The Underdark

The Underdark

This was mostly (over 95%) written by The Desertborn Midbari Asaqyi Rajara Sundari (friend of the divine). Her official title is Friend of the Divine, but she is also a friend of the underdark. She is also a well-trained and talented geologist and geobiologist, a planetologist It is slightly repetitive because I combined 4 different conversations.

ChemoLithoAutotrophs

It may seem like we're all standing on solid ground right now, but we're not. The rocks and the dirt underneath us are crisscrossed by countless tiny little fractures and empty spaces. And these empty spaces are filled with astronomical quantities of microbes.

The deepest that we found microbes so far is five kilometers down. 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.

You may not have ever thought about these microbes that are deep inside the planet'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, you should be proud. It pales in comparison to the number of microbes that are covering the entire surface of the planet, like in our soils. Collectively, these weigh about two billion tons.

It turns out that the majority of microbes on the planet aren't even in the soil or our guts or sewage treatment plants. Most of them are actually inside the planet's crust. Collectively, these weigh 40 billion tons.

This is one of the biggest biomes on the planet.

The possibilities for what life is like down there, or what it might do for us, are limitless.

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 (an eccentric choice for a pet but good eating), 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 planet, rocks included, before the end of the week.

In fact, many of them probably haven't even undergone a single cell division since the time of first landing nearly 3000 years ago. Which sounds just crazy.

It is challenging to wrap your head around things that are so long-lived.

I thought of an analogy that helped me. It's like trying to figure out the life cycle of a tree ... if you only lived for a day.

So like if your 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.

We know this is ridiculous, but that is because we live for longer than a year. We know that trees are just waiting for summer so they can reactivate. If our lifespan were significantly shorter than that of trees, we might be completely oblivious to this totally mundane fact.

When we say that these deep subsurface microbes are just dormant, are we like the hypothetical 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, their seasons more on the scale of ice ages, 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.

There's actually an evolutionary payoff to being extraordinarily slow. We should not equate being slow with being unimportant.

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

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. A crazy way to live, but shockingly seems to work out for a lot of microbes in planet. Many billions of tons of biome live this way, it is obviously not as impractical as it sounds.

The other possibility is for a microbe to just say, "Nah, We don't need the surface world, we’re good down here." For microbes that go this route, they have to get everything that they need in order to survive from inside the planet.

Some things are actually easier for them to get. They're more abundant inside the planet, like water or nutrients, like nitrogen and iron and phosphorus, or places to live. These are things that people literally kill each other to get ahold of up at the surface world.

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.

As anyone who has spent anytime during the day on the surface of Araxes, we get maybe too much energy from the sun.

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.

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 many different elements. They can do this with sulphur, iron, manganese, nitrogen, carbon, and bizarrely some of them can use pure electrons, straight up. 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.

We know that plants do more than just make food. They also make a waste product, oxygen, which the rest of us are 100 percent dependent upon in case you hadn’t noticed. 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.

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.

Am I talking about biology, or am I talking about geology? This stuff really blurs the lines. To do this thing, I have to be a biologist who studies microbes that kind of act like rocks, then I should probably start studying geology.

Volcanoes are no doubt the most interesting part of geology. Many volcanoes on planet arise because a continental tectonic plate crashes into another continental plate. As this continental 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.

Subduction Zones are like portals into the deep planet, where materials are exchanged between the surface and the subsurface world.

I was invited by some of my colleagues to come and work with them on some of the volcanoes.

We wanted to ask the very specific question: Why is it that the carbon dioxide that comes out of this deeply buried 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?

That lake in the crater is made of pure battery acid, we were measuring.

And at some point while we were working inside the crater, I turned to my colleague 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 crater lake of battery acid, the biggest eruption this volcano had had in 60-some-odd years. The entire crater lake that we had been sampling vaporizes completely.

We were pretty sure this was not going to happen on the day that we were actually in the volcano, because we monitor our volcanoes very carefully.

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

In addition to these volcanoes there are tons of cozy little hot springs all over the place, very popular with seeqs. Some of the water in these hot springs is actually bubbling up from this deeply buried tectonic plate.

