Karen Lloyd [ 29 JUL 2019 | Microbiology ] It may seem like we’re all standing on solid earth right now, but we’re not. The rocks and the dirt underneath us are crisscrossed by tiny little fractures and empty spaces. And these empty spaces are filled with astronomical quantities of microbes, such as these ones. The deepest that we found microbes so far into the earth is five kilometers down. So like, if you pointed yourself at the ground and took off running into the ground, you could run an entire 5K race and microbes would line your whole path. So you may not have ever thought about these microbes that are deep inside earth’s crust, but you probably thought about the microbes living in our guts.

If you add up the gut microbiomes of all the people and all the animals on the planet, collectively, this weighs about 100,000 tons. This is a huge biome that we carry in our bellies every single day.

We should all be proud.

But it pales in comparison to the number of microbes that are covering the entire surface of the earth, like in our soils, our rivers and our oceans. Collectively, these weigh about two billion tons. But it turns out that the majority of microbes on earth aren’t even in oceans or our guts or sewage treatment plants. Most of them are actually inside the earth’s crust. So collectively, these weigh 40 billion tons.

This is one of the biggest biomes on the planet, and we didn’t even know it existed until a few decades ago. So the possibilities for what life is like down there, or what it might do for humans, are limitless. This is a map showing a red dot for every place where we’ve gotten pretty good deep subsurface samples with modern microbiological methods, and you may be impressed that we’re getting a pretty good global coverage, but actually, if you remember that these are the only places that we have samples from, it looks a little worse.

If we were all in an alien spaceship, trying to reconstruct a map of the globe from only these samples, we’d never be able to do it. So people sometimes say to me, “Yeah, there’s a lot of microbes in the subsurface, but … aren’t they just kind of dormant?” This is a good point. Relative to a ficus plant or the measles or my kid’s guinea pigs, these microbes probably aren’t doing much of anything at all.

We know that they have to be slow, because there’s so many of them.

If they all started dividing at the rate of E. coli, then they would double the entire weight of the earth, rocks included, over a single night. In fact, many of them probably haven’t even undergone a single cell division since the time of ancient Egypt. Which is just crazy. Like, how do you wrap your head around things that are so long-lived? But I thought of an analogy that I really love, but it’s weird and it’s complicated.

So I hope that you can all go there with me. Alright, let’s try it.

It’s like trying to figure out the life cycle of a tree … if you only lived for a day. So like if human life span was only a day, and we lived in winter, then you would go your entire life without ever seeing a tree with a leaf on it. And there would be so many human generations that would pass by within a single winter that you may not even have access to a history book that says anything other than the fact that trees are always lifeless sticks that don’t do anything.

Of course, this is ridiculous.

We know that trees are just waiting for summer so they can reactivate. But if the human life span were significantly shorter than that of trees, we might be completely oblivious to this totally mundane fact. So when we say that these deep subsurface microbes are just dormant, are we like people who die after a day, trying to figure out how trees work? What if these deep subsurface organisms are just waiting for their version of summer, but our lives are too short for us to see it?

If you take E. coli and seal it up in a test tube, with no food or nutrients, and leave it there for months to years, most of the cells die off, of course, because they’re starving. But a few of the cells survive. If you take these old surviving cells and compete them, also under starvation conditions, against a new, fast-growing culture of E. coli, the grizzled old tough guys beat out the squeaky clean upstarts every single time. So this is evidence there’s actually an evolutionary payoff to being extraordinarily slow. So it’s possible that maybe we should not equate being slow with being unimportant.

Maybe these out-of-sight, out-of-mind microbes could actually be helpful to humanity.

OK, so as far as we know, there are two ways to do subsurface living.

The first is to wait for food to trickle down from the surface world, like trying to eat the leftovers of a picnic that happened 1,000 years ago. Which is a crazy way to live, but shockingly seems to work out for a lot of microbes in earth. The other possibility is for a microbe to just say, “Nah, I don’t need the surface world. I’m good down here.” For microbes that go this route, they have to get everything that they need in order to survive from inside the earth.

