{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,22]],"date-time":"2026-08-22T17:22:31Z","timestamp":1787419351742,"version":"build-2736575974"},"reference-count":61,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,7,12]],"date-time":"2026-07-12T00:00:00Z","timestamp":1783814400000},"content-version":"vor","delay-in-days":192,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2023YFD1902903"],"award-info":[{"award-number":["2023YFD1902903"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42177252"],"award-info":[{"award-number":["42177252"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["41877144"],"award-info":[{"award-number":["41877144"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"\u201cLeading Goose\u201d R&D program of Zhejiang Province of China","award":["2023C02039\u201301"],"award-info":[{"award-number":["2023C02039\u201301"]}]},{"name":"Major Science and Technology Projects of China National Tobacco Corporation","award":["1102021010152 (LS-12)"],"award-info":[{"award-number":["1102021010152 (LS-12)"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>From a \u201cOne Health\u201d perspective, antibiotic resistance genes (ARGs) harbored by the plant microbiome pose a significant threat to public health, yet their ecological mechanisms under fungicide stress remain largely unexplored. Here, a comprehensive framework integrating selection, dispersal, antagonistic interactions, and horizontal gene transfer (HGT) is established to elucidate the ecological risks and assembly mechanisms of the tomato resistome under fungicide stress, using multi-omics and several validation experiments. The indirect\/direct ecological risks of ARGs in aboveground tomato tissues increase by 1.69\u201393.81-fold and 1.29\u2013123.49-fold under fungicide exposure, respectively, compared to the control. Dispersal and selection emerge as the dominant ecological processes shaping the resistome under fungicide stress, driven by antibiotic-resistant bacteria (ARB) with streamlined and multifunctional metabolic traits, respectively. A fluorescently labeled ARB migration model and an indigenous ARB-based conjugation model demonstrate that fungicides promote the upward dispersal of native ESKAPE pathogens and intensify HGT among them, facilitating the emergence of multidrug-resistant bacteria. Validation experiments confirm that fungicides induce metabolic reprogramming of flavonoid biosynthesis in roots, which enhances HGT by modulating various physiological phenotypes. These findings underscore the ecological risks posed by fungicides in promoting ARG dissemination within the plant microbiome through multiple ecological mechanisms.<\/jats:p>","DOI":"10.1093\/ismejo\/wrag182","type":"journal-article","created":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T11:59:25Z","timestamp":1783684765000},"source":"Crossref","is-referenced-by-count":0,"title":["Bridging ecological processes to elevated antibiotic resistance risk in tomato microbiome under fungicide stress"],"prefix":"10.1093","volume":"20","author":[{"given":"Conglai","family":"Zheng","sequence":"first","affiliation":[{"name":"Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs Key Laboratory and Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang Engineering Research Center for Biological Control of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou 310058 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiajin","family":"Song","sequence":"additional","affiliation":[{"name":"Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs Key Laboratory and Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang Engineering Research Center for Biological Control of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou 310058 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mei","family":"Shan","sequence":"additional","affiliation":[{"name":"Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs Key Laboratory and Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang Engineering Research Center for Biological Control of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou 310058 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Houpu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University , Hefei 230036 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengting","family":"Qiu","sequence":"additional","affiliation":[{"name":"Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs Key Laboratory and Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang Engineering Research Center for Biological Control of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou 310058 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luqing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs Key Laboratory and Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang Engineering Research Center for Biological Control of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou 310058 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunlong","family":"Yu","sequence":"additional","affiliation":[{"name":"Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs Key Laboratory and Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang Engineering Research Center for Biological Control of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou 310058 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiuguo","family":"Wang","sequence":"additional","affiliation":[{"name":"Tobacco Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Qingdao 266101 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hua","family":"Fang","sequence":"additional","affiliation":[{"name":"Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs Key Laboratory and Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang Engineering Research Center for Biological Control of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou 310058 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,7,12]]},"reference":[{"key":"2026082212364508800_ref1","volume-title":"Global Action Plan on Antimicrobial Resistance","author":"WHO","year":"2015"},{"key":"2026082212364508800_ref2","doi-asserted-by":"publisher","first-page":"1432","DOI":"10.1038\/s41564-019-0503-9","article-title":"Defining and combating antibiotic resistance from one health and Global Health perspectives","volume":"4","author":"Hernando-Amado","year":"2019","journal-title":"Nat Microbiol"},{"key":"2026082212364508800_ref3","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1016\/j.tplants.2019.02.010","article-title":"Antibiotic resistomes in plant 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