A systematic analysis of marine lysogens and proviruses

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 and Huahua Jian ()
Additional contact information
Yi Yi: Shanghai Jiao Tong University
Shunzhang Liu: Shanghai Jiao Tong University
Yali Hao: Shanghai Jiao Tong University
Qingyang Sun: Shanghai Jiao Tong University
Xinjuan Lei: Shanghai Jiao Tong University
Yecheng Wang: Shanghai Jiao Tong University
Jiahua Wang: Shanghai Jiao Tong University
Mujie Zhang: Shanghai Jiao Tong University
Shan Tang: Shanghai Jiao Tong University
Qingxue Tang: Shanghai Jiao Tong University
Yue Zhang: Shanghai Jiao Tong University
Xipeng Liu: Shanghai Jiao Tong University
Yinzhao Wang: Shanghai Jiao Tong University
Xiang Xiao: Shanghai Jiao Tong University
Huahua Jian: Shanghai Jiao Tong University

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-41699-4

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