Irrigation water quality shapes soil microbiomes: a 16 S rRNA-based biogeographic study in arid ecosystems

Abstract Soil microbiome plays a crucial role in ecosystem; however, the responses of the soil microbiome to nonconventional irrigation water sources remain poorly understood. This study employed 16 S rRNA sequencing to investigate microbial community shifts in soil samples collected from four geographically distinct locations affected by different irrigation water sources: saline ground water affected by seawater (SW), a brackish water lake (BW), a wastewater drain (WW), and a freshwater canal that receives inflows from multiple agricultural drains (FW). Our findings revealed distinct microbial signatures shaped by water quality, with Firmicutes dominating WW soils (49.2%) due to metal resistance (DESeq2, p = 3.67 × 10 − 4 ), whereas Chloroflexi and Cyanobacteria thrived in BW environments (LEfSe, LDA > 4, p = 8.23 × 10 − 6 ), reflecting adaptations to chloride-rich conditions. FW soils enriched Acidobacteria and Verrucomicrobia, which are associated with moderate salinity and nutrient cycling, whereas SW samples harbored halotolerant Actinobacteria and Deinococcus-Thermus (DESeq2, p = 1.47x − 05 ). Statistical analyses revealed key potential biomarkers, including Streptococcus (WW, DESeq2 p = 3.67x − 24 ), RB41 (BW, LEfSe p = 1.62x − 13 ), and Candidatus_Udaeobacter (SW, DESeq2 p = 1.47x − 05 ). Physicochemical drivers such as salinity (R² =0.319, p = 0.00041) and heavy metals (Pb/Mn in WW) strongly influence community structure. Notably, WW irrigation reduced alpha diversity (Shannon index: 4.79–5.41 vs. 6.65–7.43 in FW; Kruskal-Wallis p = 0.0056), highlighting pollutant-induced stress. These findings highlight the balance between water reuse and soil health, offering a foundation for microbiome-driven bioremediation approaches in arid environments. By utilizing native, stress-resilient microbial communities, our research promotes sustainable agricultural practices in water-limited regions.