Deep Dive: Could ocean viruses be used for carbon capture?

Interviewees:

Guillermo Dominguez-Huerta, researcher at the Oceanographic Center of Malaga

Kim Thamatrakoln, assistant professor and phytoplankton molecular eco-physiologist at Rutgers University

Dave Scanlan, professor of marine microbiology at the University of Warwick in the UK

Matt Sullivan, a professor of microbiology from Ohio State University

Christopher Preston, a professor of environmental philosophy at the University of Montana

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Transcript:

Ok, so you’re at the beach. It’s a gorgeous day. The sun is warm. The sand feels soft underfoot.

Cool water rushes up around your ankles as you wade towards the waves.

You reach down and scoop up some salty seawater.

In that handful, there might be a few grains of sand, some floating bubbles.

And, something else that you won’t be able to see: millions of viruses.

Guillermo: It’s huge, the amount of viruses you have in a handful of sea water or a mouthful of sea water. Imagine you’re at the beach and you’re surprised by a wave. You have more or less 50 million viruses, s o it's huge. It's like the most abundant biological entity of the planet, really.

The oceans are teeming with them. By some estimates, a liter of sea water in coastal areas holds around 10 billion viruses – more than the number of people on the planet… And in the whole ocean?

Guillermo: We think it's about 10 to the 30 virus particles in the whole ocean.

Guillermo Dominguez-Huerta researches marine viruses at the Oceanographic Center of Malaga, which is part of Spain’s National Research Council. And 10 to the 30, by the way, is a number equal to 1 followed by 30 zeroes.

Guillermo: That means that if you put one virus, physical virus, one after another, forming a line, you could form a distance of 69 galaxies - galaxies the size of our galaxy. That means the number is huge, obviously. There is no way in the mind how many viruses, how is it possible that so many viruses can fit in a planet? It's possible because they are tiny. So, that's the estimate we have: 10 to the 30.

But before you turn and flee from the waves, vowing never to set foot in the sea again, you should know… these viruses aren’t after us.

Guillermo: That's what people tell me every time I tell them about my work - that the ocean is full of viruses. They all say: we are going to die because we cannot consume water or anything. It's not at all like that. It's just those viruses, marine viruses, are not interested in humans. They are interested in the things you can see in the marine environment, they’re not worried about humans.

They’re not even interested in dolphins or fish. Their targets are mainly microbes – like bacteria and phytoplankton.

Marine viruses are infecting these microorganisms all the time. In fact, about a third of the microbes in the ocean are infected by viruses right now. There’s a mind-boggling number of infections every second. To be exact – around 10 to the 23 infections. So a 1, followed by 23 zeros - there are this many infections every second.

These predator-prey interactions are happening out of sight, in our oceans. But so what? Why should we care?

Kim: I think it’s critically important to understand how viruses are mediating that sort of life and death in the ocean, because that is the base of the carbon cycle, the base of the food web, and sort of the beginning of the carbon cycle in the ocean.

Viruses are pretty powerful. Their abundance means they’re influencing the entire marine eco-system, in ways that scientists are still trying to understand.

Findings suggest these invisible agents can alter the flow of carbon in the ocean. And some researchers are now investigating the possibility of using viruses to engineer microbial communities in the ocean, to boost carbon capture, and help fight climate change. But is this a good idea?

This is Living Planet. I’m Neil King.

Oceans are a major carbon sink. They absorb around 30 percent of our carbon dioxide emissions from the atmosphere every day and capture 90 percent of the heat generated by those emissions. This means the oceans are big buffers against climate change. And without them, global heating would be a lot worse.

The oceans are so great at sucking up CO2 and regulating our climate because of something called the biological carbon pump.

This pump moves carbon from the atmosphere to the depths of the ocean, where it can be stored for hundreds or thousands of years, or longer.

The stars of this process are microbes called phytoplankton.

These guys use CO2 in ocean surface waters to photosynthesize, much like plants and trees on land. And they release oxygen: they actually provide us with 50% of the oxygen in the atmosphere.

