On Journey to the Microcosmos, we love microbes.

We love to see them swim and wander and live out their unique lives. But we’ve also had to make peace with the fact that the microcosmos is not a peaceful utopia.

This is a world where microbes are both residents and food, which means that occasionally, we’ll have to spend our time together watching organisms, whose bodies are fractions upon fractions upon fractions of a millimeter in size, turn into vicious predators. So today, in honor of both predator and prey, we’re going to be revisiting some of our favorite videos about eating in the microcosmos. Grab a snack, and join our microbes as they snack.

And we’ll start by revisiting some of the clever strategies that microbes use to gather their prey. Despite huge differences in morphology and biological structures, all living organisms do the same three basic things; they get food, digest it, and excrete waste materials. Living organisms require energy to live.

Some produce their own food, usually through photosynthesis, we call these autotrophs, but many organisms cannot make their own food. We call these heterotrophs and they...eat. Among heterotrophic single-celled eukaryotes, food is taken into the cell in various methods but once it’s there, it's wrapped by a membrane and forms something called a food vacuole.

Then the cell flushes digestive enzymes inside the food vacuole to start the digestion. Nutrients are taken into the cytoplasm and the waste material left in the vacuole then basically fuses with the outer membrane of the cell and what's left in the vacuole is discharged into the environment In some cases, like inside this beautiful single-celled Nassula ornata which feeds on filamentous cyanobacteria, content of the food vacuole reacts with the digestive enzymes and changes color. But that process takes time.

Because each vacuole formed at a different time, they are in different stages of digestion which gives this cell it’s colorful polka dots. But how do these heterotrophic organisms get their food? Well, in spite of a remarkable amount of diversity, a lot of microorganisms use one of the same three strategies for getting their food.

Some of this will be familiar to the macro world some of it will not. One of the less familiar is filter feeding which allows larger organisms to consume suspended food particles or much smaller organisms. There are filter-feeders in the macro-world, baleen whales come to mind.

But while a whale must swim through giant clouds of small organisms, in the microcosmos, your food can come to you. Some filter feeders use hair-like structures called cilia to create a vortex that brings other microorganisms or food particles to the cell mouth. These cilia are specialized for this task and their beating creates a current that expediently and beautifully directs every nearby thing into the waiting mouth of the microorganism.

The cilia are often too small for us to see, but you can see their effects. Take a look at these Paramecia. They're consuming tiny, tiny bacteria. and you can see their cilia causing small organisms to tumble across them.

You can also see all of their food vacuoles on the inside, and if you look very carefully, you can see a new food vacuole forming, getting filled up with those tiny, bacterial cells. Some of the best and most obvious filter feeders are rotifers, micro-animals that use cilia to create swirling vortices around their mouth parts. You can see how successful this feeding strategy is by it’s belly full of algae cells.

Every time its mouth fills with more algae, it contracts to swallow the food. Now observe these single-celled organisms called stentors, they are much bigger than most other microorganisms. You can actually see them with the naked eye. and they also use filter feeding to push all of their algal food into their cell mouths.

Our second feeding mechanism, maybe the most familiar, and the most exciting is called raptorial feeding. Raptorial feeders selectively capture prey and hunt other organisms. In this video you can see Dileptus hunting.

It paralyzes one organism with the touch of its trunk-like proboscis, and then it pulls that organism into itself in a process called phagocytosis. Many of these microorganisms are armed with something called toxicysts. These are little harpoon-like structures filled with toxins and they are located on a particular part of the cell which the microorganism uses for hunting.

These tiny harpoons are then fired when they come in contact with prey organisms which then become immobilized. This is Bursaria, it’s a single-celled organism with a huge mouth, and things have not gone well for the Paramecium that is now inside it. The Paramecium dies immediately because of the toxicysts on the inside of the Bursaria, so at least it was quick.

Now get ready for some truly gorgeous footage of a micro-animal’s day going south. First Paradileptus immobilizes the rotifer with fired toxicysts and the animal is swallowed by the single-celled organism as it swims away. This is a Frontonia which is a close relative of Paramecia, but lacks the filter-feeding habits of its relatives and feeds predaciously on large diatoms and filamentous cyanobacteria such as Oscillatoria here.

Though, in this case, it turns out this Frontonia bit off a little more than he could chew. Another raptorial feeding style is called histophagy. Histophagous organisms such as these single-celled Coleps attack injured but live animals or other single-celled organisms, sucking off hunks of tissue rather than consuming whole organisms.

