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As strange as the creatures of the microcosmos are, their lives still revolve around the same fundamentals that ours do. There’s food, reproduction, and death. Yes, even microbes, hardy as they can be, experience death. In some ways, they invented it.

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SOURCES:
https://www.smithsonianmag.com/smart-news/how-kill-tardigrade-180964069/
https://www.jstage.jst.go.jp/article/jop/51/0/51_e001/_html/-char/en
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https://link.springer.com/article/10.1007/BF01279469
https://www.ncbi.nlm.nih.gov/pubmed/7400244
https://www.ncbi.nlm.nih.gov/pubmed/7311876
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248701/
https://pubmed.ncbi.nlm.nih.gov/23864564/
https://pubmed.ncbi.nlm.nih.gov/23246407/
https://elifesciences.org/articles/20023
https://www.google.com/books/edition/Nematode_Trapping_Fungi/O13FBAAAQBAJ
https://en.wikisource.org/wiki/The_Voice_in_the_Night
https://www.tandfonline.com/doi/full/10.1080/21501203.2011.562559
https://www.hopkinsmedicine.org/health/wellness-and-prevention/sun-safety
https://www.microscopyu.com/references/cellular-phototoxicity
https://onlinelibrary.wiley.com/doi/full/10.1046/j.1365-313X.2003.01868.x
https://www.cancer.gov/publications/dictionaries/cancer-terms/def/reactive-oxygen-species
https://pubmed.ncbi.nlm.nih.gov/19393747/
https://bioone.org/journals/zoological-science/volume-21/issue-8/zsj.21.823/Defense-Function-of-Pigment-Granules-in-the-Ciliate-Blepharisma-japonicum/10.2108/zsj.21.823.full

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As strange as the creatures of the microcosmos are, their lives still revolve around the same fundamentals that ours do.

There’s food, there's reproduction, and there's death. Yes, even microbes, hardy as they can be, experience death.

In some ways, you could say they invented it. And on our journey through the microcosmos, we’ve watched those deaths through many lenses. Some are slow, calm affairs, while others are explosive or creepy.

And today, we’re going to try something new for our channel. We have gathered a few of our favorite episodes about death in the microcosmos so that we can see where our journey has taken us. So yeah, this is the kind of video you can turn on, and leave on for awhile.

This first video is also one of our oldest, so you’ll notice that a lot of footage in it looks very different from what we show these days because thanks to the support of our viewers, we’ve been able to upgrade our microscope multiple times over the course of this show. So the microscope may be different. But the death, well, the death remains the same.

This round little unicellular creature came to us via a plankton net, a mesh with tiny, microscopic holes through which we ran hundreds and hundreds of liters of water, letting us collect anything too large to pass through. We haven’t been able to identify this species yet, making it a bit of a mystery. But the bigger mystery is still to come because this little creature is about to undergo that most universal and unknowable experience of all, death.

Death comes to the microcosmos in many forms. Like this Stentor Polymorphous, slowly expelling the contents of its once trumpet-like body into the surrounding environment. Or this dead larva, whose exoskeleton is now an inanimate host to two unicellular organisms.

Even the mighty tardigrade, which has survived as a species through multiple mass extinctions, is not immune to death. This is, of course, the natural order of things. Predators hunt, and their prey attempts to survive, with varying levels of success.

This is Loxophyllum meleagris, a large unicellular organism that we’ve shown before eating a rotifer. This one is practically stuffed with those multicellular creatures, we counted five rotifers inside of it. But sometimes the predator becomes the prey, and even the Loxophyllum meleagris has to find ways to ensure its survival when other species come after it.

This seemingly unlikely threat is the Lacrymaria olor. Its name in Latin means “tears of a swan”, a name that suits both its teardrop shape and its neck-like extension, which gets up to eight times longer than its body in search of prey. Sometimes, we can see its neck poking out of the dirt on our microscope slide.

But even knowing that, you’d be forgiven for thinking it unlikely that something so small could pose a problem for those larger Loxophyllum. And yet, the Lacrymaria manages to take quite a chunk out of the Loxophyllum. The Loxophyllum though, survives thanks to its ability to regenerate the piece that was taken, but not all prey gets so lucky.

Here, this rotifer has been killed by a heliozoan, destined to become food, a fate that this flagellate is about to share as it becomes captured by a heliozoan that is in the middle of cell division. The flagellate has been trapped by those long extensions, called axopods, that radiate out from the heliozoan’s body. As the flagellate comes further in, it will be engulfed by the cells into its own food compartment called a vacuole.