Kim: So, we like to say that every other breath you take is oxygen produced from an organism in the ocean, which, you know, would be phytoplankton.

Kim Thamatrakoln is an assistant professor and phytoplankton molecular eco-physiologist at Rutgers University in the US.

Kim: So, they take up carbon dioxide and they use that in photosynthesis to produce energy and organic matter. And so, by doing so, we call that fixing carbon. So, they take CO2 out of the atmosphere and sort of process it to make their cell parts.

When these phytoplankton die, they can sink to the sea floor.

Kim: So, we're talking about thousands of meters, that carbon that they have in their cell parts can be carried with them and we call that sequestering carbon in the deep ocean.

Ok, so these microbes are there, going about their business, sucking up CO2 and helping to regulate the climate of a planet. But, there’s a predator out to get them: Viruses.

Most of the time viruses are inert particles, drifting along in the current. Until bam! They come into contact with, say, phytoplankton or bacteria. Once they infect a living cell, they spring to life, and begin reproducing like crazy.

Guillermo: Viruses, we know that they do at least three things in nature. They kill their hosts. Most of them, but not all of them, have to kill their host in order to propagate and form new viruses.

The second thing viruses do is transfer genes from one host to another, like genetic engineering.

Guillermo: So, you can transform your host if that happens… and then you have a third impact, which is actually pretty important, which is the metabolic reprogramming.

So, viruses can hack their host’s metabolism, reprogram how it processes energy, and redirect that energy toward the reproduction of more viruses.

These three interactions can have different results, and they can also influence the ocean’s “carbon pump.”

Here’s one example of how: When viruses kill their microbe hosts, these microbes burst open – releasing carbon and other matter that’s too light to sink to the sea floor. So instead, it remains on the ocean’s surface, where it can be breathed back into the atmosphere, and contribute to further warming.

Guillermo: By this hypothesis, just a hypothesis, viruses let's say push the biological carbon pump into that direction, back to the atmosphere, because that dissolved organic carbon can easily be transformed again to CO2 by other bacteria and then passed again to the atmosphere. So, it prevents the carbon export to the bottom.

It’s important to point out that a lot is still unknown when it comes to the role viruses play in the oceans. Scientists have only started to seriously study marine viruses in the last 25 years or so, and Guillermo says they’ve not even begun to scratch the surface.

Guillermo: So, I just want to say that viruses are very diverse and very abundant on this planet. And we environmental virologists or virus ecologist as you want to refer to us, we are very much at the beginning because we haven't discovered even the 1%. We are very far away from knowing the 1%. So, the role, the impact of viruses on the ecosystem, we are very much at the beginning, we are at the infancy of learning this. Many things are going to be discovered from this topic for sure.

One discovery, by a team of scientists in the UK, showed that viruses infecting phytoplankton were also preventing these microbes from trapping, or “fixing,” CO2 in their cells.

They found that the viruses – in this case ones they took from the English Channel and the Red Sea - were hijacking the host’s metabolism, encoding genes involved in photosynthesis, and directing that energy toward creating new viruses instead.

Dave: The viruses think, ‘well, actually I'd rather use this energy to make more of myself,’ which basically means to replicate its DNA and make proteins for its own needs. And so that's why we think these viruses inhibit CO2 fixation in these cells.

This is Dave Scanlan, he’s a professor of marine microbiology at the University of Warwick in the UK. And he was an author of the study that came out of the research.

Dave: And given the abundance of these organisms, you know globally, they are really major, major phototrophs on planet Earth. And if you think of the number of infections that are going on at any one period in time, if CO2 fixation is stopped in those organisms, that's a substantial amount of carbon that's not being fixed.

It's tricky to calculate the exact impact, Dave says, because it’s hard to know how many phytoplankton would be infected at any one time in the ocean. But his team gave a wide range, estimating that these viruses are preventing the fixation of between 20 million metric tons and just over 5 billion metric tons of carbon each year.