Some things are actually easier for them to get.

They’re more abundant inside the earth, like water or nutrients, like nitrogen and iron and phosphorus, or places to live. These are things that we literally kill each other to get ahold of up at the surface world. But in the subsurface, the problem is finding enough energy. Up at the surface, plants can chemically knit together carbon dioxide molecules into yummy sugars as fast as the sun’s photons hit their leaves. But in the subsurface, of course, there’s no sunlight, so this ecosystem has to solve the problem of who is going to make the food for everybody else. The subsurface needs something that’s like a plant but it breathes rocks.

Luckily, such a thing exists, and it’s called a chemolithoautotroph.

Which is a microbe that uses chemicals — “chemo,” from rocks — “litho,” to make food — “autotroph.”

And they can do this with a ton of different elements. They can do this with sulphur, iron, manganese, nitrogen, carbon, some of them can use pure electrons, straight up. Like, if you cut the end off of an electrical cord, they could breathe it like a snorkel.

These chemolithoautotrophs take the energy that they get from these processes and use it to make food, like plants do. But we know that plants do more than just make food. They also make a waste product, oxygen, which we are 100 percent dependent upon. But the waste product that these chemolithoautotrophs make is often in the form of minerals, like rust or pyrite, like fool’s gold, or carminites, like limestone. So what we have are microbes that are really, really slow, like rocks, that get their energy from rocks, that make as their waste product other rocks. So am I talking about biology, or am I talking about geology?

This stuff really blurs the lines.

So if I’m going to do this thing, and I’m going to be a biologist who studies microbes that kind of act like rocks, then I should probably start studying geology. And what’s the coolest part of geology?


This is looking inside the crater of Poás Volcano in Costa Rica. Many volcanoes on earth arise because an oceanic tectonic plate crashes into a continental plate. As this oceanic plate subducts or gets moved underneath this continental plate, things like water and carbon dioxide and other materials get squeezed out of it, like ringing a wet washcloth. So in this way, subduction zones are like portals into the deep earth, where materials are exchanged between the surface and the subsurface world.

So I was recently invited by some of my colleagues in Costa Rica to come and work with them on some of the volcanoes.

And of course I said yes, because, I mean, Costa Rica is beautiful, but also because it sits on top of one of these subduction zones.

We wanted to ask the very specific question: Why is it that the carbon dioxide that comes out of this deeply buried oceanic tectonic plate is only coming out of the volcanoes? Why don’t we see it distributed throughout the entire subduction zone? Do the microbes have something to do with that? So this is a picture of me inside Poás Volcano, along with my colleague Donato Giovannelli.

That lake that we’re standing next to is made of pure battery acid.

I know this because we were measuring the pH when this picture was taken. And at some point while we were working inside the crater, I turned to my Costa Rican colleague Carlos Ramírez and I said, “Alright, if this thing starts erupting right now, what’s our exit strategy?” And he said, “Oh, yeah, great question, it’s totally easy. Just turn around and enjoy the view.”

“Because it will be your last.”

And it may sound like he was being overly dramatic, but 54 days after I was standing next to that lake, this happened. Audience: Oh! Freaking terrifying, right?

This was the biggest eruption this volcano had had in 60-some-odd years, and not long after this video ends, the camera that was taking the video is obliterated and the entire lake that we had been sampling vaporizes completely.

But I also want to be clear that we were pretty sure this was not going to happen on the day that we were actually in the volcano, because Costa Rica monitors its volcanoes very carefully through the OVSICORI Institute, and we had scientists from that institute with us on that day.

But the fact that it erupted illustrates perfectly that if you want to look for where carbon dioxide gas is coming out of this oceanic plate, then you should look no further than the volcanoes themselves.

