Long-Term Fertilizer Use Altered Soil Microbial Community Structure but Not α-Diversity in Subtropical Southwestern China

Despite the general consensus that fertilizer is the most important driver of the evolution of soil microbial communities, the specific effects of long-term fertilizer use on microbial communities remain unclear. Here, we collected soil samples from fertilized (NPK) and unfertilized (NF) plots in a subtropical farmland in southwestern China. NPK plots were consistently treated with chemical fertilizer (nitrogen, phosphorous, and potassium) for the 20 years; NF plots were left unfertilized for the same period. To explore the effects of long-term fertilizer use on soil microbial community structure, microbial community composition in the topsoil was assessed using the bacterial 16S rRNA gene and the full-length fungal ITS1 gene. In conjunction, we measured various soil chemical properties. We found that metrics associated with soil fertility (i.e., total nitrogen, total phosphorus, total potassium, available nitrogen, available phosphorus, and available potassium) were significantly greater in the NPK samples as compared to the NF samples, but that soil pH was significantly lower. We also found that long-term fertilizer use reshaped soil microbial community composition but did not alter community α-diversity. Notably, the bacterial phyla Nitrospirae and Planctomycetes and the fungal phylum Ascomycota were closely associated with the NPK plot, influenced by soil organic matter, total nitrogen, available potassium, and available phosphorus, while the bacterial phyla Bacteroidetes and Chloroflexi and the fungal phyla Glomeromycota and Basidiomycota were closely associated with the NF plot, influenced by soil pH. Our results provide long-term data clarifying the microbial regulation mechanisms underlying the response of farmland soil to long-term fertilizer use in subtropical China.