Methane Eaters

The harvesting and processing of natural gas and petroleum account for the largest source of methane emissions around the globe, as methane is the primary component of natural gas. Photo credit: Patrick Hendry

The harvesting and processing of natural gas and petroleum account for the largest source of methane emissions around the globe, as methane is the primary component of natural gas. Photo credit: Patrick Hendry

What comes to mind when someone brings up climate change? Among the many images flashing through your brain – polar bears trapped on too-small icebergs, hurricanes devastating Caribbean islands, and summer sidewalks so hot you could fry an egg on them – I bet methane isn’t one of them.

Methane is a potent greenhouse gas: in fact, it is more than 20 times more powerful than carbon dioxide at trapping heat in our atmosphere, which, as we’ve established, is driving climate change on a global scale (if you don’t believe climate change is real and happening, please see this article). Methane is the silent killer of the greenhouse gases: it is colorless, odorless, and can be difficult to detect, but it is nonetheless wreaking havoc on our world by creating a thick blanket in our atmosphere that warms the earth.

We are in desperate need of developing technologies to both reduce emissions of methane and actively remove it from the atmosphere.

Methane is produced just about everywhere in the natural world, including wetlands, rivers and lakes, wildfires, oceans, and even by animals, but the earth has ways of regulating the amount of methane that makes it into the atmosphere. Methane-eating bacteria, called methanotrophs, are found in any ecosystem that produces methane and ensure that most of the methane produced is converted into something else (like sugars), before it is released into the atmosphere.

Methanotrophs represent Earth’s primary mechanism for regulating the cycling of methane across the globe. Unfortunately, human emissions of methane from livestock, agriculture, landfilling, and the burning of fossil fuels have far exceeded the Earth’s natural mechanisms for dealing with methane, and have driven the system out of balance.

Methylomicrobium alcaliphilum 20ZR, a methane-eating bacteria, may provide a powerful way for us to reduce atmospheric methane and mitigate climae change. Photo credit: Paula Welander

Methylomicrobium alcaliphilum 20ZR, a methane-eating bacteria, may provide a powerful way for us to reduce atmospheric methane and mitigate climae change. Photo credit: Paula Welander

Pictured to the right is Methylomicrobium alcaliphilum 20ZR, or as it is fondly referred to, 20ZR) a type of methanotroph that may offer a solution to the global methane crisis. This bacteria uses methane as a primary energy source, similar to how plants use sunlight or we use sugars, to fuel its metabolism.

This is remarkable, considering methane is a difficult molecule to break apart, but through a set of complex steps, this bacteria is able to convert methane into organic compounds and thus bind it up in a form that does not pollute the atmosphere. Scientists are currently looking into ways we could boost the efficiency of this process of methane oxidation in methanotrophs, both for remediation of the environment as well as the development of net-zero emission strategies – making sure that the methane we produce through industry is handled before it escapes to the atmosphere.

Research on methanotrophs is diverse, but most of it focuses on boosting the growth rate and the methane oxidation machinery (or the ability to convert methane into something else) of these bacteria. If we can make them grow and divide faster, they will be able to eat more methane, and the same goes for making their internal processes more efficient.

One of the world’s leading researchers of methanotrophs, Dr. Marina Kalyuzhnaya, leads a lab at San Diego State University that is looking into novel ways of improving 20ZR for use in repairing the environment. Some of these include testing how these methanotrophs grow in different conditions or when exposed to different nutrients. Other projects experiment with growing methanotrophs in co-culture with other bacteria to see if they might work together better than on their own. Some projects are even genetically engineering these bacteria to try and produce more efficient strains.

Landfills are the third largest producer of methane gas around the world, due to the microorganisms that inhabit them and decompose the waste, generating methane. Photo credit: Hermes Rivera

Landfills are the third largest producer of methane gas around the world, due to the microorganisms that inhabit them and decompose the waste, generating methane. Photo credit: Hermes Rivera

You may be wondering what these bacteria can convert methane into; it turns out the answer to this question is pretty diverse.