There, it will be lysed open and its contents digested by the heliozoa. In the end though, the natural order comes for predators too. Here, another heliozoan’s dying cellular body attracts the various decomposers of the microbial world.

Aside from predators, there are many other factors that lead a single-celled organism to die, changes in temperature, oxygen concentration, pH, water quality, so much more. This single-celled organism is swollen because the water surrounding it is entering the cell via osmosis. Many organisms have water pumps called contractile vacuoles that they use to push water back out and prevent that swelling.

But as in the case of this organism, sometimes those contractile vacuoles stop working, and when that happens, the cell swells and explodes. Other times, the cause of death is harder to determine, like this Paradileptus that spent several hours swimming before going still, its shape beginning to change until it melts away, seeming to kill not only the Paradileptus but this small green cell swimming nearby, but leaving other smaller flagellates seemingly unaffected. And this brings us back to the beginning, with our mystery organism that is about to undergo a death laden with more mysteries.

At first, the cell looks like it’s just melting away, dissolving into something that resembles a microbial Milky Way, except that for a few seconds, it almost looks like the cell membrane is able to close itself back up. We think, though we can’t know for sure, that some of the mechanisms inside the cell are still working, and that the organism is trying to recover. But alas, survival is not in the cards.

Its membrane goes through lysis, releasing its insides into the surrounding environment. This death is unlike any other kind of death we’ve observed under our microscope, and we’re still not sure what caused it. Perhaps there were so many organisms in the sample that they depleted the oxygen, and this organism could not continue cellular respiration.

But perhaps it was something else. Death at every size holds its own mysteries, but it also reveals. The observations we make, even the guesses we come up with, tell us about the way these microbes interact with their environment, the way their own bodies work, and the connections that exist between them.

It is only ever in the mysteries that knowledge is waiting to be found. So we just saw a small fraction of how many ways there are for microbes to die. But maybe now you’re asking yourself a more fundamental question: what even is death?

Well, weirdly, none of us will ever fully know the answer. But that doesn’t mean we can’t try to use what we know of chemistry and life to begin to describe it, as we’ll see in our next video. This is a ciliate, Loxodes magnus.

It is about to die. Of course, depending on your time scale, we’re all about to die. To the grand canyon, or the sun, things that have existed for millions or billions of years, we are each weird little bubbles of peculiar chemistry that form and then pop, form, and then pop.

But this ciliate, and with our new microscope you can really see those cilia beating, is about to pop right before your eyes. It looks fine right now. You can even see, inside it, it’s last meal, a Trachelomonas.

So we don’t think it’s starving to death. It seems to be trucking along just fine. Loxodes Magnus are microaerophilic organisms, preferring a low concentration of dissolved oxygen in their environment, but not too low.

So maybe the concentration on the slide was too high, though we’ve witnessed many others who have been just fine in our preparations. So no, we can’t tell you why this ciliate is about to die, but we can tell you that right here, that’s where James, our master of microscopes, first saw something strange. The moment the ciliate shifted direction, a little trail of cell membrane and cytoplasm.

No reason. Nothing grabbed it, it didn’t snag on anything. But a little bit of what was once a part of the organism was suddenly, no longer a part of it.

That cytoplasm is full of complicated molecules that are what chemists would call, far from equilibrium. Equilibrium is the situation in which chemicals no longer have a tendency to react over time. In general, a thing that you can say for sure is that all the stuff outside of living cells is either at chemical equilibrium, or it is headed there.

Whereas stuff inside cells is not at equilibrium, and it’s not headed there either. How are all of these chemicals that, if left alone, would rapidly reach equilibrium managing to not do that? Life.

That is what life is. A bunch of chemicals that take in energy in order to keep each other from reaching equilibrium. Quick break from our friend, the way we define life in biology classes is, wrong.

It’s not even really a definition, it’s a set of qualifying factors. Life has to take in energy. Life has to reproduce, it must respond to its environment, it must consist of cells.

This is not a definition, it’s an attempt to draw a line, to create a boundary. And that makes sense for things that are actually amorphous and complicated, like social constructs. But life is not a construct of our opinions, but of reality.

Life is a chemical system that uses energy to keep itself from reaching chemical equilibrium. Why do they do it? Oh, well maybe let’s not go that deep, at least not today.

