Academic Journal
Virus-mediated fate of antimicrobial resistance genes in livestock manure anaerobic digestion.
| Τίτλος: | Virus-mediated fate of antimicrobial resistance genes in livestock manure anaerobic digestion. |
|---|---|
| Συγγραφείς: | Tang Q; State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Life Science and Technology, Guangxi University, Nanning, 530005, China., Zhang Y; State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China., Garza DR; Université Paris-Saclay, INRAE, PROSE, Antony, 92761, France., Ruan C; Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland., Liu B; State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China., Rocha U; Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, 04318, Germany., Shen P; College of Life Science and Technology, Guangxi University, Nanning, 530005, China., Wei Y; State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China., Deng Y; State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China., Zhang J; State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China. Electronic address: jyzhang@rcees.ac.cn., Richnow HH; Atmospheric Chemistry Department (ACD), Leibniz Institute for Tropospheric Research (TROPOS), Permoserstraße 15, Leipzig, 04318, Germany; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China. |
| Πηγή: | Water research [Water Res] 2026 Oct 15; Vol. 305, pp. 126401. Date of Electronic Publication: 2026 Jul 02. |
| Τύπος έκδοσης: | Journal Article |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: Pergamon Press Country of Publication: England NLM ID: 0105072 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1879-2448 (Electronic) Linking ISSN: 00431354 NLM ISO Abbreviation: Water Res Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: Oxford, Pergamon Press. |
| Ιατρικοί όροι (MeSH): | Manure*/microbiology , Drug Resistance, Microbial*/genetics, Animals ; Anaerobiosis ; Livestock ; Swine |
| Περίληψη: | Antimicrobial resistance (AMR) poses a critical global health challenge, with livestock manure acting as a significant environmental reservoir for antimicrobial resistance genes (ARGs). Anaerobic digestion (AD) is a pivotal process for mitigating ARG dissemination at the livestock-environment-human interface. This study aims to elucidate the global dynamics of ARGs in AD systems, focusing on virus-host interactions and arms race, to identify actionable strategies for AMR control. We analyzed 205 metagenomic (4.5 Tb) and 36 meta-transcriptomic (640 Gb) datasets, including 15 newly generated datasets, revealing that pig manure AD harbors the highest ARG abundance (0.668 ARGs/16S rRNA), while AD systems generally exhibit limited transcriptional activation of ARGs. We constructed a viral dataset for livestock manure AD (GVD_LMAD), comprising 59,316 DNA and 727 RNA viral operational taxonomic units (vOTUs). Virus-host interactions established by CRISPR-Cas spacer, tRNA and homology matches revealed 889 lytic infections of antimicrobial-resistant bacteria (ARB) compared to only 18 ARG transduction events. Further analysis showed that the relative abundance of vOTUs assigned to the reduction role (4.11% ± 3.19%) was substantially higher than that of reproduction (0.72% ± 0.64%) and transduction (0.19% ± 0.30%), demonstrating that, among viral processes, lysis outweighs transduction in contributing to ARG abundance reduction in AD. Furthermore, an antiviral defense system (ADS) catalogue (GADSC_LMAD), derived from 2760 high-quality metagenome-assembled genomes (MAGs) containing 39,307 ADS, with ADS prevalence in ARB (7.8 ± 6.0 per MAG), indicating an intensified virus-host arms race in AD that may shield ARB from phage lysis. The resulting CRISPR-Cas immune network with expressed spacers targets foreign ARG-carrying sequences (primarily plasmids and ICEs), suggesting a mechanism that restricts horizontal gene transfer (HGT) via conjugation and transformation, despite shielding ARB from phage lysis. Collectively, these findings highlight that viral communities significantly contribute to ARG reduction through phage lysis relative to transduction, while the ADS-mediated arms race, despite protecting ARB, constructs a biological firewall that potentially limits HGT of ARGs. This study provides novel insights into virus-host dynamics as a key mechanism for controlling ARG dissemination in AD systems. (Copyright © 2026 Elsevier Ltd. All rights reserved.) |
| Competing Interests: | Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. |
| Contributed Indexing: | Keywords: Anaerobic digestion; Antimicrobial resistance genes; Antiviral defense systems; Livestock manure; Metagenomics & meta-transcriptomics; Viral community |
| Substance Nomenclature: | 0 (Manure) |
| Entry Date(s): | Date Created: 20260709 Date Completed: 20260909 Latest Revision: 20260909 |
| Update Code: | 20260909 |
| DOI: | 10.1016/j.watres.2026.126401 |
| PMID: | 42424815 |
| Βάση Δεδομένων: | MEDLINE |
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