Abstract
The spreading of antimicrobial resistance (AMR) in crops and food products represents a global concern. In this study, we conducted a survey of resistomes in maize rhizosphere from Michigan, California, the Netherlands, and South Africa, and investigated potential associations with host bacteria and soil management practices in the crop field. For comparison, relative abundance of antibiotic resistance genes (ARGs) is normalized to the size of individual metagenomes. Michigan maize rhizosphere metagenomes showed the highest abundance and diversity of ARGs, with the detection of blaTEM-116, blaACT-4/-6, and FosA2, exhibiting high similarity (≥ 99.0%) to those in animal and human pathogens. This was probably related to the decade-long application of manure/composted manure from antibiotic-treated animals. Moreover, RbpA, vanRO, mtrA, and dfrB were prevalently found across most studied regions, implying their intrinsic origins. Further analysis revealed that RbpA, vanRO, and mtrA are mainly harbored by native Actinobacteria with low mobility since mobile genetic elements were rarely found in their flanking regions. Notably, a group of dfrB genes are adjacent to the recombination binding sites (attC), which together constitute mobile gene cassettes, promoting the transmission from soil bacteria to human pathogens. These results suggest that maize rhizosphere resistomes can be distinctive and affected by many factors, particularly those relevant to agricultural practices.
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Data availability
All sequencing data are available on JGI and NCBI with their corresponding GOLD analysis project IDs and NCBI accession numbers, respectively, indicated in Table S1.
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Acknowledgements
This work was supported by the US Department of Agriculture (USDA, NIFA-2019-67020-30475) and the National Science Foundation (NSF, CBET-1903597). Dung Ngoc Pham was sponsored by the Mark B. Bain Graduate Fellowship from the Hudson River Foundation. We thank Dr. James Tiedje (Michigan State University) and Dr. Amélie Gaudin (University of California, Davis) for the permission of using the associated metagenomic data. Funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
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This work was funded by National Institute of Food and Agriculture, NIFA-2019-67020-30475, Division of Chemical, Bioengineering, Environmental, and Transport Systems, CBET-1903597, Hudson River Foundation.
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DP: conceptualization, software, formal analysis, data curation, investigation, validation, visualization, writing-review and editing. QW: conceptualization, software, formal analysis, data curation, writing-original draft, and visualization. ML: conceptualization, resources, writing-review and editing, and supervision, project administration, and funding acquisition. All authors have read and agreed to the published version of the manuscript.
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Pham, D.N., Wu, Q. & Li, M. Global profiling of antibiotic resistomes in maize rhizospheres. Arch Microbiol 205, 89 (2023). https://doi.org/10.1007/s00203-023-03424-z
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DOI: https://doi.org/10.1007/s00203-023-03424-z