Enhanced Fe acquisition and reduced Na+ toxicity are required for improving the tolerance of plants to saline–alkaline stress (Li et al., 2016). In this study, the SA03-inoculated plants exhibited higher Fe accumulation and lower Na+ levels under saline–alkaline stress. qRT-PCR analyses showed that the transcription levels of Fe acquisition-related genes and Na+/H+ antiporter genes were significantly up-regulated in the inoculated plants compared with the non-inoculated plants. To clarify how microbial induction of ABA and NO regulated these adaptive responses, the transcription of genes associated with Fe acquisition and Na+/H+ antiporters were investigated in plants treated with FLU or c-PTIO. The expression levels of Fe uptake-related (IRT1, FRO2, and AHA2) [Figure 10; F(11,24) = 202.47, P < 0.05], Fe transport-related (YSL1, YSL2, FRD3 and NAS1) [Figure 10; F(15,32) = 71.20, P < 0.05], and Na+/H+ antiporter (NHX1, NHX2 and NHX5) [Figure 10; F(11,24) = 251.41, P < 0.05] genes were remarkably increased in the inoculated plants under the stress compared with the non-inoculated plants. However, their transcription levels were markedly down-regulated in the inoculated plants after FLU treatment. Upon exposure to c-PTIO, the transcription of Fe acquisition-related and Na+/H+ antiporter genes was greatly repressed in the inoculated plants, but no significant difference was observed for the transcription of Fe transport-related genes. Moreover, either FLU or c-PTIO treatment reduced the expression of Na+/H+ antiporter genes in the inoculated plants under the stress.