Genomic Insights into a Desert-Adapted Sinorhizobium Strain from the Tunisian Sahara

Abstract

Nitrogen fixation by rhizobia in symbiosis with legumes is essential for nitrogen cycling and sustainable agriculture and plays a critical role in the survival of native leguminous plants in the arid and Saharan environments of Tunisia. The Sinorhizobium meliloti strain IRAMC:0087, initially isolated from the root nodules of the Saharan shrub Calobota saharae in southern Tunisia, can establish nodulation with Vachellia tortilis subsp. raddiana, a tree well-suited to extreme desert climates, and colonize roots of Trifolium subterraneum endophytically. Phenotypic analyses of IRAMC:0087 demonstrate its resilience to high salinity, drought, and elevated temperatures. To further explore the genetic foundation of its adaptations, we sequenced the strain's complete genome (7.3 Mb), which comprises five replicons: a main chromosome (3,650,495 bp), a chromid pSymB (1,674,059 bp), and another large plasmid, plasmid Accessory A (1,247,198 bp), and two smaller plasmids, pSymA (597,953 bp) and plasmid Accessory B (197,378 bp), with an overall GC content of 61.94%. In total, we identified 6,558 protein-coding genes, 56 tRNAs, and 9 rRNAs, along with a prophage region of 53.3 kb showing homology with Sinorhizobium phage phiLM21. Gene clusters associated with rhizosphere interactions, production of secondary metabolites, plant growth promotion, and symbiosis were found within the genome. Notably, one additional plasmid encodes stress tolerance-related genes, including those for trehalose and osmoprotectant synthesis, likely enhancing the strain's capacity to withstand extreme environmental conditions. The ability of IRAMC:0087 to engage in both endophytic and symbiotic interactions with desert-adapted hosts highlights its unique adaptations. Comparative genomic studies with other rhizobial strains may uncover new genetic elements involved in symbiosis under harsh climates.