{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T05:19:43Z","timestamp":1787721583027,"version":"build-2784847793"},"reference-count":38,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T00:00:00Z","timestamp":1787529600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Key Research and Development Plan Project","award":["2023YFD1702000"],"award-info":[{"award-number":["2023YFD1702000"]}]},{"DOI":"10.13039\/501100006606","name":"Natural Science Foundation of Tianjin","doi-asserted-by":"crossref","award":["25 CYBJC00320"],"award-info":[{"award-number":["25 CYBJC00320"]}],"id":[{"id":"10.13039\/501100006606","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["42577460"],"award-info":[{"award-number":["42577460"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"award":["42577460"],"award-info":[{"award-number":["42577460"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Basic Research Program of Yunnan Province","award":["202601AT070059"],"award-info":[{"award-number":["202601AT070059"]}]},{"name":"Basic Research Program of Yunnan Province","award":["202301AT070245"],"award-info":[{"award-number":["202301AT070245"]}]},{"name":"Central Public-interest Scientific Institution Basal Research Fund","award":["1610022026022"],"award-info":[{"award-number":["1610022026022"]}]},{"DOI":"10.13039\/501100005196","name":"Chinese Academy of Agricultural Sciences","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100005196","id-type":"DOI","asserted-by":"crossref"}]},{"id":[{"id":"https:\/\/ror.org\/0313jb750","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background: Manure-amended agricultural soil is a critical reservoir of antibiotic resistance genes (ARGs), posing escalating threats to environmental health and food safety. However, the temporal trajectories of ARG prevalence throughout the complete reproductive cycle of cash crops, and their mechanistic linkages with fertilization regimes and microbial community succession, remain inadequately understood. Methods: To bridge this knowledge gap, we conducted an in situ field experiment over the entire growth period of Chinese cabbage at a long-term manure-amended farm in Tianjin, China. Six contrasting fertilization strategies were evaluated: unfertilized control (CK1), unfertilized baseline control (CK2), traditional full-rate combined manure\u2013chemical fertilization (TF), traditional half-rate combined manure\u2013chemical fertilization (T1), half-dose sole manure fertilizer (T2), and half-dose sole chemical fertilizer only (T3). Results: Our results demonstrated that ARG abundance and associated mobile genetic elements (MGEs) exhibited a pronounced transient surge immediately post-fertilization, yet reverted to baseline levels by harvest, revealing a tangible resilience of the soil resistome. Notably, the optimized half-organic fertilization (T2) effectively curtailed the proliferation of manure-derived pathogenic taxa while preserving beneficial keystone phyla (e.g., Acidobacteria and Proteobacteria), indicating a trade-off between nutrient provisioning and ecological filtering. Co-occurrence network analysis further identified MB-A2-108, Saccharimonadales, and Rokubacteriales as pivotal hosts for multidrug-resistant ARGs, underscoring that microbial interspecific interactions\u2014rather than taxonomic richness alone\u2014are the primary drivers of resistome succession. Quantitative risk assessment confirmed that the T2 regimen reduced the composite ARG contamination index (CFzone) by 25% relative to conventional full fertilization (TF), while maintaining comparable cabbage yields. Conclusions: Collectively, our findings advocate for precision organic fertilization as a nature-based solution that synchronizes nutrient supply with crop demand, curtails ARG propagation, and mitigates long-term agroecological risks.