Antje Boetius: Discovering methane-munching microbes

In this edition of The Naked Scientists, deep sea microbiologist Antje Boetius explains how she discovered methane-consuming microbes, and why the seafloor is such a precious and important ecosystem...

Will - What were you down there looking for at the bottom of the ocean?

Antje - In various missions, the purpose was to find sea floor areas with a lot of methane where we could extract, find the so-called methanotrophs. So organisms, microorganisms, that feed on methane without using oxygen. And to find them, we looked for special cues in the landscape, for example, that a lot of methane would bubble out because it means there is a lot of methane under high pressure that can dissolve in the water and that will then enrich the microbes that eat the methane. And so that's why we were looking for such spots. And that brings you to extreme environments that are quite funky because they bubble and they have bacterial mats or huge assemblies of animals that feed on bacteria. And that was mostly the type of research I did, finding those spots and finding the microbes I needed to work with on land in a laboratory.

Will - How did you even know what to look for though? Because if you said, to me, I think there's going to be microbes at the bottom of the sea that are unlike any others that don't need oxygen to subsist. How do you go about theorising that and then going down to find them?

Antje - If you're a microbiologist, then you know that nature has microbes of specific functions where exactly the energy sources are right. So if I look for a microbe that should eat methane without oxygen, where would you go? You would go to a place that has a lot of methane and no oxygen, for example, in deep basins that have no oxygen like in the plexi or in sediments that have lots of organic matter so that oxygen is consumed. So basically that is part of our expertise. If we know what microbes we are looking for, we know what landscapes to look for.

Will - So how do these work then, these microbes?

Antje - Yeah, so the surprising thing is for decades some geologists had an idea of what to look for when one would look for these methane-munching microbes, it was considered by the microbiologists that it couldn't be that microbes would eat methane without oxygen for the energy, the low energy that would be provided to the microorganisms to thrive, to grow, to fix CO2. And so the geologist had traces, the microbiologists said, 'impossible, biology can't do such things.' But I did exactly what I said. So I thought if I were to find such microorganisms, I must go to the place in the sea with the most abundant methane for very long times and the least availability of oxygen. And it was a time when there was a lot of excitement finding gas hydrates, so frozen methane in the sea floor. And so I was on one of those expeditions where the geologist wanted to map out the surface near gas hydrates. And I thought, that's where I need to look, because if there is so much methane that it is frozen as ice in the sea floor, there should be the microbes eating it because they would not find another place where there would be so much food for them.

Will - And I'd be naïve to assume that you did your experimental work on the sea floor, but once you'd taken your samples back up to terra firma, what did you do? How did you find out exactly how they worked?

Antje - So at that time I was working a lot with isotopes. And so I had an idea, it was published by colleagues of mine who are friends today. They had an idea about metabolism. And so I tried with a suite of potential microbial food that I offered, which had radio labeling, so small amounts of radioactivity where I could measure would be eaten and taken up by the microbes consumed respired. And so I tried a lot of different things and then I found out what was expected. They cannot do this metabolism alone. They need a partner. And so when I then had the samples and looked under the microscope, this was then what put the piece together. It was not one organism that was carrying out that fascinating biochemistry. It was actually a symbiosis of two. And so that solved the problem of also why no one could find them nor cultivate them because if you have two to grow together, it's extra complicated. And so luckily they grow well in a lab and they don't necessarily need the pressure of the deep sea.

Will - So this is twice as complicated as I originally thought because there are two organisms needed in order for this process to work. As best you can to a Luddite like me, how does the actual chemistry work?

Antje - The question was if there is methane and the product of the methane consumption is CO2, which we knew it was because often these environments with these microbes, they have huge amounts of carbonate. We knew that there must be some way to bring in oxygen into the reaction, right? So you have methane, which is CH4, and you have carbonate coming out, you need a molecule that provides oxygen. And it cannot be oxygen because it doesn't exist in these sediments. So then it is obvious to an oceanographer like me, that there is a very abundant source of sulphur in the sea water. We call it sulfate. So it is S for sulphur and then oxygen in that molecule, SO4. And that is what they actually use. But to do it, they need a friend. It is a sulphate-reducing bacterium that has the right enzymes to get the oxygen from the sulphur to their buddies that want to consume methane. And thereby they do this chemistry together. The other thing that is still a bit of a mystery today. So you have two types, two entirely different types of life. They actually are in two different domains of life. So the one is a bacterium, as I said, the other one an Archaeum. And to know that the two of them, and it is exactly one species with another species, that they find each other in the sea and that they live together and that they occur everywhere globally. Just a handful of types that do this process. And they always have one counterpart. So then the question arises how do they find each other? Do they always grow together? Can we separate them? How do they transfer the electrons between them? So there's still a bunch of questions that have not been answered today. It just teaches you that life, when it has time, can develop the most amazing capacities and carry out globally relevant biochemistry. And it's life. It is some taxa that we even didn't know of before that we saw. And so we should have some respect for this amazing diversity of life that runs the planet from which we profit.

Will - Do you have any favourite theories as to how they found one another, so to speak?

Antje - Well, because it's microbes, it's cells that have no eyes, not much of sensors. They need to find each other. And so how could they? It must be surface-born recognition because there's no other way as they cannot search or signal. And so it must be on the surface. And we have made some progress with some seeing some kind of wires running from one cell to the other. You have to understand how small this life is. So the cells are a few micrometres in diameter, and the wires are then really nanowires. But we know today from also from other bacteria that bacteria can form wires and even collect energy for metals. And so potentially we have missed this ability of a single cellular life to actually tap into chemistry by forming some kind of cables or wires, really. And this is not fully researched and fully answered, but we have seen that some can produce extracellular structures with which they potentially tap into energy and also send electrons between the cells.