20,000 Viruses Under The Sea: Mapping The Ocean’s Viral Ecosystem

IRA FLATOW: This is Science Friday. I’m Ira Flatow. Later in the hour, we’ll talk about a small town with a big cannabis business and take a closer look at medical marijuana. But first, you know the oceans contain many mysteries, right? And every month, it seems, explorers find a new sea creature or two lurking in the deep. And in fact, earlier this year came word of an incredible treasure trove of new species– I mean more than 5,000.

It came with a surprise. They weren’t octopuses or angelfish or anemones. Instead, these researchers have found viruses. And not just any viruses– RNA viruses. That’s the same type that our friend SARS-COV-2 falls into.

Here with more about the significance of this viral motherlode is SciFri’s Christie Taylor. Hi there, Christie.

CHRISTIE TAYLOR: Hey, Ira.

IRA FLATOW: You know, I was a bit shocked to hear how many RNA viruses they found. Should we be surprised that there are so many viruses in the deep blue sea?

CHRISTIE TAYLOR: Step one, Ira, I would say don’t panic. We’ve known about viruses in the ocean for a pretty long time. DNA viruses– that’s the other major type– have been studied for decades. But the RNA viruses in the ocean are new and exciting because they’ve been so hard to pin down. The new research is the result of many, many water samples and some advanced machine learning tools to sort out all the RNA sequences these researchers found.

IRA FLATOW: Fair enough. But what are all these viruses doing down there? Why get so excited about viruses?

CHRISTIE TAYLOR: That’s a really great question, Ira, especially given how much our lives have really been changed by just one virus in the last three years. I talked to Dr. Ahmed Zayed about this. He’s a microbiologist and research scientist at Ohio State University.

And what excites him about all these viruses is something that has nothing to do with us, but rather the way viruses may be affecting the ecosystems when they infect plants and animals in the ocean. It may even connect to climate change at the end of the day. And here he is explaining that.

AHMED ZAYED: So we know about DNA viruses that they can manipulate their hosts and can change the element cycling, so the rates of element cycling in the ocean. One of these elements is carbon, which is really important because of how essential the ocean is for regulating the climate and for basically sucking carbon dioxide from the atmosphere.

So that’s for DNA viruses. The RNA virus discovery was lagging for multiple reasons. One of them is that the tools were not there, actually, to see RNA viruses with enough confidence, and also because of the nature of these viruses. So these viruses are made of RNA, which is less stable in the environment than DNA. So DNA viruses and their particles, they can stay for longer than RNA viruses. So that is kind of why, also, it was hard to see RNA viruses in natural samples as compared to DNA viruses.

And we had an amazing opportunity to explore these viruses in the ocean because we had this amazing data set that was collected by the Tara Oceans experts. We had samples from the surface down to 1,000 meters deep, covering large geographic range. And it holds the answers for a lot of interesting questions.

CHRISTIE TAYLOR: So you took this data set, which involves sampling seawater from dozens of locations all over the planet– deep water, shallow water, stretching from the North to the South Pole. And you found lots and lots and lots of RNA viruses. Tell me about the abundance of what you found.

AHMED ZAYED: So we started first by looking at all of the RNA that is coming from the plankton in our samples. So we had different eukaryotic groups, and also, we had bacteria. And we looked across all of these. And we basically tried to distinguish between the RNA that belongs to the host and the RNA which belongs to the virus, which is representing the viral genome.

And we ended up having around 5,500 of these species ranked clusters for RNA viruses. That’s an incredible amount of viruses to find.

CHRISTIE TAYLOR: Yeah, it sounds like it.

AHMED ZAYED: I mean, to put things into perspective, we know that there are around 3,500 virus species that are deposited in public databases. So that was an incredible number to see.

CHRISTIE TAYLOR: Are you talking about 3,500 ocean viruses in public databases?

AHMED ZAYED: All RNA viruses, that’s correct.

CHRISTIE TAYLOR: So you found more than double the known number of RNA viruses.

AHMED ZAYED: Yeah, relative to what is deposited in public databases. Yeah. So that was an incredible number to see. And we started to explore the diversity of these species ranked clusters at different taxonomic levels. And our viruses were not just so many, but they were really diverse. So they extended– we proposed five new phyla on top of the five that were already known.

CHRISTIE TAYLOR: A phyla as a whole taxonomic category of organisms. For people who maybe don’t understand how different that is, how does that compare to things like, we found another variant of COVID-19, for example?

AHMED ZAYED: I would say if we would look at the phyla within the kingdom of Animalia, they can be as different as arthropods from humans.

CHRISTIE TAYLOR: And arthropods include ants, for example.

AHMED ZAYED: Yeah, exactly. Yeah.

CHRISTIE TAYLOR: Well, then just looking at where you found these species, are there some parts of the ocean that seemed to have more virus than other parts of the ocean?