But if you go to Costa Rica, you may notice that in addition to these volcanoes there are tons of cozy little hot springs all over the place. Some of the water in these hot springs is actually bubbling up from this deeply buried oceanic plate. And our hypothesis was that there should be carbon dioxide bubbling up with it, but something deep underground was filtering it out. So we spent two weeks driving all around Costa Rica, sampling every hot spring we could find — it was awful, let me tell you. And then we spent the next two years measuring and analyzing data.

And if you’re not a scientist, I’ll just let you know that the big discoveries don’t really happen when you’re at a beautiful hot spring or on a public stage; they happen when you’re hunched over a messy computer or you’re troubleshooting a difficult instrument, or you’re Skyping your colleagues because you are completely confused about your data. Scientific discoveries, kind of like deep subsurface microbes, can be very, very slow.

But in our case, this really paid off this one time.

We discovered that literally tons of carbon dioxide were coming out of this deeply buried oceanic plate. And the thing that was keeping them underground and keeping it from being released out into the atmosphere was that deep underground, underneath all the adorable sloths and toucans of Costa Rica, were chemolithoautotrophs.

These microbes and the chemical processes that were happening around them were converting this carbon dioxide into carbonate mineral and locking it up underground. Which makes you wonder: If these subsurface processes are so good at sucking up all the carbon dioxide coming from below them, could they also help us with a little carbon problem we’ve got going on up at the surface? Humans are releasing enough carbon dioxide into our atmosphere that we are decreasing the ability of our planet to support life as we know it. And scientists and engineers and entrepreneurs are working on methods to pull carbon dioxide out of these point sources, so that they’re not released into the atmosphere.

And they need to put it somewhere.

So for this reason, we need to keep studying places where this carbon might be stored, possibly in the subsurface, to know what’s going to happen to it when it goes there.

Will these deep subsurface microbes be a problem because they’re too slow to actually keep anything down there? Or will they be helpful because they’ll help convert this stuff to solid carbonate minerals?

If we can make such a big breakthrough just from one study that we did in Costa Rica, then imagine what else is waiting to be discovered down there. This new field of geo-bio-chemistry, or deep subsurface biology, or whatever you want to call it, is going to have huge implications, not just for mitigating climate change, but possibly for understanding how life and earth have coevolved, or finding new products that are useful for industrial or medical applications.

Maybe even predicting earthquakes or finding life outside our planet. It could even help us understand the origin of life itself.

Fortunately, I don’t have to do this by myself.

I have amazing colleagues all over the world who are cracking into the mysteries of this deep subsurface world. And it may seem like life buried deep within the earth’s crust is so far away from our daily experiences that it’s kind of irrelevant.

But the truth is that this weird, slow life may actually have the answers to some of the greatest mysteries of life on earth.

Dr. Karen Lloyd is an Associate Professor in the Department of Microbiology at The University of Tennessee, Knoxville. She received her BA, in 2000, from Swarthmore, her MA and Ph.D. at the University of North Carolina, Chapel Hill and did her Postdoc at Aarhus University, in Denmark.

Her research integrates geomicrobiology, molecular biology, and geochemistry to determine how microorganisms influence marine geochemical cycles.

The goal is to link uncultivated microorganisms to their geochemical functions and explore how these communities react to changing environmental conditions.

Subseafloor ecosystems likely contain the majority of Earth’s prokaryotic biomass, but their geochemical effects are largely untested. Lloyd’s Lab focus on the following questions:

  1. What are the carbon sources and electron acceptors/donors for uncultured microbial groups?
  2. Do these organisms use previously undocumented or recalcitrant energy and carbon sources?
  3. Are these organisms living at life’s energetic limits?

Lloyd’s Lab uses single-cell technologies to link an organism’s function with its genetic identity without having to grow it in pure culture. The focus is on organiccarbon degradation, production or consumption of greenhouse gases, metal cycling, and novel microbial energy sources. And study sites include deep-sea hydrocarbon seeps and hydrothermal vents, as well as nearshore sites.

Breathing Rocks
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