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 round, sampling every seeq hot spring we could find. Awful job, but someone with seniority and grant funding had to do it.

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 relaxing at some seeq’s beautiful hot spring; they happen when you're hunched over a messy computer or you're troubleshooting a difficult instrument, or you're cortexing your colleagues because you are completely confused about your data.

Scientific discoveries, kind of like deep subsurface microbes, can be very, very slow.

This really paid off. We discovered that literally tons of carbon dioxide were coming out of this deeply buried plate. And the thing that was keeping them underground and keeping it from being released out into the atmosphere was that deep underground, 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 the ongoing carbon problem we've got going on up at the surface?

Human activity releasing carbon dioxide into our atmosphere that can decreasing the ability of our planet to support life as we know it.

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.

For this reason (and others), 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?

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 planet have coevolved, or finding new products that are useful for industrial or medical applications.

The Rocks, sand and soil beneath our feet in the ground is home to a massive, mysterious world of microbes -- some of which have been in the planet's crust for hundreds of thousands maybe millions of years

The Cauldron Spring

The Cauldron Spring is one of the some places on the planet where we have access to where these subterranean organisms interact with the surface world.

The Cauldron Spring arose when one tectonic plate crashed into another tectonic plate. As the subducting tectonic plate moves under the other tectonic plate, materials such as water, carbon dioxide and other minerals are squeezed out of it. These subduction zones are access portals to the underdark where materials are exchanged between the surface and subsurface worlds.

Besides volcanos, the subduction zone also has many hot springs where the water bubbles up from these deeply burried subduction zones, which are the usually sites for wati. The ChemoLithoAutotrophs filter out the carbon dioxide which would otherwise bubble up with the water, which would make the wati uninhabitably toxic. The ChemoLithoAutotrophs filter lock up the carbon dioxide by converting it into solid carbonate minerals such as limestone.

Not all such springs are so benevolent, some Lithoautotrophic microbial consortia metabolize energy-rich pyrites to form sulfites, which form potentially corrosive sulfuric acid when dissolved in water and exposed to aerial oxygen. Which is why some springs are essentially cauldrons of battery acid. They have their other uses, but are uninhabitable.

The ChemoLithoAutotrophs are what make it so that the Carbon Dioxide squeezed out of the subducting tectonic plate are only emitted from the volcano and not distributed throughout the entire subduction zone.

Most wati are dependent on such springs. These oases are precious gifts from the Aototrophes deep in the Underdark subduction zone.

The ChemoLithoAutotrophs exhalation byproduct is not oxygen like plants or carbon dioxide like animals, but other minerals such as rust or pyrite or carbonates like limestone.

These ChemoLithoAutotrophs are extremely resilient (like rocks) with an ultra-slow metabolism (like rocks) that get their energy from rocks, that produce as their biological process other rocks. This blurs the lives between biology and geology.

The ChemoLithoAutotrophs fill the niche as the anchor of the foodchain usually occupied by plants. They use chemical reactions using sulphur, iron, manganese, nitrogen, and carbon. Some can absorb electrons directly.

The total mass of surface and near-surface microbes is about 2 billion tons. The total mass of deep crust microbes is about 40 billion tons.

The total biomass of the planet is about 300 billion tons, of which about 50 billon tons is the total annual primary biological production of biomass. These Autotrophs make up about one eighth of the planet’s total biomass. The metabolism of these deep crust autotrophs is very slow. Some of the samples I collected have not undergone a cell division since probably before the colonization era.

Prochlorococcus

Araxes has at least 2 billion billion billion Prochlorococcus, sand plankton, the most abundant photosynthetic species on the planet, which provides the majority of the planetary oxygen and are the very bottom of the food chain, the so-called sand-plankton. Prochlorococcus eac have about 2000 genes, 1000 of these genes they share in common, the rest are adapted depending on the particular environmental conditions. Collectively the Prochlorococcus have over 80,000 genes, which is more than people. Prochlorococcus produce 100 times more carbon dioxide than vascular plants we typically think of and cultivate. The Prochlorococcus encapsulate most of the surface moisture, and are the planet’s primary oxygen producers and provide most of food and water to the grazing creatures that live in the upper 200 meters of the planet.

