This transcript was generated automatically and lightly edited for readability.

Oliver Strimpel: This is Geology Bites with Oliver Strimpel. The fossil record of complex life goes back far beyond the Cambrian explosion, to as far back as 1,600 million years ago in the late Paleoproterozoic, with the first appearance of eukaryotes. The conventional view is that these early eukaryotes did not undergo significant ecological and taxonomic expansion until hundreds of millions of years later, starting around 800 million years ago. The reasons for this expansion are unclear, but one idea is that it reflects the appearance of microscopic predators that drove both diversification and evolutionary innovation around this time. A key aspect of this evidence is the discovery of signs of predation in tiny microfossils. Susannah Porter was the first to discover this very early predation. She is a professor in the Department of Earth Science at the University of California, Santa Barbara. Susannah Porter, welcome to Geology Bites.

Susannah Porter: Thank you, Oliver. I'm delighted to be here.

Oliver Strimpel: In a previous podcast with Rachel Wood, we talked about the fossil record going back as far as the soft-bodied creatures that inhabited the Ediacaran, in the late Neoproterozoic, about 600 million years ago, just before the start of the Cambrian. But you are looking at much earlier and much more primitive fossils. What sort of time period are we talking about, and what sort of fossils are these?

Susannah Porter: Yeah, 600 million years is actually quite young from my point of view. I work on fossils that are as old as 1,600 million years or older, so the billion years or so before animals first appear on this planet. The fossils that I focus on are the remains of eukaryotes. That's one of the major branches in the tree of life, and it's the one that includes us animals, as well as plants and fungi, and then a variety of protozoa and algae, collectively known as protists, microbial eukaryotes. These fossils are almost entirely soft-bodied. They do not leave mineralized skeletons throughout this interval.

Oliver Strimpel: So we know that bacteria had existed for a long time, as recorded, for example, by sedimentary features formed by microbial mats, known as stromatolites, that go back as far as about three and a half billion years ago. But here we're talking about eukaryotes. Forgive this really basic question, but how do we know these microfossils were eukaryotes and not bacteria, or indeed archaea, which also go back as far as the bacteria?

Susannah Porter: That's actually a really good question, because it's not always easy to distinguish bacterial fossils from eukaryotic fossils. Partly this is because some of the diagnostic traits of eukaryotes, like a nucleus or the presence of mitochondria, those organelles, are not preservable, by and large. And so we're left with just looking at some aspects of their body shape, and this can include ornamentation: spines, branching structures that come off the vesicle, the wall of the cell that is preserved. We know that these structures can be made by modern eukaryotes; we have examples of that, and they are unknown in modern bacteria or archaea. So we feel pretty comfortable assigning those fossils to the eukaryotic clade. But there are a number of fossils that we find where we can't say; they could be bacteria, and they could be eukaryotes.

Oliver Strimpel: So you just said that these fossils don't have skeletons. In fact, this is hundreds of millions of years before biomineralization was, shall we say, invented, and hard skeletons appeared on the scene. So what kind of material did these early creatures produce that was tough enough to preserve their shape for long enough to appear in the fossil record?

Susannah Porter: Yeah. So it's kind of similar to, say, what pollen is made of. You think about trees, flowering plants: they produce these little structures that are highly resistant and that actually form a pretty rich fossil record. I'm not saying that these fossils are pollen or have the exact same composition, but it's similar to that. They're organic-walled, and they're made of resistant compounds that can withstand a lot of microbial degradation, for example. Part of the reason is that a lot of the fossils that we find are resting cysts. They are supposed to be resistant structures, so that the organisms themselves can sort of hibernate and not get attacked by, say, bacterial degraders.

Oliver Strimpel: I mean, just to get a feel, assuming they were big enough to feel, if you had one between your fingers, would they be like grains of sand, or would they be more kind of squishy?