AHMED ZAYED: So we actually looked at the abundance of these viruses across all of our samples, not necessarily how abundant viruses in one ocean basin versus the other, but rather at how abundant different viral groups– so these virus phyla– across ocean basins.

And to our surprise, we found that two of the novel phyla that we have suggested in our study to hold the most abundant viruses, on average, across the global ocean. So one phylum, which we called Taraviricota, was on average the most abundant across the temperate and tropical waters. And the other phylum that we also proposed, Arctiviricota, the viruses of this phylum were also, an average, the most abundant across the Atlantic-Arctic part of the ocean.

That was also surprising, because there have been studies for RNA viruses in the ocean before. They were focusing on specific oceanic regions or just focused on specific ocean organisms. All of these previous studies never have seen the viruses that we found in our study before. So it was shocking for us to find such abundant viruses flying under the radar for so long.

CHRISTIE TAYLOR: Mm-hmm. And what I think I’m hearing you say is that the most abundant viruses are ones we’ve never actually seen before.

AHMED ZAYED: Yes, that’s correct.

CHRISTIE TAYLOR: That’s incredible. One question I feel like this very much begs– people are going to hear new viruses found in the ocean and maybe panic a little bit because we think about COVID-19 as a new virus that emerged from an animal host. These are not viruses that we need to worry about. Is that correct?

AHMED ZAYED: Most probably, yeah, because the gap is really big between things that are– the set of hosts that we explored in the ocean and humans and primates. But also, some of these viruses infect multicellular organisms, and some of them infect fish and infect larvae. So there are multicellular organisms that can be infected by these viruses as well. And they can have several levels of ecological impacts. It’s not just about cycling elements and changing the rate of the biological carbon pump, for example.

CHRISTIE TAYLOR: Well, yeah, and you keep mentioning– you’ve mentioned carbon a couple times now. And I did want to get back to this idea that viruses are part of ecosystems. They’re very numerous. They may be very small, but they are in all of these cells in these ecosystems in the ocean. Can you talk a little bit more about what we know about the ways these viruses may be shaping their ecosystems?

AHMED ZAYED: So our knowledge is mainly based on DNA viruses. We know about DNA viruses that they can influence their hosts in several ways. And that can really impact the carbon cycling in the ocean.

We know that some viruses can carry genes that we call auxiliary metabolic genes. They are similar to the metabolic genes that the hosts carry. And they can change the rates of this process. So you can imagine that they can slow down or speed up carbon transformation once it takes over the host’s metabolism. So that’s one way.

Other viruses can just infect the host and lyse the cells so it releases its content. So all of that carbon that was fixed inside the cell is now available for other microbes that can respire. So it gets released back to the atmosphere as carbon dioxide.

Other viruses, more interestingly, were found to blow up the cells and form a sticky material that actually makes bigger aggregates. So all of these blown-up cells stick together, and these bigger aggregates and heavier aggregates sink to the ocean. So it’s actually helping the carbon to get exported to the deep ocean. This is really important as a process because ocean plankton are responsible for exporting around 25% of the carbon dioxide that is emitted by humans. So you can imagine the central role of viruses, potentially central role of viruses, for gluing these cells together and making the export of these aggregates to the ocean easier.

CHRISTIE TAYLOR: So what I think I’m hearing you say is that depending on the virus, it could make the carbon that is within the cell get to the bottom of the ocean faster, as opposed to being released into the atmosphere.

AHMED ZAYED: Yes. Yes, that’s correct. So in 2016, there have been a study in Nature that specifically looked at the contribution of different planktons to the process or the association with exporting carbon to the deep ocean. And to our surprise, we found that viruses were actually the best predictors of carbon export across the global ocean.

CHRISTIE TAYLOR: What other questions does this research create for you? And is answering them going to require more boats full of seawater samples?

AHMED ZAYED: Ah, so yeah. So there are so many different questions. So we are also trying to understand what is the ecological footprint of these RNA viruses through the lens of the hosts that they infect, but also by just looking at how the virus communities form, what are the environmental parameters that dictate the assemblage of these different viral communities. There are so many things that are still unanswered.

And we might be able to answer some of these questions using the data sets that we have created and now made public to the entire scientific community. And some other questions would require us to collect more samples or sequence them differently or develop new tools to try to answer some of these new questions.

CHRISTIE TAYLOR: Well, good luck with that. And thank you again so much for joining me on the show.

AHMED ZAYED: Thank you so much, Christie, for having me.

CHRISTIE TAYLOR: Dr. Ahmad Zayed is a microbiologist and research scientist at the Ohio State University. He joined me from Columbus, Ohio.

IRA FLATOW: So there’s a lot more to viruses than disease, it turns out. Thank you so much, Christie.

CHRISTIE TAYLOR: Thank you, Ira.

IRA FLATOW: SciFri’s Christie Taylor.

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