Most of the nutrients and water consumed by the Prochlorococcus are produced by the deep-crust ChemoLithoAutotrophs in a comfortable symbiotic relationship. It also indirectly acts as the planet’s information network.

Plants, fungi, and most microbal life lack a nervous system to communicate. Instead, chemical signals are passed within and between the colonies. These are often chemical reactions between colonies but sometimes symbiogenetic exchanges within colonies.

Unlike most macrocellular life, microbal life does not depend upon linear inheritance of genes, but instead can actually exchange segments of genes from other organisms thru symbiogenesis. Changes in environmental, particularly changes and shifts in the chemical makeup of the environment often results in an accelerated symbiogenetic exchange of these genes between micro-organisms. This results in chemical signals being passed within and between colonies.

My professional education in planetology combined with my spiritual training, the net result is that in many ways we can read the planet. With study and practice, you can learn to taste the difference or even feel it. In some rare cases, sense it but not know why.

The pulse of the planet can be taken at these subduction outcroppings of the underdark. Today however, we don’t need any such esoteric skills. Look at this. Goop.

Prochlorococcus’ ancestors changed the planet in ways that made it possible for us to evolve, and hidden in its genetic code is a blueprint that may inspire ways to reduce our dependency on fossil fuel.

But the most amazing thing is that there are three billion billion billion of these tiny cells on the planet,.

Four billion years ago, there was no life on the planet,there was no oxygen in the atmosphere. Then came Photosynthesis which changes that planet into the one we enjoy today, teeming with life, teeming with plants and animals?

About two and a half billion years ago, some of these ancient ancestors of Prochlorococcus evolved so that they could use solar energy and absorb it and split water into its component parts of oxygen and hydrogen. And they used the chemical energy produced to draw CO2, carbon dioxide, out of the atmosphere and use it to build sugars and proteins and amino acids, all the things that life is made of. And as they evolved and grew more and more over millions and millions of years, that oxygen accumulated in the atmosphere. Until about 500 million years ago, there was enough in the atmosphere that larger organisms could evolve. There was an explosion of life-forms, and, ultimately, we appeared on the scene.

While that was going on, some of those ancient photosynthesizers died and were compressed and buried, and became fossil fuel with sunlight buried in their carbon bonds. They're basically buried sunlight in the form of coal and oil.

Today's photosynthesizers, their engines are descended from those ancient microbes, and they feed basically all of life on the planet.

Your heart is beating using the solar energy that some plant processed for you, and the stuff your body is made out of is made out of CO2 that some plant processed for you.

Basically, we're all made out of sunlight and carbon dioxide. Fundamentally, we're just hot air.

So as terrestrial beings, we're very familiar with the plants on land: the trees, the grasses, the pastures, the crops.

There's an invisible pasture of microscopic photosynthesizers called phytoplankton that fill the upper 200 meters of the surface, and they feed the entire ecosystem. Some of the animals live among them and eat them, and others scurry up to feed on them at night, while others sit in the deep and wait for them to die and settle down and then they chow down on them.

These tiny phytoplankton, collectively, weigh less than one percent of all the plants on land, but annually they photosynthesize as much as all of the macroscopic plants.

Every year, they fix 50 billion tons of carbon in the form of carbon dioxide into their bodies that feeds the ecosystem.

How does this tiny amount of biomass produce as much as all the macroscopic plants?

Well, they don't have trunks and stems and flowers and fruits and all that to maintain. All they have to do is grow and divide and grow and divide. They're really lean little photosynthesis machines. They really crank.

So there are thousands of different species of phytoplankton, come in all different shapes and sizes, all roughly less than the width of a human hair.

Flow cytometry was developed for biomedical research for studying cells like cancer cells, but it turns out we were using it for this off-label purpose which was to study phytoplankton, and it was beautifully suited to do that.

