Background The Mu Us Desert, located in the arid and semi-arid zones of northern China, represents a critical yet fragile ecosystem characterized by extreme climatic conditions, sparse vegetation, and high susceptibility to anthropogenic disturbances. As a transitional ecotone, this region plays a pivotal role in maintaining regional ecological security. However, large-scale infrastructure projects, such as power transmission tower construction, have exacerbated soil degradation, leading to reduced microbial activity, nutrient depletion, and loss of fungal biodiversity. In efforts to rehabilitate degraded lands, nitrogen-fixing microbial agents and nitrogen fertilizers are commonly used as soil amendments to influence soil microbial communities. However, the specific effects of these amendments on sandy soils in arid conditions and their effects on microbial communities are still not well understood.

Methods This study was conducted in the disturbed areas surrounding power transmission tower bases in the Mu Us Desert. Through controlled experiments involving the application of nitrogen-fixing agents and nitrogen fertilizers, coupled with advanced high-throughput sequencing technology, we analyzed the effects of these two nitrogen addition methods on soil physicochemical properties, fungal diversity, and community structure. Physicochemical analyses included measurements of microbial biomass carbon, microbial biomass nitrogen, soil organic carbon, total nitrogen, total phosphorus, total potassium, ammonium, nitrate, pH, available phosphorus, and available potassium.

Results 1) The results showed that the application of nitrogen-fixing agents significantly increased soil microbial biomass carbon, microbial biomass nitrogen, soil organic carbon, ammonium nitrogen, and soil hardness (P < 0.05). Conversely, the application of nitrogen fertilizer significantly increased total soil nitrogen, total soil phosphorus, and nitrate nitrogen (P < 0.05). 2) Interestingly, neither treatment significantly affected soil inorganic carbon, total soil potassium, available soil phosphorus, available soil potassium, or pH (P > 0.05). Both nitrogen-fixing agents and nitrogen fertilizer significantly altered the fungal community structure (P < 0.01), increasing the relative abundance of Basidiomycota and unclassified fungal taxa while decreasing Ascomycota (P < 0.05). Notably, inoculant application further significantly reduced fungal community stability (P < 0.001) and increased fungal α-diversity metrics (observed species richness, Chao1, and Shannon indices) (P < 0.05). 3) Mantel test and Random Forest analysis identified that microbial biomass carbon, soil organic carbon, ammonium nitrogen, and nitrate nitrogen as key drivers of soil fungal α-diversity, community structure, and stability, with soil organic carbon and ammonium nitrogen exerting particularly strong effects on fungal community structure.

Conclusions Combined use of nitrogen-fixing inoculants and nitrogen fertilizer enhances key soil properties and fungal diversity more effectively than fertilizer alone. The inoculant boosts microbial biomass and soil hardness while reducing fungal stability, offering a superior strategy for soil quality improvement and ecological restoration in arid regions. These findings challenge the conventional focus on nutrient supplementation alone, advocating for integrated approaches that balance microbial inoculation with nutrient management. This research provides a mechanistic framework for designing precision restoration strategies in the Mu Us Desert and analogous regions, emphasizing the need for long-term monitoring of microbial feedback to ensure sustainable ecological recovery.