When they attack an animal, they enter wounds and ingest tissue often attacking in groups because their chemical sensing abilities attract many of them from a distance, like microscopic vultures. When a number of them gather in one place, it’s hard to avoid another macro-world analog...piranhas, devouring everything soft in no time at all. There is a huge variety of raptorial feeding, this is just the beginning, but we wanted to show you one more before we move on.

This is Vampyrella, an amoeba with a suitable name. It specializes in feeding on filamentous algae. First, it bores a hole through the algal cell wall and then slurps out the gooey, nutritious cytoplasm.

Our final feeding mechanism, for today at least, is diffusion feeding, in which the predator just sits in the same place, relying on the prey to accidentally make contact. This is a Heliozoa, it’s a single celled amoeboid and because of its resemblance to the sun due to the rays coming out of its cell, it’s sometimes called the “sun animalcule”. The rays are called axopodia.

These are sometimes used in locomotion and, in this case, for hunting prey. Axopodia, are cytoplasmic extensions, meaning they’re a part of the cell membrane, even though they look like they’re sticking out of it. Each one has a central supporting rod of microtubules that gives it this rigid structure.

The axopodia are coated in organelles that discharge toxins when touched, which impair or even paralyze Heliozoa's prey. After the organism is captured, those microtubules are drawn back into the cell, thus retracting the axopodia and allowing the cell to swallow the unlucky organism, or prey is just engulfed by extrusions from the cell called pseudopodia. In this video, a rotifer has been captured by a Heliozoa and it is slowly getting eaten by it.

Now this is something that happens fairly frequently, but we did capture something unusual here. While it was stuck to Heliozoa's axopodia, this rotifer actually lays its egg. But neither egg nor the rotifer is going to escape this.

Surprisingly heartbreaking. This is a Suctorian, it is a ciliate just like Paramecium and Stentor. These organisms have hair-like cilia during the early stage of their life, but as adults they develop bundles of tentacles.

Just like in Heliozoa these tentacles are supported by an internal cylinder of microtubules. The tip of the tentacles have extrusomes; these are special structures that attach to and immobilize any other ciliates that touch them. The tentacles eventually penetrate the cell membrane of the prey, and then the contents of the prey is sucked out through the tentacle.

In the clip, a suctorian has caught 4 individual Vorticella with its tentacles and is slowly sucking their cytoplasm. It looks a little like the vorticella have the suctorian surrounded, but in fact, they are powerless to escape it. It’s a dangerous world out there.

The complex chemicals created by organisms to sustain their life necessarily are useful to other organisms, as building blocks and as fuel. And so predation evolved. It’s beautiful, it’s constant, and it’s brutal.

Now that we’ve seen how the hunters of the microcosmos get their food, let’s experience the more challenging part of the predator-prey dynamic: getting eaten. For the organisms in our next video, finding themselves in the belly of the beast is just the start of a more grueling process, one that converts their bodies into nutrients. Tardigrades are famous for their capacity to survive.

If you look them up, you will be inundated with long lists of the many things scientists have thrown their way to see if the tardigrade will survive. We’ve made some lists like those ourselves. Tardigrades on the moon, tardigrades in extreme heat.

You’ve heard about them. We’ve talked about them. What else is there?

Well, here’s a surprising fact you might not have known. For certain species of tardigrades, like the one in the middle of your screen right now, you can tell the difference between a male and a female by looking at their toes. That’s right.

The toes. These tardigrades are called Milnesium, and the males of these species have a pair of claws on their feet that are shaped a little bit differently from the rest of the claws, with only one hook on each claw instead of the usual two. But after taking a closer peek at this tardigrade’s toes, we can confirm that she is a female tardigrade.

Now, that’s a fun fact for us as we watch the clip. But it does not actually do anything for the poor rotifers that are surrounding this tardigrade, who are currently stretching themselves in and out of danger. Around the tip of a tardigrade’s mouth are small bumps that we think act like little sensors.

And when those bumps make contact with a rotifer, out pops the tardigrade’s stylet—a needle that pokes out from the tubular mouth opening. That stylet pokes into the rotifer, and from there the tardigrade uses a circular structure called a pharynx in its head to create strong suction. And then, the stylet goes from functioning as a needle to functioning as a portable, built-in straw that lets the tardigrade suck out the inside of its prey.

You can see some of the bodily fluid leaving the rotifer as the tardigrade’s stylet pumps away like a beating heart. And when she is done, the rotifer remains, like an empty coffee cup. This method of eating works quite well for the tardigrade, letting her eat quickly from the prey that is directly in front of her.