Suffice it to say, a system that did this developed on this planet and now, billions of years later, it is still doing it. We have many things in common with this ciliate, and not to belabor the point, but one of those things is that we will die. You’ve may have noticed by now that this video isn’t about what life is, it’s about what death is.

It’s just that, first, we had to define life. Life is chemicals working together to take in energy to keep themselves far from equilibrium. Death is not the return to chemical equilibrium.

The process of decay can last decades. Likewise, many parts of my body will return to equilibrium over the course of my life, I’m shedding skin cells right now and so are you. The atoms and molecules of my body are replaced with new ones over and over and over again.

But I will only die once. Likewise, our ciliate has been shedding cytoplasm and cell membrane for minutes now, and that shed cytoplasm is dead, no doubt. But the organism lives.

Its chemistry continues. For now. Death is the moment when the system that maintains the far from equilibrium state ceases existence.

And we can imagine that at many scales. That can happen to individual bits of an organism, as it is happening to the chemicals spilling out of our Loxodes right now. It can also happen to an individual cell in an organism.

And that happens all the time. It is happening right now inside you. It can also happen to an organism.

That’s what we usually think of as death, with our focus, so often, on the individual. But we can keep moving up the scale and find yet other kinds of death. When a common genetic system that was useful for keeping many similar but individual organisms alive ceases to exist, that is an extinction.

A kind of death. And when the system that has kept all life on earth far from equilibrium for billions of years, that system that we all share of nucleic and amino acids, when that ceases to exist, that will be something else. A terrible kind of death that we do not even have a name for.

But it will be a death. The largest death, I suppose, until heat death, when everything in the universe has found equilibrium. Our ciliate is about out of time now.

I don’t know when we can call it, when we can pronounce the time of death, but this seems as good a time as any. Here, we have death. The system that was using energy to keep itself from reaching equilibrium has ceased to exist.

Hey, welcome back. If you’ve come out of that video with some existential dread about the state of the universe, that is very reasonable. However, on our next stop in this journey, we’re going to argue that sure, chemical equilibria are scary, but if you’re a nematode, maybe you should worry about fungi first.

There are plenty of horror stories that begin innocuously enough. A new home, a camping trip with friends, a doll purchased at an estate sale…. This one starts with some ponds, the same set of ponds that James, our master of microscopes, has been sampling every week for the past three years.

Which means that he’s collected so many microbes from these waters that you might think they’d get a bit boring or redundant. But you should never underestimate nature’s capacity for surprise. Recently, James came home with some samples from these ponds.

And as usual, he prepared some slides and checked on the organisms within, finding some nematodes like this one slithering about on the slide. And all seemed well, so he stored the slides and his new friends in a humidity chamber and waited to observe them after a few more days. But two days later, all would not be well.

This is where we build our suspense. In a movie, this would be the moment where we assess the unsettling basement or the dark woods, and then consider retreating to safety. This is the creepy doll, only there hasn’t been any thumps in the middle of the night, so everything seems okay, right?

We’re looking at the spores of a fungus, one belonging to the group Arthrobotrys. And when it’s just floating around like this, it seems quite harmless—especially when compared to the nematodes we showed earlier, which are part of a whole family of worms that are notorious for their parasitic lifestyle. And if you were to write off Arthrobotrys as a potential threat, you would be correct… most of the time.

It does spend much of its life aligned with the dead, but only to sustain itself on the remains of decayed life and organic matter. Arthrobotrys species are found all around the world, occupying everything from soil to animal feces in the many varied climates that make up our planet. And wherever it is, the fungus ensures that nutrients like nitrogen from dead organisms and other waste cycle through ecosystems.

But when nitrogen is scarce, these fungi will resort to hunting it down from living sources. And what better prey than the nematode, a fellow dweller of the soil and one of the most abundant animals on earth? When James put his slides into the humidity chamber, he had no notion of what these nematodes would be facing, and so no expectation of what he would find.

But when the slides came back out, what he observed was something he’d only seen once before, in a drawing done two years ago by one of his close friends, Katelyn Solbakk. In it, you can see a nematode whose body has been clinched into segments by some kind of bulbous, thing. What you’re seeing is the fungus’ most brutal design.

But to get there, it must morph from decomposer to predator, no longer consuming what has already been dead, but actively killing. It begins by weaving a trap out of itself. It threads the hyphae of its mycelium out and then back in, forming a living loop that repeats to form a net.

