The dual-threat: How saline water irrigation compromises soil health and seed cotton yield under mulched drip irrigation in Xinjiang, China

Saline water has become a significant resource for agricultural irrigation in arid regions. However, its potential negative impact on soil health remains a concern. Therefore, understanding its effects on soil properties and microbial communities is essential. A two-factor experiment was conducted in 2023 and 2024, incorporating four levels of irrigation water salinity: 1.3 dS m –1 (S1), 3.5 dS m –1 (S2), 5.7 dS m –1 (S3), and 9.8 dS m –1 (S4), as well as three irrigation amounts: 450 mm (W1), 360 mm (W2), and 270 mm (W3) to analyze the impact of saline irrigation water on soil microorganisms and to elucidate the underlying mechanisms. Our results revealed that the relative abundance of dominant species in both fungal and bacterial communities decreased with increasing irrigation water salinity, with the exceptions of Eurotiomycetes (fungal community), Actinobacteriota , and Gemmatimonadota (bacterial community). Additionally, the relative abundance of all dominant species declined with reduced irrigation amount, except for Gemmatimonadota in the bacterial community. Redundancy analysis (RDA) revealed that the variables, including soil water-stable macroaggregates (WR0.25), pH, Na⁺, Ca²⁺, and nitrate reductase (NR), explained over 10 % of the variance in fungal community structure, while WR0.25, NO₃⁻-N, Na⁺, Ca²⁺, and NR accounted for over 10 % of the variance in bacterial community structure. Moreover, the alpha diversity of both fungal and bacterial communities decreased as irrigation water salinity increased and irrigation amount decreased. The structural equation model (SEM) revealed that irrigation water salinity and irrigation amount directly or indirectly affect microbial community diversity by altering soil physical, chemical, and enzymatic properties. The application of saline water irrigation significantly deteriorated soil quality and cotton yield. Irrigation with water of 3 g/L salinity did not significantly affect cotton yield, whereas high salinity levels (≥5 g/L) led to a significant reduction in yield, notably, the highest yields in both years were observed under the S2W1 treatment. This study provides valuable practical guidance for the use of saline water in agricultural irrigation in arid areas. • Saline water irrigation affects the soil microbial community structure. • Saline water irrigation decreases soil microbial community diversity. • Saline water irrigation significantly reduces soil quality and yield.