Rotation-driven changes in physicochemical properties modulate soil microbial diversity and community complexity in tobacco-woad soils

ABSTRACT Continuous tobacco monocropping leads to soil degradation and yield reduction. To address this, we evaluated the effects of tobacco ( Nicotiana tabacum L.)-woad ( Isatis tinctoria L.) rotation (A2, A4) compared to tobacco monoculture (A1) and woad monoculture (A3) on soil health and crop quality over a multi-year period. Methods involved comparative analysis of soil nutrients, enzyme activities, microbial community structure, and crop chemical composition and economic value. Key results demonstrated that tobacco-woad rotation significantly improved soil fertility. The tobacco-woad rotation could increase the content of organic matter, alkaline available nitrogen, available phosphorus, and available potassium in the soil, which were increased by 1.44%, 17.96%, 4.61%, and 16.20%, respectively, compared to tobacco monoculture. Soil urease and catalase activities, particularly urease (increased by 2.31 times), were significantly enhanced during the tobacco pre-growth period under rotation. Soil microbial communities were significantly restructured under tobacco-woad rotation versus monocropping. Bacterial phyla Acidobacteria, Gemmatimonadota, and Methylomirabilota were enriched in tobacco-woad rotation (A2) relative to tobacco monoculture (A1), while Chloroflexi, Methylomirabilota, and Verrucomicrobiota increased in woad-tobacco rotation (A4) versus woad monoculture (A3). Fungal shifts featured decreased Ascomycota and Basidiomycota with increased Mortierellomycota in both rotations, alongside reduced Chytridiomycota in A4. Rotation enriched key bacterial genera ( MND1 , Nitrospira , Subgroup-10 , and RB41 ) and fungal taxa ( Mortierella , Saccharomyces , and Saitozyma ). Crucially, rotation harmoniously improved the chemical composition of both tobacco and woad leaves, increasing reducing sugars, total sugars, nicotine, potassium, and the sugar ratio in tobacco. The proportion of high-quality tobacco leaves post-curing increased by 10.24% (A2), contributing to a significantly higher total crop production value. In conclusion, tobacco-woad rotation effectively alleviates soil degradation associated with continuous tobacco cropping by enhancing soil nutrient availability, boosting key enzyme activities, and optimizing the structure and interactions of the soil microbial community. These soil improvements collectively drive superior crop quality and economic returns, supporting their adoption as a sustainable agricultural practice. IMPORTANCE (i) The effects of rotation of tobacco with woad on the quality of tobacco production were clarified using physiological and biochemical analyses. (ii) The effects of rotating tobacco with woad on soil microorganisms were revealed by microbiome sequencing of tobacco soils. Tobacco-woad rotation significantly improved the relative abundance of soil-dominant bacteria and decreased the relative abundance of harmful fungi. (iii) An efficient cultivation model of tobacco and woad suitable for Shandong was established by combining soil microbiomics with tobacco plant growth and development. Rotation of tobacco to woad gave the best results.