‘Viral dark matter’ - Hidden world of giant viruses discovered in seawater

15 May 2017 | 89

From a teaspoon of seawater, scientists have discovered a hidden world of giant viruses. Using a newly developed technique called single virus genomics, researchers picked out individual viruses from seawater collected from the Gulf of Maine (off the East Coast of the US) and analysed their genomes. The discovery was unique since no cultivation of the viruses was required, this was the first time such giant viruses had been isolated from the ‘wild’. The research also revealed that every giant virus analysed by the team was different and new to science. Strikingly, some of the genomes also revealed new infection mechanisms or enzymes not previously observed in viruses. A whole new world of viruses has been revealed!

Despite their size, giant viruses have remained hidden from view as current sampling techniques have rendered them invisible: they are too large to pass through standard filters normally used to study viruses, consequently they have been caught on the filters, but their genomes have been confused with cellular material.  Furthermore, “It is akin to discovering a vibrant ecosystem of new animals in your front garden that thrive by mimicking plants” suggested Professor Willie Wilson, lead author in this study carried out at the world-renowned Single Cell Genomics Center (SCGC) at Bigelow Laboratory for Ocean Sciences in Maine, US, “because they have the appearance of plants, nobody searching for animals would give them a second look” he said, explaining the analogy.

Most of the newly discovered viruses belong to a group called the Mimiviruses, originally named since they mimic bacteria to persuade their protist (single-celled organism) hosts to eat them. Indeed, these viral leviathans are larger than many marine bacteria and probably initially seem like a tasty morsel. However, in a culinary twist, the predator turns into prey as the dangerous snack infects its host. Many of the previously discovered Mimiviruses have been isolated on a susceptible and easily cultivatable amoeboid pathogen of humans; an amoeba that is unlikely to be the Mimivirus’ natural host in the ocean. One challenge marine scientists still have, is to determine what the natural hosts of these marine Mimiviruses actually are. Looking for clues in the genomes of individual viruses, with tools developed in this study will help to address this challenge. In addition, exploration of these genomes will identify novel and diverse metabolisms of these newly investigated viruses.

Use of single virus genomics is a paradigm shift in how we obtain genomic sequence information from aquatic viruses. The term ‘viral dark matter’ is often used to describe the unknown oceanic virosphere; it clearly has massive effects in the ocean but they are difficult to observe, and even more difficult to measure. Single virus genomics gives us a new ‘lens’ that will open up a universe of possibilities and importantly increase viral gene space. 

“There is a lot of uncharted biodiversity on our planet that we can’t get hold of because the cultivation of marine viruses is so difficult” noted Professor Wilson; “by using technology developed in our study, reconstruction of individual virus genomes from a sample of seawater is now possible. Using this data, inferences can be made on not only the numbers and kinds of viruses that inhabit a particular ecosystem, but also on who and how these viruses infect; it is a powerful technique”.

Prior to this pioneering study, most environmental virus genomic information came from metagenomic analysis of viruses, where the total virus fraction from a water sample was filtered, concentrated and sequenced. However, this method was typically riddled with cellular contamination and often jumbled viral genomes together. Wilson’s study used flow cytometry to sort individual viruses that are free from cellular contamination. Wilson’s team predict this method will revolutionise the way viruses are investigated in future. It will be widely applicable throughout environmental virology and medical fields.

The paper: Genomic exploration of individual giant ocean viruses is published in The ISME Journal doi:10.1038/ismej.2017.61 

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