Microbes that silence methane – a natural climate fix for pig farms

Methane from pig slurry may seem to be a minor farmyard nuisance – but it is a hidden giant in the climate story. With a global warming potential 27 times that of carbon dioxide (CO₂), methane accounts for most of the greenhouse-gas equivalents released from livestock manure.

Worldwide, pig farming accounts for about 15% of ammonia emissions and up to 80% of farm-level methane emissions – a major hotspot for climate pollution.

At Aarhus University, researchers found a surprising ally – one that farmers already know from food production: microbes themselves. The same kind of microscopic life that creates methane in slurry can also be used to stop it.

“We thought, what if we could make biology control biology?” says Herald W. Ambrose, Assistant Professor at Aarhus University’s Department of Biological and Chemical Engineering, who led the experimental work. “If we could turn the microbial process inside the slurry against itself, we might silence methane where it starts.”

Together with Clarissa Schwab from Aarhus University’s Department of Animal and Veterinary Sciences, Herald W. Ambrose and his team added Limosilactobacillus reuteri – a bacterium normally used in food and probiotics – together with glycerol, triggering a natural antimicrobial system called reuterin inside the slurry that nearly stopped methane formation.

“This is one of the most underestimated climate hotspots in livestock production,” says Herald W. Ambrose. “In our experiments, methane emissions dropped by 70–95%, and we also saw less CO₂ and, in several cases, less ammonia. What we show here is basically microbes helping us control other microbes – a safe, scalable and realistic solution that fits into the slurry ecosystem.”

On a typical farm in Denmark, that kind of reduction could mean tonnes less methane from a single slurry pit each year – a small microbial tweak with an outsized climate effect.

From chemistry to biology

On most farms today, methane is curbed with chemicals. Acidification works – it slows the microbes down – but it also corrodes tanks, adds safety risks and hampers biogas production.

“We were hearing the same critique again and again,” says Herald W. Ambrose. “Chemical fixes work, but they are still chemicals. They do not adapt to the slurry, and they create new problems downstream.”

That frustration sparked a shift in thinking, so Herald W. Ambrose joined forces with Clarissa Schwab and her team in food biotechnology to test whether biology could regulate itself instead.

“We wanted a living solution that fits into the slurry ecosystem rather than fighting it,” Herald W. Ambrose says.

This was the first step toward an unexpected collaboration – one that would turn a waste problem into a microbial climate solution.

Why the problem lies beneath the pigs

Pig farming’s climate footprint does not arise from the animals themselves but from what happens underneath them. Beneath the barn floor, in the warm, less ventilated slurry pits, unseen microbial communities from pig droppings quietly exhale methane and ammonia into the air.

Most mitigation strategies today focus on acidifying the slurry with sulfuric acid, which stops microbial activity by lowering the pH. The problem is that acidification also brings corrosion, safety hazards and long-term soil effects when the slurry is used as fertiliser.

“It is not the pigs themselves but the microbes in the slurry tanks that generate the problem. They thrive without oxygen and convert carbon from manure into methane,” explains Herald W. Ambrose. “When you acidify slurry, you do not solve the problem; you move it. The sulfur content rises, biogas can be hindered and you add safety issues in handling corrosive chemicals.”

In search of cleaner options, Herald W. Ambrose and his colleagues spent years testing physical and chemical additives that could cut emissions.

“Our path was really a transformation,” he says. “We went from acidification to surfactants, to biosurfactants and finally to a better biological method.”

An accidental meeting sparks a new idea

That shift toward biology controlling biology began almost by accident. A departmental seminar brought together researchers from the sections of Environmental Engineering and Industrial Biotechnology. One of Clarissa Schwab’s postdoctoral researchers, Maria Florencia Bambace, presented a project on reuterin – a natural antimicrobial compound produced by L. reuteri. The poster caught Ambrose’s attention.

“We were initially sceptical,” Herald W. Ambrose recalls. “I did not think a probiotic bacterium could survive in slurry. But we decided to test it anyway, step by step – first with reuterin alone, then with the live bacterium plus glycerol – and that is when the whole idea came alive.”

Clarissa Schwab laughs at the memory. “This project started completely bottom-up,” she says. “No grand initiative, just a meeting at a department retreat at which two lines of research crossed. People said it would not work, but we thought, why not test it? Sometimes that is how real innovation happens.”

From that informal start grew collaboration that bridged two distinct scientific worlds – environmental methane control and microbial food preservation – united by one insight: if you can make microbes police one another, you may be able to clean up the world’s dirtiest climate emitter from the inside out.

Testing the probiotic fix

To test whether biology could indeed silence methane, the researchers recreated a miniature version of a pig slurry pit in the laboratory – mimicking the space beneath barn floors – and measured the gases escaping day by day.

“We recreated the slurry pit conditions in sealed laboratory reactors and continuously measured methane, CO₂ and ammonia,” says Clarissa Schwab. “The clever thing is that reuterin is formed directly inside the slurry – you do not have to make it first; the bacteria do it themselves.”

The team combined L. reuteri – a probiotic bacterium with a long record of safety in food production – with glycerol, a cheap by-product of biodiesel manufacturing. When L. reuteri consumes glycerol, it produces reuterin, a mix of powerful antimicrobial compounds that can disrupt methane-producing microorganisms. The scientists followed both the chemistry and the microbial communities inside the slurry over several weeks, tracking how the balance of gases shifted.

