Altitude modulates growth and bioactive compounds in two Gastrodia elata forms through the microenvironment and soil microbes

Introduction Gastrodia elata Bl. is a medicinal-edible heterotrophic orchid with distinct vertical distribution, but unstable yield and inconsistent quality in cultivation limit its industrial development. The mechanisms by which altitude modulates growth and bioactive compound accumulation in different G. elata forms remain unclear. Methods We conducted a two-factor field experiment (two forms: G. elata f. glauca , G. elata f. elata ; three altitudes: 650, 1653, 1953 m) in the Qinba Mountains, using a consistent commercial Armillaria sp . strain to isolate bacterial effects. We analyzed microclimate, soil properties, soil enzyme activities, culturable bacterial communities, and tuber bioactive compounds (gastrodin, parishins) across developmental stages. Results Form-specific altitudinal responses were observed: total yield peaked at high altitude (1953 m; 2668.11 ± 317.10 g), while bioactive compounds were enriched at middle altitude (1653 m)—with optimal accumulation at the Large Baima stage (f. glauca ) and Mima stage (f. elata ). Soil pH was the primary correlative factor for f. glauca quality (explaining 52%–70.5% of variation in RDAs), whereas integrated carbon-acquiring enzyme activity (16.6%) was key for f. elata —consistent with PLS-SEM evidence of an indirect “soil properties→enzyme activities” pathway for f. elata quality. Culturable tuber-associated bacteria (dominated by Pseudomonadota, least diverse at middle altitude) correlated divergently with yield and quality: positively with yield but negatively with quality in f. glauca ; weakly positive with yield and strongly (non-significantly) positive with quality in f. elata ( p < 0.05). Discussion Our findings clarify form-specific correlative networks linking altitude, microenvironment, soil microbes, and plant performance, providing targeted guidance for ecological cultivation to balance high yield and quality in G. elata .