Mild organic substitution is advantageous for sustainable agricultural development. In order to determine the proper fertilization strategy, it is essential to investigate the impact of substituting chemical fertilizers with varying levels of organic manure on soil nutrients, microbial communities, and crop productivity. Four treatments were implemented: no fertilizer, sole chemical fertilizer, 20% organic manure substitution, and 40% organic manure substitution. Bacterial and fungal communities were characterized through high-throughput sequencing of the 16S rRNA gene V3–V4 region and the V4 region, respectively. The 20% and 40% organic manure substitutions increased soil organic matter (SOM) content, total nitrogen (TN) content, and reduced soil pH compared to the control (CK). The 20% organic manure substitution showed the most significant improvements in soil alkaline phosphatase, urease, and invertase activities. Soil nutrient enhancement increased bacterial alpha diversity, with a milder impact on fungal alpha diversity compared to bacteria. Different fertilization treatments elevated the relative abundance of bacterial Bacteroidetes (8.11%, 21.25%, and 1.88%), Actinomycetes (12.65%, 26.36%, and 15.33%), and fungal Ascomycota (16.19%, 10.44%, and 12.69%), known for degrading recalcitrant organic matter. The sole chemical fertilizer treatment increased the pathogenic Cheatotryiales. Shared species, primarily from bacterial Actinomycetes, Firmicutes, Proteobacteria, and fungal Ascomycota phyla, were found at 20% and 40% organic manure substitution levels. Specifically, the 20% organic manure substitution level promoted the relative abundance of beneficial plant growth-promoting taxa, Oxalobacteraceae and Massilia, and suppressed pathogens, with an increase in the relative abundance of the Purpureocillium genus and Mortierellomycota. These findings suggest that a 20% OF substitution can maintain crop yield, enhance soil nutrients and enzyme activities by fostering beneficial soil bacteria, inhibiting soil-borne pathogens, and refining microbial community structure.

The partial substitution of chemical fertilizers with organic manure is an important strategy for improving agricultural sustainability. However, its effect on heavy metal (HM) pollution and its potential risk to human health remain unclear. Therefore, a field study was conducted to evaluate the effects of partial organic fertilizer substitution (0, 10%, 20%, 30%, and 40%) on health risks posed by HMs, including Zn, Cu, Ni, Cd, Pb, As, and Cr. The results showed that organic fertilizer substitution significantly increased Cu, Cd, Pb, and As accumulations in the soil. The Zn, Cu, Pb, and As contents were significantly higher in grains grown under organic fertilizer substitution (40%) conditions. The HM contents in the soil and grains were below the safety threshold limits in all treatments. Furthermore, the health risk caused by the exposure to As, Cu, and Zn accounted for 86% of the hazard index (HI) value. The HI value was significantly greater at a substitution ratio of 40% than in the no-nitrogen fertilizer treatment. Ingestion of the wheat grains grown at substitution ratios ≥ 30%) increased the carcinogenic risk of As and the total carcinogenic risk. In conclusion, organic fertilizer substitution at high ratios significantly increased the non-carcinogenic and carcinogenic risks associated with ingesting wheat grain. The optimal organic fertilizer substitution ratio (20%) maintained crop yields and improved soil fertility without increasing the non-carcinogenic or carcinogenic risks to human health. These findings highlight the importance of understanding the impacts of optimal organic fertilizer management in wheat growing systems.