But a net is only one part of a trap, the other part is the lure. The fungi can find nematodes by following traces of their pheromones like they’re breadcrumbs. And more nefariously, they can mimic the smell of certain food cues to draw the worm in, like a siren working through scent instead of song.

The nematode has no reason to suspect anything, even as it swims closer and closer and eventually through the fungal rings. But as it does, the movement of worm and water triggers the rings to constrict. The worm is trapped, but the worst is still yet to come.

The fungus’ hyphae begin to grow off from the loop, puncturing the worm’s cuticle and paralyzing it. The threads swell up into a bulb that produces more hyphae to spread through the rest of the nematode. And then the fungus feeds and feeds, quickly digesting the rest of the nematode’s body from within.

It is a gruesome death. Here is one nematode, just recently trapped. And here is the worm again, four days later.

You can see the infection bulb where the fungus first punctured and expanded. And the whole body of the worm seems taken over, no longer a clear tube, but instead a corpse that has become home to its cause of death. The Arthrobotrys fungi are not the only ones capable of trapping and feeding upon nematodes.

There is a whole range of nematode-trapping fungi with their own methods, though the species Arthrobotrys oligospora is perhaps the most plentiful of these fungi and also the best studied. Maybe it’s just us, but it’s somewhat unsettling to realize that this insidiousness is all the work of a fungus, a thing that can seem so inert compared to the wiggling, active worm that it targets. But fungi do have a kinship with horror stories.

Their frequent role as decomposers naturally connects them with the dead. Plus, they come equipped with their own creeping sense of dread with images of mycelia weaving through bodies. And authors have drawn inspiration from the notion of fungal horror.

There are many works--like the famous Gothic tale We Have Always Lived in the Castle, or the short story “The Voice in the Night,” or recent novels like Mexican Gothic and Wanderers— that draw on everything from poisonous mushrooms to colonizing fungi to create their terror. But whatever we seek to scare ourselves with in fiction, horror has its purpose in nature. As we’ve pointed out, nematodes are one of the most abundant animals on earth.

They play an important role in decomposition...but they’re also the source of many diseases—both in animal bodies and in plants. So having them be slightly less abundant is important to our ecosystem as well. In fact, scientists have been studying these fungi to develop better nematode-fighting strategies for agriculture.

So as is the case with many good horror villains, there is a version of this story where the nematode-trapping fungus is the hero. Unless, of course, you’re the nematode. And for our last video, our microbes are dying at the hands of an unusual enemy.

It’s James, with an UV laser, in the laboratory. Maybe it sounds like a microscopic version of the game Clue, but there’s a point to it all, we swear. Blepharisma have appeared on our channel several times before.

In fact, this channel got its start thanks to a video that James, our master of microscopes, once posted of a Blepharisma dying. Around three million people watched that video, including me, your host Hank Green. So if you enjoy this channel, you can thank that dead Blepharisma.

But perhaps you should wait for another day to thank them. Because in about ten seconds, you’re going to watch a Blepharisma explode. Here it is, glowing with autofluorescence underneath UV light.

You can see its oblong shape and oral groove outlined in red…but not for long. The red becomes brighter and brighter, but it also looks like it’s starting to expand. And then suddenly, the walls of the blepharisma burst, the organism popping like a crimson balloon.

The blepharisma bubbles and pours into its surroundings and it all happens within a matter of seconds. Let’s watch it again. Dead or dying microbes are a common enough sight in our journey through the microcosmos.

And there are many potential culprits behind these deaths: predators, accidents, environmental changes, the inevitable march of life into death. But the culprit this time… well, it was us. Us and the UV light that is part of our new fluorescence microscope upgrade.

And our UV light has been very exciting for us. In particular, it’s allowed us to look for methanogens, or Archaea, which sometimes take up residence inside protists. Under normal light, it’s hard to tell the tiny archaea and the tiny bacteria apart.

But under UV light, the archaea will shine blue. So UV can reveal new aspects of the microcosmos. But if you’ve ever fallen asleep on a beach or just stayed out in the sun a bit too long, you may have also experienced the darker side of UV light.

No one wants a sunburn, but fortunately, we have defenses, like hair, and melanin, and sunscreen which can block or absorb UV rays before they cause further damage in our cells. We also, and this is crucial, have more than one cell...so if some of them die, which when you get a sunburn they do, the rest of our bodies can live on. Not all organisms have these sorts of protections.

