Insight into the Gastrodia elata microbiome and its relationship with secondary metabolites

The plant microbiome plays an important role in plant growth and development, stress response, and secondary metabolite accumulation. Gastrodia elata is a mycoheterotrophic orchid plant with medicinal values. G. elata appears to have a close and complicated relationship with microorganisms but, so far, it is poorly understood. In this study, the temporal dynamics of both endophytic bacterial and fungal communities during the growth of G. elata subjected to two different cultivation patterns were analyzed, and further metagenomics were used to characterize the microbiome of the rhizosphere. Also, the relationship between G. elata endophytes and secondary metabolites was initially explored. The results showed that the plant growth stage had a much stronger influence on multiple microbial attributes (alpha-diversity, community composition and potential functions, determinism/stochasticity processes and co-occurrence networks) than cultivation patterns. Metagenomic analysis indicated that the cultivation process of G. elata distinctly changed the soil microbial composition and functions, and microbial species and functional diversity were strongly correlated with soil pH and nutrients. Furthermore, correlation analysis showed that the secondary metabolites (e.g., gastrodin and parishin) and biomass of G. elata tubers were significantly and positively correlated with several endophytic bacterial taxa belonging to Streptococcus, Vibrio, and ‘uncultured’ (Lactobacillales) . In conclusion, our findings systematically revealed the composition and potential functions of the microbiome associated with G. elata . This study has provided valuable information to guide the microbial isolation and culture of G. elata , and promote sustainable development for the cultivation of G. elata and other orchids. • Plant growth stage had a much stronger influence on microbial communities than cultivation patterns. • Crop process of Gastrodia elata clearly changed soil properties and microbial composition and functions. • Secondary metabolites and biomass of G. elata tubers were positively correlated with several endophytic bacteria. • There is potential to use the microbiome to promote growth and quality improvement of G. elata .