Abstract:[Background] Endophytic microorganisms in the roots can promote the seedling growth and improve the environmental adaptability of orchids. [Objective] To reveal the structures of endophytic microbial communities in three medicinal orchids (Coelogyne occultata, Arundina graminifolia, and Gymnadenia conopsea) and screen out functional strains. [Methods] Illumina MiSeq high-throughput sequencing was employed to analyze the structures of endophytic microbial communities in the roots of the three orchids. Conventional methods were adopted to isolate the endophytic bacteria and fungi from the roots, and the functional microorganisms were screened. [Results] The endophytic microbial communities of C.occultata and A.graminifolia clustered into one group at the genus level. In C.occultata, A.graminifolia, and G.conopsea, the dominant endophytic bacterial genera were Mycobacterium (Coe: 70.65%), Burkholderia-Caballeronia-Paraburkholderia (Aru: 26.35%), and Gordonia (Gym: 6.65%), respectively; the dominant endophytic fungal genera were Fusarium (Coe: 21.07%), unclassified Helotiales (Aru: 46.74%), and Morchella (Gym: 91.21%), respectively. Bacterial isolates Pseudomonas nunensis Coeb11, Rahnella sikkimica Coeb32, and Rouxiella silvae Coeb22 had the functions of dissolving phosphorus, fixing nitrogen, and secreting indole-3-acetic acid. The hyphae of the fungal isolate Cladophilophora chaetospira Aruf26 could colonize the cells of Dendrobium officinale as the dark septate endophyte. [Conclusion] This study revealed the structures of endophytic microbial communities in the roots of three medicinal orchids and screened the functional microorganisms. The findings provide a scientific basis for the protection of medicinal orchids, biomimetic cultivation under forests, and development and utilization of functional microorganisms.