Or if they do, they’re designed for exposure to the sun, not the intense scrutiny of our UV light. So when James wants to hunt Archaea, he has to be careful. He can quickly shine the UV light to see if anything blue appears.

But he has to quickly shut it off. Because as we’ve seen, even a few seconds of exposure to the UV light will kill off his pond buddies. We want to note that as we said earlier, death is a common reality of the microcosmos…we just usually prefer to walk in on a microbe dying rather than being the cause of death.

But for this episode, we decided to make an exception and use our UV light for an extended period of time, with the knowledge that it would kill the microbe we were watching. Because these explosions illustrate the cost of doing business with light. The word for this business is phototoxicity.

Death by light. And while it can happen under other monochromatic lights, the particular wavelength and intensity of our UV light makes it much more harmful to our organisms than our other red, blue, or green light sources. This death starts with excitation.

When the light hits the organism, it can potentially excite chemical structures inside the cell, sending electrons up and down, and producing fluorescent colors in the process. But the colors aren’t the only thing that gets created. If there’s oxygen around, it will react with the excited fluorescent molecule, creating what are known as reactive oxygen species.

In biology, reactive oxygen species are byproducts of different cellular processes that metabolize oxygen, which can make them part of normal life. There are even reactive oxygen species that are involved in signaling pathways. But the “reactive” in their name is key to what makes an excess amount of them dangerous.

If you are an organism, and you are, there are a lot of reactions you want to have happen in your cells. You want your DNA to link together correctly, you want your enzymes to find the right substrates. But reactive oxygen species are happy to react with all of those molecules too, damaging them and getting in the way of the chemistry that we need to survive.

What phototoxicity will look like depends on the organism and the light being directed at it. For the organisms we’ve been showing here, like this homalozoon, the overall effect of this intense UV light seems to be unanimous: the cell swells up and bursts open, like a galaxy erupting on our slide. But while the overall effect is the same, the internal machinations are likely different, triggered by a complex interplay of different chemicals that nonetheless react to our light source in a similar, catastrophic fashion.

While we’re not sure of the culprits behind the homalozoon’s death, we can identify one of the chemicals that likely sets off the blepharisma’s death. It’s the reddish pigment molecule called blepharismin that gives the ciliate its color under more normal circumstances. Outside of the UV light, you can see the membrane-bound pigments neatly distributed along the rows that stretch from one end of the blepharisma to the other.

But under our UV light and with oxygen in the environment, the blepharismin reacts to form reactive oxygen species, and death follows quickly from there. But while toxic in our experiment, we should note that the blepharismin serves a key purpose for the blepharisma: defense. These pigment molecules are toxic to some of Blepharisma’s predators in both the light and the dark.

That makes the pigment somewhat like UV light: necessary for survival, yet also a delicate negotiation. But in the same way that we manage our relationship with the sun, scientists have learned ways to manage these phototoxic reactions. They’ve had to in order to understand how we can use fluorescence microscopy to study cells and organisms.

They’ve learned how to modulate wavelength and intensity and duration, along with many other factors, to wield light in a way that better serves their purposes. In the case of the blepharisma, for example, scientists found that using a moderate light for around 1 hour wasn’t much of a problem for them. But with more time under the light, the cells would eventually die.

It’s easy to think of the microcosmos as a separate world from us, even when we know that the microscope is a bridge between large and small. But these deaths at the hand of our supposed bridge are a cautionary sign that we are encountering microbes in a world that is both natural and manufactured at the same time. The way that we light that world impacts the way we see the organisms, and it also shapes their lives—reminding us that they are stronger often than we can fathom, but fragile nonetheless.

And that brings us to the end of our tour of death in the microcosmos today, an end to a story of ends, you might say. But maybe what we’ve seen today is that there really is no end, is there? Just pauses on individual stories that nonetheless endure in the remains of the world left behind.

Thank you for coming on this journey with us as we explore the unseen world that surrounds us. And thank you to all of our patrons who make videos like the ones we’ve watched today possible. This channel could not exist without your support and we are so thankful for it.

If you’d like to join the list of patrons you’re currently seeing on your screen, you can go to patreon.com/journeytomicro. And if you’d like to see more from our Master of Microscopes, James, you can check out Jam & Germs on Instagram, and if you’d like to see more from us, there’s probably a subscribe button somewhere nearby.