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Background  Soil salinization is a worldwide problem that is intensifying because of the effects of climate change. An effective method for the reclamation of salt-affected soils involves initiating plant succession using fast growing, nitrogen fixing actinorhizal trees such as the  Casuarina . The salt tolerance of  Casuarina  is enhanced by the nitrogen-fixing symbiosis that they form with the actinobacterium  Frankia . Identification and molecular characterization of salt-tolerant  Casuarina  species and associated  Frankia  is imperative for the successful utilization of  Casuarina  trees in saline soil reclamation efforts. In this study, salt-tolerant and salt-sensitive  Casuarina  associated  Frankia  strains were identified and comparative genomics, transcriptome profiling, and proteomics were employed to elucidate the molecular mechanisms of salt and osmotic stress tolerance.    Results  Salt-tolerant  Frankia  strains (CcI6 and Allo2) that could withstand up to 1000 mM NaCl and a salt-sensitive  Frankia  strain (CcI3) which could withstand only up to 475 mM NaCl were identified. The remaining isolates had intermediate levels of salt tolerance with MIC values ranging from 650 mM to 750 mM. Comparative genomic analysis showed that all of the  Frankia  isolates from  Casuarina  belonged to the same species ( Frankia casuarinae ). Pangenome analysis revealed a high abundance of singletons among all  Casuarina  isolates. The two salt-tolerant strains contained 153 shared single copy genes (most of which code for hypothetical proteins) that were not found in the salt-sensitive(CcI3) and moderately salt-tolerant (CeD) strains. RNA-seq analysis of one of the two salt-tolerant strains ( Frankia sp.  strain CcI6) revealed hundreds of genes differentially expressed under salt and/or osmotic stress. Among the 153 genes, 7 and 7 were responsive to salt and osmotic stress, respectively. Proteomic profiling confirmed the transcriptome results and identified 19 and 8 salt and/or osmotic stress-responsive proteins in the salt-tolerant (CcI6) and the salt-sensitive (CcI3) strains, respectively.    Conclusion  Genetic differences between salt-tolerant and salt-sensitive  Frankia  strains isolated from  Casuarina  were identified. Transcriptome and proteome profiling of a salt-tolerant strain was used to determine molecular differences correlated with differential salt-tolerance and several candidate genes were identified. Mechanisms involving transcriptional and translational regulation, cell envelop remodeling, and previously uncharacterized proteins appear to be important for salt tolerance. Physiological and mutational analyses will further shed light on the molecular mechanism of salt tolerance in  Casuarina  associated  Frankia  isolates.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-4056-0) contains supplementary material, which is available to authorized users.

bmc genomics

Genomic, transcriptomic, and proteomic approaches towards understanding the molecular mechanisms of salt tolerance in Frankia strains isolated from Casuarina trees