<\/jats:p>","DOI":"10.3390\/antibiotics15090821","type":"journal-article","created":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T13:20:43Z","timestamp":1787577643000},"page":"821","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Optimized Organic Fertilization Mitigates Antibiotic Resistance Gene Dissemination in Manure-Amended Soils: A Field Study on Nutrient\u2013Microbiome\u2013Antibiotic Resistance Gene Nexus During Cabbage Reproductive Cycle"],"prefix":"10.3390","volume":"15","author":[{"given":"Han","family":"Wang","sequence":"first","affiliation":[{"name":"Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keqiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China"},{"name":"National Field Observation and Research Station (Yunnan Dali) for Agro-Ecosystem, Dali 671004, China"},{"name":"Key Laboratory of Low-Carbon Green Agriculture in North China, Ministry of Agriculture and Rural Affairs, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muheng","family":"Liu","sequence":"additional","affiliation":[{"name":"Chifeng Municipal Agriculture and Animal Husbandry Bureau Plant Protection and Plant Quarantine Center, Chifeng 024000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shenwei","family":"Cheng","sequence":"additional","affiliation":[{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6713-5100","authenticated-orcid":false,"given":"Cheryl Marie","family":"Cordeiro","sequence":"additional","affiliation":[{"name":"NIBIO, Norwegian Institute of Bioeconomy Research, N-1430 \u00c5s, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2313-7512","authenticated-orcid":false,"given":"Erik","family":"Sindh\u00f8j","sequence":"additional","affiliation":[{"name":"NIBIO, Norwegian Institute of Bioeconomy Research, N-1430 \u00c5s, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junfeng","family":"Liang","sequence":"additional","affiliation":[{"name":"Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanfang","family":"Zeng","sequence":"additional","affiliation":[{"name":"National Field Observation and Research Station (Yunnan Dali) for Agro-Ecosystem, Dali 671004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shizhou","family":"Shen","sequence":"additional","affiliation":[{"name":"Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China"},{"name":"National Field Observation and Research Station (Yunnan Dali) for Agro-Ecosystem, Dali 671004, China"},{"name":"Key Laboratory of Low-Carbon Green Agriculture in North China, Ministry of Agriculture and Rural Affairs, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-1815-887X","authenticated-orcid":false,"given":"Suli","family":"Zhi","sequence":"additional","affiliation":[{"name":"Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China"},{"name":"National Field Observation and Research Station (Yunnan Dali) for Agro-Ecosystem, Dali 671004, China"},{"name":"Key Laboratory of Low-Carbon Green Agriculture in North China, Ministry of Agriculture and Rural Affairs, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"107986","DOI":"10.1016\/j.envint.2023.107986","article-title":"The Dynamics and Transmission of Antibiotic Resistance Associated with Plant Microbiomes","volume":"176","author":"Chen","year":"2023","journal-title":"Environ. Int."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"133335","DOI":"10.1016\/j.jhazmat.2023.133335","article-title":"Effects of Heavy Metal and Disinfectant on Antibiotic Resistance Genes and Virulence Factor Genes in the Plastisphere from Diverse Soil Ecosystems","volume":"465","author":"Ni","year":"2024","journal-title":"J. Hazard. Mater."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.1016\/j.envpol.2017.09.074","article-title":"Temporal Succession of Soil Antibiotic Resistance Genes Following Application of Swine, Cattle and Poultry Manures Spiked with or without Antibiotics","volume":"231","author":"Zhang","year":"2017","journal-title":"Environ. Pollut."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"108126","DOI":"10.1016\/j.envint.2023.108126","article-title":"Risk Assessment and Dissemination Mechanism of Antibiotic Resistance Genes in Compost","volume":"178","author":"Xu","year":"2023","journal-title":"Environ. Int."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"j2440","DOI":"10.1136\/bmj.j2440","article-title":"Antibiotic Residues in the Environment of South East Asia","volume":"358","author":"Lundborg","year":"2017","journal-title":"BMJ"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1128\/MMBR.00056-13","article-title":"Integrons: Past, Present, and Future","volume":"78","author":"Gillings","year":"2014","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1111\/j.1574-6976.2009.00175.x","article-title":"Gene Cassettes and Cassette Arrays in Mobile Resistance Integrons","volume":"33","author":"Partridge","year":"2009","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Wang, H., Huo, Q., Wang, T., Lv, G., Li, W., Ren, J., Zhang, S., and