Habitat adaptation determines dark septate endophyte mediated stabilization of the soil-root-plant continuum under sulfate salinity

Background Global soil salinization is intensifying, yet the mechanisms determining whether beneficial plant–microbe symbioses remain functional under extreme ionic stress remain poorly understood. Methods Using the halophyte Suaeda salsa and two ecologically distinct dark septate endophytes (DSEs), we evaluated symbiotic performance across a Na ₂ SO ₄ gradient (0-0.4 M) by integrating physiological, ionomic, rhizosphere, and untargeted metabolomic analyses. Symbiotic outcomes were strongly dependent on fungal habitat adaptation. Results The halophytic isolate Alternaria chlamydospora SC11 maintained stable colonization and consistently enhanced plant survival and growth under increasing salinity, whereas the non-adapted isolate As17463 progressively lost functionality. SC11 sustained K, N, and P homeostasis despite high Na ⁺ accumulation, preserved root structural integrity and rhizosphere enzymatic activity, and promoted persistent activation of pyrimidine and nucleotide-sugar metabolism. Integrative analyses revealed strong coupling between rhizosphere properties and host metabolic responses, indicating coordinated regulation across the soil-root-plant continuum. Conclusion Persistent colonization by habitat-adapted DSEs strengthens the osmoregulatory capacity, nutrient homeostasis, and functional stability of S. salsa under severe sulfate salinity. This study provides mechanistic criteria for selecting effective fungal inoculants and offers theoretical guidance and practical support for microbial-assisted restoration and sustainable management of saline-alkali environments.