Dave: This is something that’s happening naturally, in the system, all of the time. So, we're currently trying to understand how that happens, which is getting quite complicated. I always think of the ocean as like a car engine and we're trying to figure out, you know, you wouldn't drive a car without understanding how the engine works. And so, we're trying to understand how this ocean engine really works. Clearly viruses do impact systems in a way that we are only really beginning to think about.

They’re currently trying to work out which virus genes are stopping the microbes from locking down CO2.

Dave: And ideally what you'd want to do is to literally what we call make mutants of those genes. We're effectively trying to knock these genes out in these viruses so that we can then attribute the phenotype, as in its inhibition process, with these genes.

We all know clearly about COVID, you know, clearly there are mutations. You know things change over time because you know they're infecting hosts that also change. And so, it's like an arms race. So clearly that's happening anyway. But as a scientist, you know, we're curious about how things work. And so, to be able to ultimately attribute a function, we need to do this. And so that's one of the things that the guys in my lab are trying to do.

Viruses appear to be influencing microbes shuttling carbon around the oceans in a range of ways. And these interactions may have a different impact, depending on which species of phytoplankton or virus are involved. We’ve just heard about two ways viruses can stop carbon from being sequestered. But, as Dave said, it’s complicated.

Because scientists have also observed viruses having the opposite effect, and accelerating the carbon pump. 

Kim: We're starting to look at ways that viruses might, when they infect, might elicit a response by the host that would potentially make the host more likely to sink. And so that would be sort of facilitating carbon sequestration.

Kim says that they’ve seen phytoplankton in the lab increase the size of their cell wall after being infected, making themselves heavier and more able to sink to the sea floor.

Another way they’ve seen phytoplankton deal with an infection isn’t so different to how we humans might respond.

Kim: And so, one of the things they do is produce like a lot of sticky material. It's kind of like when you and I get sick, we get kind of mucusy, we get a little sticky. So, the same thing with phytoplankton, they can produce these exopolymeric substances that make them sticky.

And that stickiness means they trap particles around them, including carbon, forming a bigger clump that is heavier and can also sink to the deep ocean.

Climate change has caused ocean temperatures to rise. That’s slowing down ocean circulation that allows surface water enriched with CO2 to move to the ocean depths. It’s also making it harder for seawater to absorb carbon dioxide from the atmosphere.

But once CO2 does end up in the ocean, its fate ultimately depends on marine microbes, like phytoplankton. As well as the viruses that infect them.

Carbon might end up sequestered, buried in the seabed for millennia. Or maybe it’ll be released back into the atmosphere.

But what if it were possible to harness viruses to lock away more carbon? To help fight climate change?

That’s an idea that’s being explored by Matt Sullivan, a professor of microbiology from Ohio State University.

Matt: We’re trying to use viruses to alter the naturally occurring microbes. The oceans are already acidifying and suffering from warmer ocean temperatures due to anthropogenic or human produced carbon dioxide in the atmosphere. When carbon dioxide from the atmosphere is absorbed by the oceans, that is what leads to acidification and that carbon dioxide in the atmosphere acts like a greenhouse and so it warms the surface waters of the ocean and that leads to stratification and that changes the microbiome already.

So, we've already shifted the ocean's microbiome. And so, what the virus angle here is, is can we use viruses to sort of tune back that microbiome, that native ocean microbiome, from this disturbed state back to a more native state and/or towards states that will produce carbon and forms of carbon that can be sunk out of the surface oceans.

The team in his lab has been creating a global catalogue of virus species in the ocean, and using a machine learning algorithm to pinpoint viruses that are most likely to enhance carbon capture.

They’re developing models to predict how it could look, say, to use these viruses to engineer or manipulate microbial communities to trap more carbon.

