Bio-organic fertilizer coupled with moderate deficit irrigation optimizes cotton root system architecture and enhances salt tolerance via rhizosphere amelioration in arid saline-sodic soils

Soil salinization severely constrains cotton ( Gossypium hirsutum L.) productivity in arid irrigated regions, while prolonged shallow drip irrigation exacerbates root superficialization and limits deep soil water utilization. However, the mechanistic pathways by which coupled water-organic management regulates root system architecture (RSA) plasticity and the optimal coupling parameters remain inadequately quantified. A two-year (2022–2023) field experiment was conducted in Alar, Xinjiang, China, to investigate coupling effects of three deficit irrigation regimes (W1, W2 and W3, targeting 90%, 75% and 60% of seasonal non-stressed crop evapotranspiration, ETc) and four soil amendments (CK: chemical fertilizer; T1: biochar 4.5 t ha⁻¹; T2: potassium humate 150 kg ha⁻¹; T3: bio-organic fertilizer—composted sheep manure plus wheat straw inoculated with a salt-tolerant Bacillus subtilis strain—3.0 t ha⁻¹) on cotton RSA using integrated shovelomics and minirhizotron phenotyping. Results demonstrated that the W2 ×T3 treatment was associated with optimized RSA, showing increased deep root length density (40–80 cm) by 37.5% (from 0.48 to 0.66 cm cm⁻³) and reduced fine root turnover rate by 27.9% (from 2.47 to 1.78 year⁻¹) compared to W1 ×CK. This "steep and deep" architecture coincided with 47.2% higher root hydraulic conductivity (3.21 × 10⁻⁴ vs. 2.18 × 10⁻⁴ kg s⁻¹ MPa⁻¹ m⁻²). Structural equation modeling revealed strong associations between amendment-induced rhizosphere improvements—including 34.0% reduced Na⁺/K⁺ ratio and 50.0% increased aggregate stability—and root deepening (path coefficient β = 0.54), which showed the strongest association with yield (β = 0.59). Random forest analysis corroborated that deep rooting index (31.2% relative importance), rhizosphere Na⁺/K⁺ ratio (18.7%), and root hydraulic conductivity (13.4%) were the top yield-associated variables, whereas total root biomass ranked last of the twelve predictors (1.1%). The W2 ×T3 treatment achieved 15.3% higher seed cotton yield (5847 vs. 5072 kg ha⁻¹), 33.7% higher irrigation water productivity (WP I , 1.31 vs. 0.98 kg m⁻³) and 19.6% higher crop water productivity referenced to measured actual crop evapotranspiration (WP ET , 1.10 vs. 0.92 kg m⁻³), with 13.8% water savings. This study identified W2 ×T3 (75% ETc target + 3.0 t ha⁻¹ bio-organic fertilizer) as the optimal strategy for sustainable cotton production in arid saline-sodic soils.