Genomic and Phenotypic Bases of Salt Tolerance in Sinorhizobium meliloti : Candidate Traits for Bioinoculant Development Addressing Saline Soils

Soil salinity poses a major challenge to the legume-rhizobia symbiosis development, thereby affecting sustainable agriculture. Selecting NaCl-tolerant strains and enhancing the native strains' fitness under salt stress are essential steps for the restoration of marginal areas. In this work, 49 Sinorhizobium meliloti strains, the rhizobial species forming symbiotic nitrogen-fixing associations with alfalfa—including 21 de novo-sequenced field isolates—were subjected to a thorough in vitro screening for salt tolerance at progressively higher NaCl concentrations. Field isolates showed genome-based geographical clustering but contrasting salt tolerance abilities. Indeed, genome-wide association (GWA) analysis on the strains' whole-genome sequencing data indicated several loci associated with the variability in salt tolerance. Candidate genes were involved in various processes including cell wall organisation, LPS biosynthesis, quorum sensing, and carbohydrate transport and metabolism. The relationship with carbohydrate metabolism was further confirmed by Phenotype Microarray analysis which indicated salt-tolerant strains having enhanced capacity in carbon source usage. These findings reveal synergistic pathways underlying salt tolerance and suggest candidate traits (e.g., quorum sensing, carbohydrate synthesis and modification) for developing bioinoculants to enhance legume performance in saline soils.