But not all organisms come equipped with a weapon that lets them turn rotifers into Capri Suns. These organisms have to turn to other methods to extract nutrients from their food. This marine ciliate is called kentrophyllum, and it came to James, our master of microscopes, in a large container full of beach sand.

On a normal day, maybe we would talk more about its funny almond shape that stretches as it swims around. But today is not a normal day because this kentrophyllum is about to be overshadowed by a rotifer. Now, where is the rotifer, you might ask?

It is inside the kentrophyllum, of course. We did not catch the moment of its capture, when the toxic needles lining the kentrophyllum darted out and paralyzed the rotifer. By the time we arrived, the rotifer had already been ingested…but it was not dead yet.

You can see it wiggling and wrestling at the broad end of the kentrophyllum, causing the ciliate’s body to wrinkle and fold in on itself. But it is trapped inside of a food vacuole now, a compartment that exists to break this rotifer down. Sure, the rotifer can try and fight against the walls of the vacuole holding it hostage.

But there’s not much it can do against the digestive enzymes pouring in, or the increasing acidity of its surroundings. A food vacuole is a hostile place to be, and for minutes, its destructive tools will go to work. In the end, the rotifer will be left in dissolved pieces to be absorbed by the kentrophyllum’s cytoplasm, sustaining the organism that was the site of its last battle.

It’s a lonely death for the rotifer, with only the kentrophyllum to witness it. Though I suppose now there is also us, sharing and immortalizing that rotifer’s last moments. And if the rotifer had not died in the body of another organism, it may have ended up like this gastrotrich.

Now to be fair, they did find themselves in a very similar situation: they are both dead. But the rotifer was eaten alive, digested from the outside

while trapped in another organism. Meanwhile, this gastrotrich is going through the exact opposite situation.

It is being eaten from the inside out, by a scavenger called a peranema. Now, as far as we know, the peranema didn’t do anything to kill the gastrotrich. It was likely already dead, though we don’t know what killed it.

But the peranema is both a hunter and a scavenger. Sometimes it can be found with other peranema as they hunt down prey, in a pack of hungry microbes. At other times, the peranema scavenges.

They are notorious for being able to squeeze their way into whatever holes they find to get into a dead organism. And in this case, the gastrotrich’s exoskeleton was the right combination of available, open, and dead for the peranema, which found its way in and decided to begin helping itself to the buffet of dead tissue around it. After all, the gastrotrich won’t be needing that tissue anymore, so the peranema might as well make good use of it.

The gastrotrich’s body has likely vanished by now. Perhaps the peranema will have finished it off entirely, or some other scavenger will have joined in on the fun. Or perhaps, it will have simply faded, like the rotifer inside the kentrophyllum, its body eventually fading into the world that encapsulates it.

But for this last moment, let’s remember the gastrotrich in a more beautiful moment under a fluorescent light, glowing in the glorious purple autofluorescence of its remains. If you think that microbes are the only organisms that eat microbes, think again. We humans have a particular fondness for one specific fungus called Saccharomyces cerevisiae, but you probably know better as “yeast.” Often when we talk about the invisible role that microbes have played in human history, we’re talking about the destruction wrought by diseases.

But as we’ll talk about in the next video, the life of Saccharomyces cerevisiae has intertwined with our own in ways that are both delicious and mysterious. Every time you eat a piece of bread or drink a glass of beer, you are participating in what might be (depending on how strict you are about your definitions) one of the longest-running microbiology experiments in human history. While the earliest scientific studies of microbes usually go back only a few centuries when it comes to yeast, the microbe at the core of some of our favorite foods and drinks, well...those past few centuries barely scratch the surface.

But before we get to that history, let’s start with some of the basic biology. Yeast are a fungus, though unlike many in that kingdom, they don’t grow the branching hyphae that characterize organisms like mushrooms. Instead, yeast grow primarily through a process of asexual reproduction called “budding.”.

While there are many yeast species found among different fungal phyla, perhaps the most well-known is Saccharomyces cerevisiae, which you might see labelled as brewer’s yeast or baker’s yeast. Along with a few other yeasts, these various strains of S. cerevisiae are what we’ve come to rely on for our beer, wine, and bread--and all through the magic of fermentation. Yeast, like many organisms, rely on different metabolic pathways to break down sugar and create energy.

These processes usually rely on oxygen. But to deal with situations where oxygen may be less readily available or some of their key metabolic processes are shut down, yeast turn to alcoholic fermentation. Fermentation helps the yeast get the energy it needs, but the particular chemical path they follow also produces ethanol and carbon dioxide.

