Microbes living on air: hidden methane consumers from caves to landscapes help to regulate Earth’s atmosphere

Deep inside caves where sunlight never reaches, microbial life has found an unexpected way to survive: by living on the air itself. Instead of relying mainly on organic matter drifting in from the outside world, some microbes appear able to draw energy directly from trace gases circulating through the cave atmosphere.

At first glance, that idea may sound exotic. But it may point to a much larger story: the same methane-consuming microbes that sustain dark cave ecosystems may also help remove methane across entire landscapes – from soils and wetlands to sediments across entire countries, including thousands of mapped locations across Denmark.

“The surprising thing is not that there are microbes in caves – it is that so many of them seem equipped to live on atmospheric trace gases,” says Sean K. Bay, a microbial ecologist at Monash University in Australia.

Only in recent years have experiments shown convincingly that microbes can draw energy from atmospheric trace gases.

“The idea that microbes can live directly off atmospheric trace gases is not entirely new,” says Kalinka Sand Knudsen, a microbiologist at Aalborg University in Denmark specialising in methane-oxidising microbes.

In the new cave study published in Nature Communications, researchers combined DNA-based analyses with direct gas measurements inside several Australian caves. Their results suggest that microbes equipped to consume methane, hydrogen and carbon monoxide are not merely present – they are actively functioning.

“When methane concentrations decrease as you move deeper into the cave, it strongly suggests that microbes there are actively consuming it,” says Caitlin Margaret Singleton, a microbial ecologist at Aalborg University in Denmark.

The findings suggest that atmospheric trace gases can support continuous microbial activity even in environments where photosynthesis is impossible. More tentatively, they also hint at a broader planetary process in which microbial communities that feed on methane may help shape the chemistry of Earth’s atmosphere – from cave interiors to open landscapes.

The puzzle of life in the dark

Caves are both isolated and connected. They are dark and often poor in nutrients, yet air still moves through them and keeps them in contact with the atmosphere. Traditionally, microbial life in caves has been explained by outside inputs such as leaves, roots, surface water or bat guano. Another explanation has been microbes drawing energy from chemical reactions involving minerals such as ammonium, sulphur or iron.

But both explanations leave gaps: many caves contain very little organic material, and inorganic energy sources often occur only in trace amounts – yet microbial communities can still be surprisingly abundant.

“For decades, we have known that caves harbour abundant life, but the energy budget has been unclear,” Sean K. Bay says. “If there is no light and no steady influx of organic carbon, there must be another, more continuous energy source.”

Over the past decade, studies in soils and polar deserts have pointed to another possibility: microbes that harvest energy directly from tiny amounts of gas in the atmosphere. Even at extremely low concentrations – parts per million or even parts per billion – gases such as hydrogen and carbon monoxide can provide a steady trickle of energy.

“What changed the field was recognising that the atmosphere itself can serve as an energy source,” Bay explains. “Once you accept that microbes can live on trace gases in air, caves become an obvious system in which to test that idea.”

If microbes in caves really can survive this way, the implications may reach far beyond subterranean ecosystems. Similar metabolisms may help to sustain microbial communities in energy-poor environments such as upland soils – including forests, grasslands and heathlands – where trace gases in the atmosphere can serve as an important energy source and where microbial activity influences methane levels in the atmosphere.

Ecosystems powered by air

Methane oxidation in caves has been reported before, and some cave systems appear to act as sinks for atmospheric methane. What has remained uncertain is whether this merely enables microbes to survive – or whether it can sustain growing ecosystems.

“The key question was whether this is just enough to stay alive, or enough to grow,” Bay says. “If microbes can both harvest energy and fix CO₂ from the air, then we are looking at a fundamentally different ecological foundation.”

Such a system would challenge a longstanding assumption in ecology: that new living matter is produced mainly with the help of sunlight.

Instead, cave ecosystems may operate on a different principle. As air circulates through cave passages, trace gases such as methane, hydrogen and carbon monoxide provide a small but continuous energy source. Microbial communities may tap into that flow, creating ecosystems powered not by light but by atmospheric chemistry.

Taken together, the observations suggest a consistent ecological transition from cave entrance to cave interior – from light-influenced microbial communities near the surface to chemically powered ecosystems deeper underground.

“This is not random patchiness,” Bay says. “It is a structured energy landscape.”

