Salinity-driven microbiome profiling of <i>Salvadora persica</i> reveals distinct tissue-associated bacterial assemblages in leaves and roots

Tissue-associated microbial communities contribute to plant adaptation in extreme environments, yet the compartment-specific organization of tissue-associated bacterial communities in desert halophytes remains insufficiently understood. This study investigated how plant tissue type may influence the tissue-associated bacterial phytobiome of Salvadora persica growing under saline desert conditions along the western coast of Saudi Arabia. Leaf and root tissues were collected and analyzed using high throughput 16S rRNA gene amplicon sequencing. After quality filtering, non-chimeric reads were processed using DADA2 for amplicon sequence variant (ASV) inference, and microbial diversity and community structure were assessed using alpha diversity indices, rarefaction analysis, beta diversity metrics, principal coordinates analysis (PCoA), and UniFrac-based clustering. Sequencing produced 68,817–108,461 high-quality non-chimeric reads per sample. Leaf tissue-associated bacterial communities were highly conserved and taxonomically simplified (10–22 ASVs; Shannon index 0.89–1.01; Faith’s PD 1.92–4.02), dominated mainly by Cyanobacteriota and Pseudomonadota. Root tissue-associated bacterial communities exhibited substantially higher richness and phylogenetic complexity (286–508 ASVs; Faith’s PD 31.03–51.05), with one root sample showing dominance of Bacillota and Bacteroidota and enrichment of anaerobic genera, while other root samples were enriched in Cyanobacteriota and Pseudomonadota alongside diverse low-abundance soil-associated phyla. Beta diversity analyses revealed compartment-associated patterns, where ordination and phylogenetic clustering suggested separation between leaf- and root-associated communities; however, permutational multivariate analysis of variance (PERMANOVA) did not detect statistically significant differences between compartments based on Bray–Curtis and unweighted UniFrac distances. Overall, the data indicates trends consistent with compartment differentiation in diversity and composition between leaf- and root-associated bacterial communities in S. persica , supporting compartment-associated structuring of tissue-associated bacterial assemblages under saline desert conditions and providing a foundation for future functional and metagenomic investigations.