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The recently proposed species Ensifer aridi represents an interesting model to study adaptive mechanisms explaining its maintenance under stressful pedo-climatic conditions. To get insights into functions associated with hyperosmotic stress adaptation in E. aridi, we first performed RNAseq profiling of cells grown under sub-lethal stresses applied by permeating (NaCl) and non-permeating (PEG8000) solutes that were compared to a transcriptome from unstressed bacteria. Then an a priori approach, consisting of targeted mutagenesis of the gene encoding alternative sigma factor (rpoE2), involved in the General Stress Response combined with phenotyping and promoter gfp fusion-based reporter assays of selected genes was carried out to examine the involvement of rpoE2 in symbiosis and stress response. The majority of motility and chemotaxis genes were repressed by both stresses. Results also suggest accumulation of compatible solute trehalose under stress and other metabolisms such as inositol catabolism or the methionine cycling-generating S-adenosyl methionine appears strongly induced notably under salt stress. Interestingly, many functions regulated by salt were shown to favor competitiveness for nodulation in other rhizobia, supporting a role of stress genes for proper symbiosis’ development and functioning. However, despite activation of the general stress response and identification of several genes possibly under its control, our data suggest that rpoE2 was not essential for stress tolerance and symbiosis’ development, indicating that E. aridi possesses alternative regulatory mechanisms to adapt and respond to stressful environments.

BackgroundNitrogen fixing bacteria isolated from hot arid areas in Asia, Africa and America but from diverse leguminous plants have been recently identified as belonging to a possible new species of Ensifer (Sinorhizobium). In this study, 6 strains belonging to this new clade were compared with Ensifer species at the genome-wide level. Their capacities to utilize various carbon sources and to establish a symbiotic interaction with several leguminous plants were examined.ResultsDraft genomes of selected strains isolated from Morocco (Merzouga desert), Mexico (Baja California) as well as from India (Thar desert) were produced. Genome based species delineation tools demonstrated that they belong to a new species of Ensifer. Comparison of its core genome with those of E. meliloti, E. medicae and E. fredii enabled the identification of a species conserved gene set. Predicted functions of associated proteins and pathway reconstruction revealed notably the presence of transport systems for octopine/nopaline and inositol phosphates. Phenotypic characterization of this new desert rhizobium species showed that it was capable to utilize malonate, to grow at 48 °C or under high pH while NaCl tolerance levels were comparable to other Ensifer species. Analysis of accessory genomes and plasmid profiling demonstrated the presence of large plasmids that varied in size from strain to strain. As symbiotic functions were found in the accessory genomes, the differences in symbiotic interactions between strains may be well related to the difference in plasmid content that could explain the different legumes with which they can develop the symbiosis.ConclusionsThe genomic analysis performed here confirms that the selected rhizobial strains isolated from desert regions in three continents belong to a new species. As until now only recovered from such harsh environment, we propose to name it Ensifer aridi. The presented genomic data offers a good basis to explore adaptations and functionalities that enable them to adapt to alkalinity, low water potential, salt and high temperature stresses. Finally, given the original phylogeographic distribution and the different hosts with which it can develop a beneficial symbiotic interaction, Ensifer aridi may provide new biotechnological opportunities for degraded land restoration initiatives in the future.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3447-y) contains supplementary material, which is available to authorized users.