Host Genotype and Compartment Regulate Bacterial Microbiome Composition, Assembly Pattern and Network Complexity in Three Salt Tolerant Date Palm Cultivars

Plant microbiomes play an important role in plant health, growth, disease and stress resistance, but interacting drivers and ecological processes shaping microbiome diversity remain elusive. In this study, we examined bacterial communities using 16S rRNA gene sequencing in bulk soil, rhizosphere, rhizoplane and endosphere of three salt-tolerant date palm cultivars. We found the highest diversity in the rhizosphere and bulk soil, while lower diversity in the rhizoplane and endophyte compartments across the three cultivars. Furthermore, the bacterial microbiome exhibited genotype and compartment-specificity, with significant differences (p < 0.05) noted in community composition between compartments of the same date palm cultivar and among cultivars. Bacterial diversity and co-occurrence network complexity progressively decreased as host selection pressure increased from the soil to epiphytes, then 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, the heatmap based on PICRUSt2 analysis showed that functional profiles clustered distinctly by compartment, with significant differences (p < 0.05) in differentially abundant metabolic pathways, reflecting the functional specialisation of plant-associated compartments. Our findings provide 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.