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

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Title: Ciprofloxacin-driven purifying selection on viral genomes accelerates soil N2O production.
Authors: Linfa Fang1,2, Lakshmanan, Prakash3,4, Hailin Zhang1, Yue Deng1,2, Ran Xiao1,2, Teng Wen5, Bin Ma6, Tida Ge7, Müller, Christoph8,9,10, Jinbo Zhang5,8, Xinping Chen1,2, Yongguan Zhu11, Xiaoxuan Su1,2 xuangood@swu.edu.cn
Source: Proceedings of the National Academy of Sciences of the United States of America. 7/22/2025, Vol. 122 Issue 29, p1-12. 39p.
Subjects: Greenhouse gases, Viral genomes, Biogeochemical cycles, Nitrogen cycle, Nitrogen in soils
Abstract: 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. [ABSTRACT FROM AUTHOR]
Copyright of Proceedings of the National Academy of Sciences of the United States of America is the property of National Academy of Sciences and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: Ciprofloxacin-driven purifying selection on viral genomes accelerates soil N<subscript>2</subscript>O production.
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  Data: <searchLink fieldCode="AR" term="%22Linfa+Fang%22">Linfa Fang</searchLink><relatesTo>1,2</relatesTo><br /><searchLink fieldCode="AR" term="%22Lakshmanan%2C+Prakash%22">Lakshmanan, Prakash</searchLink><relatesTo>3,4</relatesTo><br /><searchLink fieldCode="AR" term="%22Hailin+Zhang%22">Hailin Zhang</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Yue+Deng%22">Yue Deng</searchLink><relatesTo>1,2</relatesTo><br /><searchLink fieldCode="AR" term="%22Ran+Xiao%22">Ran Xiao</searchLink><relatesTo>1,2</relatesTo><br /><searchLink fieldCode="AR" term="%22Teng+Wen%22">Teng Wen</searchLink><relatesTo>5</relatesTo><br /><searchLink fieldCode="AR" term="%22Bin+Ma%22">Bin Ma</searchLink><relatesTo>6</relatesTo><br /><searchLink fieldCode="AR" term="%22Tida+Ge%22">Tida Ge</searchLink><relatesTo>7</relatesTo><br /><searchLink fieldCode="AR" term="%22Müller%2C+Christoph%22">Müller, Christoph</searchLink><relatesTo>8,9,10</relatesTo><br /><searchLink fieldCode="AR" term="%22Jinbo+Zhang%22">Jinbo Zhang</searchLink><relatesTo>5,8</relatesTo><br /><searchLink fieldCode="AR" term="%22Xinping+Chen%22">Xinping Chen</searchLink><relatesTo>1,2</relatesTo><br /><searchLink fieldCode="AR" term="%22Yongguan+Zhu%22">Yongguan Zhu</searchLink><relatesTo>11</relatesTo><br /><searchLink fieldCode="AR" term="%22Xiaoxuan+Su%22">Xiaoxuan Su</searchLink><relatesTo>1,2</relatesTo><i> xuangood@swu.edu.cn</i>
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  Data: <searchLink fieldCode="DE" term="%22Greenhouse+gases%22">Greenhouse gases</searchLink><br /><searchLink fieldCode="DE" term="%22Viral+genomes%22">Viral genomes</searchLink><br /><searchLink fieldCode="DE" term="%22Biogeochemical+cycles%22">Biogeochemical cycles</searchLink><br /><searchLink fieldCode="DE" term="%22Nitrogen+cycle%22">Nitrogen cycle</searchLink><br /><searchLink fieldCode="DE" term="%22Nitrogen+in+soils%22">Nitrogen in soils</searchLink>
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  Data: 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. [ABSTRACT FROM AUTHOR]
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  Data: <i>Copyright of Proceedings of the National Academy of Sciences of the United States of America is the property of National Academy of Sciences and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1073/pnas.2503199122
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        Text: English
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        PageCount: 39
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      – SubjectFull: Greenhouse gases
        Type: general
      – SubjectFull: Viral genomes
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      – SubjectFull: Biogeochemical cycles
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      – SubjectFull: Nitrogen cycle
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      – SubjectFull: Nitrogen in soils
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              Text: 7/22/2025
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