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A systematic analysis of marine lysogens and proviruses

Author

Listed:
  • Yi Yi

    (Shanghai Jiao Tong University)

  • Shunzhang Liu

    (Shanghai Jiao Tong University)

  • Yali Hao

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

  • Qingyang Sun

    (Shanghai Jiao Tong University)

  • Xinjuan Lei

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

  • Yecheng Wang

    (Shanghai Jiao Tong University)

  • Jiahua Wang

    (Shanghai Jiao Tong University)

  • Mujie Zhang

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

  • Shan Tang

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

  • Qingxue Tang

    (Shanghai Jiao Tong University)

  • Yue Zhang

    (Shanghai Jiao Tong University)

  • Xipeng Liu

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

  • Yinzhao Wang

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

  • Xiang Xiao

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University
    Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai))

  • Huahua Jian

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

Abstract

Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, we systematically analyze existing genomic sequences of marine prokaryotes to compile a Marine Prokaryotic Genome Dataset (MPGD, consisting of over 12,000 bacterial and archaeal genomes) and a Marine Temperate Viral Genome Dataset (MTVGD). At least 40% of the MPGD genomes contain one or more proviral sequences, indicating that they are lysogens. The MTVGD includes over 12,900 viral contigs or putative proviruses, clustered into 10,897 viral genera. We show that lysogens and proviruses are abundant in marine ecosystems, particularly in the deep sea, and marine lysogens differ from non-lysogens in multiple genomic features and growth properties. We reveal several virus-host interaction networks of potential ecological relevance, and identify proviruses that appear to be able to infect (or to be transferred between) different bacterial classes and phyla. Auxiliary metabolic genes in the MTVGD are enriched in functions related to carbohydrate metabolism. Finally, we experimentally demonstrate the impact of a prophage on the transcriptome of a representative marine Shewanella bacterium. Our work contributes to a better understanding of the ecology of marine prokaryotes and their viruses.

Suggested Citation

  • Yi Yi & Shunzhang Liu & Yali Hao & Qingyang Sun & Xinjuan Lei & Yecheng Wang & Jiahua Wang & Mujie Zhang & Shan Tang & Qingxue Tang & Yue Zhang & Xipeng Liu & Yinzhao Wang & Xiang Xiao & Huahua Jian, 2023. "A systematic analysis of marine lysogens and proviruses," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41699-4
    DOI: 10.1038/s41467-023-41699-4
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    1. Hanpeng Liao & Chen Liu & Shungui Zhou & Chunqin Liu & David J. Eldridge & Chaofan Ai & Steven W. Wilhelm & Brajesh K. Singh & Xiaolong Liang & Mark Radosevich & Qiu-e Yang & Xiang Tang & Zhong Wei & , 2024. "Prophage-encoded antibiotic resistance genes are enriched in human-impacted environments," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Jiandui Mi & Xiaoping Jing & Chouxian Ma & Fuyu Shi & Ze Cao & Xin Yang & Yiwen Yang & Apurva Kakade & Weiwei Wang & Ruijun Long, 2024. "A metagenomic catalogue of the ruminant gut archaeome," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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