Viruses can be delicious as well as deadly

Now that we’ve been held hostage by a virus for seven months that feel like seven years, many of us could use some good old-fashioned retribution. Well, it turns out there is a satisfying place where the viruses are the ones that have to worry about social distancing, and that place is the ocean.

In seawater, viruses massively outnumber cellular life. There are an estimated 1030 virions there. Their victims are usually bacteria or other microbes. Every second this viral swarm infects 1023 such creatures, killing 20 percent of the ocean’s microbial biomass each day (ocean microbes reproduce so quickly and often that they maintain an equilibrium nevertheless). It’s hard to imagine such a horde could escape the culinary attentions of everything in the sea.

Viruses also have some features that make them potentially appealing entrees. Compared to cellular life forms, they are rich in phosphorous and nitrogen, making them nutritious as well as abundant little nibbles.

Yet it’s long been thought marine viruses serve only one function: killing. Like the sludgy recycling pit in Waterworld, their role has been seen by ecologists as “viral shunt,” a fancy way of saying viruses are good at converting living creatures into drifting bits of the “pool of dissolved organic matter.”

But a recent report in the journal Frontiers in Microbiology suggests the reverse can also occur: viruses are microbe chow.

Until now, I had never considered viruses as a potential foodstuff, and apparently, few scientists had either. Although at least five studies had suggested that microbes may prey on viruses, until this most recent report, no one had followed up to discover just how widespread or important the process actually is.

A team of American and Spanish scientists finally decided to examine whether grim reaping was truly viruses’ only function, and to what extent any alternative was the case, by screening the cells of marine microbes for associated viral genes.

The microbes in question were not bacteria or archaea, the simplest cells. Rather, they were protists: tiny life forms that—similar to their much larger cousins known as plants and animals—have complicated cellular furniture called organelles that house DNA, produce energy and do all sorts of other jobs.

This team analyzed a variety of protists from water samples from the Gulf of Maine and the Mediterranean Sea. Viral genes were detected alongside 51 percent of protist cells from the gulf and 35 percent from the sea.

Two groups, the Picozoa and the Choanozoa, were always found associated with viruses, and contained many more viral sequences per cell than other groups.

Though obscure to humans, choanozoans and picozoans are important and abundant in the ocean. Picozoa are the size of bacteria, minuscule even for protists. These creatures, in spite of being prolific enough to make up half of the biomass in nutrient-poor coastal waters, were completely new to science as of 2007.

Choanozoa, also called choanoflagellates, are the closest living relatives of animals and sport a jaunty collar and tail with which they both move and capture prey. They too are tiny, yet choanozoa are estimated to filter 10–25 percent of coastal surface water each day, a staggering sum.

In this study, choanozoans averaged an incredible 28 viral sequences per cell; picozoans 5.7. However, as only 22 out of 1,698 protist genomes detected belonged to these two groups, these results are certainly suggestive but by no means definitive.

What could explain the presence of these viruses in the many protists studied? One might expect that if they were parasites rather than supper, we would observe a wide variety of sequences for targeting many potential hosts. If they were food, on the other hand, we might expect just a few sequences as grazers and predators indiscriminately gobble the most abundant viruses.

In this study, most of the viruses detected were nearly identical, few were specific to particular protists, and many infect only bacteria: bacteriophages and gokushoviruses. Also detected was a new and somewhat mysterious group called CRESS DNA viruses, whose hosts are diverse. These too had nearly identical sequences.

To assume near-identical viruses were infecting all the cells studied in this report would imply that some viruses are capable of infecting organisms from different phyla, the taxonomic rank just below kingdom, the authors say. No known virus can do this.

What are some other alternatives? It’s possible the viruses inserted themselves into the protists’ genomes, a feat that the chickenpox virus is famous for (it can reemerge years after the initial infection as shingles). Many other viruses can end up as permanent residents of their host’s genome, which from the viral perspective is ideal as it confers immortality without the continual bother of trying to find a new host. But the near-identical sequences detected once again argue against this, because random mutations in viruses isolated within particular genomes should result in a variety of sequences.

Perhaps the viruses ended up in the protists because they were eating bacteria that happened to be infected by viruses. But many of the protists contained viral genes without any bacterial genes. It’s also possible the viruses were randomly assorted into the sample wells along with the protists. But the fact that some protist lineages were found with many more viruses than others seems to argue against that.

Perhaps there’s something about the surfaces of Picozoans and Choanozoans that makes them especially sticky to viruses. But the way these protists eat makes viral ingestion more likely, the authors argue. They are suspension feeders: they eat whatever they can swallow that is unlucky enough to bump into them. Since previous studies have shown choanozoans and picozoans are certainly capable of consuming viruses, their universal presence and abundance suggests that is exactly what the protists are doing.

Choanozoans and Picozoans may not be unique in their eating habits, either. Several other protist groups in this study also contained more viral sequences than would be expected by chance, but because these other protists feed in many ways, the authors refrained from making inferences about the viruses’ presence.

In retrospect, it’s not entirely surprising that massively abundant, defenseless, drifting bonbons of protein and nucleic acid would be scarfed up by something. A paper also published this year in Scientific Reports even showed that marine sponges were extremely efficient at removing viruses from seawater and concluded it was possible they too are eating viruses.

Protists … sponges … how many more creatures out there have food pyramids that include viruses? Why didn’t we know this? And how can we get in on the action?

The idea of viruses as food for anything is a bit mind-warping, but it’s also a rich source of schadenfreude at a moment where humans could really, really use some. While we are at the undisputed mercy of one virus, it’s satisfying to think about legions of others meeting their ends in the gullet of a living, breathing cell.