Deciphering the root microbiome and its relationship with active compound accumulation in medicinal Dendrobium officinale (Orchidaceae) from different regions

Abstract

Dendrobium officinale is a well-known traditional Chinese medicinal plant of Orchidaceae that displays unique mycorrhizal symbiosis with compatible fungi under natural conditions. In this study, we investigated endophytic fungi in the roots and bacteria in the rhizosphere of D. officinale from 15 different regions using high-throughput sequencing as well as combined content analysis of polysaccharides and flavonoids and morphological traits of host plants to screen the candidate core microbes related to bioactive compound accumulation. The results showed that endophytic fungi Nectriaceae, Pleurotaceae, Aspergillaceae,Trichocomaceae, Cladosporiaceae, Hypocreaceae and mycorrhizal fungi Serendipitaceae, Ceratobasidiaceae, Stereaceae, Tuberaceae, Trichocomaceae have the greatest abundance, making them the core fungal community of D. officinale roots. In the rhizosphere of D. officinale , 4 bacterial phyla including Proteobacteria, Chloroflexi, Bacteroidota, and Actinobacteriota and 24 families including Acetobacteraceae, Acidobacteriaceae, Acidothermaceae, Beijerinckiaceae, Pseudomonadaceae, Rhizobiaceae, Sphingomonadaceae, Streptomycetaceae, etc. constitute the core bacterial communities. The fungal and bacterial communities between samples of D. officinale from Daodi and non-Daodi areas were significantly different, and the mycorrhizal fungi Ceratobasidiaceae is significantly enriched in samples from Daodi regions, having a positive correlation with the polysaccharide content of D. officinale . Fungi belonging to the Serendipitaceae family have a significant positive correlation with schaftoside content and Rhizoctonia has a positive correlation with rutin content of D. officinale . A co-cultural experiment using D. officinale inoculated with Serendipita WX-7 showed that mycorrhizal fungi can stimulate the accumulation of flavonoid active compounds. This study can help enrich the geoherbalism theory of traditional Chinese medicine(TCM) and be of practical significance in improving medicinal quality and future ecological planting that uses microbial synthesis technology. • Genuine medicinal materials is recognized with better quality and clinical effect but its formation reasons is unclear. • We characterized the microbial composition of medicinal plant D. officinale from 15 regions using high-throughput sequencing. • The core fungal community (e.g. Serendipitaceae) and core bacterial communities (e.g. Proteobacteria) were identified. • The fungal and bacterial communities in D. officinale samples from Daodi and Non-Daodi areas were significantly different. • Co-cultural experiments showed that the fungus Serendipita WX-7 can stimulate the flavoid accumulation of D. officinale .

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