Investigation of the Plant-Growth-Promoting Potential of Plant Endophytic Keystone Taxa in Desertification Environments

The Qinghai–Tibetan Plateau (QTP) is under serious desertification stress, which has been receiving increasing attention. Although the restoration of surface vegetation is crucial, the growth of plants is often hindered by unfavorable nutrient-deficient conditions. The plant-associated endophytic microbiome is considered the secondary genome of the host and plays a significant role in host survival under environmental stresses. However, the community compositions and functions of plant-endophytic microorganisms in the QTP desertification environments remain unclear. Therefore, this study investigated the endophytic microbiome of the pioneer plant Gueldenstaedtia verna on the QTP and its contribution to host growth under stressful conditions. The results showed that nutrient-deficient stresses strongly influenced the microbial community structures in the rhizosphere. The impacts of these stresses, however, decreased from the rhizosphere community to the plant endophytes, resulting in consistent plant endophytic microbial communities across different sites. Members of Halomonas were recognized as keystone taxa in the endophytic microbiome of G. verna. Correlation analysis, metagenome-assembled genomes (MAGs), and comparative genome analyses have shown that the keystone taxa of the plant endophytic microbiome may promote plant growth through pathways such as nitrogen fixation, IAA, and antioxidant production, which are important for improving plant nutrient acquisition and tolerance. This finding may provide a crucial theoretical foundation for future phytoremediation efforts in desertification environments on the Qinghai-Tibet Plateau.