Macrogenome-based study on the mechanism of Bacillus velezensis SX13 in regulating rhizophere environment and cucumber growth under different cultivation environments

Microbial activities are the dynamic core of nutrient cycling in organic substrates, and the exploitation of plant growth-promoting rhizobacteria strains contributes to sustainable agricultural development. This study aimed investigate the effect and mechanism of Bacillus velezensis SX13 in nutrient cycling and plant promotion under different substrate supply conditions. The effects of reduced substrate supply (sCK), inoculation with SX31 under conventional substrate dosage (Bv) and reduced substrate dosage conditions (sBv), respectively, on the rhizospheric microenvironment and plant growth were investigated using conventional substrate dosage as a control (CK). Results showed no significant difference in the diversity indexes (Chao1 and Shannon) of the rhizospheric microbial community among the four treatments. However, nonmetric multidimensional scaling analysis and principal coordinate analysis revealed that compared with CK treatment, the inoculation of SX13 strains and reduced substrate supply reshaped the diversity structure of microbial communities. Furthermore, inoculation with B. velezensis SX13 under both substrate supply conditions increased the abundance of Proteobacteria, Acidobacteria, and Firmicutes. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the gene abundance in the pathways related to the carbon and nitrogen cycle was generally upregulated after inoculation with B. velezensis SX13. Carbohydrate-metabolizing enzyme analysis based on the Carbohydrate-Active Enzymes Database also indicated that the rhizosphere inoculation of B. velezensis SX13 significantly up-regulated the top genes related to carbohydrate esterases, carbohydrate binding modules, glycoside hydrolases, glycoside transferases, and polysaccharide lyases. Further mining of macrogenomic data for enrichment of key genes in carbon and nitrogen metabolism pathways revealed that SX13 elevated the abundance of genes involved in nitrogen metabolism processes, such as nitrification, nitrogen fixation, nitrogen assimilation and organic nitrogen mineralization, and carbon metabolism pathways, such as C5 branched-chain dicarboxylic acid metabolism, phosphatidylinositol metabolism, fructose and mannose metabolism, and glycolate and dicarboxylic acid metabolism. As a result, the activities of carbon and nitrogen cycle-related enzymes such as cellobiohydrolase, glucosidase, urease, L-leucine amino peptidase, and 1 4-N-acetylglucosaminidase were increased, which in turn accelerated nutrient cycling. B. velezensis SX13 and its mediated improvement of the rhizospheric microenvironment resulted in the up-regulation of root CsNRT family genes (such as CsNRT1.1, CsNRT1.4a, CsNRT1.4b, CsNRT1.5a, CsNRT1.5b, CsNRT1.5c, and CsNRT1.8c), which accelerated nitrogen uptake, accumulation, and utilization efficiency and ultimately improved the yield and quality of cucumber. The effect of SX13 strain was more stable and efficient under conventional substrate supply conditions than under reduced substrate supply conditions.