The yeast doesn’t need these byproducts—in fact, too much ethanol could be toxic for them. But what is waste to a yeast is treasure to us, and that shift in metabolic activity has been making our bread rise and our brains woozy for millennia. Molecular studies of pottery jars found in China found that they may have held some kind of fermented beverage as far back as 7000 BCE.

And archaeological evidence has turned up for leavened bread from 2000 BCE in Egypt and 1000 BCE in North Western China. It’s easy to see why our use of yeast has persisted for millennia. To quote one group of scientists, it helped us make food and drinks with a “enriched sensorial palate” and also a “euphoriant effect.” But the long-standing ubiquity of yeast also emphasizes how mysterious their origins are.

We don’t actually know how yeast became involved with our cooking. We just know that it was ancient, likely starting with wine, and would come to span continents, potentially spreading through trade. The results were food and drinks produced through a series of observations about how factors like temperature, time, and air might affect the final product.

To quote Samuel Johnson’s 18th century dictionary, barm--a type of yeast--is “the ferment put into drink to make it work, and into bread to lighten and swell it.” At the time they didn’t know what was actually in yeast or how it worked to shape those results. We just knew it was a thing that provided…something…somehow…. Moreover, the earliest glimpses of yeast under the microscope seemed to support the idea that yeast was just some sort of chemical, a fermenting agent, not a biological entity of its own.

When Antoni van Leeuwenhoek observed yeast in the 17th century, he thought they were just bits of globular particles. Against the new and incredible bits of life he was seeing for the first time through the microscope, yeast seemed useful but ultimately unliving. But over the next few centuries, as more scientists worked to try and understand how fermentation actually worked, they identified not just the chemical reactions that shaped the process, but that yeast was an actual living organism essential to fermentation.

Eventually, Louis Pasteur would put all the pieces together, publishing a paper titled “The Memoir of the Fermentation of Alcohol”, or something like that, but in French. It was published in 1857 and it established the interplay between chemistry and biology that allowed yeast to turn to alcoholic fermentation to survive. He would also later uncover another form of fermentation carried out by bacteria, which is called lactic acid fermentation.

Pasteur’s work didn’t just change our understanding of how bread was made, it would go on to inform our understanding of germ theory, and how the invisible world of microbes connects to the grim realities of disease. From this early history, yeast have gone on to become perhaps one of the most studied eukaryotic organisms in modern biological research. Saccharomyces cerevisiae in particular has had an illustrious research career.

In 1996, its genome was fully sequenced, making it the first eukaryotic organism to be genetically mapped out. Part of what makes yeast such great research organisms is that they are easy to grow and manipulate--both through environmental and genetic means--which has allowed us to use them to study everything from DNA replication to prion diseases. In the same way that cultures have refined the ways we use yeast in our food and drinks, scientists have refined the way we use yeast in our lab experiments.

They’ve even developed genetic engineering techniques that repurpose yeast to brew the ingredients for everything from perfumes to antimalarial drugs. When you consider just how far we’ve come with yeast, you might begin to wonder: did we domesticate them? After all, our early days of yeast use likely coincided with our early days of plant and animal domestication.

So in the same way that we’ve come to rely on domesticated animals for food and labor, maybe yeast are our microbial workhorses. The answer to that question is one scientists are still studying, in part because the history of yeast is so large and mysterious, and in part because domestication has a very specific definition in these conversations. One paper we found describes it as “human selection and breeding of wild species to obtain cultivated variants that thrive in man-made environments, but behave sub-optimally in nature,” now that’s quite a number of nuanced requirements to check off.

But with this definition in mind, beer yeast seems to show the most evidence for having been domesticated, which is likely connected to specific aspects of the brewing process that have limited the exposure of the domesticated yeast to wild yeast. But all yeasts considered, the genetic analysis of beer yeast strains show that this domestication is actually relatively recent—as in, it only happened a few centuries ago. While it did happen before we even knew that yeast was a living thing that we were domesticating, it still came long after we started using yeast to make beer, leaving much of the organism’s history still a mystery.

It is often tempting to think that we have a microbial world and a human world that intersect only in chemical reactions and biological connections. But yeast reminds us that microbes are more than just a scientific reality, they are a cultural one--even when we didn’t know they were around. Yeast have created our foods, shaped our traditions, and both bonded and divided us.

And how we use and change yeast will only continue to shape our lives. Their future, tied so much to our own, is every bit as grand and mysterious as their past has been. There is but one inevitable way to end all this, with poop.