To test whether microbes were truly using atmospheric gases in this way, researchers needed to combine several lines of evidence – from genetic analyses to direct measurements of how gases move and change inside caves.

Do microbes really live on air?

To determine whether cave microbes truly live off the air, the researchers combined several lines of evidence: DNA-based analysis, direct gas measurements and laboratory experiments designed to test whether the microbes were actually consuming those gases.

They sampled four aerated caves in southeastern Australia – two limestone caves and two lava tubes – collecting sediments and microbial biofilms along transects from the entrance into the dark interior.

“We did not want to rely on DNA alone,” Sean K. Bay says. “We needed to know both what the microbes are capable of – and what they are actually doing.”

By piecing together DNA from the cave samples, the researchers reconstructed more than 1,400 microbial genomes. These genomes revealed enzymes capable of consuming methane, hydrogen and carbon monoxide – the key chemical steps that allow microbes to extract energy from gases in the air.

Researchers then compared these genes with known ones to confirm that they really belonged to microbes capable of using methane, rather than merely looking similar to methane-oxidation genes.

“When you analyse these genomes, you have to be very careful,” says Kalinka Sand Knudsen. “You need to look at the genes in a proper evolutionary context to see whether they might have the potential to perform that function.”

Following the disappearing methane

But genetic potential alone cannot show that the process is actually happening.

Researchers therefore measured how methane, hydrogen and carbon monoxide concentrations changed along the cave passages.

“The fact that they actually measured how methane levels changed in different parts of the cave system was really convincing,” says Caitlin Margaret Singleton. “When methane decreases as you move deeper into the cave, it strongly suggests that microbes there are actively consuming it.”

Sediment samples were also incubated in laboratory experiments to test whether cave microbes actively consumed methane.

“The genomic data tell you what the microbes could do,” Bay says. “But when you see methane actually disappearing in those samples, you know that metabolism is really happening.”

By combining DNA analysis, field measurements and laboratory experiments, the researchers were able to connect what the microbes seemed capable of doing with what they were actually doing rather than relying on DNA alone.

A hidden energy system in caves

The results revealed a striking shift in microbial activity as researchers moved deeper into the caves.

Near cave entrances, where some sunlight and organic material may still reach the environment, microbial communities showed genetic signatures associated with photosynthesis. Deeper inside the caves, however, those signals largely disappeared. Instead, genes involved in methane, hydrogen and carbon monoxide oxidation became increasingly common.

More than half of the reconstructed microbial genomes contained enzymes capable of consuming one or more trace gases from the air. Two groups stood out in particular: methanotrophs that consume methane and bacteria specialising in using hydrogen, both of which appear well suited to caves in which energy is scarce.

Direct measurements inside the caves supported the genomic evidence: methane concentrations were consistently lower deeper in the cave systems than near the entrance, suggesting that microbial communities were actively consuming the gas.

Laboratory incubations of cave sediments showed the same pattern: when samples were placed in sealed containers, methane concentrations in the air above them steadily declined.

An ecosystem powered by trace gases

Together, these observations suggest that cave ecosystems are structured along predictable energy gradients. Near the surface, microbial communities rely partly on sunlight and organic matter. Deeper underground, however, the dominant energy source appears to be the slow but continuous supply of trace gases circulating through cave air, although this interpretation still relies on combining several indirect and direct lines of evidence.

Many of the microbes involved in these processes also belonged to previously unknown or poorly characterised lineages.

“We were seeing organisms with the genetic machinery to oxidise methane that did not fit neatly into previously described groups,” says Sean K. Bay.

The abundance of these organisms also surprised researchers.

“They were present in relatively high abundance,” Bay says. “This suggests that they are not just barely surviving in these environments but are actually an important part of the ecosystem.”

Together, the findings suggest that atmospheric trace gases can sustain microbial metabolism in caves even in the absence of sunlight or major organic inputs – a strategy that may also operate far beyond subterranean environments.

From cave air to the methane cycle

If cave ecosystems can be powered by trace gases drifting through the air, the implications extend far beyond subterranean microbiology.

Methane is one of the most powerful greenhouse gases in Earth’s atmosphere, and methane-consuming microbes form the only biological mechanism capable of removing it directly from the air.

“Microorganisms are the only biological sink for atmospheric methane,” says Caitlin Margaret Singleton. “They are the only organisms that can take it up directly from the atmosphere.”

