Divergence in the tomato rhizosphere microbial community structure driven by three soil types

Loess, calcareous, and laterite soils are common in Guangxi, southern China, where tomatoes are widely cultivated. To understand how these soil types affect tomato growth and the associated microbial communities, we analyzed soil fertility and the rhizosphere microbiome. Tomatoes in calcareous soil exhibited higher β-glucosidase activity and microbial biomass carbon, whereas those in laterite soil showed increased acid phosphatase activity and microbial biomass phosphorus. Actinobacteriota, Proteobacteria, and Acidobacteriota were the dominant bacterial phyla across all soils, while Ascomycota and Basidiomycota predominated among fungi. Each soil type hosted distinct microbial communities: loess was enriched with the bacterial genera Ramlibacter and Bradyrhizobium and the fungus Alternaria; calcareous soil favored the bacterium Rubrobacter and the fungus Fusarium, and laterite supported bacteria such as Bacillus and Sphingobium, along with the fungus Curvularia. Given its higher phosphorus availability and the presence of beneficial microbes like Bacillus, laterite soil appears to provide a more favorable environment for tomato cultivation compared to loess and calcareous soils.

Soil type is a critical but often overlooked factor influencing tomato productivity in southern China, where diverse soils such as loess, calcareous soil, and laterite are extensively cultivated. Understanding how these soils shape rhizosphere microbial communities and soil nutrient dynamics is essential for improving crop performance. This study provides the first comparative assessment of tomato-associated microbiomes across these major soil types in Guangxi. Our findings reveal that each soil fosters distinct microbial assemblages and enzyme activities, with laterite particularly enriched in beneficial taxa such as Bacillus and associated with enhanced phosphorus availability. These insights highlight the importance of soil-specific microbial processes in supporting tomato growth and offer a scientific basis for selecting and managing soils to optimize productivity. The results also contribute to broader efforts to harness rhizosphere microbiomes for sustainable agricultural improvement.