Microbial communities perform essential ecosystem services, including nutrient cycling, pathogen suppression, and stabilization of soil aggregates and degradation of xenobiotics. Changes in microbial community structure or function can result in detectable changes in soil chemical and physical properties, thus providing an early sign of soil improvement or an early warning of soil degradation. Red–yellow soil dominates in Fujian Province, which is located in the subtropics of China. In tropical and subtropical regions, the topsoil can be easily eroded because of the enhanced soil weathering that causes nutrient leaching and destruction of aggregate structure in the soil. Soil aggregates are groups of soil particles that bind to each other more strongly than to adjacent particles. Aggregate stability refers to the ability of soil aggregates to resist disintegration when disruptive forces associated with tillage and water or wind erosion are applied.