Abstract Investigating how soil microorganisms respond to different cropping systems is essential for advancing sustainable agricultural practices. Most prior studies have focused on the surface layers of soil microbiota across various cropping systems, leaving the distribution of these communities at different depths largely unexplored. This study aims to systematically analyze the depth‐related distributions of microbiota in tobacco soil under both rotating and continuous cropping systems, employing Illumina NovaSeq sequencing for 16S rRNA and ITS genes. The findings revealed a strong correlation between microbial community composition and sampling depth, with pH being a significant factor. In the rotating cropping system, bacterial diversity and abundance increased with depth. Conversely, the 15–30 cm layer in continuous cropping soils exhibited the lowest bacterial diversity compared to other depths. Fungal diversity was also found to be lower in the 0–15 cm layer than in deeper layers. The dominant bacterial phylum identified was Proteobacteria, while the predominant fungal phyla were Ascomycota and Rozellomycota. Microbes that play a role in nutrient cycling, such as Gemmatimonas , Anaerolinea , and Leptolinea , were more abundant in rotation‐cropping soils. In contrast, antagonistic microorganisms like Babeliales and Sphingomonas might serve as indicators in continuous cropping systems. These results offer important insights for monitoring soil health in the context of sustainable agriculture.
Zhang et al. (Fri,) studied this question.