How scientists are tackling methane emissions with killer viruses and seaweed diets

A cow's gut is an utterly alien world. Within the bovine digestive tract, dozens of organisms jockey for position, digesting and fermenting the grass and feed that passes through. Some of these microbes convert sugars into other molecules, others hoover up carbon dioxide and hydrogen and, as a result, produce methane. 

Cows, and other ruminants, belch out that methane -- a particularly troublesome problem on a warming planet. Methane is a potent greenhouse gas, with even more warming potential than carbon dioxide. The vast majority of methane emissions come from human activities like burning fossil fuels and via consumer waste, but ruminant emissions are a significant contributor, accounting for about 15%. 

Fortunately, the methane-producing microbes within the gut are themselves "food," hunted by even tinier enemies: viruses. 

The viruses land on the microbe, like a NASA rover landing on Mars, pierce the organism's exterior and inject their own genetic code. As part of this process, they destroy the microbes. Scientists believe they could ally with the viruses to control the methane-producing microbes, or methanogens, in the guts of livestock or synthesize new compounds that diminish methane emissions. And that's not the only potential ally they've turned to.

Researchers are also investigating the potential of algae to neutralize methane in the gut. Introducing small amounts of red seaweed to stock feed reduced methane emissions by about 80%. Developing mitigation strategies like these could cut agricultural methane emissions without harming the animal's overall health.

As world leaders, activists and academics meet in Glasgow, Scotland, for COP26, the UN's premiere climate change conference, CNET Science is examining some of the technological advances being developed to help tackle the climate crisis. While technology might help us adapt or mitigate the effects of climate change, alone it's not a solution to the problem. Drastic reduction in carbon emissions is required for the world to limit global warming to 1.5 degrees Celsius by the end of the century -- the chief goal of the 2015 Paris Agreement.

Nevertheless, researching and developing new technologies will enable more tools to be added to the climate change toolkit. The microbe-murdering viruses that naturally dwell within a cow's gut may be one such tool. Algae, another. So how can we use them?

It's not a phage, it's a lifestyle

Life is divided into three "domains." Eukarya, which includes everything from mushrooms to frogs to cows and humans, contains only a tiny fraction of all organisms on Earth. It's dwarfed by the other two domains: bacteria and archaea. 

These two domains consist of all the single-celled microbes, invisible to the naked eye, that have colonized practically every corner of the planet. Bacteria and archaea look similar under a microscope, but they differ in the way their cell walls are constructed.

Archaea are found in some of the most extreme environments on the planet -- some species thrive in the boiling waters near hydrothermal vents, while others can withstand extreme levels of ionizing radiation. A cow's gut isn't quite as wild as some of these environments, according to Rosalind Gilbert, at Queensland's Department of Agriculture and Fisheries, but it is an unusual environment filled with a diverse array of microorganisms.

The archaea are the chief methane production factories. They take up carbon dioxide and hydrogen produced by the other bacteria (and fungi) and spit out methane. This process can see between 2% and 12% of energy in the feed lost -- that's energy that could be converted to protein to help a cow bulk up or to milk for dairy products. Destroying the methane factories or preventing them from operating means the cow gets more energy from its feed and releases less in the way of greenhouse gas emissions.

And that's where the viruses come in. "Wherever you have bacterial populations, you'll have viral populations associated with them," says Gilbert. It's the same story for archaea. Viruses love to hunt them too.

Viruses that attack bacteria and archaea are known as "phages," from the Greek "to devour." Identifying the phages in a cow's gut that naturally attack the methanogens would provide a unique way to reduce methane emissions. 

Gilbert recently led a search for phages in a cow's gut, but says it was a difficult project because the microbes the viruses feed on are hard to grow in a lab. Unfortunately, her team was unable to locate any phages, but, she says, it could be possible in the future to find viruses that will infect and burst the archaea open. 

Examining the DNA of these phages may yield even better results.