Most methane in the atmosphere is eventually destroyed through chemical reactions high in the atmosphere. But microbes living in soils, wetlands and sediments also remove substantial amounts every year, acting as one of the planet’s most important natural methane filters.

“These microbial systems remove around 30 to 40 teragrams of methane from the atmosphere annually,” Singleton says. “That is roughly the equivalent mass of about 250,000 well-fed female blue whales.”

From caves to landscapes

The cave ecosystems studied represent an extreme example of this metabolism, but the same strategy – microbes extracting energy from methane and other trace gases – also appears across many natural environments.

The processes observed in dark cave systems may reflect a much broader planetary phenomenon in which microbial communities help to regulate methane in the atmosphere.

Understanding where these microbes live – and how ecosystems support them – therefore has implications that reach far beyond caves and into the global methane cycle.

To explore that question, researchers turned from subterranean ecosystems to entire landscapes, analysing environmental DNA from thousands of sites across Denmark to map where methane-consuming microbes live and how they contribute to the planet’s natural methane filter.

Hunting methane-consuming microbes across landscapes

Although the cave study shows how microbes can survive on trace gases in extreme environments, similar metabolisms also operate in upland natural soils such as forests, grasslands and heathlands, where the atmosphere itself forms the main source of trace gases such as methane, hydrogen and carbon monoxide.

Methane-consuming microbes are widespread in soils, wetlands and sediments, where they form one of the planet’s natural methane filters. These organisms, known as methanotrophs, use methane both for energy and as a building material for growth.

Methane is a particularly powerful greenhouse gas. Molecule for molecule, it traps far more heat in the atmosphere than CO₂, and rising concentrations are responsible for a substantial share of current global warming.

“Nearly a third of the global warming we are experiencing is linked to increased methane concentrations in the atmosphere,” says Kalinka Sand Knudsen.

Why scientists still struggle to identify methane-consuming microbes

Despite their importance, scientists still know surprisingly little about which methane-consuming microbes dominate natural ecosystems.

Most of the methanotrophs studied in detail so far have been cultivated in laboratories – but those organisms are not always the ones that dominate in nature.

“The organisms we can grow in the laboratory are often not the ones that dominate in natural environments,” Knudsen says. “So if we want to understand the methane sink in nature, we need better ways of identifying the microbes that are actually living there.”

To address that gap, researchers turned to a large environmental DNA dataset collected across Denmark, aiming to map the diversity and distribution of methane-consuming microbes across entire landscapes.

Mapping Denmark’s methane-consuming microbes

To map methane-consuming microbes across Denmark, the researchers analysed environmental DNA from more than 10,000 sites collected as part of the Microflora Danica project.

“We had collaborators all across Denmark collecting samples,” says Caitlin Margaret Singleton. “In total we ended up with more than 10,000 environmental samples.”

The dataset includes soils, sediments and wetlands from a wide range of natural and human-modified habitats.

Rather than isolating microbes one by one in the laboratory, the researchers analysed all the DNA in each sample, enabling them to examine whole microbial communities directly from the environment.

“The powerful thing about metagenomics is that it captures the DNA of everything in that environment,” Singleton says. “Once you have that dataset, you can go back and look for almost any organism or metabolic pathway you are interested in.”

By screening this national dataset for genes involved in methane metabolism, the researchers were able to begin mapping where methane-consuming microbes live across Denmark’s landscape.

Finding the microbes that consume methane

To identify methane-consuming microbes in the Danish dataset, researchers searched the environmental DNA for genetic markers associated with methane metabolism.

The most important of these markers is a gene encoding methane monooxygenase – the enzyme that initiates methane oxidation.

“First we look for the gene that encodes methane monooxygenase,” says Kalinka Sand Knudsen. “This indicates that methane oxidisers might be present.”

Because environmental sequencing often produces only small fragments of microbial genomes, researchers then reconstructed longer genome sequences from promising samples.

“You start with short fragments indicating that methane oxidation might be happening,” Knudsen explains. “Then you go deeper and reconstruct the full microbial genome.”

This approach enabled the team to identify not only the methane-oxidation genes themselves but also the rest of the machinery needed to process carbon from methane and obtain energy from it.

“If a microbe oxidises methane, it needs the rest of the metabolic pathways to process that carbon and obtain energy,” Knudsen says. “So we check whether the genome also contains those downstream genes.”

