A synthetic microbial community derived from the roots of Kalidium gracile enhances its salt tolerance by modulating gene transcription and reshaping the rhizosphere soil microbiota.

Abstract

Soil salinization and alkalinization are severe environmental problems in the desert-oasis transition zone of the Hexi Corridor, China. Rhizosphere microbial communities are key regulators of plant adaptation to saline-alkali environments. However, the functional microbial resources and ecological mechanisms underlying the contribution of the rhizosphere microbiome associated with Kalidium gracile to its saline adaptation remain poorly understood. In this study, we characterized the rhizosphere microbiome of K. gracile inhabiting severely saline-alkali soil and isolated two Bacillus strains with strong plant growth-promoting potential, which were subsequently used to construct a synthetic microbial community (SynCom). Inoculation experiments under salt stress demonstrated that SynCom increased plant biomass and chlorophyll content and modulated host transcriptional responses associated with the "growth-defense trade-off." Shortly after inoculation, plant growth-related pathways were suppressed, while CAT and POD activities surged by 45% and 213%, respectively. At later stages after inoculation, the expression of growth-related pathways was significantly upregulated. Metagenomic sequencing revealed that SynCom reshaped the rhizosphere microbial community, with the relative abundances of the halophilic bacteria Halomonas and Marinobacter increasing by 317% and 1162%, respectively. The abundances of functional genes involved in soil carbon, nitrogen, phosphorus, and sulfur nutrient cycling were all significantly increased. Collectively, these findings indicate that SynCom enhances plant salt tolerance through a multi-layered regulatory mechanism by coordinating host physiological responses and rhizosphere microbial functions. Collectively, these findings reveal a multi-level regulatory mechanism through which SynCom enhances plant salt tolerance by coordinating host physiological responses and rhizosphere microbiome functions.