Optimizing flue-cured tobacco planting patterns: enhanced rhizosphere nutrient availability and microbial community dynamics

Introduction Continuous monoculture of flue-cured tobacco causes soil degradation and microbial dysbiosis. While crop rotation can alleviate these obstacles, how different cropping patterns regulate soil carbon (C) and nitrogen (N) metabolic functions remains unclear. Methods A four-year field experiment compared tobacco monoculture (CK), tobacco–maize rotation (TM), tobacco–rice rotation (TR), and tobacco–sweet potato intercropping (TP). Soil physicochemical properties, enzyme activities, metagenomic sequencing, and microbial network analysis were integrated. Results TR significantly improved soil health: pH (+6.6%), organic matter (+22.1%), and urease activity (+12.5%). It enriched beneficial microbes ( Pseudomonadota +16.4%, Mucoromycota +327%) and upregulated C-cycle ( korA +42.3%) and N-assimilation genes ( amoC +460%), while suppressing denitrification ( nirK ). TM increased available P/K but enriched oligotrophic taxa and reduced sucrase activity. TP triggered pathogenic fungi ( Olpidium +160%), depleted beneficial microbes, and broadly suppressed C/N metabolic genes ( cbbL –94.5%, nirS –21.8%). Discussion Cropping patterns differentially reshape microbial communities and metabolic functions, determining their efficacy against continuous cropping obstacles. TR establishes efficient C/N cycling with “high assimilation, low denitrification,” whereas TP induces pathogenic proliferation and metabolic suppression. This provides a functional framework for designing cropping systems to enhance soil health and tobacco productivity.