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Unique plastisphere viromes with habitat-dependent potential for modulating global methane cycle

Author

Listed:
  • Xue-Peng Chen

    (University of Science and Technology of China
    Chinese Academy of Sciences)

  • Dong Zhu

    (Chinese Academy of Sciences
    CAS Haixi Industrial Technology Innovation Center in Beilun
    University of Chinese Academy of Sciences)

  • Shu-Yue Liu

    (Chinese Academy of Sciences)

  • Ming-Ming Sun

    (Nanjing Agricultural University)

  • Mao Ye

    (Chinese Academy of Sciences)

  • Lu Wang

    (Chinese Academy of Sciences
    CAS Haixi Industrial Technology Innovation Center in Beilun)

  • Da Lin

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Tian-Lun Zhang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Matthias C. Rillig

    (Freie Universität Berlin
    Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB))

  • Yong-Guan Zhu

    (University of Science and Technology of China
    Chinese Academy of Sciences
    CAS Haixi Industrial Technology Innovation Center in Beilun
    University of Chinese Academy of Sciences)

Abstract

Plastispheres, novel niches in the Anthropocene, harbor microbial communities with unique functional signatures. As the most abundant biological entity on Earth, viruses are key regulators of microbial community composition and metabolism. However, little is known about viral communities and their functions in the plastisphere. Here, we investigate the composition and functional profile of plastisphere viral communities through microcosm experiments combined with global plastisphere metagenomics data. We find that the plastisphere recruits a distinct viral community with 86.9% novel viral operational taxonomic units compared to control substrates. The plastisphere viral community modulates host methane metabolism through auxiliary metabolic genes and distinctive interactions with hosts. These auxiliary metabolic genes for methane cycling are prevalent in global plastisphere viral communities. Notably, the plastisphere microbiome adopts the life history strategy of copiotrophs in the nutrient-poor water environment, making the water plastisphere a potential hot spot for methane emission compared to the soil plastisphere. Our phage transplantation experiments reveal that lysogenic viruses significantly contribute to enhancing the methanogenic capacity of microorganisms and promoting methane emission of the water plastisphere. Overall, we decipher the role of viruses in the plastisphere and reinforce the necessity of incorporating viral contributions when assessing the effects of plastisphere communities on global biogeochemical cycles.

Suggested Citation

  • Xue-Peng Chen & Dong Zhu & Shu-Yue Liu & Ming-Ming Sun & Mao Ye & Lu Wang & Da Lin & Tian-Lun Zhang & Matthias C. Rillig & Yong-Guan Zhu, 2025. "Unique plastisphere viromes with habitat-dependent potential for modulating global methane cycle," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-63215-6
    DOI: 10.1038/s41467-025-63215-6
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    1. Javier Lopez-Simon & Marina Vila-Nistal & Aleksandra Rosenova & Daniele Corte & Federico Baltar & Manuel Martinez-Garcia, 2023. "Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    2. Xiaoxuan Su & Leyang Yang & Kai Yang & Yijia Tang & Teng Wen & Yingmu Wang & Matthias C. Rillig & Lena Rohe & Junliang Pan & Hu Li & Yong-guan Zhu, 2022. "Estuarine plastisphere as an overlooked source of N2O production," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    3. E. Marie Muehe & Tianmei Wang & Carolin F. Kerl & Britta Planer-Friedrich & Scott Fendorf, 2019. "Rice production threatened by coupled stresses of climate and soil arsenic," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    4. Florian Tesson & Alexandre Hervé & Ernest Mordret & Marie Touchon & Camille d’Humières & Jean Cury & Aude Bernheim, 2022. "Systematic and quantitative view of the antiviral arsenal of prokaryotes," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    5. Cong Wang & Qing-Yi Yu & Niu-Niu Ji & Yong Zheng & John W. Taylor & Liang-Dong Guo & Cheng Gao, 2023. "Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    6. Zhi-Ping Zhong & Jingjie Du & Stephan Köstlbacher & Petra Pjevac & Sandi Orlić & Matthew B. Sullivan, 2024. "Viral potential to modulate microbial methane metabolism varies by habitat," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    7. Ernest D. Osburn & Steven G. McBride & Mohammad Bahram & Michael S. Strickland, 2024. "Global patterns in the growth potential of soil bacterial communities," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    8. Shicong Du & Xinzhao Tong & Alvin C. K. Lai & Chak K. Chan & Christopher E. Mason & Patrick K. H. Lee, 2023. "Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    9. Kristopher Kieft & Zhichao Zhou & Rika E. Anderson & Alison Buchan & Barbara J. Campbell & Steven J. Hallam & Matthias Hess & Matthew B. Sullivan & David A. Walsh & Simon Roux & Karthik Anantharaman, 2021. "Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    10. Eleanor A. Sheridan & Jérémy A. Fonvielle & Samuel Cottingham & Yi Zhang & Thorsten Dittmar & David C. Aldridge & Andrew J. Tanentzap, 2022. "Plastic pollution fosters more microbial growth in lakes than natural organic matter," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
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