Methane-eating bacteria discovery could help capture gas from the air

Bacteria that convert methane in the air into useful products could be a vital tool for reducing our greenhouse gas emissions, if we can crack how they do it. A new discovery could kickstart efforts to engineer methane-harvesting bacteria, fight greenhouse emissions, and “mine” the air for useful compounds.

The problem with methane: Methane is an incredibly potent greenhouse gas. Compared with carbon dioxide (CO₂), it is around 25 times more effective at trapping the sun’s heat inside Earth’s atmosphere.

Emitted by sources ranging from cattle and coal mines to pipelines and landfills, methane now makes up roughly 20% of all the greenhouse gases we emit – making it a key contributor to the warming climate. 

One potential solution involves capturing the methane we produce, and converting it into other chemicals. The key difficulty here is that the bonds within methane molecules are incredibly strong, making these chemical reactions difficult to control.

Yet nature has shown us that harvesting methane is possible. Each year, specialised bacteria named “methanotrophs” consume roughly 30 million tons of atmospheric methane, and convert it into less harmful compounds. In some cases, these can even be exploited for our benefit. 

The challenge: Already, researchers have begun to explore how methanotrophs could be used to convert atmospheric methane into compounds like methanol – potentially providing a cheap and abundant source of fuel. 

However, these efforts are currently limited by their low yields and inefficiency, preventing them from becoming competitive from an economic perspective. Researchers need to optimise the chemical reactions taking place within the bacteria, to maximise how much methane is being converted. 

That will require detailed knowledge of particular enzymes used by methanotrophs, named pMMO. These large, complex proteins are known to bind to methane at specific sites, and are crucial for catalysing the chemical reactions that convert methane. 

The team identified an as-yet undetected “binding site” on the enzyme.

The problem is that these enzymes are embedded within the delicate outer membranes of the bacteria. 

To study their structures on atomic scales, researchers so far have had to use damaging techniques to remove the enzymes from their hosts. When torn from its natural environment in this way, pMMO’s activity completely stops, making it virtually impossible for researchers to understand how it interacts with methane.

The study: A team led by Amy Rosenzweig at Northwestern University have now made an important step towards overcoming this problem. 

Their solution involves a more careful procedure, where the extracted enzymes are embedded into tiny nanodiscs of lipids – the same fatty molecules that comprise cell membranes. The idea was that the nanodiscs would resemble the enzymes’ native environment closely enough for the enzyme to keep reacting with methane. 

Using a 3D imaging technique named “electron cryotomography,” Rosenzweig’s team could closely study the behaviour of the enzymes, at a level of detail that allowed them to visualise the motions of individual atoms. The researchers discovered that, when embedded in the nanodiscs, the pMMO enzymes behaved completely differently from counterparts that had been removed from cell membranes entirely. 

Crucially, by interacting with the lipids surrounding them, these enzymes retained their ability to interact with methane molecules. For the first time, this allowed the team to identify an as-yet undetected “binding site” on the enzyme, where methane molecules likely undergo the reaction that converts them into methanol. 

Fine-tuned bioengineering: The team’s discovery could have far-reaching implications for our ability to capture methane directly from the atmosphere. Through an improved understanding of pMMO’s natural binding behaviour, researchers in future studies could engineer new, artificial enzymes based on pMMO. When embedded into the cell membranes of methanotrophs, these enzymes could be far better suited to converting atmospheric methane into useful products. 

By fine-tuning chemical reactions in this way, researchers could significantly boost the efficiency and yield of existing biomanufacturing processes, making them economically competitive. In turn, this could provide strong incentives for many industries to harvest the methane they produce at its source, rather than letting it go to waste — and heating up the atmosphere.

Rosenzweig’s team ultimately hope that their methods for observing methane-eating enzymes in their natural habitats will inspire a new wave of efforts to capture methane from the atmosphere directly – potentially helping to close the loop on our greenhouse gas emissions. 

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