To elucidate the mechanisms underlying the SA03-induced stress tolerance of plants, comparative transcriptomic analyses were used to identify DEGs associated with the adaptive responses of plants to the stress. Here, the inoculation with SA03 activated several major biological processes associated with salt and drought stress, Fe acquisition, wounding, and response to ABA under saline–alkaline stress. It is well known that ABA plays a cardinal role in the regulation of abiotic stress responses and tolerance in plants. The increased ABA levels can activate a wide array of many stress-responsive genes in plants, which contributes to abiotic stress tolerance. In addition, ABA has been demonstrated to regulate Fe deficiency responses in Arabidopsis plants (Lei et al., 2014). Intriguingly, ABA can also enhance the activity of plasma membrane H+-ATPase to release protons along root tips (Xu et al., 2013). In this study, transcriptomic analyses showed that the ATPase activity was significantly increased in the SA03-inoculated plants under saline–alkaline stress. Recent studies have indicated that plasma membrane H+-ATPase plays a vital role in the adaptation of plant roots to alkaline conditions by modulating proton secretion (Fuglsang et al., 2007; Yang et al., 2010), indicating that the ABA-induced H+-ATPase activity can increase the release of protons into plant rhizosphere for counteracting adverse impacts imposed by alkaline pH conditions. More recently, some PGPR strains markedly induce ABA accumulation in host plants under abiotic stress (Salomon et al., 2014; Cohen et al., 2015; Park et al., 2017). Salomon et al. (2014) have reported that B. licheniformis Rt4M10 reduces water losses in drought-treated grapevine plants by induction of ABA synthesis. Azospirillum brasilense ameliorates drought stress in Arabidopsis thaliana mainly through enhancement of ABA levels (Cohen et al., 2015). Moreover, the inoculation with Bacillus aryabhattai SRB02 induces a great increase of ABA level and further activates ABA-mediated stomatal closure in soybean, which contributes to better heat stress tolerance (Park et al., 2017). These results have indicated that application of PGPR can enhance the tolerance of host plants to various abiotic stresses by activating ABA-mediated signaling pathways. Thus, the increased tolerance of SA03-inoculated plants against saline–alkaline stress may result from alteration of ABA levels.