Effects of long-term application of organic fertilizer from distillers’ grains on the soil microbiome

Distillery residues represent an underexplored circular-economy resource for organic soil amendment, yet their long-term dose-dependent effects on soil microbial communities remain poorly characterized. Here we report a five-year field experiment (2020–2024) in which Maotai distillery-residue organic fertilizer was applied at five rates (4500–13,500 kg/ha) to a sorghum monoculture on yellow soil in Guizhou Province, China, alongside unfertilized control and chemical fertilizer (NPK) treatments. Soil bacterial and fungal communities were characterized by shotgun metagenomic sequencing. We found that Organic fertilizer application restructured microbial communities in a dose-dependent manner: high application rates (≥ 11,250 kg/ha) increased bacterial abundance by 11–17% relative to the control, whereas all organic treatments reduced fungal abundance by 46–75%. The soil health index (bacteria-to-fungi ratio) increased by 69–266% under organic fertilizer treatments. Redundancy analysis identified soil pH as the dominant driver of bacterial community variation (explaining 82%), while available nitrogen primarily controlled fungal community differentiation (73%). KEGG pathway analysis indicated that medium-to-high application rates were associated with enrichment of nitrogen metabolism and MAPK signaling–related genes. These findings demonstrate that distillery-residue organic fertilizer can serve as an effective soil amendment within a circular-economy framework, with application rates of 9000–11,250 kg/ha representing an optimal range that balances microbial diversity with functional gene enrichment.