Gymnadenia conopsea (L.) R. Br. is an important perennial terrestrial photosynthetic orchid species whose microbiomes are considered to play an important role in helping its germination and growth. However, the assemblage of G. conopsea root-associated microbial communities is poorly understood. The compositions of fungal and bacterial communities from the roots and corresponding soil samples in G. conopsea across distinct biogeographical regions from two significantly different altitudes were characterized at the vegetative and reproductive growth stages. The geographical location, developmental stage and compartment were factors contributing to microbiome variation in G. conopsea. Predominant fungal taxa include Ascomycota, Basidiomycota, Mortierellomycota and Chytridiomycota, whereas Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Verrucomicrobia, Chloroflexi, TM7 and Planctomycetes were predominant bacterial taxa. Using G. conopsea as a model, the structural and functional composition in G. conopsea root-associated microbiomes were comprehensive analyzed. Contrary to previous studies, biogeography was the main factor influencing the microbial community in this study. Besides, compartment and developmental stage should also be considered to analyze the variation of microbiota composition. Although the microbial composition varied greatly by location, the symbiotic microorganisms of G. conopsea still have certain specificity. This study gives an abundant information of G. conopsea root-associated microbiomes and provides new clues to better understanding the factors affecting the composition and diversity of fungal/bacterial communities associated with orchids. Our results also laying a foundation for harnessing the microbiome for sustainable G. conopsea cultivation. Moreover, these results might be generally applicable to other orchidaceae plants.

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Background: Gymnadenia conopsea (L.) R. Br. is an important perennial terrestrial photosynthetic orchid species whose microbiomes are thought to play an important role in promoting its growth and health. However, the assemblage of G. conopsea root-associated microbial communities is poorly understood. Results: The compositions of fungal and bacterial communities from the roots and corresponding soil samples of G. conopsea across distinct biogeographical regions from two significantly different altitudes were characterized at the vegetative and reproductive growth stages. The geographical location, developmental stage and compartment were factors contributing to microbiome variation in G. conopsea. Predominant fungal taxa include Ascomycota , Basidiomycota , Mortierellomycota and Chytridiomycota , whereas Proteobacteria , Bacteroidetes , Acidobacteria , Actinobacteria , Verrucomicrobia , Chloroflexi , TM7 and Planctomycetes were predominant bacterial taxa. The fungi classes of Leotiomycetes , Agaricomycetes , Eurotiomycetes and Mortierellomycetes, as well as bacterial taxa Actinobacteria were more abundant in G. conopsea from higher altitude location. Moreover, Dark septate endophytes and Arbuscular mycorrhiza may have important role for G. conopsea to adapt to high altitude environment. Conclusions: Using G. conopsea as a model, we report a comprehensive analysis of the structural and functional composition of the G. conopsea root-associated microbiomes. Contrary to previous studies, biogeography was the main factor influencing the microbial community in this study. Although the microbial composition varied greatly by location, the symbiotic microorganisms of G. conopsea still have certain specificity. This study offers a robust knowledge of G. conopsea root-associated microbiomes and lends guidelines to the investigation of adaptation mechanism of G. conopsea in high altitude environment. Our results also laying a foundation for harnessing the microbiome for sustainable G. conopsea production. Moreover, these results might be generally applicable to other Orchidaceae plants.