Li, J. (2024). Effects of Combination of Water-Retaining Agent and Nitrogen Fertilizer on Soil Characteristics and Growth of Winter Wheat under Subsoiling Tillage in South Loess Plateau of China. Agronomy, 14.","DOI":"10.3390\/agronomy14061287"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1016\/j.envpol.2016.01.007","article-title":"Effects of Manure and Mineral Fertilization Strategies on Soil Antibiotic Resistance Gene Levels and Microbial Community in a Paddy\u2013Upland Rotation System","volume":"211","author":"Lin","year":"2016","journal-title":"Environ. Pollut."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.scitotenv.2015.04.046","article-title":"Occurrence of (Fluoro)Quinolones and (Fluoro)Quinolone Resistance in Soil Receiving Swine Manure for 11 Years","volume":"530\u2013531","author":"Xu","year":"2015","journal-title":"Sci. Total Environ."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"163334","DOI":"10.1016\/j.scitotenv.2023.163334","article-title":"Long-Term Field Application of Manure Induces Deep Selection of Antibiotic Resistomes in Leaf Endophytes of Chinese Cabbage","volume":"882","author":"Zhang","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"5701","DOI":"10.1128\/AEM.01682-13","article-title":"Impact of Manure Fertilization on the Abundance of Antibiotic-Resistant Bacteria and Frequency of Detection of Antibiotic Resistance Genes in Soil and on Vegetables at Harvest","volume":"79","author":"Marti","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"6933","DOI":"10.1021\/es1007802","article-title":"Abundance and Diversity of Tetracycline Resistance Genes in Soils Adjacent to Representative Swine Feedlots in China","volume":"44","author":"Wu","year":"2010","journal-title":"Environ. Sci. Technol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"135927","DOI":"10.1016\/j.scitotenv.2019.135927","article-title":"Increased Soil PH and Dissolved Organic Matter after a Decade of Organic Fertilizer Application Mitigates Copper and Zinc Availability despite Contamination","volume":"709","author":"Laurent","year":"2020","journal-title":"Sci. Total Environ."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Coyte, K.Z., Stevenson, C., Knight, C.G., Harrison, E., Hall, J.P.J., and Brockhurst, M.A. (2022). Horizontal Gene Transfer and Ecological Interactions Jointly Control Microbiome Stability. PLoS Biol., 20.","DOI":"10.1371\/journal.pbio.3001847"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1007\/s11274-024-04214-5","article-title":"Dynamic Interaction of Antibiotic Resistance between Plant Microbiome and Organic Fertilizers: Sources, Dissemination, and Health Risks","volume":"41","author":"Ullah","year":"2025","journal-title":"World J. Microbiol. Biotechnol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Wang, Y., Xu, Y., Jiang, L., Yang, Y., Shi, J., Guan, X., Sun, T., Zhao, H., Wang, Y., and Liu, Y. (2024). Effect of Mild Organic Substitution on Soil Quality and Microbial Community. Agronomy, 14.","DOI":"10.3390\/agronomy14050888"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"105301","DOI":"10.1016\/j.resconrec.2020.105301","article-title":"Replacing Synthetic Fertilizer by Manure Requires Adjusted Technology and Incentives: A Farm Survey across China","volume":"168","author":"Zhang","year":"2021","journal-title":"Resour. Conserv. Recycl."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"112538","DOI":"10.1016\/j.ecoenv.2021.112538","article-title":"Tracking Antibiotic Resistance Genes (ARGs) during Earthworm Conversion of Cow Dung in Northern China","volume":"222","author":"Tian","year":"2021","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref_20","unstructured":"Rub\u00e6k, G.H., and Kristensen, K. (2017). Protocol for Bicarbonate Extraction of Inorganic Phosphate from Agricultural Soils, DCA-Nationalt Center for F\u00f8devarer og Jordbrug."