Combined metagenome and metabolome analyses reveal the effects of three Bacillus spp. on the rhizosphere microenvironment and plant growth of cucumber (Cucumis sativus L.)

To identify plant growth-promoting bacteria with strong environmental adaptability and high efficiency and to understand their regulatory mechanisms, single or combined inoculation experiments were conducted with three strains, Bacillus tequilensis JZ31, Bacillus pumilus JZ38 and Bacillus albus JZ264, which were isolated from the rhizosphere soil samples of saline-alkali tolerant plants. The regulatory mechanisms of the three strains affecting the rhizosphere microenvironment and plant growth were systematically analyzed based on the metagenomes and metabolomes on the premise of determining the functions of phosphorus and potassium solubilization, and IAA secretion of the strains and their promotional effects on seedling growth and field production. Results of analyzing the microbial alpha diversity (Chao1 and Shannon) and beta diversity (NMDS and PcoA) in rhizosphere showed that the relative abundance of rhizosphere microorganisms tended to change more evenly (JZ31) or selectively increase the relative abundance of some microorganisms (JZ38 and JZ264) under the condition that the microbial abundance was not affected. We analyzed the abundance differences of top20 microorganisms in 207 phyla and 3825 genera enriched by different treatments, and further screened the biomarkers specifically enriched by the three strains based on Lefse and MetagenomeSeq analysis. The results showed that the three strains selectively recruited many microorganisms related to decomposition of organic nutrients, promotion of plant growth, secretion of growth regulatory factors and biological control functions, respectively, and reduced the relative abundance of pathogens and microorganisms significantly enriched in the control treatment with unknown functions or adverse to the conversion of nutrients. The results of pathway enrichment characterization and functional profiling of 3,652,168 genes annotated to the KEGG database in the metagenomes and the enrichment and functional profiling of 1,893 metabolites enriched in the metabolomes collectively indicated that the three strains selectively activated pathways associated with quorum sensing, gene expression, and nutrient cycling, and drove the functional focus of differential metabolites to promote plant growth, enhance plant immunity, and form a healthier bio-barrier in rhizosphere, which in turn facilitated organic nutrient release and nutrient uptake and utilization by plants, and ultimately, plant growth and production. Overall, the growth-promoting and yield-enhancing effects of JZ38 and JZ264 were better than those of the JZ31 strain. These findings may provide new biological resources for promoting sustainable agricultural development, and provide important information for elucidating the regulation of rhizosphere microenvironment and plant growth by the three strains.