Rhizobium moroccans sp. nov.: a plant-growth-promoting endophyte from Peganum harmala in an arid environment

Abstract

The diversity and ecological roles of Rhizobium species beyond legume symbiosis remain insufficiently characterized, particularly in arid ecosystems. Here, we report the isolation and comprehensive characterization of strain AGC32, an endophytic bacterium recovered from surface-sterilized roots of the medicinal xerophyte Peganum harmala growing in Moroccan drylands. The isolate is a non-halophilic, aerobic, Gram-negative bacterium with optimal growth at 30-35{degrees}C, pH 5.0, and 1% NaCl. Phylogenomic analysis placed AGC32 within the genus Rhizobium. However, average nucleotide identity values below 96%, digital DNA-DNA hybridization values below 70%, and the absence of assignment to any validly published type strain supported its classification as a novel species, for which the name Rhizobium moroccans sp. nov. is proposed. Comparative genomics revealed substantial genome rearrangements relative to its closest relative, Rhizobium deserti, indicating distinct evolutionary trajectories. The high-quality draft genome encodes pathways associated with nitrogen limitation (including complete allantoin utilization), polyphosphate metabolism, oxidative and osmotic stress tolerance, and organic acid utilization. Phenotypic assays corroborated genomic predictions, demonstrating preferential metabolism of organic acids, utilization of carbohydrates, and plant growth-promoting traits including nitrogen fixation and solubilization of phosphorus, potassium, and silicon. These findings expand the ecological knowledge of Rhizobium and reveal adaptation to a non-legume host in an arid environment. IMPORTANCEBacteria of the genus Rhizobium are widely known for forming nitrogen-fixing symbioses with legumes. However, their roles in non-leguminous desert plants remain poorly understood. We isolated and characterized a new species, Rhizobium moroccans, from the roots of the medicinal plant Peganum harmala growing in Moroccan drylands. This bacterium shows genetic and physiological traits that support survival under drought and nutrient limitation and displays multiple plant-beneficial properties. Our results demonstrate that Rhizobium species are not restricted to legumes but can form intimate associations with medicinal plants in extreme environments. The discovery of this novel species highlights desert plants as reservoirs of previously unrecognized microbial diversity and suggests potential applications for sustainable agriculture in arid regions.