Partial replacement of chemical fertilizers with different types of animal manure enhances soil ecological multifunctionality and foxtail millet yield by improving soil environment and regulating microbial functions

Background The growing livestock industry has boosted manure production, leading to environmental health issues. Composted livestock manure application can enhance soil quality and crop yield, but the regulatory mechanisms of the different types of animal manure on the soil ecological multifunctionality (EMF) and microbial functions in foxtail millet fields remain unknown. We assessed variations in soil environmental factors, microbial community responses, and their contributions to foxtail millet nitrogen use efficiency (NUE) across a two-year experiment with distinct manure treatment regimes. Results The findings revealed that organic replacement treatments mitigated soil alkalization and improved soil nutrients and enzyme activities, resulting in higher soil quality and EMF, with the pig manure treatment performing best. Improved soil conditions enhanced microbial community diversity and network stability, strengthened soil carbon and nitrogen cycling, and thus improved soil EMF, which directly promoted foxtail millet NUE. Soil physicochemical properties and microbial functions (mainly carbon and nitrogen cycling) were key direct drivers of EMF. Notably, key microbial phyla like Proteobacteria were significantly enriched in organic replacement treatments, playing a key role in stabilizing microbial network structures and maintaining community functions. Additionally, pH changes were the primary driver influencing soil microbial communities. Conclusions This study confirmed that organic fertilization enhanced soil EMF by mitigating alkalization, boosting soil nutrients and enzymes, and optimizing microbial traits, thereby improving crop NUE and yield. Locally, pig manure maximized yield, while cow manure optimized grain quality. Our findings provide valuable guidance for scientific fertilization practices and the safeguarding of ecological integrity.