecological strategies of endophytic and rhizosphere soil bacteria during the reproductive development of the plant.

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.