Matt: What's new and interesting now is that we can look at the microbial nutrient and energy fluxes. And what that does is it allows us to understand all the different forms of carbon that could be happening, and how carbon dioxide is transformed from one form into another. And what's exciting is that as those models become more sophisticated and experiments help us constrain those models, we're able to understand where in sort of metabolic network space, can we tune this carbon pump or speed up this carbon pump in a way that it might create carbon forms that end up in biomass and sink out of the water column or would get re-mineralized and released back into the atmosphere.

And what's particularly exciting for me is that as we start to do these on smaller scales or in large data sets, we're learning that viruses play a bigger role in sinking carbon than we thought that they might a couple of decades ago.

It’s very early days. Matt stresses that his team is laying out the science and testing the models’ predictions. It’s a long-term project.

Matt: These are difficult experimental measurements to make - complex communities could have thousands of different microbes and or viruses that are there. And they're all playing different roles and so we're trying to study these systems in their natural form or in situ, and it's really, it's a complex problem.

He says the idea has potential, but it’s not yet clear whether adding these viruses to the ocean could have unintended consequences.

Matt: As a scientist, you know, I think that the potential for this idea is quite high, meaning that I'm seeing more and more our ability to make metabolic predictions and to model these systems even though they're incredibly complex. And the part that's hard for me to predict is we don't know about the unintended consequences yet and models can make suggestions about what those might be, but we need to follow up on those to some degree to start to improve the models in a way that allows us to track and really trust those unintended consequences that are predicted.

The kinds of viruses that we'd be adding would infect bacteria and or Archaea, and so these are the small microbial forms of life which live in the kinds of wildlife that we normally think of. And so, I don't think that adding these microbial viruses will drastically impact wildlife.

The other part that's hard for me to say is you don't know how acceptable these kinds of approaches would be. If you're going to add viruses to seawater at any scale, what will the unintended consequences be and how will that impact systems, and particularly when a lot of this has to be done in international waters, where the rules of the game politically are complicated.

So, what do others working in this field make of the possibility of engineering the ocean’s microbiome to combat climate change?

Guillermo: I'm not opposed to using viruses for any kind of environmental application. That would be too much. I would say that I'm skeptical to use viruses for geoengineering. I mean using viruses for changing big characteristics of Earth, you know, like the amount of CO2 we have in the atmosphere, nothing less. So, I’m a bit skeptical.

Guillermo used to work as a research scientist at Ohio State University, and he said he has his doubts. One issue he raises is that a manipulated marine microbiome may not have much impact if warmer waters mean the ocean can’t take up as much CO2.

Guillermo: So, if the ocean is not in the physical state to absorb more CO2 or oxygen or anything, it won't, you know what I mean? And right now, this is the situation that we have.

And then there’s the fact that viruses evolve and mutate. So, would it even be possible to control or manage them in an environment as vast as the ocean?

Matt: Viruses, like other forms of life, can evolve and mutate. I think what we tend to think of, though, are viruses that infect us or infect animals or plants. Those tend to evolve and mutate quite rapidly and that's because they're a different kind of virus. They’re RNA or single stranded DNA viruses, which, for genetic reasons, have an ability to mutate much faster than the kinds of viruses we're proposing to work with. Most viruses that infect the bacteria that we would be trying to dial up or down are double stranded DNA viruses and those tend to evolve much, much slower. We're using naturally occurring viruses and those would mutate as they do in a natural system. And so, they may jump from one host to another, but it would be a pretty closely related host. And these would be for bacterium to bacterium, as opposed to into the kinds of wildlife that we might be more worried about.

Kim Thamatrakoln from Rutgers University points out that we’re already using viruses in the medical field, for example with viral therapy and drug delivery systems. And that using them for environmental problems is worth studying.

Kim: Viruses have been, you know, useful for human health purposes and whether viruses can be useful in combating climate change, I think it's worthy of investigating. I think, you know, I mean the situation with climate change is very real and very dire. Something dramatic is going to have to happen for us to solve it, it’s not gonna be these little incremental changes, like something massive is going to have to take place in order for us to reverse the impacts of climate change. And I don't think that gives somebody, you know, carte blanche to just go and do whatever they want. But I think it's worth studying and trying to understand from a basic science point of view.

