Crop Rotation Improved the Rhizosphere Soil Microenvironment Under Continuous Pepper Monoculture in Southwest China

ABSTRACT Continuous cropping obstacle (CCO), characterized by soil degradation and microbial dysbiosis, severely restricts the sustainable production of pepper ( Capsicum annuum L.) in Southwest China. Given the high ecological vulnerability and unique soil properties of karst mountainous regions, identifying suitable rotation strategies to overcome CCO is an urgent yet underexplored research focus. This study aimed to investigate the efficacy of different cropping systems in mitigating CCO by reshaping the rhizosphere microenvironment. A field experiment was conducted with four treatments: unfertilized control (CK), pepper monoculture with fertilization (PP), oilseed rape‐pepper rotation (OP), and green manure‐pepper rotation (GP). Soil physicochemical properties, pepper yield, and the bacterial community structure were comprehensively analyzed using high‐throughput 16S rRNA sequencing. The results demonstrated that compared to PP, both OP and GP significantly enhanced pepper yield with increases of 98.5% and 124.1%, respectively. Notably, the GP treatment exhibited the most pronounced alleviation of CCO, significantly improving soil pH (to 7.01) and increasing organic matter (OM) and microbial biomass carbon (MBC). Although α‐diversity showed minor differences, β‐diversity (PCoA and NMDS) revealed a significant separation of bacterial community structures under different cropping systems, with GP showing the most distinct shift from PP. Linear discriminant analysis Effect Size (LEfSe) and DESeq2 further identified specific bacterial biomarkers and differentially abundant OTUs enriched in the rotation systems. Crucially, the GP system enriched beneficial bacterial taxa, particularly Actinobacteriota and Proteobacteria, which are known for their roles in nutrient cycling and disease suppression. Redundancy analysis (RDA) indicated that soil properties, particularly pH, OM, and MBC, were the primary drivers shaping the bacterial community composition. These findings suggest that incorporating green manure into crop rotation is an effective strategy to overcome pepper CCO by improving soil physicochemical conditions and fostering a beneficial bacterial community, thereby enhancing productivity and soil health.