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Leveraging a massive global dataset of 420 metagenomes and 42 viromes, we decipher the phage-host evolutionary arms race during ecological succession. While composting reduces total antimicrobial resistance genes (ARGs), it is bottlenecked by the selective enrichment of thermophilic antimicrobial-resistant bacteria (ARB), which dominate the residual maturation-phase resistome (\u223c 60%). Among 106,387 identified viral operational taxonomic units (vOTUs), lytic interactions (39.5%) quantitatively override transduction (&amp;lt; 0.5%) in driving ARB decline. Correspondingly, the relative abundance of ARG-reducing vOTUs (7.24%) is orders of magnitude higher than that of vOTUs involved in transduction (0.06%) (p &amp;lt; 0.001). However, intense viral predation drives surviving ARB to evolve enriched antiviral defense systems (ADS) against lysis. Intriguingly, this immune shield acts as a genetic firewall, likely restricting the horizontal acquisition of ARGs via transformation or conjugation. Our findings redefine composting as an intense evolutionary arena and suggest that precision strategies targeting the thermophilic reservoir are essential for maximizing ARG mitigation and safer manure recycling.<\/jats:p>","DOI":"10.1021\/acs.est.6c04304","type":"journal-article","created":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T07:02:10Z","timestamp":1788764530000},"page":"26552-26565","source":"Crossref","is-referenced-by-count":0,"title":["Virus-Mediated Fate\nof Antimicrobial Resistance Genes\nin Livestock Manure Composting"],"prefix":"10.1021","volume":"60","author":[{"given":"Qihe","family":"Tang","sequence":"first","affiliation":[{"name":"Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , , ,","place":["Beijing, China, 100085"]},{"name":"Guangxi University , , ,","place":["Nanning, China, 530005"]},{"name":"Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , , ,","place":["Beijing, China, 100085"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luoyao","family":"Wen","sequence":"additional","affiliation":[{"name":"Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , , ,","place":["Beijing, China, 100085"]},{"name":"Guangxi University , , ,","place":["Nanning, China, 530005"]},{"name":"Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , , ,","place":["Beijing, China, 100085"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yixuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , , ,","place":["Beijing, China, 100085"]},{"name":"Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , , ,","place":["Beijing, China, 100085"]},{"name":"University of Chinese Academy of Sciences , ,","place":["Beijing, China, 100049"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiedong","family":"Lu","sequence":"additional","affiliation":[{"name":"Guangxi Academy of Agricultural Sciences\/Guangxi Key Laboratory of Arable Land Conservation , , , ,","place":["Nanning, Guangxi, China, 530007"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peihong","family":"Shen","sequence":"additional","affiliation":[{"name":"Guangxi University , , ,","place":["Nanning, China, 530005"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0900-7412","authenticated-orcid":true,"given":"Yuansong","family":"Wei","sequence":"additional","affiliation":[{"name":"Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , , ,","place":["Beijing, China, 100085"]},{"name":"Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , , ,","place":["Beijing, China, 100085"]},{"name":"University of Chinese Academy of Sciences , ,","place":["Beijing, China, 100049"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hans Hermann","family":"Richnow","sequence":"additional","affiliation":[{"name":"Leibniz Institute for Tropospheric Research (TROPOS) , , Permoserstra\u00dfe 15 , ,","place":["Leipzig, Germany, 04318"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7959-2701","authenticated-orcid":true,"given":"Junya","family":"Zhang","sequence":"additional","affiliation":[{"name":"Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , , ,","place":["Beijing, China, 100085"]},{"name":"Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , , ,","place":["Beijing, China, 100085"]},{"name":"University of Chinese Academy of Sciences , ,","place":["Beijing, China, 100049"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,7]]},"reference":[{"key":"2026092210102093500_cit1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abq8015","article-title":"Global Biogeography and Projection\nof Soil Antibiotic Resistance Genes","volume":"8","author":"Zheng","year":"2022","journal-title":"Sci. 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Spectrum."},{"key":"2026092210102093500_cit3","doi-asserted-by":"publisher","first-page":"1199","DOI":"10.1016\/S0140-6736(24)01867-1","article-title":"Global burden of bacterial\nantimicrobial resistance 1990\u20132021: a systematic analysis with\nforecasts to 2050","volume":"404","author":"Naghavi","year":"2024","journal-title":"Lancet"},{"key":"2026092210102093500_cit4","doi-asserted-by":"publisher","first-page":"100947","DOI":"10.1016\/j.lanmic.2024.07.010","article-title":"Antimicrobial Resistance:\nA Concise Update","volume":"6","author":"Ho","year":"2025","journal-title":"Lancet"},{"key":"2026092210102093500_cit5","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1038\/s41893-025-01751-1","article-title":"Livestock Antimicrobial Use Embodied in Global Supply Chains","volume":"9","author":"Zhang","year":"2026","journal-title":"Nat. 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Technol."},{"key":"2026092210102093500_cit13","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1016\/j.jhazmat.2017.11.020","article-title":"Abundance,\nand Persistence of Antibiotic Resistance Genes in Various Types of\nAnimal Manure Following Industrial Composting","volume":"344","author":"Qian","year":"2018","journal-title":"J. Hazard. Mater."},{"key":"2026092210102093500_cit14","doi-asserted-by":"publisher","DOI":"10.48130\/biocontam-0026-0003","article-title":"Reconsidering\nPhage-Host\nEvolutionary Triad for Antimicrobial Resistance Control","volume":"2","author":"Zhang","year":"2026","journal-title":"Biocontaminant"},{"key":"2026092210102093500_cit15","doi-asserted-by":"publisher","first-page":"5397","DOI":"10.1038\/s41467-024-49840-7","article-title":"Phage Predation\nAccelerates the Spread of Plasmid-Encoded\nAntibiotic Resistance","volume":"15","author":"Ruan","year":"2024","journal-title":"Nat. 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