Human World

Pamela Silver: New fuels from extreme deep sea life

“Biology is the best chemist out there,” said Harvard scientist Pamela Silver. The U.S. Department of Energy funds Silver’s research exploring the use of deep-ocean extremophiles to create new biofuels. She described the bacteria she works with as being “like little batteries” that move electrons around. Silver’s goal is to genetically program these ocean bacteria to recover carbon from air or water and process it into fuel. This interview is part of a special EarthSky series, Biomimicry: Nature of Innovation, produced in partnership with Fast Company and sponsored by Dow. Silver spoke with EarthSky’s Jorge Salazar.

Pamela Silver

Describe the project you’re leading …

Our project explores reverse engineering of bacteria for fuel. It’s a DOE-funded project called the ElectroFuels Project. It derives from an aspiration by the DOE [U.S. Department of Energy] to think about deriving biofuels from organisms other than the standard ones.

The standard industrial organisms might be e-coli, yeast, or even photosynthetic bacteria. But there are many other kinds of bacteria in the world, often called extremophiles, which live deep in the ocean, in vents, or in soil.

Some of these bacteria are capable of moving electrons in and out of them. The idea is that those electrons could provide reducing power or energy coupled with the fixation of CO2, or carbon, to produce a biofuel.

What’s new about this research?

The research is quite different than what has gone on prior to this, and that’s what attracted it to us. It’s also fairly blue skies for the Department Of Energy. It’s funded by something called the ARPA-E Program, which is meant to fund more adventurous-style research. What’s new here is the idea that we would use these different kinds of microbes or extremophiles in different ways, to take in electricity, affix carbon and produce a fuel. That’s a huge undertaking. But it’s different than using sugarcane as the carbon source for fuel, or using sunlight, which is what you would use with plants, or photosynthetic bacteria.

How does this work? How will the deep sea bacteria make fuels?

Marine bacteria Shewanella

There are three things we need these bacteria to do. We need them to somehow take in electricity or electrons. That’s one part that we need to do. Second, they need to have carbon because you need the carbon to produce the fuel. And then we need to engineer them to produce the fuel.

The Department Of Energy is quite keen that the fuel be what’s called ‘transportation compatible.’ That has to do in part with the way fuel is handled in the United States. It’s very centralized. It’s hard to use fuels that are corrosive to plastic or to things that are in cars already. That’s what we mean by transportation compatible fuels. So we chose Octanol as our fuel, because it should be high energy and compatible with the existing infrastructure.

How to get the cells to take in electrons is very challenging. First of all, we have to establish that they can do it, and that they can do it at a rate and at an extent that is good enough to use the energy to produce the fuel. This means coupling of a living organism — in this case a microbe — with an electrode, a solid state man-built thing, which has been done but never at a commercial scale. Then, thirdly, depending on the organism, we either have to use an organism that already fixes carbon or engineer carbon fixation into the cells.

What are these organisms like?

In our case, we chose Shewanella. I should say there are several other research groups involved in this effort. — the ElectroFuels effort — and they use different kinds of bacteria. Some use one that are called Ralstonia. Some use Geobacter.

But the common feature of these bacteria is that they are somehow capable of moving electrons through them. Shewanella is best known for taking electrons and actually pumping them out of the cell. It’s a way that the cell copes in its metabolism with extra-reducing equivalence in the cell.

In Shewanella, in part, they pump out electrons. People have actually used that fact to use Shewanella to transfer electrons from a living organism to an electrode. We want to do the opposite. We want have them take up electrons. We think that’s possible because they already have this mechanism for moving electrons around, so we think it’s possible to reverse that. And in fact we’ve shown that.

Shewanella also had its genome sequenced, which is a very high priority. We know everything about the organism in terms of its genome. It’s also amenable to the technologies of bioengineering – it’s biotechnology friendly. That’s important in this project.

What does it mean to be biotechnology friendly?

It means that we can introduce genes or pieces of DNA — genes that provide certain functions for the cell. We can take those genes and put them in the cell and get it to do things we want it to do.

For example, in the case of Shewanella, we wanted to fix carbon. There are about five different ways that the earth uses to fix carbon. The most common one uses an enzyme called RuBisCo and the Calvin cycle. We would like to try engineer that into Shewanella.

But there are also other newly discovered pathways that we are also trying to engineer. This will be the first time that these other pathways have ever been engineered into another organism. There is a science component to this. It’s not all about application.

This ability to transfer DNA from one kind of organism to another in a predictable way is at the core of what we do.

Tell us more about why these deep-sea bacteria, Shewanella oneidensis, are so interesting to scientists who research energy?

In genetically modifying these organisms we would like to program them to do certain specific functions. In our case, we need to program them to take up carbon, because you need carbon to produce the fuel molecules. The fuel molecules are all carbon based. It’s what we get out of the ground. It’s what oil is – fossilized carbon. And the process of using fuel is the burning of carbon.

So we need to recover carbon, ideally from the atmosphere, and process that carbon into a fuel molecule. Organisms don’t normally do that. Some do it to some extent but these organisms don’t.

What’s the goal of the research you’re doing, and how do you see it ultimately being used?

I want to preface this by saying there are multiple groups, so that the government is really covering it’s bets. Some will succeed and some won’t. And that’s good. When you do high-risk research you need that. But it’s an amazing idea from the point of view of the government to have thought of this.

There are other sources of biofuels. You have plants, which harvest sunlight. You might have heard about cyanobacteria, or photosynthetic bacteria that grow in large ponds. This brings up the possibility of having genetically engineered organisms in the environment. Some people may be uncomfortable with that. The advantage of this process would be that the organism would not necessarily have to be exposed to the environment. It doesn’t need light to grow. It could be sitting underground, and the source of electricity could be anything. It could be solar. It could be wind. As long as you can access the organism, the organism is sort of acting like a battery or a little production factory into which you would pump electricity, and then it would pump fuel out. But it’s sequestered, so you don’t have to deal with this problem that the public might see as of having a lot of a particular genetically engineered organism that might get out if it were say, in an open pond or something. That assumes you’re going to use open pond farming for say photosynthetic microbes. You may or may not; you might build a closed bioreactor, which is a big challenge and people should be working on that too. I think there’s no one solution, by the way. This is may provide one part of a bigger solution.

What are your thoughts on biomimicry, learning how nature does things and applying that knowledge to human problems?

The biomimicry part in our case would come from the fact that these organisms already use electrons. They act like little batteries. We’re using that aspect of biology to solve this particular problem of biofuels.

May 24, 2012
Human World

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