Plant-associated microbial communities vary across compartments, mycorrhizal types, and species identities in alpine meadows of the Qinghai-Tibetan Plateau.

Plant-microbe symbioses can enhance plant adaptability. However, whether root-associated microbes form specific associations with plants of different mycorrhizal types remains controversial. Furthermore, it is currently unknown whether plants with different mycorrhizal types show heterogeneity in their phyllosphere microbial communities. In this study, we independently conducted in two alpine meadows, simultaneously collecting root and phyllosphere samples from plants with different mycorrhizal types, and used amplicon sequencing to characterize patterns of microbial community variations. We observed a strong compartment differentiation, with roots dominated by symbiotrophic fungi, phyllospheres by saprotrophic fungi, and the two compartments harboring distinct groups of plant-beneficial bacteria. Within each compartment, mycorrhizal types and species identity of plants can influence both fungal and bacterial community compositions. Specifically, plants with different mycorrhizal types or even different plant species within the same mycorrhizal type (especially ectomycorrhizal) tend to harbor distinct mycorrhizal fungi and root endophytes, particularly dark septate endophytes, challenging the traditional views that ectomycorrhizal fungi in alpine regions and dark septate endophytes have limited host specificity. Furthermore, our study revealed that bacteria showed broader niche breadths and stronger cross-compartment sharing than fungi, but fungi exhibited higher connectivity and more frequently acted as keystone nodes in inter-kingdom co-occurrence networks. This study deepens our understanding of how mycorrhizal types of host plants relate to variations in the microbial communities of entire plants. Future research should further elucidate the molecular mechanisms underlying differential microbial associations and explore their ecological roles in alpine ecosystems.