Compartment-Specific Assembly and Functional Potential of the Bacteriome of Citrullus colocynthis in a Semi-Arid Ecosystem

Abstract

Plants inhabitng in arid and semi-arid ecosystems, such as Citrullus colocynthis (L.) Schrad., are adapted to drought, heat, salinity, and nutrient limitation. Their associated microbial communities may further support plant persistence under these harsh conditions. Here, we characterized the bacterial communities associated with leaf endosphere, rhizosphere and roots of C. colocynthis growing in a semi-arid region of Moroccan using 16S rRNA gene amplicon sequencing, culture-dependent isolation, and genome-informed functional profiling of selected isolates. The results revealed a structured microbiome, with rhizosphere harboring the highest bacterial diversity, roots representing an intermediate selective habitat, and the leaf endosphere containing a more restricted assemblage. Communities were dominated by members of the phyla Pseudomonadota, Actinomycetota, Bacillota, and Bacteroidota. Several families associated to plant colonization, nutrient mobilization, and stress tolerance, including Pseudomonadaceae, Microbacteriaceae, Rhizobiaceae, Devosiaceae, and Xanthomonadaceae, showed compartment-specific enrichment. Although soil physicochemical properties influenced bacterial community structure, they explained only part of the variation observed, suggesting that bacteriome assembly is shaped by both environmental conditions and host filtering processes. Culture-bdependant analyses recovered diverse endophytic genera, mainly Achromobacter, Pseudomonas, and Glutamicibacter, most of which were also detected in the amplicon sequencing dataset. Genome-based profiling identified traits related to stress response, osmoprotection, nutrient-related metabolism, colonization, and plant-microbe interactions. Together, these findings highlight C. colocynthis as a reservoir for functionally relevant bacterial diversity with ecological and biotechnological potential in semi-arid environments. ImportanceUnderstanding how plants survive in arid and semi-arid ecosystems is increasingly important in the context of climate change and land degradation. This study demonstrates that Citrullus colocynthis hosts a structured and functionally diverse bacteriome across the leaf endosphere, rhizosphere, and root compartments. By combining amplicon sequencing, cultivation, and genome-informed functional analyses, we identified bacterial taxa and traits associated with stress tolerance, nutrient acquisition, and plant colonization. The recovery of cultivable endophytes with adaptive genomic features highlights the potential of desert plant-associated microbiota as a source of beneficial microorganisms for sustainable agriculture and biotechnological applications in water-limited environments.