Ciprofloxacin- driven purifying selection on viral genomes accelerates soil N2O production

• 成果类型: Article
• 署名作者: Fang, Linfa; Lakshmanan, Prakash; Zhang, Hailin; Deng, Yue; Xiao, Ran; Wen, Teng; Ma, Bin; Ge, Tida; Mueller, Christoph; Zhang, Jinbo; Chen, Xinping; Zhu, Yongguan; Su, Xiaoxuan
• 署名单位: Southwest University - China; Southwest University - China; Guangxi Academy of Agricultural Sciences; University of Queensland; Nanjing Normal University; Zhejiang University; Ningbo University; Justus Liebig University Giessen; Justus Liebig University Giessen; University College Dublin; University College Dublin; Chinese Academy of Sciences
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-11940
• DOI: 10.1073/pnas.2503199122
• 发表日期: 2025-07-22
• 关键词: analysis reveals; codon usage; resistance; denitrification; nitrification; adaptation; mutations; context; genes

摘要

Viruses are ubiquitous regulators of microbial dynamics and may thus greatly influence global microbial- driven greenhouse gas emissions. Anthropogenic stressors, such as chemical contamination, are likely to amplify these viral contributions; however, their global significance and underlying mechanisms remain elusive. Utilizing 15N tracing, metagenomics, and laboratory assays, we explore soil viral communities and their evolutionary potential under the stress from antibiotic ciprofloxacin (CIP), focusing on their roles in regulating nitrogen cycling and N2O production. Through isolation and reinoculation of soil viruses, we demonstrate that CIP stimulates soil denitrification- derived N2O production, with 18 to 29% of the increase attributed to viral activity. Under CIP stress, soil viruses shift toward a lysogenic lifestyle, promoting mutualism with denitrifiers by horizontally transferring viral denitrification- related auxiliary metabolic genes (AMGs). The observed synonymous mutations in these AMGs, driven by CIP, suggest enhanced purifying selection, likely optimizing codon usage to align with host preferences. This optimization likely enhances the expression of denitrifying AMGs and increases N2O production. This study provides insights into the overlooked role of viral dynamics and genomic mutations in modulating N2O production under stressful environments, highlighting their evolutionary significance and impact on biogeochemical cycles in the Anthropocene.