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The hunt for giant viruses in the ocean

A mysterious danger is facing algae blooms in the oceans: giant viruses. A new "forensic detection" method makes it possible to locate the fingerprints of large viruses in the specific tiny algae that they attack

They said that they came from outer space, that they are actually bacteria and that they challenge the very definition of viruses. Although until the beginning of the 21st century they were not at all known to science, but the giant viruses (giant viruses), or affectionately gyros, are here to stay. While most viruses contain little genetic material, which is needed to produce only a few proteins, discoveries from about two decades ago indicated the existence of viruses with a lot of genetic material - up to 100 times that of other viruses - and that their size exceeds that of certain bacteria.

This is how the bloom collapses: four giant hexagon-shaped viruses that have replicated in a unicellular alga (the rough texture on the right) are on their way out to infect more algae. Three of the viruses are normal and ready for action - and one is white and empty of DNA. Photo: Dr. Daniela Shatz
This is how the bloom collapses: four giant hexagon-shaped viruses that have replicated in a unicellular alga (the rough texture on the right) are on their way out to infect more algae. Three of the viruses are normal and ready for action - and one is white and empty of DNA. Photo: Dr. Daniela Shatz

Many of the giant viruses are found in the oceans, where they infect, among other things, various species of single-celled algae - photosynthetic creatures responsible, among other things, for about half of the work of producing oxygen and fixing carbon in our world. The giant viruses are able to cause the rapid collapse of algae mats that extend over tens of thousands of kilometers in the oceans, thereby affecting extensive ecosystems in the sea, air and land. Nevertheless, much is hidden from the visible when it comes to the natural hosts of the giant viruses - that is, those specific marine species that each virus tends to infect. In a new study in the laboratory of Prof. Assaf Verdi From the Department of Plant and Environmental Sciences at the Weizmann Institute of Science, the researchers used RNA sequencing technology at the single cell level in samples collected during algae blooms in fjords in Norway, and thus mapped in unprecedented detail the relationships between the giant viruses and the algae species each infects.

""The processes of climate change lead to the release of ancient pathogens from the melting glaciers at the poles. The new method will make it possible to identify them more easily and thus assess the environmental threat posed by them"

Until recently, the most effective way to examine the population of viruses and algae in water was by examining all the genetic material in samples full of creatures and viruses isolated from the ocean. "Studies of this type advanced our knowledge of the distribution of algae and viruses in water, but provided missing information," explains Prof. Verdi. "We could learn from them about the variety of common species in the sample, but we could not detect an active infection and therefore we were limited in our ability to measure the effect of the viruses on the rashes and their crusting. We also did not have the ability to identify populations that were less common in the sample, who is the natural host of each virus, and whether the viruses are actively present in the cells."

The line between a giant virus and a tiny algae: families of unicellular algae (left) and the giant viruses they host (right) as discovered in the study
The line between a giant virus and a tiny algae: families of unicellular algae (left) and the giant viruses they host (right) as discovered in the study

In order to overcome these limitations, and to examine the relationships as they exist in the natural environment, the researchers sailed to the Norwegian fjords and proactively stimulated algae blooms in their natural location by adding nutrients to the water and imitating the conditions that lead to the bloom. When they returned to the laboratory, they sequenced the RNA of the cells in the samples - that is, the molecules that indicate the active genes in the organisms sampled at a given time. In contrast to normal RNA sequencing, in which all the RNA from all the organisms in the sample are combined into one "mash", the researchers used sequencing at the single cell level - an advanced, high-resolution method that allows the researchers to tag each and every cell, and identify which R- AN appeared only in it.

Flowering the fjords: a team of researchers from Prof. Assaf Vardi's laboratory collects samples in Norway
Flowering the fjords: a team of researchers from Prof. Assaf Vardi's laboratory collects samples in Norway

Thanks to the sequencing, the researchers were able to identify the active genes in the cells and by comparing them to existing databases to identify which species each algae in the samples belonged to. But the researchers were not satisfied with mapping the hosts - they demanded to receive the guest list as well. Amir From, a PhD student in Prof. Verdi's lab, and who led the research, explains: "We realized that through a careful analysis of the RNA we can extract double information from the data - not only to identify the type of algae, but also to distinguish whether the algae were infected by a giant virus, and if so, what giant virus is it." Before the study, there was no database for the classification of giant viruses that infect algae, so the researchers turned to a virus evolution expert from Virginia Tech, Prof. Frank Aylward, who together with his team put together a unique database for identifying giant viruses based on the RNA extracted from the cells.

Of the tens of thousands of cells examined, many belonged to the dominant algae in that bloom, Emiliania huxleyi , that the giant virus that infects her has already been identified by Verdi's laboratory in research recently published. This time the lab focused on virus-host pairs that appeared in minute amounts in the samples. In total, the researchers found 972 infected cells, of which 71 did not belong to the dominant algae in the bloom, including several pairs of hosts and giant viruses that were not known until now; For example, they discovered that the Imitervirales-07 virus infects cells from the Katablepharidaceae family. When the researchers examined the RNA of the virus in these cells, they discovered that it works to produce proteins that directly affect the fate of cells, including proteins that can cause cells to commit suicide (programmed cell death) - an unprecedented viral effect on a host cell. In addition, the researchers found a smoking gun: they showed a connection between the appearance of the virus in the tested samples and a collapse in the host algae population shortly thereafter.

Having successfully faced the computational challenge of characterizing cells infected with samples from a tiny amount of RNA, the researchers believe that the method they developed will also be used to identify relationships between algae and viruses and other disease-causing agents (pathogens) in other regions of the world, including in extreme climate environments such as the poles and alpine lakes . "The processes of climate change lead to the release of ancient pathogens from the melting glaciers at the poles. The new method will make it possible to identify them more easily and thus assess the environmental threat posed by them," says Prof. Verdi.

Dr. Gore Hebroni, Dr. Flora Vincent and Dr. Daniela Schatz from Prof. Verdi's lab at the Weizmann Institute of Science and Dr. Carolina Martinez-Gutierrez from Prof. Aylward's lab at Virginia Tech contributed to the research.