A book within a book

Viruses that infect archaea are some of the most poorly understood microorganisms on Earth. Only a few dozen archaeaphages that attack methanogens have been discovered and described. Thanks to leaps in DNA sequencing techniques over the past decade, scientists are beginning to learn more about them -- even if they can't find them under a microscope.

Sometimes when an archaeaphage infects a microbe, it integrates into the organism's DNA and leaves behind a fingerprint of its existence. If you think of DNA like a book, it's as if the phage copy-pasted its own book inside the archae's; a copy of The Sorcerer's Stone inside The Goblet of Fire. This copy of DNA is known as a prophage.

Researchers can work backward and study the prophage to identify proteins and enzymes that might be used to attack the microbe's outer membrane. Gilbert says it's easier to find the viral enzymes that break open methanogens rather than finding the viruses and cultivating them to do our bidding.

A search for enzymes has already yielded positive initial results. 

One research group, from New Zealand, was able to isolate an enzyme that can burst open methanogens and place it inside a nanoparticle. When the nanoparticle was delivered to cultures of methanogens in the lab, it was able to inhibit methane production. Notably, the proof-of-concept work showed the enzyme had broad effects against different methanogen species. 

"It hasn't been developed into something that can be delivered into cows right now," says Gilbert.

Seafeed

Something that is already being delivered to cow feed comes fresh from the sea. 

In mid-2020, scientists showed that adding small amounts of red seaweed, Asparagopsis taxiformis, to cow feed reduced methane emissions by up to 98% -- without any negative health effects. 

Another study, published in the journal PLOS One in March 2021, showed a reduction of methane production in beef steer of more than 80%. The trial took place over three weeks, and the microbial communities didn't appear to evolve any resistance to the seaweed.

There are some significant advantages over the use of natural viruses or viral enzymes, too. You don't need a laboratory to make it, and it's common throughout the tropical climates of the world, limiting carbon-intense supply chain movements. Companies like FutureFeed, set up by Australia's chief scientific body, CSIRO, in 2020, are already trying to establish the seaweed supply chain.

The seaweed contains a sweet-smelling chemical, known as bromoform, that blocks the methane production pathway in archaea and, in culture, has been shown to reduce the abundance of methanogens. This also helps to free up carbon dioxide and hydrogen in the gut, which provides energy for other microorganisms and may even help the cow bulk up. "It is energetically beneficial, because instead of losing the carbon, they're using it themselves," says Gilbert.

Importantly, when tested in beef cattle, the seaweed additive didn't change the meat quality or the sensory properties of the steaks -- a win for both farmers and consumers. 

However, one of the key questions to be answered is whether the bromoform released in the cow's gut can make its way back out and into the atmosphere. Bromoform can become an ozone-depleting substance, so calculating its potential effects on the atmosphere will be important before farmers make a definitive switch to seaweed.

Another compound, known as 3-nitrooxypropanol (3-NOP), produces a similar effect in ruminant animals, but it has a more modest reduction in emissions and may affect milk production and fat content. Research into both is ongoing.  

Control the methanogens

It's likely that by 2050 there will be an additional 2 billion people living on the planet. Those extra 2 billion stomachs will require food, and, as developing nations like China and India, continue to prosper, demand for meat could rise by almost 75%.

It's a simple equation, as it stands: More meat means more methane. 

The alien world within a cow's gut provides an opportunity to help decouple this rise in meat production from a rise in methane. In recent decades, scientists have explored the wildlife that call the alien world home. Understanding the killer viruses that attack microbes and the discovery of a potent methane-inhibiting seaweed are just two ways we're learning to counteract the cow burp.

But alone these advances will not be enough to prevent the worst effects of climate change. We may still need to reduce meat intake, increase the efficiency of livestock feed, improve land use practices and maybe even up the amount of synthetic meats, from places like Impossible Foods, that we include in our diets. 

If we can't control the methanogens and don't drastically curb our carbon emissions, it could be our world that becomes ever more alien -- hotter, drier and a lot more extreme.