Organic fertilizer compost alters the microbial composition and network structure in strongly acidic soil

Soil acidification impairs plant growth and agricultural sustainability, whereas organic fertilizers can ameliorate soil quality. Nonetheless, the response of microbial populations to organic fertilization in acidified soil remains elusive. This study selected facility soils that underwent acidification, and native vegetation (Native) soils were used as controls. We investigated the effects of the sole application of inorganic fertilizers, sole application of organic fertilizers, and combined application of organic and inorganic fertilizers on the microbial diversity of rhizosphere soils of tomato (Solanum lycopersicum. L). The effects of applying organic fertilizers on the function of microbial communities and the structure of related networks were analyzed. Results indicated that organic fertilizer enhanced bacterial network complexity, metabolic function, and convergence of the community structure of Native soils. Beneficial biomarkers Gemmatimonadetes, Armatimonadetes, Sphingomonadales, Patescibacteria, Pezizomycetes, and Agaricomycetes were identified by linear discriminant analysis effect size screening. Applying organic fertilizer alters microbial composition, enhancing microbial abundance and network stability in acidified soil. This research reveals the intrinsic mechanism of yield enhancement by organic fertilizers and provides a basis for screening biocontrol strains.