Main conclusion The composition, diversity and co-occurrence patterns of the rhizosphere microbiota of E. ulmoides were significantly influenced by environmental factors, and which were potentially associated with the contents of pharmacological active ingredients. Eucommia ulmoides is an important perennial medicinal plant. However, little is known about the interactions among microbiota, environmental factors (EFs), and pharmacological active ingredients (PAIs) of E. ulmoides. Herein, we analyzed the interactions among rhizosphere microbiota-EFs-PAIs of E. ulmoides by amplicon sequencing and multi-analytical approach. Our results revealed variations in the dominant genera, diversity, and co-occurrence networks of the rhizosphere microbiota of E. ulmoides across different geographical locations. Notably, available nitrogen exerted the strongest influence on fungal dominant genera, while pH significantly impacted bacterial dominant genera. Rainfall and relative humidity exhibited pronounced effects on the alpha-diversity of fungal groups, whereas available phosphorus influenced the number of nodes in fungal co-occurrence networks. Altitude and total phosphorus had substantial effects on the average degree and nodes in bacterial co-occurrence networks. Furthermore, the dominant genera, diversity and co-occurrence network of rhizosphere microbiota of E. ulmoides were significantly correlated with the content of PAIs. Specifically, the abundance of rhizosphere dominant genera Filobasidium, Hannaella and Nitrospira were significantly correlated with the content of pinoresinol diglucoside (PD). Similarly, the abundance of Vishniacozyma and Bradyrhizobium correlated significantly with the content of geniposidic acid (GC), while the abundance of Gemmatimonas was significantly correlated with the content of aucubin. Moreover, the bacterial co-occurrence network parameters including average degree, density, and edge, were significantly correlated with the content of GC and aucubin. The alpha-diversity index Chao1 also displayed a significant correlation with the content of PD. These findings contribute to a more comprehensive understanding of the interactions between medicinal plants and microbes.
