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

TL;DR

This study identifies genetic and metabolic traits in Sinorhizobium meliloti that help the bacteria survive in salty soils, which could improve legume growth in such environments.

Contribution

The study identifies candidate genes and metabolic traits associated with salt tolerance in Sinorhizobium meliloti using genome-wide and phenotypic analyses.

Findings

Genome-wide association analysis identified loci linked to salt tolerance, including genes involved in cell wall organization and quorum sensing.

Salt-tolerant strains showed enhanced carbon source usage, indicating broader metabolic adaptability.

Phenotype Microarray confirmed a connection between salt tolerance and carbohydrate metabolism.

Abstract

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.

Genome‐wide association analysis on 49
Sinorhizobium meliloti
strains (21 de novo sequenced) reveals extensive phenotypic heterogeneity in salt tolerance, closely associated with quorum sensing, cell surface stability and adaptation. Salt‐tolerant strains exhibit a wider metabolic capacity, especially in carbon sources exploitation, underscoring their potential for adaptability in harsh conditions.

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