Soil disinfestation and optimized nutrient management reduces nitrogen leaching and shapes soil microbial community composition in greenhouse cucumber production systems.

High nutrient input leads to problems such as excessive accumulation of soil nutrients, and imbalance of microbial communities. However, there remains significant gaps in the impact of soil disinfestation and optimized nutrient management measures on the growth and soil conditions of greenhouse cucumber. This study investigated the effects of non-disinfected soil with conventional nutrient treatment (CK), after disinfection with conventional chicken manure application (FP), after disinfection with bio-organic fertilizer application (BF), and after disinfection with organic materials application (OM) on cucumber growth performance, soil nutrients, and microbial communities. The results indicated that compared to the CK, FP, BF, and OM could significantly increase cucumber yield, dry weight, nitrogen uptake, and the nutritional yield of potassium, calcium, and magnesium, with BF showing the most pronounced effect. BF effectively alleviated the migration of dissolved inorganic nitrogen in the 0-200 cm soil layer, thereby reducing its loss. In addition, BF reduced the accumulation of nutrients such as total nitrogen, available phosphorus, available potassium, and available magnesium in the 0-20 cm soil layer. The optimization measures altered the species diversity of the soil microbial community. In the BF group, microorganisms showed a negative correlation with soil properties, while OM was positively correlated with pH and C/N, with norank_c__Subgroup_6 and Gaiella being the dominant bacteria. Functional analysis revealed that carbon and nitrogen metabolism functions were significantly enriched in BF-associated bacteria compared to all other groups. These findings provide new insights and strategies for saving resources, improving crop quality, and reducing nutrient accumulation and waste.