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DNA viral community enhances microbial carbon fixation capacity via auxiliary metabolic genes in contaminated soils

Author

Listed:
  • Jia-nan Lu

    (Sun Yat-sen University)

  • Yuanqing Chao

    (Sun Yat-sen University)

  • Li Tian

    (Sun Yat-sen University)

  • Xi Zhong

    (Sun Yat-sen University)

  • Ziwu Chen

    (Sun Yat-sen University)

  • Huan He

    (South China Agricultural University)

  • Bi Huang

    (Sun Yat-sen University)

  • Mengyao Li

    (Sun Yat-sen University)

  • Zekai Feng

    (Sun Yat-sen University)

  • Huayuan Feng

    (Sun Yat-sen University)

  • Chang Hu

    (Sun Yat-sen University)

  • Shunkang Zhou

    (South China Agricultural University)

  • Liqi Zhang

    (Sun Yat-Sen University)

  • Yulu Yang

    (Sun Yat-sen University)

  • Zhepu Ruan

    (South China Agricultural University)

  • Kengbo Ding

    (Sun Yat-sen University)

  • Ying Yang

    (Sun Yat-Sen University)

  • Ke Yuan

    (Sun Yat-Sen University)

  • Wenshen Liu

    (Sun Yat-sen University)

  • Hua Qi

    (South China Agricultural University)

  • Yue Cao

    (Sun Yat-sen University)

  • Ying-heng Fei

    (Guangzhou University)

  • Ning Ling

    (Lanzhou University)

  • Shizhong Wang

    (Sun Yat-sen University)

  • Ye-tao Tang

    (Sun Yat-sen University)

  • Tiangang Luan

    (Sun Yat-sen University)

  • Zhihong Xu

    (Griffith University)

  • Rongliang Qiu

    (Sun Yat-sen University
    South China Agricultural University)

Abstract

Soil is the largest organic matter repository on land and the virosphere is an essential component of soil carbon cycling. While a few carbon-related auxiliary metabolic genes (AMGs) in viruses are reported to potentially influence the hosts, the effects of virus-host interactions on soil carbon fixation, particularly in carbon-deficient contaminated soils, need further validation. Here, we explore the impact of viruses on carbon fixation in contaminated soils from 58 metal mining areas across eastern China. Eleven different functional categories of carbon fixation AMGs are identified via metagenomic analysis in 323 contaminated soil samples. Enzymatic activities of three key AMGs (i.e., rbcL, ppdK and TKT) are experimentally characterized, indicating the positive role of these genes in carbon fixation. Furthermore, transcriptomic sequencing reveals that after active virus inoculation the carbon fixation genes significantly up-regulate (~73%, p

Suggested Citation

  • Jia-nan Lu & Yuanqing Chao & Li Tian & Xi Zhong & Ziwu Chen & Huan He & Bi Huang & Mengyao Li & Zekai Feng & Huayuan Feng & Chang Hu & Shunkang Zhou & Liqi Zhang & Yulu Yang & Zhepu Ruan & Kengbo Ding, 2025. "DNA viral community enhances microbial carbon fixation capacity via auxiliary metabolic genes in contaminated soils," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-64938-2
    DOI: 10.1038/s41467-025-64938-2
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    as
    1. B. Knowles & C. B. Silveira & B. A. Bailey & K. Barott & V. A. Cantu & A. G. Cobián-Güemes & F. H. Coutinho & E. A. Dinsdale & B. Felts & K. A. Furby & E. E. George & K. T. Green & G. B. Gregoracci & , 2016. "Correction: Corrigendum: Lytic to temperate switching of viral communities," Nature, Nature, vol. 539(7627), pages 123-123, November.
    2. Martin Steinegger & Johannes Söding, 2018. "Clustering huge protein sequence sets in linear time," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    3. Gene W. Tyson & Jarrod Chapman & Philip Hugenholtz & Eric E. Allen & Rachna J. Ram & Paul M. Richardson & Victor V. Solovyev & Edward M. Rubin & Daniel S. Rokhsar & Jillian F. Banfield, 2004. "Community structure and metabolism through reconstruction of microbial genomes from the environment," Nature, Nature, vol. 428(6978), pages 37-43, March.
    4. Cynthia M. Kallenbach & Serita D. Frey & A. Stuart Grandy, 2016. "Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls," Nature Communications, Nature, vol. 7(1), pages 1-10, December.
    5. Mark A. Bradford & William R. Wieder & Gordon B. Bonan & Noah Fierer & Peter A. Raymond & Thomas W. Crowther, 2016. "Managing uncertainty in soil carbon feedbacks to climate change," Nature Climate Change, Nature, vol. 6(8), pages 751-758, August.
    6. Lydia Steffens & Eugenio Pettinato & Thomas M. Steiner & Achim Mall & Simone König & Wolfgang Eisenreich & Ivan A. Berg, 2021. "High CO2 levels drive the TCA cycle backwards towards autotrophy," Nature, Nature, vol. 592(7856), pages 784-788, April.
    7. Zhengang Wang & Thomas Hoffmann & Johan Six & Jed O. Kaplan & Gerard Govers & Sebastian Doetterl & Kristof Van Oost, 2017. "Human-induced erosion has offset one-third of carbon emissions from land cover change," Nature Climate Change, Nature, vol. 7(5), pages 345-349, May.
    8. B. Knowles & C. B. Silveira & B. A. Bailey & K. Barott & V. A. Cantu & A. G. Cobián-Güemes & F. H. Coutinho & E. A. Dinsdale & B. Felts & K. A. Furby & E. E. George & K. T. Green & G. B. Gregoracci & , 2016. "Lytic to temperate switching of viral communities," Nature, Nature, vol. 531(7595), pages 466-470, March.
    9. Sarah R. Weiskopf & Forest Isbell & Maria Isabel Arce-Plata & Moreno Di Marco & Mike Harfoot & Justin Johnson & Susannah B. Lerman & Brian W. Miller & Toni Lyn Morelli & Akira S. Mori & Ensheng Weng &, 2024. "Biodiversity loss reduces global terrestrial carbon storage," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    10. Marguerite V. Langwig & Faith Koester & Cody Martin & Zhichao Zhou & Samantha B. Joye & Anna-Louise Reysenbach & Karthik Anantharaman, 2025. "Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    11. Shaoming Gao & David Paez-Espino & Jintian Li & Hongxia Ai & Jieliang Liang & Zhenhao Luo & Jin Zheng & Hao Chen & Wensheng Shu & Linan Huang, 2022. "Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    12. Simon Roux & Jennifer R. Brum & Bas E. Dutilh & Shinichi Sunagawa & Melissa B. Duhaime & Alexander Loy & Bonnie T. Poulos & Natalie Solonenko & Elena Lara & Julie Poulain & Stéphane Pesant & Stefanie , 2016. "Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses," Nature, Nature, vol. 537(7622), pages 689-693, September.
    13. Forest Rohwer & Rebecca Vega Thurber, 2009. "Viruses manipulate the marine environment," Nature, Nature, vol. 459(7244), pages 207-212, May.
    Full references (including those not matched with items on IDEAS)

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