Susannah Porter: I think of them as being more kind of squishy, the way plant material feels, so kind of halfway between a really rigid skeleton and a really soft, jelly-like thing. Part of the way we can tell this is that when they are preserved in, say, mudstones or shales, very fine-grained laminated rocks, we find them squished; we find them flattened. Whereas something that made a mineralized skeleton will often still retain its shape.

Oliver Strimpel: So have you gone into the field yourself to find these microfossils in such sedimentary rocks?

Susannah Porter: Yeah. One of my favorite field areas is in the Grand Canyon, in the oldest fossiliferous sedimentary rocks there, known as the Chuar Group, which are exposed in the eastern Grand Canyon. Traveling to the Chuar Group is kind of like going to the Moon. It's really hard to get there. You have to plan river trips; you have to access the rocks from the water, and it's a two-and-a-half-hour hike from the water out to the rocks. But once you get there, it's fantastic. The exposure is beautiful. And these rocks are so fossiliferous that pretty much any sample that I grab will have these very tiny microfossils, a diversity of them, preserved.

Oliver Strimpel: Are they relatively rare? Does it require some pretty unusual preservation conditions?

Susannah Porter: First of all, the amount of rock of this age is pretty low. Most of the land is covered in rocks that are 600 million years old or younger. So rocks like these, in this case 750-million-year-old rocks from the Grand Canyon, are pretty sparsely distributed around the planet. And then you need the rocks not to have been cooked too much. It's important that they didn't see temperatures that were too high, because that can destroy the fossils. Also, you need a certain type of rock, a certain lithology. You'll typically find fossils like these in very fine-grained rocks, like mudstones or claystones or shales; sandstones, for example, don't bother looking in. And then there's work being done right now trying to figure out, if you're faced with, say, a whole section of shales, which are the ones you want to target. We are finding, sort of counterintuitively, that the shales that are the least organic-rich, the shales that are sort of green or gray in color, have the best fossils. In the ones that are really organic-rich, chock-full of organic matter, we typically won't find fossils at all. You'll find other organic crud in there, but not the fossils.

Oliver Strimpel: Do you know why that is?

Susannah Porter: We think that if there's a lot of organic matter in these sediments, then it sort of feeds the bacteria, and the bacteria can then easily degrade any would-be fossils that might fall into the mix. Whereas if it's very organic-poor, it's sort of like a food desert, and so the fossils don't necessarily encounter bacteria that would eat them up. That's just one hypothesis. We're still trying to figure out what's going on.

Oliver Strimpel: So what happens next? You identify these rocks, you grab a few kilograms, or however much, of this rock in the field, and you take it back to your lab. What do you have in your lab? How do you analyze these fossils?

Susannah Porter: Yeah, so this is the funny thing. It's very different from, say, studying trilobites or dinosaurs, where you know you have the fossil out in the field when you've collected it. We collect these rocks, and because these fossils are so tiny, I mean, you literally cannot see them with your eyes, they're smaller than a speck of dust, I don't necessarily know if I've gotten anything. But we take them back to the lab, and we can process them in a couple of different ways. For the mudstones, one common approach is to put them in 50% hydrofluoric acid, which is quite a dangerous acid. If you get 10 milliliters spilled on you, you can potentially die, so you have to be very, very careful. But that hydrofluoric acid dissolves away all the minerals and leaves behind the organic matter, and then we can sift through that to find the fossils. Another, much less dangerous, approach is to cut very thin sections of the mudstones and mount them on a glass microscope slide. Then you can shine a light through it, look under the microscope at what is basically an ancient seafloor bedding plane, and look for evidence of fossils there.

Oliver Strimpel: So can you magnify enough using a conventional light microscope, or do you need to use an electron microscope?

Susannah Porter: It's a good question. You can certainly magnify enough to see the fossils, and you can often make out the ornamentation of the fossils, the spines, and maybe designs on the walls, and that is often enough to do taxonomy, to figure out what species you have. But I became rather frustrated using the light microscope, because it has a maximum resolution of about a micron, and there are a lot of features that are tinier than a micron, or about a micron in size. I was just dying to know what these walls really looked like up close. And so we would take some of what we call the macerate, the results of the acid dissolution, strew it on scanning electron microscope stubs, and look at it under the scanning electron microscope. Then you can look at submicrometer features. And I should say a micrometer is a thousandth of a millimeter, so we're looking at very, very tiny features that we would not be able to see at all under a light microscope.

