Unveiling microbial complexity within Astragalus propinquus and Glycyrrhiza uralensis roots

Background Astragalus propinquus (AP) and Glycyrrhiza uralensis (GU), members of the Fabaceae family, are widely used for their therapeutic properties. However, the endophytic microbial communities in their roots remain largely unknown. Herein, we compared the structure and properties of root-associated bacterial and fungal communities of AP and GU, specifically excluding the microbial communities thriving in the rhizosphere, using both culture-dependent and -independent methods. Results A metabarcoding-based approach revealed a higher abundance of Proteobacteria in the root microbiome of GU than in that of AP. Fungal communities showed similar distinctions, with AP and GU predominantly harboring Ascomycota and Basidiomycota, respectively. The bacterial community in AP exhibited significantly higher diversity than in GU and included unique taxa, e.g., Steroidobacterales and Micromonosporales. However, the bacterial community in GU was relatively less diverse and dominated by Xanthomonadales. Differential abundance analysis revealed that the plant species significantly impacted 301 bacterial and 228 fungal amplicon sequence variants (ASVs) in AP and GU. Among these, B5_f_Comamonadaceae was markedly more enriched in AP than in GU. A random forest model analyzing bacterial ASVs with significant differences in abundance indicated that most bacterial ASVs were enriched in AP. A pan-microbial community of 1,243 ASVs was identified, including 96 co-detected ASVs between AP and GU, with 3 core ASVs (B2_f_Pseudomonas, B5_Comamonadaceae, and B70_Cutibacterium). The fungal community comprised 435 ASVs, with 98 shared ASVs and 8 core ASVs (F5_Paraphoma, F6_f_Lysurus, F22_Alternaria, F30_Phaeosphaeria, F53_Cladosporium, F36_Moesziomyces, F55_f_Neocucurbitaria, and F56_Malassezia). Hub nodes were identified to elucidate the roles of microorganisms within microbial networks. In AP, B152_o_Burkholderiales, F14_Exophiala, and F33_Fusarium were the key hub nodes, whereas, in GU, B36_Paenibacillus was the central hub node. The comparative analyses of in vitro culture data and molecular sequencing results showed overlapping patterns, with Pseudomonas dominant in AP and Bacillus in GU. Conclusions These findings highlight distinct microbial communities between AP and GU, with each species exhibiting unique bacterial and fungal orders and differences in microbial network complexity and diversity. These differences suggest the potential functional contributions, e.g., nutrient cycling and secondary metabolite production, of root-associated microbial communities, likely impacting the therapeutic properties of these plants.