Organic–mineral fertilization modulates microbial communities and nutrient-cycling genes in saline–alkali soil

Abstract

Soil salinization severely constrains crop production in arid regions by degrading soil structure, increasing pH and salt stress, and impairing microbial processes. Co-application of organic and mineral fertilizers is widely promoted to rehabilitate saline–alkali soils, but the microbial and functional mechanisms remain poorly resolved. Here, we conducted a pot experiment with sorghum–sudangrass grown in saline–alkali soil under five fertilization regimes supplying equal total nitrogen but different proportions of organic nitrogen. Soil physicochemical properties were measured at the seedling and maturity stages, and rhizosphere bacterial communities and C , N and P cycling functional genes at maturity were characterized by 16S rRNA gene sequencing and SmartChip high-throughput quantitative PCR. Organic–mineral fertilization decreased soil pH and total salt content and increased soil organic matter, total nitrogen and available phosphorus relative to mineral fertilizer alone, with the strongest improvements under the 50% organic–50% mineral nitrogen regime. Organic inputs enhanced bacterial Shannon diversity and evenness and significantly shifted community composition, enriching copiotrophic and potentially beneficial taxa such as Actinobacteriota, Firmicutes, Bacillus and Pseudarthrobacter. The balanced regime also increased the relative abundance of key genes involved in carbon degradation and fixation, nitrogen fixation and phosphorus mineralization and polyphosphate metabolism (e.g. xylA, acsA, mct, nifH, phoD, ppx), whereas mineral-only fertilization favored genes associated with nitrification, denitrification and methane oxidation (e.g. amoA2, nirK, nirS, pmoA), indicating a greater potential for nitrogen losses. Integrated multivariate analyses consistently identified soil pH, total salt, organic matter and total nitrogen as primary regulators of bacterial communities and functional gene profiles, exerting both direct effects and indirect effects via shifts in community structure. These findings demonstrate that moderate organic–mineral co-application, particularly the 50% organic–50% mineral nitrogen regime, simultaneously improves soil conditions, restructures microbial communities and strengthens nutrient-cycling potential in saline–alkali soil, providing a mechanistic basis for optimizing fertilization strategies in salt-affected sorghum–sudangrass systems.