Some hormone signaling pathways in host plants are tightly regulated by some PGPR strains, and thus affecting various physiological processes (Poupin et al., 2016; Zhou et al., 2016a). ABA plays a cardinal role in abiotic stress responses in plants (Zhang et al., 2006). In this study, transcriptomic analyses indicated that the inoculation with SA03 might affect cellular ABA levels in plants, and further regulate stress-related signaling pathways. To test the hypothesis, the ABA content in plants was measured. The roots of inoculated plants exhibited slightly higher ABA content than that of non-inoculated plants before saline–alkaline treatment, whereas no significant difference was observed in shoots (Table 2). After 2 and 4 weeks of saline–alkaline treatment, the ABA content was significantly higher in shoots [F(5,54) = 369.14, P < 0.05] and roots [F(5,54) = 123.34, P < 0.05] of the inoculated plants than that of the non-inoculated plants (Table 2). Furthermore, we explored the effects of fluridone (FLU), an inhibitor of ABA biosynthesis, on the inoculated plants under saline–alkaline stress. It was observed that treatment with 10 μM FLU abolished the SA03-induced stress tolerance of plants (Figure 8A). Many studies have indicated that NO serves as an important signal molecule to regulate abiotic stress responses, Fe uptake and remobilization in plants (Graziano and Lamattina, 2007; Tanou et al., 2009; Chen et al., 2010; Wang et al., 2017). For this reason, we examined if NO was involved in the SA03-mediated stress responses in plants. Intriguingly, the inoculation with SA03 could not increase the tolerance of plants to saline–alkaline stress after treatment with 150 μM c-PTIO, a scavenger of NO. That was similar to the phenotypes observed for the FLU-treated plants (Figure 8A).