Impact of long-term application of manure and inorganic fertilizers on common soil bacteria in different soil types

Understanding the impact of long-term fertilization in different soil types and its effect on soil bacteria and crop production is critical for designing sustainable agricultural practices across diverse landscapes. Here, we investigated the impact of 25–37 years of continuous fertilizer treatments in three parent materials (Phaeozem, Cambisol, and Acrisol) on crop yield, soil properties, and soil bacteria (i.e., the total 16 S rRNA gene abundance, community structure, and its relationship with soil nutrient) across diverse Chinese agriculture areas. Four consistent treatments were included: unfertilized control (CK), inorganic nitrogen fertilizer (N), manure (M), and manure plus nitrogen (MN). The crop yields were significantly increased under MN treatments at the rates of 147 kg/ rotation (3 years) in Phaeozem and 90.6 kg/ rotation (1 year) in Acrisol, while the crop yields remained constant or decreased for CK and N treatments. The relative abundance of Acidobacteria_Gp6 and Planctomycete were significantly higher in manure treatments than in chemical fertilizer treatment. Through the structural equation model (SEM) analysis, species in module 1 were directly correlated with crop yield, and both module 2 and module 3 species were indirectly correlated with crop yield via SOM and NO3- contents. Proteobacteria, Acidobacteria, and Firmicutes were dominant bacterial groups in the three modules, respectively. This study reveals the complex role of keystone ecological clusters of soil bacteria on crop yields and identifies the common bacterial taxa that respond to long-term fertilization and thereby, as potential targets for improving soil fertility across soil types.