Long-term sod-based rotation promotes beneficial root microbiomes and increases crop productivity

Cotton root microbiomes were investigated in two long-term rotation systems established in 2000, a bahiagrass (Paspalum notatum Flugge)-bahiagrass-peanut (Arachis hypogaea L.)-cotton (Gossypium hirsutum L.) rotation (sod-based rotation, SBR) and a peanut-cotton-cotton rotation (conventional rotation, ConR), from 2017 to 2019. Our results demonstrate that bacterial communities were primarily structured by interannual variability, while fungal alpha and beta diversity were sig- nificantly affected by both rotation and interannual variability, with greater fungal diversity and distinct fungal communities in SBR compared to ConR across three sampling years. Cotton roots in SBR also harbored more complex and stable micro- bial networks. These increased resistance to environmental changes driven by interannual variability, such as temperature and precipitation. Beneficial microbial communities (e.g., Opitutaceae, Pseudonocardiaceae, Rhizobiaceae, Bacillaceae, Comamonadaceae, Serendipitaceae, and Glomeraceae) that may promote plant growth, improve tolerance to abiotic stress, and enhance pathogen defense were associated with cotton roots in SBR, along with fewer pathogenic microbes. These beneficial microbial communities (core microbiomes) together with complex and stable microbial networks were signifi- cantly and positively correlated with cotton yield across three sampling years, suggesting that long-term conversion to SBR shaped root microbiomes in a way that increased cotton productivity. This study improves our understanding of the microbial mechanisms that underlie the agronomic and economic benefits observed when integrating perennial grasses to diversify the conventional peanut-cotton rotation.