Here's how it works: You inject a sample in this tiny little capillary tube, and the cells go single file by a laser, and as they do, they scatter light according to their size and they emit light according to whatever pigments they might have, whether they're natural or whether you stain them. And the chlorophyl of phytoplankton, which is green, emits red light when you shine blue light on it.

We used this instrument for several years to study our phytoplankton cultures, just studying their basic cell biology.

All that time, we thought, well wouldn't it be really cool if we could take an instrument like this out on a ship and just squirt seawater through it and see what all those diversity of phytoplankton would look like. We managed to get my hands on what we call a big rig in flow cytometry, a large, powerful laser with a money-back guarantee from the company that if it didn't work on a ship, they would take it back.

We didn't think it would, because we thought the ship's vibrations would get in the way of the focusing of the laser, but it really worked like a charm. And so we mapped the phytoplankton distributions across the ocean. For the first time, you could look at them one cell at a time in real time and see what was going on -- that was very exciting.

One day, we noticed some faint signals coming out of the instrument that we dismissed as electronic noise for probably a year before we realized that it wasn't really behaving like noise. It had some regular patterns to it. To make a long story short, it was tiny, tiny little cells, less than one-one hundredth the width of a human hair that contain chlorophyl. That was Prochlorococcus.

Prochlorococcus are the smallest and most abundant photosynthetic cell on the planet.

At first, we didn't know what they were.

Over the years, we and others, many others, have studied Prochlorococcus and found that they're very abundant over wide, wide ranges in the open ecosystems. They're particularly abundant in what are called the open gyres.

Collectively, they weigh more than the planet’s human population and they photosynthesize more than all of the crops we cultivate.

Over the years, as we were studying them and found how abundant they were, we wondered how can a single species be so abundant across so many different habitats.

And as we isolated more into culture, we learned that they are different ecotypes. There are some that are adapted to the high-light intensities, and there are some that are adapted to the low light. And then we learned that there are some strains that grow optimally along the equator, where there are higher temperatures, and some that do better at the cooler temperatures as you go north and south.

As we studied these more and more and kept finding more and more diversity, we wondered how diverse are these things.

Sequence their genomesand we really looke under the hood and look at their genetic makeup.

And we've been able to sequence the genomes of cultures that we have, but also recently, using flow cytometry, we can isolate individual cells from the wild and sequence their individual genomes, and now we've sequenced hundreds of Prochlorococcus.

And although each cell has roughly 2,000 genes -- that's one tenth the size of the human genome -- as you sequence more and more, you find that they only have a thousand of those in common and the other thousand for each individual strain is drawn from an enormous gene pool, and it reflects the particular environment that the cell might have thrived in, not just high or low light or high or low temperature, but whether there are nutrients that limit them like nitrogen, phosphorus or iron. It reflects the habitat that they come from.

If each cell is a smartphone and the apps are the genes, when you get your smartphone, it comes with these built-in apps and near identical main hardware. Those are the ones that you can't delete.

Even if you don't want them, you can't get rid of them. Those are like the core genes of Prochlorococcus. They're the essence of the phone. But you have a huge pool of apps to draw upon to make your phone custom-designed for your particular lifestyle and habitat.If you travel a lot, you'll have a lot of travel apps, if you're into financial things, you might have a lot of financial apps,

If you're like me, you probably have a lot of weather apps, hoping one of them will tell you what you want to hear, or is at least more convincing about what they are forecasting.

So just as your smartphone tells us something about how you live your life, your lifestyle, reading the genome of a Prochlorococcus cell tells us what the pressures are in its environment. It's like reading its diary, not only telling us how it got through its day or its week, but even its evolutionary history.

We've sequenced hundreds of these cells, and we can now project what is the total genetic size -- gene pool -- of the Prochlorococcus federation, as we call it. It's like a superorganism. And it turns out that projections are that the collective has 80,000 genes. That's four times the size of the human genome. And it's that diversity of gene pools that makes it possible for them to dominate these large regions and maintain their stability year in and year out.