Reprogramming of Gene Transcripts and Metabolites by the Wild Soybean Endophyte Pseudomonas sp. 77S3 Improves Soybean Salt Tolerance

Soybean is a critical source of protein and vegetable oil worldwide. Expanding its cultivation into salinity lands represents a promising strategy for increasing production; however, soil salinity severely limits soybean growth by disrupting physiological and metabolic homeostasis. Although beneficial endophytes can enhance plant stress adaptation, the molecular mechanisms by which they reprogram host responses under salinity remain poorly understood. In this study, we isolated Pseudomonas sp. 77S3 from salt-tolerant wild soybean and demonstrated its exceptional ability to significantly improve growth and salt tolerance in cultivated soybean under salt stress, using both fresh and fermented formulations. Integrated transcriptomic and metabolomic analyses revealed that 77S3 inoculation systemically reprograms gene expression and metabolic networks in soybean roots. Key to this reprogramming was the enhancement of nitrogen metabolism, orchestrated largely by the nitrate transporter NRT1.5, which facilitated nitrogen reallocation under stress. Functional studies using nrt1.5 knockdown lines confirmed that NRT1.5 is essential for 77S3-mediated improvements in salt tolerance, ion homeostasis, root architecture remodelling, and carbon-nitrogen rebalancing. Additionally, 77S3 increased antioxidant capacity, modulated phytohormone signalling, particularly in auxin and ethylene pathways, and improved phosphorus and potassium solubilisation. These multi-level adaptations collectively enhance salinity resilience in soybean. Our findings provide novel insights into the mechanistic basis of endophyte-induced salt tolerance and support the use of Pseudomonas sp. 77S3 as a sustainable bioinoculant for soybean production in saline agriculture.