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Exploring the Archaeal Virosphere by Metagenomics

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Viral Metagenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2732))

Abstract

During the past decade, environmental research has demonstrated that archaea are abundant and widespread in nature and play important ecological roles at a global scale. Currently, however, the majority of archaeal lineages cannot be cultivated under laboratory conditions and are known exclusively or nearly exclusively through metagenomics. A similar trend extends to the archaeal virosphere, where isolated representatives are available for a handful of model archaeal virus-host systems. Viral metagenomics provides an alternative way to circumvent the limitations of culture-based virus discovery and offers insight into the diversity, distribution, and environmental impact of uncultured archaeal viruses. Presently, metagenomics approaches have been successfully applied to explore the viromes associated with various lineages of extremophilic and mesophilic archaea, including Asgard archaea (Asgardarchaeota), ANME-1 archaea (Methanophagales), thaumarchaea (Nitrososphaeria), altiarchaea (Altiarchaeota), and marine group II archaea (Poseidoniales). Here, we provide an overview of methods widely used in archaeal virus metagenomics, covering metavirome preparation, genome annotation, phylogenetic and phylogenomic analyses, and archaeal host assignment. We hope that this summary will contribute to further exploration and characterization of the enigmatic archaeal virome lurking in diverse environments.

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Acknowledgments

YW was supported by the National Natural Science Foundation of China (41376135, 31570112, and 41876195). The preparation of this chapter was supported by the Emergence(s) project MEMREMA from Ville de Paris to MK.

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Authors and Affiliations

  1. Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France

    Yifan Zhou, David Prangishvili & Mart Krupovic

  2. Sorbonne Université, Collège Doctoral, Paris, France

    Yifan Zhou

  3. College of Food Science and Technology, Shanghai Ocean University, Shanghai, China

    Yongjie Wang

  4. Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China

    Yongjie Wang

  5. Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China

    Yongjie Wang

  6. Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia

    David Prangishvili

Authors
  1. Yifan Zhou
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  2. Yongjie Wang
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  3. David Prangishvili
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  4. Mart Krupovic
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Corresponding author

Correspondence to Mart Krupovic .

Editor information

Editors and Affiliations

  1. Institute for Sustainable Plant Protection, National Research Council, Bari, Italy

    Vitantonio Pantaleo

  2. Institute for Sustainable Plant Protection, National Research Council, Torino, Italy

    Laura Miozzi

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Zhou, Y., Wang, Y., Prangishvili, D., Krupovic, M. (2024). Exploring the Archaeal Virosphere by Metagenomics. In: Pantaleo, V., Miozzi, L. (eds) Viral Metagenomics. Methods in Molecular Biology, vol 2732. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3515-5_1

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  • DOI: https://doi.org/10.1007/978-1-0716-3515-5_1

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3514-8

  • Online ISBN: 978-1-0716-3515-5

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