Highlights: • Desert ecosystems are subjected to high water stress, limiting plant growth. • Drought increases the abundance of drought-tolerant Actinobacteria and Acidobacteria. • Microbiota of Haloxylon salicornicum roots and rhizosphere is responsive to water. • Symbionts taxa are differentially expressed following watering. • Little studied dark septate endophytes may be important plant symbiont. Abstract: Soil microbiota plays a fundamental role in nutrient cycles and plant fitness. However, the response of bacterial and fungal communities interacting with plants to an increase in the water regime in natural ecosystems has yet to be extensively studied. To address this matter, we studied the response of rhizospheric and root endophytic microbial communities to simulated intense precipitation in a natural desert environment. We used amplicon sequencing to identify bacterial (16S) and fungal (ITS) communities of Haloxylon salicornicum (Moq) Bunge ex Boiss., a pivotal plant species in natural ecosystems with a high potential for land restauration. Bacterial community composition included mostly Actinobacteriota in roots and Chloroflexi in rhizospheres, whereas fungal communities were mostly represented by Ascomycota. The decomposition of beta diversity revealed a significant share of i) turnover for bacteria between compartments, ii) nestedness for fungi according to compartments, and iii) nestedness for bacteria in both rhizosphere and roots according to watering. Differential abundances analyses between watering conditions identified respectively i) 29 and 37 differentially abundant bacterial families, and ii) 7 and 6 differentially abundant fungal families for rhizosphere and roots. Watering induced a rapid response from little characterized microbiota potentially involved in nutrient recycling, such as rhizobia and dark septate endophytes. These results provided evidence of the fundamental role of rare and intense precipitation in modifying the microbial composition of roots and rhizosphere of one desert plant species. Moreover, little studied taxa potentially crucial to the plant health in desert environments such as dark septate endophytes and Planctomycetota were identified as pioneer taxa colonizing freshly emitted roots. Collectively, our results help to improve the understanding of desert taxa response to water availability, and may guide future research on natural ecosystems restauration. Graphical abstract: https://ars.els-cdn.com/content/image/1-s2.0-S0929139324001434-ga1.jpg