Wee, single-celled creatures may chow down on viruses

Teeny, single-cell creatures floating in the ocean may be the first organisms ever confirmed to eat viruses.

Scientists scooped up the organisms, known as protists, from the surface waters of the Gulf of Maine and the Mediterranean Sea off the coast of Catalonia, Spain. They found a slew of viral DNA associated with two diverse groups of protists, called choanozoans and picozoans; the same DNA sequences cropped up in many members of the two groups, despite some of these single-cell organisms not being closely related.

"It would be like organisms as distantly related as trees and humans, or even more distantly related than that," said lead author Julia Brown, a bioinformatician at the Bigelow Laboratory for Ocean Sciences in Maine. "It's very, very unlikely that those viruses are capable of infecting all the organisms we found them in." After running a number of tests, Brown and her colleagues concluded that the protists likely consumed the viruses as food, rather than picking them up by chance or being infected by them. The team says their findings, published online today (Sep. 24) in the journal Frontiers in Microbiology, could reshape how we think about the entire ocean food web, the network of who-eats-who that connects everything from tiny bacteria to plants to blue whales. 

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However, one expert told Live Science that the study doesn't conclusively prove that the protists actually ate the viruses. 

"The detection of viral sequences in ... cells alone can hardly answer the question of how these virus particles entered the cell," Christian Griebler, a freshwater microbial ecologist at the University of Vienna, who was not involved in the study, said in an email. More work will be needed to show how and whether these protists gobble up viruses, and if so, how much nutrition they gain from these microscopic snacks, he said.

A new node in the food web? 

Protists that have a nucleus to hold their DNA, known as eukaryotes, have been shown to take up viral DNA in the past, Griebler noted. However, scientists don't know much about how the cells take in the viruses in the first place, he said. Protists that filter feed may suck in free-floating viruses from the surrounding water, or they may take up viruses that hitch a ride on other tiny particles of matter in the ocean. In addition, viruses called bacteriophages infect bacterial cells, and protists that eat bacteria may inadvertently take in those viruses, he added. 

But a big question remains as to how significant a food source viruses may be to the protists that can ingest them, Brown said. 

The small number of past studies on protist consumption of viruses took place in controlled laboratory settings, "but these [protist] isolates did not represent what's abundant in the ocean, and there were no conclusions made as to how relevant it is to what happens out in the real world," senior author Ramunas Stepanauskas, a senior research scientist at the Bigelow Laboratory for Ocean Sciences, told Live Science. To find real-world evidence of protists eating viruses, Stepanauskas and his team took to the open ocean.  

In all, the team collected nearly 1,700 individual protists from the Gulf of Maine and the Mediterranean Sea; they captured cells belonging to more than 10 different groups of protists, although choanozoans and picozoans primarily appeared in water samples from the Gulf of Maine. The team then sent the water samples through an instrument called a flow cytometer, which sorts any cells floating in the water based on their physical characteristics. From there, they analyzed the DNA associated with each sorted cell; that included the DNA of the cell itself, any microbes stuck to its surface and any organisms trapped within the organism. 

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This genome collection technique "does not discriminate between genomic DNA and any other DNA that's already in the cell, so that's why we were also able to see viral DNA and any associated bacteria that might be there," Brown said. Overall, viral DNA appeared in about 51% of the protists from the Gulf of Maine and 35% of those from the Mediterranean, with most of those viruses being bacteriophages, or viruses that infect bacteria. But within the groups of choanozoans and picozoans, 100% of the samples contained viral DNA sequences, but little trace of bacterial DNA, by comparison. This hints that the protists took in the viruses, in isolation, rather than by eating infected bacteria.  

"We see ... elevated levels of viruses in these two groups, and consistently across all the members of the groups," especially compared with other protists, Brown said. Having also ruled out the possibility that all these protists were being directly infected by viruses, the team considered that the viruses could either be stuck to the outside of the cells or accidentally sorted with the cells while in the flow cytometer. But they found that "the levels of viruses that we see in those cells is above the number that would be sorted by accident," Brown said. The varying levels of virus between different protist groups also makes it unlikely that the pathogens stuck to the protists at random, she added.

Still some unknowns 

Despite these data, Griebler said that there are still alternate explanations as to how viral DNA ended up in protists, including the possibility that the protists consumed infected bacterial cells. To definitively rule out this possibility, the study authors would have to check whether the viral sequences found in protists also appear abundant in bacterial cells, and how often those bacterial cells appear in the protists' cellular bellies, he said. Moreover, if these viruses do represent a food source, the amount of nutrients viruses provide must still be calculated, Griebler added.   

"A back-of-the-envelope calculation reveals that a protozoan cell that eats virus particles instead of bacterial cells needs to take up 100 (or more) virus particles to get the same amount of carbon when eating one bacterial cell," he noted. "It seems very unlikely that protozoa" — eukaryotic protists — "can cover their carbon and nutrient demand from a virus diet."

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That said, while choanozoans are known to consume bacteria, the diet of picozoans remains somewhat mysterious. One report, published in 2007 in the journal PLOS ONE, found that the picozoa feeding apparatus is too small to capture bacterial cells, but large enough to engulf particles less than 0.000006 inches (150 nanometers) in diameter, which could include viruses. "Picozoa are a really mysterious group of protists in the ocean," Stepanauskas noted. They can make up to 15% of a given protist community, especially those in coastal waters, so learning whether or not picozoans devour viruses could reshape our understanding of how nutrients flow through the ocean at large, he said.

"If you combine the biomass of marine protists or marine viruses, that biomass is much greater than all the whales combined," Stepanauskas said. "The larger organisms that we see with the naked eye … they totally depend on the microscopic organisms" to send nutrients up through the food web.

Finding that viruses not only infect cells but could be viewed as a critical node in the food web represents "a different way of thinking," he added. By eating viruses, protists could send ripple effects through the entire marine ecosystem, both by limiting the number of viruses available to infect bacterial cells and by shuffling nutrients from viruses to higher levels of the food web, Brown said.

Originally published on Live Science.