Compartment-Specific Bacterial Communities and Their Functional Potential in the Desert Plant Citrullus colocynthis

Plants inhabiting arid and semi-arid ecosystems rely on their associated microbiota to withstand drought, heat, salinity, and nutrient limitation. We investigated the bacterial communities associated with the foliar tissues, roots, and rhizospheric soil of the desert plant Citrullus colocynthis (L.) Schrad. growing in semi-arid Morocco using 16S rRNA gene amplicon sequencing, culture-dependent isolation, and genome-informed functional profiling of selected tissue-associated isolates. Bacterial communities exhibited strong compartmentalization, with the rhizospheric soil harboring the highest diversity, followed by roots and foliar tissues. Across compartments, communities were dominated by Pseudomonadota, Actinomycetota, Bacillota, and Bacteroidota, while several bacterial families showed compartment-specific enrichment consistent with roles in plant colonization, nutrient cycling, and stress adaptation. Soil physicochemical properties were significantly associated with community composition but explained only part of the observed variation, indicating an additional role for host-mediated selection in microbiome assembly. Cultivation recovered diverse bacteria from root and foliar tissues, mainly belonging to Achromobacter , Pseudomonas , and Glutamicibacter , most of which were also detected by amplicon sequencing. Genomic analyses identified traits associated with stress tolerance, osmoprotection, nutrient acquisition, colonization, and plant growth promotion. These findings reveal a structured and functionally diverse bacteriome in C. colocynthis and highlight this desert-adapted plant as a promising source of beneficial microorganisms for future experimental evaluation under water-limited conditions.