Genomic plasticity, stress tolerance, and a distinctive pSymA in the symbiotic bacterium Sinorhizobium meliloti IRAMC:0087

Abstract

Arid ecosystems promote the emergence of rhizobial strains adapted to severe abiotic stress while retaining symbiotic competence. Here, we characterize IRAMC:0087, a rhizobial strain isolated from root nodules of the Saharan shrub Calobota saharae in southern Tunisia. Phenotypic assays showed high tolerance to heat, salinity, and osmotic stress, together with plant growth-promoting traits including indole-3-acetic acid production, phosphate solubilization, and siderophore secretion. In vivo assays demonstrated effective nitrogen-fixing nodulation of Vachellia tortilis , whereas Medicago and Trifolium species were not nodulated despite growth promotion through non-symbiotic mechanisms. Confocal microscopy confirmed root colonization and nodule occupancy, indicating host-dependent infection behavior. To better understand the physiological behavior of this strain, its complete genome sequence was generated, revealing a 7.37 Mb circularized genome comprising five replicons: a 3.65 Mb chromosome, two megaplasmids corresponding to pSymA (0.59 Mb) and pSymB (1.67 Mb), and two accessory plasmids, with an overall GC content of 62%. Phylogenomic, Average Nucleotide Identity (ANI), and digital DNA–DNA hybridization (dDDH) analyses assigned IRAMC:0087 to Sinorhizobium meliloti . However, comparative genomics revealed marked structural and functional divergence of pSymA_IRAMC:0087 from S. meliloti 1,021, with greater similarity to S. garamanticum and S. numidicum . NodC phylogeny placed the strain within symbiovar tunisiaense , consistent with its distinct host range. Genome annotation further identified determinants linked to stress tolerance, rhizosphere competitiveness, bioactive metabolite production, signaling, and symbiosis, including genes located on accessory plasmids. These findings highlight IRAMC:0087 as a desert-adapted rhizobium with distinctive symbiotic properties and strong ecological fitness, providing insights into rhizobial evolution in arid environments.