Metagenomic analysis reveals soil acidification alters rhizosphere microbial communities, functional dynamics, and nutrient cycling in sugarcane agroecosystems

Intensive continuous cropping-induced soil acidification significantly impairs soil health and reduces sugarcane yield and sugar content. However, a comprehensive understanding of how acidification mechanistically alters the integrated soil ecosystem remains poorly understood. To address this knowledge gap, we investigated the effects of soil acidification on soil physicochemical properties, elemental composition, and the structure and function of microbial communities in sugarcane roots, rhizosphere, and bulk soil in Laibin, Guangxi. The results showed that soil acidification significantly reduced soil nutrient content, including available potassium, organic matter, alkaline nitrogen, magnesium, calcium, and selenium, in both rhizosphere and bulk soil. Concurrently, toxic metals (mercury, cadmium, arsenic, and aluminum) exhibited significant accumulation in acidified soils. On the other hand, soil acidification disrupted the functional balance of carbon, nitrogen, sulfur, and phosphorus cycling. It also significantly increased the richness of pathogens and viruses in both rhizospheric and endophytic microbes, while notably decreased the abundance of Bradyrhizobium, Pajaroellobacter , and Mesorhizobium in both root and rhizosphere soils. Correlation analyses indicated that Bradyrhizobium and Mesorhizobium exhibited positive relationships with agronomic traits such as sugarcane yield. Furthermore, acidification significantly narrowed microbial niche breadth and, as shown by neutral community modeling, shifted bacterial community assembly from stochastic to deterministic processes across roots and soil. These findings advance understanding of the ecological functions of root-associated microbial communities in acidified soils and their role in maintaining soil health and sugarcane productivity.