Plant Microbiome of the Arabian Peninsula Desert Reveals Unique Structural and Functional Adaptations Supporting Climate Resilience

Background Climate change is expanding arid regions globally, intensifying drought, salinity, and heat stress that threaten ecosystem stability and food security. Desert plants of the Arabian Peninsula have evolved physiological and microbial adaptations that enable survival under such extremes. This study investigates the endophytic microbial communities of four representative xerophytic species; Zygophyllum mandavillei, Tribulus zeyheri, Limeum arabicum, and Cyperus conglomeratus, to identify functional traits that promote their climatic resilience. These perennial species were selected because they inhabit similar arid environments and share xerophytic traits such as reduced leaf area, fibrous root systems, and high drought tolerance, making them ideal models for examining interactions between plants and their associated microbes in desert ecosystems. Methods High-throughput environmental DNA (eDNA) sequencing was performed on 27 plant samples, generating 3,660,664 high-quality reads. Taxonomic clustering resolved the sequences into 30 phyla, 15 classes, 20 orders, 27 families, and 21 genera. Diversity analyses were conducted to evaluate microbial richness and community structure, and functional inference was performed using PICRUSt2. Results Dominant microbial taxa included Alphaproteobacteria, Actinomycetia, Cyanophyceae, and Gammaproteobacteria, groups known for nitrogen fixation, carbon cycling, and resistance to desiccation and heat. Alpha-diversity analyses revealed significant variation in species richness among the host plants, while beta-diversity metrics showed distinct clustering patterns, indicating host-specific microbial assembly shaped by plant genotype and microhabitat. Functional prediction suggested enrichment of pathways related to amino acid, carbohydrate, and lipid metabolism, oxidative phosphorylation, DNA repair, and secondary-metabolite biosynthesis, supporting metabolic versatility and stress adaptation. Conclusions These findings provide a comprehensive genomic overview of endophytic bacterial communities associated with key desert plants of the Arabian Peninsula and establish a foundation for future functional validation and sustainable applications of desert microbiomes under climate change.