Multiomics Integration Unravels the Systemic Mechanisms of <i>Bacillus paramycoides</i> JYZ-SD5 in Enhancing Salt Tolerance in <i>Metasequoia glyptostroboides</i>

Soil salinization is a major driver of global soil degradation and significantly affects agricultural productivity and ecosystem stability. The use of plant growth-promoting rhizobacteria (PGPR) represents a promising strategy for mitigating salt stress and reclaiming saline soils. This study investigated the mechanisms by which Bacillus paramycoides JYZ-SD5, a PGPR strain that promotes growth under salt stress, achieves this effect in Metasequoia glyptostroboides. We combined bacterial genome sequencing with transcriptomic analysis of M. glyptostroboides to identify key genes and pathways involved in this interaction. The JYZ-SD5 genome (5.83 Mb chromosome, five plasmids, 35.16% G+C content) encodes genes for the production of compatible solutes and exopolysaccharides (EPS), the regulation of ion (Na+, Cl-) transport, and the production of volatile organic compounds (VOCs). Under salt stress, JYZ-SD5 produces high levels of EPS and compatible solutes (proline, betaine, trehalose), effectively sequestering sodium ions. The VOCs produced by JYZ-SD5 further alleviate salt stress in M. glyptostroboides, significantly improving seedling root development and biomass under 0.6% NaCl. Transcriptomic analysis revealed 76 genes that were differentially expressed following JYZ-SD5 inoculation under salt stress and were involved mainly in nutrient uptake, hormone regulation, reactive oxygen species (ROS) scavenging, and osmotic regulation. Untargeted metabolomic analysis revealed the activation of the ascorbic acid pathway and proline metabolism. These results offer new insights into the molecular mechanisms by which PGPR enhance salt tolerance in M. glyptostroboides and highlight the potential of B. paramycoides JYZ-SD5 as a bioinoculant for sustainable agriculture and the reclamation of saline soils.