Oliver Strimpel: Which brings me to the topic that we're talking about today, which is predation. What exactly do you mean by the term predation when it comes to such microscopic life forms?

Susannah Porter: By predator, I mean something that is going around killing other organisms. When I use the word predator, I'm distinguishing it from a grazer. A grazer is an organism that is eating the primary producers, at the bottom of the food chain, whereas a predator is something that is eating, say, the grazers; it's eating other organisms that are eating organisms. So, higher up in the food chain. With respect to the fossils that I've been studying, I think what is significant here is that the evidence of predation is predation on eukaryotes, on these protists. Before this time, we knew certainly that eukaryotes were around, and they were eating bacteria; bacteria were getting grazed on. But we didn't know whether those eukaryotes themselves were getting eaten by anybody. And so this is the first evidence that we actually have another tier in the food chain.

Oliver Strimpel: And what actually is the evidence for predation?

Susannah Porter: There are several different lines of evidence. Initially, for my PhD work, I focused on some fossils from the Grand Canyon that are called vase-shaped microfossils. They do look just like little flower vases, with an opening at one end where you put in the flowers, right? And it turns out that these are shells, or tests, made by amoebae, kind of similar to the way snails make their own shells. There are amoebae today that make their own shells, often quite beautifully decorated, and these vase-shaped microfossils look just like these testate amoebae. And the modern testate amoebae are predators. They'll eat bacteria, but they'll also eat other protists. In fact, they'll capture little animals. They live today in films on moss, in peat bogs and forests, so they're pretty important predators in these microbial ecosystems. So that was sort of indirect evidence that we already had, that we must have had predators around.

But I mentioned the scanning electron microscope work. I started diving into that to do a taxonomic description of the variety of organic-walled microfossils that I found in the Chuar Group. And it's one of these serendipitous things: I was zooming up really close, trying to see what the ornamentation was like on these fossils, and I started noticing that a number of them had perfectly circular holes, about a tenth of a micron to half a micron in size. The holes seemed to go in at different angles, maybe, or be slightly beveled. It was clear that they weren't part of the ornamentation of the fossil itself. They were often randomly distributed on a single fossil. They were found in some specimens of a species but not all, and they were found in a variety of different species. It was very different from the kind of holes that, say, minerals growing in the sediment might make in a protist fossil. For me, the linchpin was that, because I had studied vase-shaped microfossils and testate amoebae during graduate school, I was familiar with some modern amoebae and their behaviors. And I knew about a group of amoebae known as vampyrellid amoebae, the vampire amoebae, they're called. They attack their prey: they attack green algae, and they also live in the soil and attack fungal spores. Anyway, they make perfectly circular holes that look exactly like the ones that I was seeing in my microfossils. That, to my mind, was pretty strong evidence of predator attack. And it's not attack like swallowing their prey. They pierce a hole in the wall of their prey and then stick in their pseudopods, finger-like extensions of the cell, pull out some of the cytoplasm, and then phagocytose it, swallow it, like a Pac-Man.

Oliver Strimpel: But how does it make the hole? I mean, it doesn't have a little microscopic drill, does it?

Susannah Porter: No, no. And "pierce" is maybe the wrong word, in the sense that it's not like they're taking a needle and poking through. What we guess is that it's secreting some kind of enzyme that is macerating, that is, dissolving, the wall. And it's interesting looking at modern vampire amoebae, which are the best studied. There are different taxa of vampire amoebae, different species, and they make holes of different sizes, and it tends to be species-specific. Some species make maybe 0.1-micron circular holes; others make much larger holes, a micron or so in size, and they use a different process. They will actually digest away a ring, and then, in the way that you might remove a manhole cover, they remove the circle that they have formed in the prey's wall and actually swallow that, and then put their pseudopods inside and grab chunks of the cytoplasm.