“We started by adding laboratory-produced reuterin directly – nothing happened. We did not stop there. We added both the microbe and the substrate simultaneously into the slurry, and that is when it worked,” recalls Herald W. Ambrose. “The simultaneous addition was the key step.”

Reprogramming the slurry ecosystem

In the experiments, the researchers compared different slurry types: fresh, old residual slurry from below the barn floor and bulk slurry collected from storage tanks. These represent the real conditions found on farms – where layers of partly decomposed waste build up and act as seedbeds for methane-producing microbes.

“Residual slurry is the inoculum holder for methanogens,” Herald W. Ambrose explains. “If you treat that layer – the material left in the pit after flushing – then whatever manure falls on top later will not have the methanogens ready to produce methane. That was the novelty of our design.”

“The goal was not a quick chemical knock-out but biological suppression that stays stable through the whole storage period,” says Herald W. Ambrose.

By the end of the tests, the team had established a simple, repeatable biological process: adding a safe bacterium and a small amount of glycerol could reshape the microbial ecosystem of pig slurry, cutting its emissions drastically – without acid, corrosion or complex handling.

Results that outperformed expectations

The outcome surprised even the researchers. When L. reuteri and glycerol worked together, gas readings on their monitors suddenly plunged – methane almost vanished. For a moment, the laboratory fell silent.

“In the best combination, we saw a 95% reduction in methane compared with untreated slurry,” says Herald W. Ambrose. “Even in fresh and aged residual slurries, we achieved around 70% to 80% reduction in methane emissions. Glycerol was consumed immediately – we detected reuterin intermediates within hours – and the suppression persisted for four weeks.”

In other words, the friendly microbe outperformed earlier natural fixes and worked almost as well as chemical acidification – but without the acid or corrosion. The researchers also found that ammonia and CO₂ emissions fell simultaneously – a rare combination of effects.

How the microbes did it

When the team examined the microbial DNA, they discovered why: methanogens – the microorganisms that form methane – were reduced, and the reactive compounds produced by L. reuteri interfered with their key enzymes, shutting down their metabolism.

“By the end of the experiments, we could hardly detect any methanogens,” explains Herald W. Ambrose. “Reuterin interferes with their enzymes, so they stop converting carbon into methane. Meanwhile other bacteria take over – the community reorganises.”

The results also held across all slurry types.

“In bulk slurry, we could barely identify methanogens; in fresh residual slurry, they were reduced but still there,” says Herald W. Ambrose. “This pattern shows that the treatment is robust under very different microbial starting-points.”

A stable, switchable biological control

Even more encouraging was the persistence of the effect. With just a single treatment, methane remained low throughout the four-week test period – the typical time slurry is stored before being spread on fields.

“We did one treatment, and for four weeks nothing happened – methane stayed low,” Clarissa Schwab notes. “This shows that the inhibition is not just a temporary shock.”

For the researchers, the implication was clear: biology can match the power of chemistry when the right microbial relationships are activated – and perhaps even surpass it in stability and environmental safety.

For Herald W. Ambrose and Clarissa Schwab, the next step is not just proving that the system works but making it practical. Laboratory success is one thing; scaling up to real barns, in which fresh manure continually mixes with older slurry, is another challenge entirely.

“Think of it as a switch,” says Herald W. Ambrose. “We want methane off during storage but on again in biogas. With biological control, we can turn it off and then back on when needed. Next we will test how dilution from fresh faeces and urine affects it and how often treatment must be repeated.”

From laboratory success to farm reality

The prospect of a controllable, reversible biological process could enable farms to minimise emissions without sacrificing biogas production later – a common drawback of acidification methods.

“This is biology regulating biology,” says Clarissa Schwab. “That makes it safer, more sustainable and easier to integrate into existing systems. If this is implemented widely, it could cut methane from pig slurry by up to 90% while reducing ammonia and CO₂ – without corrosive chemicals.”

Nevertheless, several hurdles remain. The glycerol used in the experiments was food grade; industrial glycerol from biodiesel production must meet strict standards before it can be spread on land. And L. reuteri, although food safe, is currently produced as an expensive probiotic – not yet at the scale or cost needed for agriculture.

“Feasibility is the challenge,” Clarissa Schwab admits. “Glycerol must be of certified quality, and L. reuteri is currently produced as a probiotic – too expensive at the volumes we would need today.”

She adds that the chemistry itself also demands care:

“Reuterin’s most active compound, acrolein, binds to proteins and DNA – that is probably why the methanogens stop. It is very reactive and unlikely to persist, but we need to quantify how much is freely present in real systems.”

Beyond pigs: the bigger methane prize

The researchers are therefore exploring alternative approaches, such as stimulating native slurry microbes that already possess the same enzymatic machinery.

“Maybe we do not need to add expensive cultures at all,” Clarissa Schwab says. “Indigenous slurry microbes and pig-derived communities already have the capacity to produce reuterin if we steer the system in the right direction.”

Although the method was designed for pigs, the underlying principle could reach further.

“For feed additives, the bigger methane prize is in cattle,” notes Herald W. Ambrose. “Enteric methane from dairy barns dwarfs slurry emissions, and adapting this mechanism to ruminant feed would be fascinating.”

Clarissa Schwab adds that the story of reuterin itself reflects a larger scientific arc. “This whole mechanism started in food biopreservation, then in gut ecology and now in agricultural biotechnology,” she says. “Same natural chemistry – just used for a new purpose.”

For the scientists – and for the farmers taking care of Denmark’s barns – the discovery feels like a beginning: a way to see livestock waste not as pollution but as a living system that can clean up after itself.