Multi-omics reveals microbial community associations with metabolite accumulation in Gastrodia elata

Gastrodia elata is a medicinal herb widely cultivated in East Asia for treating headache and dizziness, and its efficacy largely depends on gastrodin, 4-hydroxybenzyl alcohol, and parishins. However, the basis for quality variation of G. elata across growth systems remains largely undetermined. Here, tubers and rhizosphere soils were collected from wild, wild‑simulated cultivated (WSC), and greenhouse cultivated (GHC) G. elata , and metabolite, transcript, and microbiome data were generated for comprehensive multi-omics analyses. We found that (1) wild G. elata accumulated significantly higher gastrodin and parishin C levels than GHC G. elata , and were enriched in organic acids and glycosides, whereas cultivated G. elata accumulated more sugars and amino acids. (2) gene expression patterns differed relatively little between wild and WSC G. elata , whereas GHC G. elata exhibited a distinct transcriptomic profile associated with defense activation. (3) wild and WSC G. elata harbored higher absolute microbial abundance (16S and ITS gene copy numbers) in the rhizosphere and were enriched in a diverse array of plant growth-promoting microorganisms. (4) microbial communities were associated with the metabolic and transcriptional divergence among growth systems. Soil properties and the rhizosphere bacterial community, particularly taxa such as Burkholderia-Caballeronia-Paraburkholderia and Roseiarcus , were closely associated with the accumulation of gastrodin and parishins. Notably, the absolute abundance of rhizosphere microbes was significantly correlated with gastrodin and parishins accumulation. In summary, this study offers a multi‑omics view of microbe–plant–metabolite associations in G. elata , providing valuable guidance for the rational design of synthetic microbial inoculants and future cultivation practices.