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Impacts of drought and manure fertilization on soil and radish resistomes

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Abstract

Antibiotic resistance is a growing global problem, with agricultural practices and climate change as substantial contributors to the spread of antibiotic resistance genes (ARGs) in the environment. We investigated the effect of drought and fertilization type (organic vs. mineral) on radish crop growth and soil prokaryotic communities, with special emphasis on the radish and soil resistomes, as measured by the relative abundance of ARGs and mobile genetic element (MGE)-linked genes. Manure fertilization significantly increased ARG relative abundances in soil, compared to mineral fertilization. Drought and the presence of radish plants emerged as key variables regulating the association between ARGs and MGE-linked genes. Nonetheless, despite radish being a belowground crop, no direct connection was observed between the soil and crop resistomes. These results suggest that soil moisture and fertilization strategies do not necessarily increase the risk of ARG transfer to human pathogens through crop consumption. Consequently, a robust risk assessment of the environmental resistome must account for all compartments within the transmission chain. Together, our findings highlight the complex interplay between agricultural practices and climatic factors in shaping the soil and crop resistome.

Data availability

Raw sequencing data are available in the SRA database (https://www.ncbi.nlm.nih.gov/sra/PRJNA1402202).

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Funding

This work was financially supported by PRADA PID2019-110055RB-C21 and PID2019-110055RB-C22 projects funded by MICIU/AEI/https://doi.org/https://doi.org/10.13039/501100011033 and Basque Government project IT648-22. Fernando Ruiz-Torrubia was the recipient of a predoctoral fellowship PRE2020-092509 funded by MCIN/AEI/https://doi.org/10.13039/501100011033.

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Authors and Affiliations

  1. Department of Conservation of Natural Resources, NEIKER – Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, Derio, P812, 48160, Spain

    Fernando Ruiz-Torrubia, Carlos Garbisu & Lur Epelde

  2. Department of Plant Biology and Ecology, University of the Basque Country, UPV/EHU, P. O. Box 644, Bilbao, 48080, Spain

    María T. Gómez-Sagasti, Unai Artetxe & José M. Becerril

Authors

  1. Fernando Ruiz-Torrubia
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  2. Carlos Garbisu
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  3. María T. Gómez-Sagasti
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  4. Unai Artetxe
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  5. José M. Becerril
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  6. Lur Epelde
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Contributions

The contributions of each author are reported according to the CRediT (Contributor Roles Taxonomy) guidelines. Conceptualization: Fernando Ruiz-Torrubia, Carlos Garbisu, José M. Becerril, Lur Epelde; Formal analysis and investigation: Fernando Ruiz-Torrubia, Unai Artetxe, Maria T. Gómez-Sagasti; Writing – original draft preparation: Fernando Ruiz-Torrubia; Writing – review and editing: Carlos Garbisu, Unai Artetxe, Maria T. Gómez-Sagasti, José M. Becerril, Lur Epelde; Funding acquisition: Carlos Garbisu, José M. Becerril, Lur Epelde.

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Correspondence to
Fernando Ruiz-Torrubia.

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Ruiz-Torrubia, F., Garbisu, C., Gómez-Sagasti, M.T. et al. Impacts of drought and manure fertilization on soil and radish resistomes.
Sci Rep (2026). https://doi.org/10.1038/s41598-026-38389-8

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  • DOI: https://doi.org/10.1038/s41598-026-38389-8

Keywords

  • Agricultural practices
  • Antibiotic resistance
  • Climate change
  • Mobile genetic elements
  • Soil microbial communities
  • Drought

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