Using Microbes to Convert Greenhouse Gases to Valuable Chemicals

Berkeley Lab project aims to bioengineer a microbe to capture methane and CO2

– By Julie Chao

What if there were a way to take greenhouse gases - gases such as carbon dioxide and methane which are warming our planet - and not only capture them but also then convert them into a useful product?

Deepika Awasthi, a scientist in Berkeley Lab’s Biosciences Area, is working on a project to engineer a microbe to capture methane and carbon dioxide and convert it to a valuable chemical. (Credit: Thor Swift/Berkeley Lab)

Lawrence Berkeley National Laboratory ÜBerkeley Lab) scientist Deepika Awasthi has a project aiming to do just that. By bioengineering a microbe, she hopes to be able to capture both methane and carbon dioxide and produce a useful chemical that can be used in everyday products, such as automobile coatings and advanced textiles.

Almost 50 gigatons of carbon dioxide and 300 million metric tons of methane are emitted globally every year. To achieve the goal of reaching net-zero emissions by mid-century, experts are increasingly recognizing that technologies to remove climate-warming gases will be needed. Berkeley Lab’s Carbon Negative Initiative aims to develop breakthrough negative emissions technologies to address our climate crisis.

Awasthi, a project scientist in the Biosciences Area with a doctorate in microbiology and cell science, was awarded a grant through Berkeley Lab’s LDRD, or the Laboratory Directed Research and Development, program. Hers is complementary to other projects in the Initiative that are trying various methods to remove carbon, such as ocean capture and an electrochemistry approach.

Q. What is the problem you’re trying to solve?

Methane is about 30 times more potent in its heat-trapping capability than carbon dioxide. That means methane is going to trap 30 times more heat than the same amount of molecules of carbon dioxide. It’s not as abundant as carbon dioxide - it’s emitted during oil and natural gas production, raising livestock, and the decay of organic waste in landfills - but it’s more dangerous, and looking at our climate crisis, we need to look at all greenhouse gases and technologies.

There are a lot of groups working on microbes that use carbon dioxide as their primary food source. I thought developing technologies for methane could be interesting, and also, could we use carbon dioxide as a secondary resource, not to feed the microbe, but integrated somewhere in the middle of the system where it can enhance the product yield?

My aim is to capture two greenhouse gases - both methane, which will be the primary food source for the microbe, and also carbon dioxide, which will be incorporated into a commercial product produced by the microbe. And the product I chose is malonic acid.

Q. What is malonic acid, and why do we want to produce it?

Malonic acid is on the Department of Energy’s list of top biochemicals that they’re looking for somebody to make as replacements for fossil fuel-based chemicals. It’s currently made by the petrochemical industry or produced by sugar fermentation. Malonic acid is potentially a multi-billion-dollar market and is used in the solvent industry, in the auto coating industry, in making video tapes, audio tapes, or films, and polymer clothing, to name a few uses. 

When you think about fossil fuels, such as oil, we refine barrels of crude oil to make gas for automobiles. The refining process also generates many chemicals as side products that have found a use in the market. So if we are thinking of finding a replacement for the fuel, we also have to find a replacement way to produce all those chemicals that we now depend upon.

We are trying to make a biochemical that is going to fix two greenhouse gases into products that we will use for the next 10, 20, or 100 years. That means we’ll sequester these gases into products that will be a replacement to petrochemicals and keep them away from the atmosphere.

Q. That certainly sounds like a win-win. How will you do that?

I am using a methanotroph, which is a microbe that feeds on methane. Specifically I’m working with one called Methylomicrobium alcaliphilum. It’s a high-pH, high-salt loving bacteria. It was first isolated at a lake in Russia by a Russian scientist.

Without going into too much detail, basically the microbe will take up methane, and then there is a very common energy pathway for processing the carbon. Along with postdoctoral researcher Shubhasish Goswami, we are doing metabolic engineering so that CO2 will be integrated in the pathway; then the cell is synthesizing the desired product and eventually secreting it in the medium. Methane is a one-carbon compound. The chemical symbol is CH 4 . Carbon dioxide, or CO2 , is also a one-carbon compound. Each molecule of malonic acid, which is a three-carbon compound, incorporates two molecules of methane and one molecule of CO2 in this bioengineering design.

Q. How would this look in a real-world setting? Where will the methane and carbon dioxide come from?

I was thinking of an anaerobic digester - these are located where waste is processed, such as municipal solid waste. When you keep it closed and airtight and then throw in a bunch of microbial communities, it digests the waste and generates a lot of methane and CO2 . The whole process happens in the absence of oxygen, so we call it anaerobic.

Anaerobic digesters can be very expensive, but if we can generate a lot of valuable product streams from it, then that makes them economically attractive.

A second possible point source is wherever natural gas is produced. Natural gas is a mixture consisting of more than 90% methane plus other volatile hydrocarbons.

Q. So what is the hard part of this project - is it the genetic engineering of the microbe?

Yes. Methanotrophs are not easy to culture or genetically engineer. Microbes like E. coli and fungi such as S accharomyce s’are very well understood and widely used for bioengineering, but methanotrophs are not there yet. E. coli can be genetically engineered in a few days, whereas with a methanotroph it might take you one to two months to do what you can reach with E. coli.

So I’m trying to take the genetic engineering techniques for methanotrophic hosts to the next level, developing methods to shorten the time and improve their foreign DNA uptake efficiency, and develop CRISPR-Cas9 genetic engineering technology. I’m hoping that with this development I can bring that two months down to two to three weeks.

If you think about hosts that utilize sugar - there’s yeast, E. coli, Pseudomonas putida , Bacillus subtilis

If I get more funding, I have an interest in exploring and expanding the genetic tools for other types of methanotrophs because I feel that each genus of microbe has an individual capability. They should be explored and maybe exploited for what they can make from methane. I want to study different types of these methane-utilizing hosts and see what they can bring to the table. 


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