Host genotype and compartment regulate bacterial microbiome composition, assembly pattern and network complexity in three salt tolerant date palm cultivars.

Plant microbiomes are important for plant health, growth, disease, and stress resistance, but the factors and ecological processes shaping the microbiome remain unclear. In this study, we examined bacterial communities using 16s RNA sequencing in bulk soil, rhizosphere, rhizoplane and endosphere of three salt tolerant date palm cultivars including Bughal White, Messalli and Razez. We found the highest diversity in the rhizosphere and bulk soil, with lower diversity in the rhizoplane and endophytes compartment across the three cultivars. Furthermore, the bacterial microbiome exhibited genotype and compartment-specificity, with significant differences (P < 0.05) noted in bacterial community composition between compartments of the same date palm cultivar and among cultivars. Bacterial diversity and the complexity of microbial co-occurrence networks progressively decreased as host selection pressure increased from the soil to epiphytes to endophytes. Specialist microorganisms dominate the community composition and play a major role in microbial interactions in each compartment. The ecological model showed that stochastic processes, primarily drift (37%), predominantly shaped microbial community assembly in bulk soil, whereas deterministic processes, mainly homogenous selection, governed microbial assembly in the rhizosphere, rhizoplane, and endosphere, contributed 59%, 60%, and 64%, respectively. Notably, PICRUSt2 analysis showed that bacterial communities clustered distinctly by compartment, with significant differences (P < 0.05) in differentially abundant metabolic pathways, reflecting the functional specialization of plant-associated compartments. Our research provides strong empirical support for the theoretical model of host selection and niche occupation in date palm microbiome assembly, with significant implications for sustainable agriculture in arid ecosystems through improved crop management and microbiome manipulation.