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The text describes the analysis of genomic sequences of marine prokaryotes to create a dataset of bacterial and archaeal genomes and viral genomes. The analysis shows that lysogens and proviruses are common in marine ecosystems, particularly in the deep sea, and have different genomic features and growth properties compared to non-lysogens. The study also identifies virus-host interaction networks and proviruses with the ability to infect different bacterial classes and phyla. The viral genomes analyzed are enriched in functions related to carbohydrate metabolism. The impact of a prophage on a marine Shewanella bacterium is experimentally demonstrated. The research contributes to understanding the ecology of marine prokaryotes and their viruses.
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.
Viruses are ubiquitous in natural environments, and their extremely high abundance, diversity, and activity make them indispensable to various Earth’s ecosystems<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Dance, A. The incredible diversity of viruses.