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Biology LibreTexts

7.16B: Viral Genomes in Nature

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  • [ "article:topic", "authorname:boundless", "Viral Genomes" ]

    Viruses are the most abundant biological entity on earth, they outnumber all other lifeforms on earth combined.


    Recognize viral genomic diversity in nature


    Key Points

    • Viruses infect all types of cellular life including animals, plants, bacteria, and fungi.
    • Metagenomic sequencing has identified that there are an enormous number of species of virus in nature, showing that a a teaspoon of water has a million species of viruses.
    • Viruses kill about 20% of the microbes that constitute the oceans microbial fauna, each day. This viral-driven biological turn over is needed for for life on earth to continue.
    • Viruses can transfer genetic material from one species to another, and as such viruses may be a main driving force of evolution.

    Key Terms

    • metagenomics: The study of genomes recovered from environmental samples; especially the differentiation of genomes from multiple organisms or individuals, either in a symbiotic relationship, or at a crime scene.
    • stool: Feces; excrement.


    Environmental Shotgun Sequencing (ESS): (A) sampling from habitat; (B) filtering particles, typically by size; (C) Lysis and DNA extraction; (D) cloning and library construction; (E) sequencing the clones; (F) sequence assembly into contigs and scaffolds

    Viruses are by far the most abundant biological entities on earth and they outnumber all the others put together. They infect all types of cellular life including animals, plants, bacteria, and fungi. However, different types of viruses can infect only a limited range of hosts and many are species-specific. Some, such as smallpox virus for example, can infect only one species – in this case humans, and are said to have a narrow host range. Other viruses, such as rabies virus, can infect different species of mammals and are said to have a broad range. The viruses that infect plants are harmless to animals, and most viruses that infect other animals are harmless to humans. The host range of some bacteriophages is limited to a single strain of bacteria and they can be used to trace the source of outbreaks of infections by a method called phage typing.

    Metagenomic sequencing is particularly useful in the study of viral communities. As viruses lack a shared universal phylogenetic marker (as 16S RNA for bacteria and archaea, and 18S RNA for eukarya), the only way to access the genetic diversity of the viral community from an environmental sample is through metagenomics. Viral metagenomes (also called viromes) should therefore provide more and more information about viral diversity and evolution. In 2002, Mya Breitbart, Forest Rohwer, and colleagues used environmental shotgun sequencing to show that 200 liters of seawater contains over 5,000 different viruses. Subsequent studies showed that there are more than a thousand viral species in human stool and possibly a million different viruses per kilogram of marine sediment, including many bacteriophages. Essentially all of the viruses in these studies were new species.


    Phocine distermper encephalitis: This is a section from a harbor seal cerebral cortex. The white areas are tissue lesions caused a phocine distermper viral infection.

    To understand the complex diversity of viruses a further look at viruses in aquatic environments shows, a teaspoon of seawater contains about one million viruses. They are essential to the regulation of saltwater and freshwater ecosystems. Most of these viruses are bacteriophages, which are harmless to plants and animals. They infect and destroy the bacteria in aquatic microbial communities, comprising the most important mechanism of recycling carbon in the marine environment. The organic molecules released from the bacterial cells by the viruses stimulate fresh bacterial and algal growth. Microorganisms constitute more than 90% of the biomass in the sea. It is estimated that viruses kill approximately 20% of this biomass each day and that there are 15 times as many viruses in the oceans as there are bacteria and archaea. Viruses are the main agents responsible for the rapid destruction of harmful algal blooms, which often kill other marine life. The number of viruses in the oceans decreases further offshore and deeper into the water, where there are fewer host organisms. The effects of marine viruses are far-reaching. By increasing the amount of photosynthesis in the oceans, viruses are indirectly responsible for reducing the amount of carbon dioxide in the atmosphere by approximately three gigatonnes of carbon per year. Like any organism, marine mammals are susceptible to viral infections. In 1988 and 2002, thousands of harbor seals were killed in Europe by phocine distemper virus. Many other viruses, including caliciviruses, herpesviruses, adenoviruses, and parvoviruses circulate in marine mammal populations.

    Viruses are an important natural means of transferring genes between different species, which increases genetic diversity and drives evolution. It is thought that viruses played a central role in the early evolution, before the diversification of bacteria, archaea, and eukaryotes and at the time of the last universal common ancestor of life on earth. Viruses are still one of the largest reservoirs of unexplored genetic diversity on earth.