Guillermo: I mean my feeling is that the situation is getting so bad environmentally that we're going to try almost everything. That's I mean, of course, with the policies and regulations we have in every region of the planet. But I think we're gonna try many things, even if we're not sure if they're gonna work. I think we're gonna try.

We’ll be right back after this message.

The ocean makes up 70% of the planet and can store more CO2 than the atmosphere and land. So, it’s no surprise that there are a number of projects under way to try and boost its carbon capture potential. These range from planting mangroves and seagrasses in coastal areas, to changing ocean chemistry. 

Some proposed options include fertilizing the ocean surface with iron to stimulate phytoplankton growth, and adding alkaline substances to the water to allow more CO2 to be absorbed. There’s also artificial upwelling and downwelling – which involves using pumps and tubes to bring water from deeper zones to the ocean surface and vice versa to promote carbon draw down. There are others too, but in many cases, these technologies are still being tested, and it’s not clear whether they can be scaled up, or what deploying them could mean for ecosystems in the open ocean.

It's also far too early to say whether ocean viruses, one day, could play a bigger role in carbon sequestration. But even if the science is eventually worked out, and any risks are addressed, does that mean we should interfere with nature?

Christopher: Even if you can make a strong case on scientific grounds, it's not obvious that systems that are this complex and systems that are shared systems are ones that humans should be meddling with.

That’s Christopher Preston, a professor of environmental philosophy at the University of Montana in the US.

Christopher: I mean, one of the lessons that we've learned is that there's a complexity to many biological systems that we don't appreciate. I like to think of some systems as being hypercomplex, and I would count the atmosphere as one of those systems. I would count the genome as one of those systems, and I would count the oceans as one of those systems. So, they're hypercomplex and even if you're fairly confident about the science, there is this question about whether humans should in fact be intentionally manipulating those hypercomplex systems. Now the counter argument to that obviously is that, well, look, haven't we already manipulated these systems? And it's true, that's what global climate change is, is a problem with an imbalance that we've created in a complex system. But that imbalance we created accidentally, and I think it's worth hesitating a little bit before saying, well, let's jump in with both feet and manipulate a complex system intentionally. I think we should be very cautious before doing that.

Christopher says that, given the role of viruses in the ocean’s carbon pump, it would be wise to study and deepen our understanding of them. At the same time, he describes the idea of using viruses to “tune” the carbon pump as a fairly “radical” one.

Christopher: It's not just a carbon removal type of minor tweak or small project. It is an ocean scale engineering project. I do think the idea that you could do this with 100% guarantee of avoiding any sorts of negative implications for ocean biology or ocean chemistry. This looks to me like an area where you couldn't provide that 100% guarantee.

He also stresses that any project that involves geoengineering in the ocean would have to be subject to a legal framework and governance protocols -- that can often take many years to work out.

Christopher: And so, that indicates that when you start talking about geoengineering in a different environment in the oceans, you’re going to have a long lag time before you would get in place particular rules and regulations. And I think it’s important to remember that lag time when you hear about a project right at the beginning.

The Intergovernmental Panel on Climate Change has warned that reducing emissions alone will not be enough to address climate change.

We know that oceans are getting warmer, causing rising seas and melting ice sheets. Elevated carbon dioxide levels have also led to ocean acidification, which has dire consequences for corals and crustaceans because it causes their skeletons to dissolve. But what about the tiniest of organisms like phytoplankton that play such an important part in our planet’s health?

Climate change is affecting them, too – and the way they respond to virus infections. But it’s an area that needs more study.

The microbial life-and-death interactions happening in the ocean are complex. And scientists are only at the start of figuring out what they could mean for the climate – and for us.

As for viruses…

Guillermo: Viruses, they really evolved fast and like this and they can overcome almost every challenge, let's say. So in any kind of world that we're living in, maybe there are not humans, maybe there are not many other kinds of species that we know today. But viruses will remain because they infect everything.