Irrigation regime modulates the effects of organic amendments on soil quality and microbial carbon-degrading gene composition in saline-alkali soils

Soil salinization severely constrains agricultural productivity, highlighting the need to understand how irrigation regimes and organic amendment types jointly influence soil quality in salt-affected agroecosystems. However, their interactive effects on microbial communities and carbon-degradation-related functional potential remain poorly understood. Here, a two-year field experiment combined two irrigation regimes, W1 (irrigation triggered at −30 kPa soil matric potential for maize; 100 mm applied at jointing and grain-filling period for wheat) and W2 (−60 kPa; 60 mm), with three organic amendments (straw, manure, and biochar). Soil physicochemical properties, extracellular enzyme activities, microbial communities, metagenomic carbohydrate-active enzyme (CAZyme) profiles, and a soil quality index (SQI) were analyzed to characterize water-carbon coupling (the interaction between irrigation regime and organic amendment input). Irrigation regime strongly influenced amendment performance. In the 0–20 cm soil layer, W1B and W2M consistently exhibited higher microbial biomass carbon (MBC), carbon-cycling enzyme activities, and SQI than W1M and W2B in both years, whereas straw showed smaller differences between irrigation regimes for most indicators. Treatment effects were limited in the 20–40 cm layer. Water-carbon coupling did not significantly alter bacterial or fungal community composition but affected the abundance of nine carbon-degrading enzyme families. Families reaching significance occurred mainly in hemicellulose degradation (five of six families) and microbial-residue recycling (three of five), whereas few cellulose and no pectin- or starch-degrading families responded. The interaction-responsive families were correlated with MBC and with two of the five measured carbon-cycling enzymes, indicating that the treatment effects were reflected in functional gene composition rather than community composition. Based on soil indicators, the effectiveness of organic amendments is strongly governed by the irrigation regime, with biochar preferred under adequate irrigation and manure under deficit irrigation. Amendment selection should therefore follow water availability, providing practical guidance for the sustainable utilization of organic amendments in salt-affected agricultural systems.