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2194","DOI":"10.1093\/bioinformatics\/btr381","article-title":"UCHIME Improves Sensitivity and Speed of Chimera Detection","volume":"27","author":"Edgar","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1093\/bioinformatics\/btt593","article-title":"PEAR: A Fast and Accurate Illumina Paired-End ReAd MergeR","volume":"30","author":"Zhang","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"e2584","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: A Versatile Open Source Tool for Metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1007\/s00374-023-01775-9","article-title":"Soil PH Differently Affects N2O Emissions from Soils Amended with Chemical Fertilizer and Manure by Modifying Nitrification and Denitrification in Wheat-Maize Rotation System","volume":"60","author":"Wu","year":"2024","journal-title":"Biol. Fertil. Soils"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1017\/S0021859615000295","article-title":"An Assessment of the Effects of Fertilizer Nitrogen Management on Nitrate Leaching Risk from Grazed Dairy Pasture","volume":"154","author":"Vogeler","year":"2016","journal-title":"J. Agric. Sci."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1186\/s12302-021-00505-y","article-title":"Environmental Fate of Tetracycline Antibiotics: Degradation Pathway Mechanisms, Challenges, and Perspectives","volume":"33","author":"Ahmad","year":"2021","journal-title":"Environ. Sci. Eur."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1016\/j.jaci.2012.10.026","article-title":"A Microbiota Signature Associated with Experimental Food Allergy Promotes Allergic Sensitization and Anaphylaxis","volume":"131","author":"Burton","year":"2013","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/j.tim.2014.05.005","article-title":"Fate and Effects of Veterinary Antibiotics in Soil","volume":"22","author":"Jechalke","year":"2014","journal-title":"Trends Microbiol."},{"key":"ref_29","unstructured":"(2018). Soil Environmental Quality-Risk Control Standard for Soil Contamination of Agricultural Land (Trial) (Standard No. GB 15618-2018)."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"113652","DOI":"10.1016\/j.envpol.2019.113652","article-title":"Temporal Effects of Repeated Application of Biogas Slurry on Soil Antibiotic Resistance Genes and Their Potential Bacterial Hosts","volume":"258","author":"Liu","year":"2020","journal-title":"Environ. Pollut."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"5721","DOI":"10.1021\/acs.est.6b05887","article-title":"The Prevalence of Integrons as the Carrier of Antibiotic Resistance Genes in Natural and Man-Made Environments","volume":"51","author":"Ma","year":"2017","journal-title":"Environ. Sci. Technol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1038\/ismej.2013.189","article-title":"Quantitative and Qualitative Impact of Hospital Effluent on Dissemination of the Integron Pool","volume":"8","author":"Stalder","year":"2014","journal-title":"ISME J."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"16270","DOI":"10.1038\/nmicrobiol.2016.270","article-title":"Continental-Scale Pollution of Estuaries with Antibiotic Resistance Genes","volume":"2","author":"Zhu","year":"2017","journal-title":"Nat. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Cyco\u0144, M., Mrozik, A., and Piotrowska-Seget, Z. (2019). Antibiotics in the Soil Environment\u2014Degradation and Their Impact on Microbial Activity and Diversity. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.00338"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"111764","DOI":"10.1016\/j.marpolbul.2020.111764","article-title":"Trace Metal Contamination in the Marine Sediments off Point Calimere, Southeast Coast of India","volume":"161","author":"Gopal","year":"2020","journal-title":"Mar. Pollut. Bull."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"100893","DOI":"10.1016\/j.psj.2020.12.006","article-title":"Prevalence, Biosecurity Factor, and Antimicrobial Susceptibility Analysis of Salmonella Species Isolated from Commercial Duck Farms in Korea","volume":"100","author":"Kim","year":"2021","journal-title":"Poult. Sci."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"111477","DOI":"10.1016\/j.ecoenv.2020.111477","article-title":"Seasonal Variation and Risk Assessment of Microplastics in Surface Water of the Manas River Basin, China","volume":"208","author":"Wang","year":"2021","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1007\/s10653-024-02239-1","article-title":"Characteristics of Tetracycline Antibiotic Resistance Gene Enrichment and Migration in Soil\u2013Plant System","volume":"46","author":"Wang","year":"2024","journal-title":"Environ. Geochem. 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