Rhizobium moroccans sp. nov., a Plant-Associated Bacterium from the Desert Medicinal Plant Peganum harmala, Reveals Genomic Adaptation to Arid Environments

Members of the genus Rhizobium are best known for nitrogen-fixing symbioses with legumes, yet their diversity and evolutionary roles in non-legume hosts remain poorly explored, particularly in arid ecosystems. We report the isolation and characterization of strain AGC32, an endophytic bacterium obtained from surface-sterilized roots of the desert medicinal plant Peganum harmala collected in Moroccan drylands. Phylogenomic analyses placed AGC32 within the genus Rhizobium but clearly distinct from described species, with average nucleotide identity values below 96% and digital DNA–DNA hybridization values below 70%, supporting its designation as a novel species for which the name Rhizobium moroccans sp. nov. is proposed. Comparative genomics revealed extensive structural genome rearrangements relative to its closest sequenced relative, Rhizobium deserti, indicating a divergent evolutionary trajectory. The high-quality draft genome encodes metabolic pathways associated with adaptation to nutrient limitation and environmental stress, including complete allantoin utilization, polyphosphate metabolism, organic acid assimilation, and multiple systems involved in oxidative and osmotic stress tolerance. Phenotypic assays corroborated these genomic predictions, demonstrating the ability to metabolize diverse organic acids and carbohydrates and to express multiple plant growth–promoting traits, including nitrogen fixation and the solubilization of phosphorus, potassium, and silicon. Collectively, these findings expand the ecological and evolutionary diversity of Rhizobium, demonstrate its capacity to associate with non-legume medicinal plants in extreme environments, and highlight desert ecosystems as reservoirs of previously unrecognized microbial diversity with potential applications in sustainable agriculture in arid regions.