Because yes, even microbes do it. Not all that we eat can be retained in our bodies, something must exit. So come for the funny videos of microbes pooping, stay for the extra lesson on how they do it without a butthole.

Ah, food, one of life’s great pleasures. Whether you’re an organism whose body can create its own food, or you make do with the consumption of other organisms, food sustains and connects life both large and small. But we’re not going to talk about food today.

We’re going to talk about what happens…after. No great meal comes without consequences. Even photosynthetic microbes produce oxygen they don’t need, a byproduct that is quite useful to many other organisms, including us.

And for organisms that have to digest their food to extract nutrients, well, there’s all sorts of stuff left behind when the process is done. In the world of the microcosmos, there are not only many varied tiny organisms. There are also many varied ways to produce even tinier poop.

And when we say “tinier,” we mean it. If you’re worried about being grossed out by this video, or you really want to make sure you’re not missing anything, just know that some of this pooping will require you to pay very close attention. Some of this will probably look similar to macroscopic bowel movements, and some will seem less so.

So let’s start with the more poop-like poop that comes from some of the multicellular members of the microcosmos, particularly the ones with digestive systems complete with specialized regions for digesting food and releasing solid waste. Our dragon-like friend the gastrotrich is doing the old scrunch-and-poop, probably after having finished a nice meal made up of bacteria or protozoa. The food came in through its pharynx and was then sent through the intestine, a straight tube full of digestive cells.

After, the remains continued their way to the end of the tube, where lies the anus--a microscopic gateway out of the gastrotrich and into the world. That’s all well and good for the more complex organisms, but how does one poop when one does not have a butthole? Well, for some single-celled organisms, one becomes the butthole.

Such is the case for amoebas. Their formlessness allows them to easily shift their shape around to take in food via phagocytosis. The amoeba here happens to have found a nice meal made of a ciliate, which is now contained in a food vacuole filling with digestive enzymes.

Those enzymes will eventually break the ciliate down, allowing the amoeba to absorb nutrients into its cytoplasm. But then what happens with the remains? Well, as we see with this amoeba here, it gets released.

Amoebas and other similar organisms use a process called exocytosis to send waste back to the membrane where it is removed from their body. You can see it again here in this Mastigamoeba, slowly gliding along the microscope slide while a round bit seems to come off up top. It almost looks like it’s leaving behind a little piece of itself, which I mean, maybe it is.

Ciliates have a more refined approach to pooping, which is to say they have the unicellular equivalent of an anus called the cytoproct. Ciliates gather food into an oral groove, and then consume it in the digestive vacuoles that travel through the cell. Eventually, when the vacuole makes its way to the cytoproct, the contents get out, and there you have ciliate poop.

The way organisms poop—the way microbes poop—are even more varied and wonderful than we’ve been able to show you here. But you might be wondering how you even get from something relatively simple like this ciliate releasing a small bit of waste to something more complex, like this tardigrade with its more compartmentalized approach to defecation. Well the answer, of course, is evolution, but it’s an answer that leads to many more unanswered questions.

Even within animals, the evolution of the anus—or in some species, the cloaca—is not well understood, as discussed in a 2015 review paper with the spectacular title, “Getting to the bottom of anal evolution”. While the anus itself is linked to the evolution of a digestive system, not all metazoans have a designated anus. The hydra gut has only one opening, which means that the organism’s mouth has to pull digestive double duty and open back up to release the waste.

And how that system fits in with the evolution of digestion overall is unclear. Much like the evolution of sex, anuses are a trait that appears and disappears in evolutionary lineages, reflecting the fact that they might be useful for some animals and less so for others. The duality of the hydra’s mouth seems to be working out great for them after all.

But having a digestive system with a distinct entrance and exit is pretty handy too. For one, it’s just a little less disgusting. But it also keeps food flowing in one direction.

And that means animals like the tardigrade and us don’t have to wait to finish digesting to eat more food. That would be annoying. We just get to keep eating, all thanks to that evolutionary mystery that is the anus.

In the end though, anus or not, everybody poops. Food, after all, might be one of life’s great pleasures, but all good things must come to an end. And perhaps, with the microcosmos, we can find some pleasure in that as well.

Thank you for coming on this journey with us as we explore the unseen world that surrounds us. The names on the screen right now, these are some of our Patreon patrons, the people who have decided to directly support this channel over at patreon.com/journeytomicro, and we thank them so much for their continued support. If you want to see more from our master of microscopes, James Weiss, check out Jam & Germs on Instagram and TikTok.

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