Oliver Strimpel: That's an incredible image: an ancient microorganism drilling a ring, pulling out a manhole cover and eating that, and then sticking an arm, if you like, a pseudopod, inside and grabbing. If that doesn't count as predation, nothing does.

Susannah Porter: Yeah. I had so much fun digging into this literature, because it gets even worse than that, from the point of view of the prey. After they've taken out the guts of the prey cell, some of them will then go inside this empty husk themselves and reproduce, you know, make babies, which then make further holes to escape out of the prey.

So I found evidence of these tiny holes. These tiny holes had been reported by other paleontologists; I wasn't the first to discover the holes, but other people had just suggested, oh, maybe it's just microbial degradation. In addition, I mentioned those vase-shaped microfossils, which themselves were predators back then, but some of them also have these really unusual holes that are half-moon-shaped. They're not circles; they're half of a circle, a semicircle, and they're in the main body of the test, and they seem to be aligned with the axis of the test. I've always been puzzled about these, but my best guess is that they are holes made by some other predator. They're much larger; they're about 30 micrometers. So a different predator, and one that maybe had a stereotyped behavior, holding the test in a certain position, such that the half-moon was always aligned in a certain way. That suggests we have several different predators in these ancient ecosystems. The predators themselves were prey for other predators.

Oliver Strimpel: I should probably have said this before, but when you say test, that's really the shell you're referring to, the one that's fossilized, right?

Susannah Porter: Yeah, that's the shell. When I talked about snails making their own shells: some amoebae make their own shells.

Oliver Strimpel: So I said in my introduction that predation may have been instrumental in the early diversification of eukaryotes and in evolutionary innovation. What sort of innovations do we see around this time?

Susannah Porter: One big one we see is actually mineralized skeletons. This is a really fascinating discovery that was first made in the '80s. They are called scale microfossils, and they're about 10 to 20 micrometers in size, and they look like little shields with a variety of decorations. Some of them have spines coming off them; some of them have little hexagonal holes throughout. The big surprise with them is that it was always assumed they were siliceous in composition, but they were restudied by Phoebe Cohen, Nick Butterfield and others in the 2000s, and they found, much to everybody's surprise, that they were phosphatic. That's bizarre, because no protists make phosphatic mineralized skeletons. But these appear in rocks of about the same age as these vase-shaped microfossils and the other predation holes. And if you look at them, they're preserved in clusters of similar types of scales, and there are dozens of species. We know that modern protists, a number of different protists throughout the tree of eukaryotes, make scales; coccolithophores are a great example. One reasonable speculation is that, at least with these scales 800 million years ago, they may have served as a defense against predation. And one thing you can point to is especially the scales that have these spines sticking out. If you imagine them armoring the cell, they increase the size of the cell. It would have been difficult to, say, swallow this creature whole, and it would have been difficult to attack them the way vampire amoebae attack. So that's one innovation which I think it's reasonable to think reflects this advent of predators.

Another is that we start to see more multicellular organisms around this time, seaweeds. Again, one adaptation for a single cell that gets preyed on is to become part of a larger creature. It's harder to attack if you're bigger, and there have been experiments where scientists have put a single-celled predator in with a bunch of single-celled algae, and the algae do evolve to form multicellular structures.

Oliver Strimpel: We often think of the early evolution of life as being critically affected by the environment, and vice versa, which is why we talk of coevolution. But what do we know about the physical and chemical environment at the time we're talking about here?

