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Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China

Author

Listed:
  • Shaoming Gao

    (Sun Yat-sen University)

  • David Paez-Espino

    (DOE Joint Genome Institute, Lawrence Berkeley National Laboratory)

  • Jintian Li

    (South China Normal University)

  • Hongxia Ai

    (Sun Yat-sen University)

  • Jieliang Liang

    (South China Normal University)

  • Zhenhao Luo

    (Sun Yat-sen University)

  • Jin Zheng

    (South China Normal University)

  • Hao Chen

    (South China University of Technology)

  • Wensheng Shu

    (South China Normal University)

  • Linan Huang

    (Sun Yat-sen University)

Abstract

Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment. The results demonstrate that prokaryotic communities dictate viral taxonomic and functional diversity, abundance and structure, whereas other factors especially latitude and mean annual temperature also impact viral populations and functions. In silico predictions highlight lineage-specific virus-host abundance ratios and richness-dependent virus-host interaction structure. Further functional analyses reveal important roles of environmental conditions and horizontal gene transfers in shaping viral auxiliary metabolic genes potentially involved in phosphorus assimilation. Our findings underscore the importance of both abiotic and biotic factors in predicting the taxonomic and functional biogeographic dynamics of viruses in the AMD sediments.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30049-5
    DOI: 10.1038/s41467-022-30049-5
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    1. Janina Rahlff & Victoria Turzynski & Sarah P. Esser & Indra Monsees & Till L. V. Bornemann & Perla Abigail Figueroa-Gonzalez & Frederik Schulz & Tanja Woyke & Andreas Klingl & Cristina Moraru & Alexan, 2021. "Lytic archaeal viruses infect abundant primary producers in Earth’s crust," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    2. Christopher T. Brown & Laura A. Hug & Brian C. Thomas & Itai Sharon & Cindy J. Castelle & Andrea Singh & Michael J. Wilkins & Kelly C. Wrighton & Kenneth H. Williams & Jillian F. Banfield, 2015. "Unusual biology across a group comprising more than 15% of domain Bacteria," Nature, Nature, vol. 523(7559), pages 208-211, July.
    3. Ben J. Woodcroft & Caitlin M. Singleton & Joel A. Boyd & Paul N. Evans & Joanne B. Emerson & Ahmed A. F. Zayed & Robert D. Hoelzle & Timothy O. Lamberton & Carmody K. McCalley & Suzanne B. Hodgkins & , 2018. "Genome-centric view of carbon processing in thawing permafrost," Nature, Nature, vol. 560(7716), pages 49-54, August.
    4. 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.
    5. Rosseel, Yves, 2012. "lavaan: An R Package for Structural Equation Modeling," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 48(i02).
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    Cited by:

    1. Mengzhi Ji & Jiayin Zhou & Yan Li & Kai Ma & Wen Song & Yueyue Li & Jizhong Zhou & Qichao Tu, 2024. "Biodiversity of mudflat intertidal viromes along the Chinese coasts," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. Jie-Liang Liang & Shi-wei Feng & Jing-li Lu & Xiao-nan Wang & Feng-lin Li & Yu-qian Guo & Shen-yan Liu & Yuan-yue Zhuang & Sheng-ji Zhong & Jin Zheng & Ping Wen & Xinzhu Yi & Pu Jia & Bin Liao & Wen-s, 2024. "Hidden diversity and potential ecological function of phosphorus acquisition genes in widespread terrestrial bacteriophages," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Zongzhi Wu & Tang Liu & Qian Chen & Tianyi Chen & Jinyun Hu & Liyu Sun & Bingxue Wang & Wenpeng Li & Jinren Ni, 2024. "Unveiling the unknown viral world in groundwater," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    4. Liyun An & Xinwu Liu & Jianwei Wang & Jinbo Xu & Xiaoli Chen & Xiaonan Liu & Bingxin Hu & Yong Nie & Xiao-Lei Wu, 2024. "Global diversity and ecological functions of viruses inhabiting oil reservoirs," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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