By combining gene searches, genome reconstruction and evolutionary analysis, the researchers were able to identify methane-consuming microbes across a wide range of Danish habitats.

A hidden methane filter

The nationwide analysis revealed that methane-consuming microbes are both widespread and far more diverse than previously recognised.

Across the thousands of environmental DNA samples, researchers identified more than 100 previously undescribed methanotrophic species. Many of these appear to be important contributors to methane consumption in natural ecosystems.

In addition, the results confirmed an important pattern: many of the methanotrophs commonly studied in laboratories are not the ones most abundant in nature.

“The organisms we can grow in the laboratory are often not the ones that dominate in natural environments,” says Kalinka Sand Knudsen. “That was one of the key motivations for this work – to understand which microbes are actually living and thriving out in nature.”

The analysis also revealed strong differences between habitats.

Where methane-consuming microbes thrive

Wetlands, peatlands and freshwater sediments hosted rich communities of microbes adapted to environments where methane is produced naturally in oxygen-poor mud and soil. In these ecosystems, methane-consuming microbes often act as a biological filter, consuming part of that methane before it escapes into the atmosphere.

“In wetlands and sediments they work as a filter,” Knudsen says. “They consume methane produced deeper in the soil before it reaches the atmosphere.”

In contrast, upland soils such as forests and grasslands were dominated by microbes capable of oxidising methane present at extremely low concentrations in the air.

These organisms appear to form an important component of the planet’s natural methane sink.

Microbes that quietly shape the atmosphere

Although each individual microbe consumes only minute amounts of methane, the combined activity of microbial communities across global landscapes has a measurable impact on atmospheric chemistry.

“Microorganisms are the only biological sink for atmospheric methane,” says Caitlin Margaret Singleton. “They are the only organisms that can take methane directly from the atmosphere.”

Most methane in the atmosphere is eventually destroyed by chemical reactions high above Earth’s surface, but microbes in soils and sediments also remove 30 to 40 teragrams of methane from the atmosphere annually.

That number is difficult to visualise, but it substantially contributes to regulating atmospheric methane.

Taken together, the cave research and the nationwide Danish analysis suggest that microbial processes operating from underground caves to soils and wetlands may help shape the chemistry of Earth’s atmosphere.

When landscapes shape the methane filter

Mapping methane-consuming microbes across Denmark does more than catalogue biodiversity. It provides the first steps toward understanding how ecosystems influence methane in the atmosphere – and how human activity might strengthen or weaken that natural filter.

Methane concentrations in the atmosphere have risen rapidly in recent decades and comprise a substantial share of current global warming.

“Nearly a third of the global warming we are experiencing is linked to increased methane concentrations in the atmosphere,” says Kalinka Sand Knudsen. “So understanding the microbes that consume methane is really important.”

The genomic map also suggests that methane-consuming microbes may respond strongly to how landscapes are managed.

In particular, disturbances to soil structure may disrupt the microbial communities responsible for methane oxidation.

“When you plough soil, it is almost like an earthquake for the microbial community,” says Caitlin Margaret Singleton. “You break apart all the biofilms and structures that microbes depend on, and their activity can drop dramatically.”

Earth’s invisible methane filter

The new genomic map also raises the possibility of identifying landscapes where methane-consuming microbes are already active – and where restoration efforts might strengthen those natural methane filters.

“What we show in this study is that we can identify which species live in which habitats,” Knudsen says. “That enables us to make much better estimates of what a natural methane-consuming ecosystem should look like.”

Such knowledge could help to guide ecosystem restoration in areas where methane-consuming microbes already exist and may expand naturally.

“If you restore land next to an ecosystem that already functions as a methane sink, those microbes may spread more easily,” Singleton says.

What scientists still need to understand

For now, however, the researchers emphasise that the work mainly provides a baseline – a detailed picture of the microbial communities that influence methane cycling.

The next step will be to explore how similar microbial systems function in other parts of the world.

“It would be fascinating to compare what we see in Denmark with other countries,” Knudsen says. “Do the same species dominate in Sweden or Germany – or even in places as far away as Australia?”

If similar microbial communities occur across many environments, that would suggest that the same atmospheric trace gases powering cave ecosystems may also help to sustain microbial methane filters across much of the planet.