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

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Abstract

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 significantly 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 microbial 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 significantly 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.

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Acknowledgements

We thank Chih-Ming Hsu, Neetika Thakur and Lesley Schumacher for their help in collecting root samples and performing DNA extraction for the cotton root samples. We also thank the staff at the North Florida Research and Education Center for maintenance of the long-term field site at Quincy.

Funding

This work was financially supported by a United States Department of Agriculture (USDA)-Southern Sustainable Agriculture Research and Education (SSARE) grant award (2017–38640-26914) to Z. Grabau, I. Small, D. Wright and H.-L. Liao, a USDA-NIFA (2019–67013-29107) award to H.-L. Liao, a USDA-SSARE (2019–38640-29878, SUB00002463) grant award to H.-L. Liao and K. Zhang, and a UF Graduate School Funding Award to K. Zhang.

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Authors and Affiliations

  1. North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL, 32351, USA

    Kaile Zhang, Sheeja George, Ian M.Small, David Wright & Hui-Ling Liao

  2. Soil and Water Sciences Department, University of Florida, Gainesville, FL, 32611, USA

    Kaile Zhang, Gabriel Maltais-Landry & Hui-Ling Liao

  3. Entomology and Nematology Department, University of Florida, Gainesville, FL, 32611, USA

    Zane J. Grabau

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  1. Kaile Zhang
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  2. Gabriel Maltais-Landry
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  7. Hui-Ling Liao
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Correspondence to Hui-Ling Liao.

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Zhang, K., Maltais-Landry, G., George, S. et al. Long-term sod-based rotation promotes beneficial root microbiomes and increases crop productivity. Biol Fertil Soils 58, 403–419 (2022). https://doi.org/10.1007/s00374-022-01626-z

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