Metabolic and antioxidant responses drive Haloxylon ammodendron’s adaptation to drip irrigation with saline and freshwater in saline-alkali soils

Saline water irrigation represents a promising strategy for addressing freshwater scarcity and rehabilitating saline-alkali lands, yet the molecular mechanisms underlying plant adaptation to varying salt conditions remain poorly understood. This study investigated the molecular responses of Haloxylon ammodendron（H. ammodendron） to freshwater versus saline water drip irrigation in saline-alkali soils using integrated transcriptomic and metabolomic analyses coupled with dynamic soil ion monitoring. Freshwater irrigation temporarily reduced soil Na⁺ and Cl⁻ levels through leaching but caused Ca²⁺ and SO₄²⁻ accumulation, while saline water irrigation initially increased Na⁺ and Cl⁻ concentrations before achieving ion rebalancing and pH stabilization. Transcriptomic analysis revealed distinct molecular responses: freshwater irrigation induced 1,305 differentially expressed genes primarily associated with secondary metabolite biosynthesis and antioxidant pathways, whereas saline water irrigation activated 825 genes enriched in carbohydrate metabolism and flavonoid biosynthesis. Metabolomic profiling showed higher numbers of differentially expressed metabolites under freshwater irrigation, particularly organic acids and amino acids. Correlation analysis demonstrated that saline water irrigation enhances salt tolerance through suppressed gene expression and metabolic pathway reconstruction, notably involving key flavonoid biosynthesis genes (SS2296411, SS3033913) that enable precise adaptation to salt fluctuations. These findings reveal that H. ammodendron maintains physiological homeostasis under salt stress by dynamically regulating secondary metabolism, energy balance, and antioxidant systems, providing theoretical foundations for optimizing saline water utilization and developing salt-tolerant crops through targeted genetic engineering. • Dynamic metabolic reprogramming and antioxidant regulation underpin H. ammodendron's salinity adaptation. • Freshwater irrigation triggers secondary metabolism; saline irrigation prioritizes carbohydrate and flavonoid pathways. • Flavonoid biosynthesis genes are differentially regulated to enhance salt tolerance under saline irrigation.