BackgroundRhizobium tropici strain CIAT 899 establishes effective symbioses with several legume species, including Phaseolus vulgaris and Leucaena leucocephala. This bacterium synthesizes a large variety of nodulation factors in response to nod-gene inducing flavonoids and, surprisingly, also under salt stress conditions. The aim of this study was to identify differentially expressed genes in the presence of both inducer molecules, and analyze the promoter regions located upstream of these genes.ResultsResults obtained by RNA-seq analyses of CIAT 899 induced with apigenin, a nod gene-inducing flavonoid for this strain, or salt allowed the identification of 19 and 790 differentially expressed genes, respectively. Fifteen of these genes were up-regulated in both conditions and were involved in the synthesis of both Nod factors and indole-3-acetic acid. Transcription of these genes was presumably activated through binding of at least one of the five NodD proteins present in this strain to specific nod box promoter sequences when the bacterium was induced by both apigenin and salt. Finally, under saline conditions, many other transcriptional responses were detected, including an increase in the transcription of genes involved in trehalose catabolism, chemotaxis and protein secretion, as well as ribosomal genes, and a decrease in the transcription of genes involved in transmembrane transport.ConclusionsTo our knowledge this is the first time that a transcriptomic study shows that salt stress induces the expression of nodulation genes in the absence of flavonoids. Thus, in the presence of both nodulation inducer molecules, apigenin and salt, R. tropici CIAT 899 up-regulated the same set of symbiotic genes. It could be possible that the increases in the transcription levels of several genes related to nodulation under saline conditions could represent a strategy to establish symbiosis under abiotic stressing conditions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2543-3) contains supplementary material, which is available to authorized users.

The Sinorhizobium fredii HH103 rkp-3 region has been isolated and sequenced. Based on the similarities between the S. fredii HH103 rkpL, rkpM, rkpN, rkpO, rkpP, and rkpQ genes and their corresponding orthologues in Helicobacter pylori, we propose a possible pathway for the biosynthesis of the S. fredii HH103 K-antigen polysaccharide (KPS) repeating unit. Three rkp-3 genes (rkpM, rkpP, and rkpQ) involved in the biosynthesis of the HH103 KPS repeating unit (a derivative of the pseudaminic acid) have been mutated and analyzed. All the rkp-3 mutants failed to produce KPS and their lipopolysaccharide (LPS) profiles were altered. These mutants showed reduced motility and auto-agglutinated when early-stationary cultures were further incubated under static conditions. Glycine max, Vigna unguiculata (determinate nodule–forming legumes), and Cajanus cajan (indeterminate nodules) plants inoculated with mutants in rkpM, rkpQ, or rkpP only formed pseudonodules that did not fix nitrogen and were devoid of bacteria. In contrast, another indeterminate nodule–forming legume, Glycyrrhiza uralensis, was still able to form some nitrogen-fixing nodules with the three S. fredii HH103 rifampicin-resistant rkp-3 mutants tested. Our results suggest that the severe symbiotic impairment of the S. fredii rkp-3 mutants with soybean, V. unguiculata, and C. cajan is mainly due to the LPS alterations rather than to the incapacity to produce KPS.

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Different Rhizobium and Bradyrhizobium strains were screened for their ability to produce melanin. Pigment producers (Mel') were found among strains of R. leguminosarum biovars viceae, trifolii, and phaseoli, R. meliloti, and R. fredii; none of 19 Bradyrhizobium strains examined gave a positive response. Melanin production and nod genes were plasmid borne in R. leguminosarum biovar trifolii RS24. In R. leguminosarum biovar phaseoli CFN42 and R. meliloti GRO15, mel genes were located in the respective symbiotic plasmids. In R. fredii USDA205, melanin production correlated with the presence of its smallest indigenous plasmid. * Corresponding author. Wild type, Mel+* Spontaneous Rif' derivative of RS24, Mel' Kmr derivative of RS240 by insertion of transposon TnS-Mob, Mel' Kanamycin-sensitive derivative of RS2400 after treatment with acridine orange, Mel-Kanamycin-sensitive derivative of RS2400 after treatment with acridine orange, Mel+ Kanamycin-sensitive derivative of RS2400 after treatment with acridine orange, Mel' Wild type, Mel+* Wild type, Mel-Nonnodulating derivative of RS169 after treatment with acridine orange, Mel-Spontaneous Stri derivative of RS169-NA545, Mel-RS169-NA4(pJERS1) (from cross RS2400 x RS169-NA4), Mel+* Wild type, Mel' 128C53 str-279 (ApRL6JI), Mel-Spontaneous Rif' derivative of B151, Mel-B1511(p42d) (from cross A. tumefaciens C58C1 x B1511), Mel+ B1511(p42d) (from cross A. tumefaciens C58C1 x B1511), Mel Wild type, Mel+ Wild type, Mel+ Spontaneous Rif' derivative of strain GRO15, Mel+* Kmr derivatives of TC281 by insertion of transposon Tn5-Mob into pRmeGRO15, pJB3JI, Mel+ Wild type, Mel+ Wild type, Mel' Wild type, Mel+* Spontaneous Rif derivative of strain USDA205, Mel-Spontaneous Rifr derivative of strain USDA205, Mel-Spontaneous Strr derivative of strain USDA205, Mel+* AB55(R68.45) (from cross E. cOli 1230 x AB55), Mel+ Spontaneous Rif derivative of strain USDA205, Mel+* Kmr transconjugants of AB034 by transposon TnS-Mob mutagenesis, Mel-Wild type, Mel+* Wild type, Mel+* Wild type, Mel+* Rif' Strr Mel-Spontaneous CM' derivative of strain GM19023, Mel AB274(pJERS1) (from cross RS2400 x AB274), Mel+* AB274(pTC1) (from cross TC282 x AB274), Mel' AB274(pTC2) (from cross TC283 x AB274), Mel' AB274(pTC3) (from cross TC284 x AB274), Mel' Eryr Cmlr pTi-cured derivative of A. tumefaciens C58, Mel-C58C1(p42d), Mel't 294 Rec-, chromosomally integrated RP4 derivative, Tpr Strr Pro-Met-Nalr (R68.45) Pro-Met-Nalr (pJB3JI) hsdS hsdM pro leu thi gal lac Y recA Strr pBR325;:TnS-Mob Used for mobilizing plasmids, Kmr P1 group R-plasmids: Apr Kmr Tcr R68.45 Kms, used for mobilizing plasmids 220-MDa indigenous plasmid of R. leguminosarum biovar trifolii RS24; Mel+ Co

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