Short-Term Maize Rotation Suppresses Verticillium Wilt and Restructures Soil Microbiomes in Xinjiang Cotton Fields

Verticillium wilt, a prevalent soil-borne disease, poses a significant challenge to cotton production in Xinjiang, China. Continuous cotton monoculture has increased disease incidence and affected soil microbial diversity in Xinjiang, while crop rotation is recognized as an effective strategy for soil pathogen control. This study investigates how a one-year maize rotation affects Verticillium wilt incidence and soil microbiome composition in cotton fields across northern and southern Xinjiang. The results demonstrated that short-term rotation significantly reduced Verticillium wilt occurrence in both northern and southern Xinjiang. Using high-throughput sequencing of fungal ITS and bacterial 16S rRNA regions, microbial community analysis revealed minimal changes in alpha-diversity but significant structural reorganization between continuous cropping (CC) and rotation (CR) systems, particularly in fungal and bacterial genera composition, with distinct spatial patterns between northern and southern fields. Crop rotation promoted beneficial taxa such as <i>Sphingomonas</i> and <i>Pseudogymnoascus</i>, while reducing the abundance of pathogens such as <i>Verticillium dahliae</i>. LEfSe study suggested <i>Tepidisphaerales</i> and <i>Lasiosphaeriaceae</i> as biomarkers for CR systems, whereas <i>Hypocreales</i> and <i>Blastocatellia</i> dominated in CC soils. Co-occurrence network analysis revealed more bacterial connectivity and modularity under CR, suggesting better microbial interactions and ecological resilience. The increased structural complexity of bacterial networks under CR indicates their greater contribution to soil health maintenance and ecosystem resilience. Our findings demonstrate that short-term crop rotation not only effectively reduces Verticillium wilt incidence but also restructures soil microbial communities, providing an actionable strategy for sustainable cotton cultivation in Xinjiang.