With a little manipulation, methanotrophs can convert methane into biofuels that we can use to power industry, and when the burning of those fuels produces more methane, we can have the methanotrophs convert it back to biofuels. This is an example of a net-zero emission strategy: we are still using fossil fuels, but we are combining them with a sustainable technology that makes it so we don’t have to pollute the atmosphere. Methanotrophs can also be engineered to produce the precursors to other compounds using methane, such as nylon, which is a very environmentally unfriendly product to make. Researchers around the world are using methanotrophs to try and produce many different organic compounds, like biopolymers, alcohols, and more diverse types of fuel.

I recently did some work in Dr. Kalyuzhnaya’s lab, and one of my research projects focused on genetically engineering 20ZR to be able to overproduce vitamin B12. Vitamin B12 is an essential compound in all organisms, as it is required for a vital step in the synthesis of DNA, as well as acting as a cofactor for several other biochemical reactions. Most organisms don’t produce it on their own because it is a very energetically expensive molecule to make, but many methanotrophs (including 20ZR) do, making them important sources of B12 in environments that other organisms can pull from.

Ideally, we wanted to engineer methanotrophs to produce more vitamin B12 so we could increase the efficiency of co-cultures with other bacteria. For example, a partnership of interest in the Kalyuzhnaya lab is between 20ZR and cyanobacteria, which eat carbon dioxide (another greenhouse gas) and produce oxygen. If 20ZR were able to provide more vitamin B12 to the cyanobacteria, they would be able to consume more carbon dioxide and release more oxygen; in this way, 20ZR and cyanobacteria can work together to remove greenhouse gases from a system and keep emissions down.

Genetically modifying this bacteria required finding the mechanisms that it uses to regulate B12 production and removing them. All organisms possess regulation mechanisms: our bodies know when to tell our eyebrows to stop growing, for example, or when we have enough insulin in our blood.

In 20ZR, B12 production is regulated by something called a riboswitch: a highly sensitive protein that can detect how much B12 is being produced. The bacteria continues to produce B12 until it reaches a certain concentration, at which the riboswitch closes (similar to an on/off switch) and prevents any more from being produced; this allows the bacteria to maintain B12 at stable levels.

In my project, I identified where in the 20ZR genome this riboswitch resides, and by cutting out the pieces of DNA on either side of the riboswitch and then ‘gluing’ them back together, I was able to remove the regulation mechanism entirely. It has yet to be seen whether this will allow the bacteria to produce more B12 than it did before, but if it can, it is a step forward in developing efficient systems for dealing with the methane crisis.

Domestic livestock produce mass amounts of methane as a result of their digestion, and humans’ mass management of livestock has resulted in elevated methane emissions. Photo credit: Antonio Grosz

Domestic livestock produce mass amounts of methane as a result of their digestion, and humans’ mass management of livestock has resulted in elevated methane emissions. Photo credit: Antonio Grosz

Ultimately, this type of research aims at improving natural systems that already exist. We don’t have to reinvent the wheel here, we just have to make it turn a little faster: by making this natural mechanism of methane conversion more efficient, we will hopefully be able to develop sustainable ways of removing methane from the atmosphere.

Dr. Kalyuzhnaya believes that an efficient strategy to decrease methane emissions would be to modify how we handle waste – processes like this that produce greenhouse gases could be coupled with organisms that use those gases to produce other compounds, like plastic, fuels, and animal feed. Similarly, Dr. Kalyuzhnaya would also like to see methanotrophy applied to agriculture, namely by “changing current agricultural practices which eliminate and restrict natural methanotrophic communities in the soil.”

Instead of introducing foreign methanotrophs into environments, she sees restoring the natural diversity of these ecosystems as a fundamental way of reducing methane, by giving the environment the tools to repair itself. 

While there is much left to be discovered about the miniscule world of methanotrophs, it has become clear that reducing how much methane is pumped into the atmosphere will be the most efficient strategy for mitigating the global methane crisis in the long term. Scientists in the Kalyuzhnaya lab and others around the world are currently dedicated to incorporating these methane-eating microbes in industrial processes in order to accomplish this goal.

“Stimulating methanotrophy is the only way to go,” Dr. Kalyuzhnaya affirms, “for me, that also means understanding the environment, and reconstructing it as close as possible to native systems.”

- Jason


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