Host selection shapes structure and network of microbial community of Epimedium plants along the soil–rhizosphere–plant continuum

Microbiota inhabiting plants are essential for plant productivity and health. Microbes in various plant compartment niches perform distinct ecological functions. However, the microbial characteristics in different niches of Epimedium plants, one of the most promising tonic herbs in traditional Chinese medicine, remain largely unknown. Here, microbial composition, diversity and co-occurrence network in the five ecological niches (bulk soil, rhizosphere soil, root, stem, and leaf) of three Epimedium plant cultivars were investigated using high-throughput sequencing. The microbial composition were predominately imprinted by compartment niches than by host cultivars. Bacterial diversity and network complexity incrementally decreased from the soils to the root to the leaf; however, fungal diversity and network complexity gradually decreased from the soils to the root to the stem but increased from the stem to the leaf. Cyanobacteria, Proteobacteria, Arthrobacter, Sphingomonas, and Gemmatimonas were bacterial keystone taxa, while Ascomycota, Davidiella, and Hymenoscyphus were fungal keystone taxa. These taxa exhibited significant compartment-specific properties and performed distinct ecological functions. The microbial communities are mostly originated from bulk soil, and subsequently filtered and enriched in various compartment niches through host selection. Compartment niches profoundly imprinted the plant-associated microbiota, which provided valuable insights into harnessing beneficial communities for Epimedium plants in sustainable agriculture and the improvement of herbal quality.