Cultivation Mode Reshapes Root Fungal Endophyte Communities in Dendrobium officinale (Orchidaceae)

Background: Symbiotic fungi play essential roles throughout the entire cycle of orchid plants, including seed germination, seedling development, and maturation. Dendrobium officinale Kimura & Migo (Orchidaceae) (D. officinale) is a rare and highly valued traditional Chinese medicinal herb. Currently, artificial breeding using tissue culture technology is widely adopted and essential in the Dendrobium industry; however, this approach may impair or disrupt the plant’s ability to establish and maintain symbiotic relationships with mycorrhizal fungi. Methods: In this study, the fungal endophyte community (FEC) in the roots of D. officinale cultivated under four different modes was analyzed using high-throughput sequencing. Correlation analyses were also carried out to examine the relationships between bioactive compounds and the FEC. Results: (1) The FEC in D. officinale roots was dominated by Ascomycota and Basidiomycota, with significant differences in abundance, diversity, and community structure among cultivation modes; (2) the FEC under greenhouse cultivation differed significantly from those under tree epiphytic cultivation in terms of fungal nutritional types and dominant taxa; (3) six major mycorrhizal fungal taxa were identified in Dendrobium roots, although non-mycorrhizal fungi accounted for approximately 97% of the community; and (4) polysaccharide content in Dendrobium stems was positively correlated with certain root fugal endophytes (Exophiala, alaromyces, Pseudodactylaria, and Fellomyces). Conclusions: This study provides a foundation for understating the growth of D. officinale under different cultivation modes and highlights the relationship between bioactive compound accumulation and fungal endophyte communities.