(1) Background: Low-calcium stress can have adverse effects on the rhizosphere environment of cucumber, subsequently impacting cucumber growth. However, plant-growth-promoting rhizobacteria can directly or indirectly enhance plant growth and induce plant tolerance, thereby mitigating the detrimental effects of low-calcium stress on cucumber growth. This study aims to elucidate the role of Bacillus amyloliquefaciens QST713 in the rhizosphere environment of cucumber under low-calcium stress, providing a theoretical basis for the application and promotion of Bacillus amyloliquefaciens. (2) Methods: This study used the 'JinYou NO.4 ' cucumber variety as test material, setting four treatments of CK, CK+Q, LCa, LCa+Q. We conducted measurements of plant height and stem diameter for four groups of cucumber plants: before treatment (0 d), and at 10 d, 20 d, 30 d, and 60 d after treatment. Additionally, we determined the biomass of cucumber plants under different treatments during the peak fruiting period. Inter-root matrix samples of cucumber were collected during the fruiting late period, and the physical and chemical properties and nutrient contents of the inter-root matrix of cucumber were determined, and bacterial microbial diversity and bacterial microbial communities were analysed using Illumina-MiSeq high-throughput sequencing technology. (3) Results: Low-calcium stress significantly inhibits the growth of cucumber plants. However, the application of Bacillus amyloliquefaciens QST713 effectively mitigates the inhibitory effects of low-calcium stress on cucumber growth. The application of Bacillus amyloliquefaciens QST713 was able to improve the physicochemical environment of the matrix and enhanced the absorption and utilisation of matrix nutrients in cucumber. The high-throughput sequencing analysis showed that the richness and diversity of bacterial communities and the number of bacteria decreased significantly under low-calcium stress, and increased significantly after the application of Bacillus amyloliquefaciens QST713. The composition of the dominant bacterial groups of the inter-root matrix of cucumber was basically the same among the four treatments, and the main difference was in the abundance of bacteria. The application of Bacillus amyloliquefaciens QST713 increased the relative abundance of bacteria that decreased under low-calcium stress, and decreased the relative abundance of bacteria that increased under low-calcium stress. (4) Conclusions: The results of this study elucidated the positive effects of Bacillus amyloliquefaciens QST713 on the growth and inter-root environment of cucumber under low-calcium stress, and provided a theoretical basis for in-depth research on the resistance of Bacillus amyloliquefaciens and its popularised application.