Susannah Porter: Well, in this time period that we're talking about, oxygen levels were still quite low, but there was some oxygen in the atmosphere and in the oceans. We know that microbial mats with oxygen-producing bacteria, cyanobacteria, were widespread. These could have been, and certainly were, home to a lot of eukaryotes. Those vase-shaped microfossils I mentioned: we find them associated with some microbial mat layers, so I can imagine them moving around, eating those bacteria and eating other protists. One interesting thing about the environment during this time is that it seems that the chemistry of the oceans was different. Phosphorus levels were a lot higher, and that's one reason why maybe those first skeletons were made of phosphate. There were many more areas of the ocean that were anoxic and had dissolved iron in them. Some parts of the ocean were not only anoxic but euxinic, with hydrogen sulfide, which has that stinky rotten-egg smell. It was a very different world, and depending on the habitats of eukaryotes, if they really were restricted to oxygen-rich oases, they might have been more restricted in space, certainly, no question, than they are today.

Oliver Strimpel: So do you think there is evidence for an environmental trigger that started this predation–defense arms race and led to the diversification and innovation that we've just been discussing?

Susannah Porter: There's some evidence that oxygen levels may have risen around this time, and you could potentially spin a story tying rising oxygen levels to the advent of predation. We know, for example, that in modern environments where oxygen levels are really low, predation pressure among the microbes is not that great. Basically, you have the primary producers and you have the grazers, and it's the environments with more oxygen that can support predation. So that's one idea: that maybe if you get oxygen levels high enough, you can get microbial ecosystems that can support those higher levels in the food web. But I still feel like it's a bit of an open question.

Oliver Strimpel: One of the things you mentioned when we were talking earlier is that what we see is subject to at least two enormous biases. One is whether something is preserved or not in the fossil record, in other words, how well it's preserved, and the other is that so many of the species around at that time are extinct.

Susannah Porter: And there's an additional bias, and that is, you know, we're talking about the record of predation. These holes are difficult to see; it may go back a lot further. In fact, one of my colleagues, Corentin Loron, has documented what look like predation holes in billion-year-old fossils. But you're right, the vast majority of modern microbial eukaryotes would not get preserved. They just don't make any preservable structures. So we're seeing a very small slice, and the slice that we are seeing is often hard to make sense of, because the fossils represent clades that have gone extinct, which maybe have some characteristics of modern eukaryotic groups but not all, and they also have some characteristics of their own that make them distinct. And so a lot of the time, for most of the early eukaryote fossil record, we don't know what we are dealing with, other than eukaryotes.

Oliver Strimpel: And even then, as you said earlier, we don't necessarily know in some cases whether a fossil is from a eukaryote, which, I think, goes to your point that it's still an open question whether these creatures needed, let's say, extra oxygen in order to evolve the way they did. I mean, maybe they had characteristics that enabled them to do just fine without oxygen.

Susannah Porter: Yeah. This is quite a fight I have been picking lately, actually: this assumption that is out there that if we go back in time a billion years, fifteen hundred million years, all those eukaryotes were aerobic, that they required oxygen. There are a couple of problems with that assumption. One is that today, if we look at anoxic environments, there are protists that are adapted to anaerobic lifestyles, that can't actually survive in the presence of oxygen. So we know that a lot of modern eukaryotes live in anoxic environments, even anoxic, sulfidic environments, with the help of bacterial symbionts. And then the other thing is that it's entirely possible that the very first eukaryote, and I'm talking about the first lineage that branched off from the closest living relatives of eukaryotes today, the archaea, may have been anaerobic itself. The last common ancestor of all living eukaryotes almost certainly needed oxygen at some point in its life. Maybe it could also deal with anoxic environments, but we can say it probably used oxygen, based on the characteristics that we think it had. But somewhere between that guy and that very early first eukaryote, there could have been a transition to requiring oxygenated environments. We don't know when that transition occurred. And so that means that some of these early eukaryotes that we see in rocks that are one and a half billion years old might have been adapted to anoxic environments. We can't assume that they required oxygen. Then, you know, if they persisted, and we see a lot of taxa, a lot of species, persisting for hundreds of millions of years through the Proterozoic, into, say, the rocks that I study in the Grand Canyon, some of those taxa might have been adapted to anoxic environments. They might have been relics of these very early eukaryotes. And what would be a really interesting thing to ask is: do we only see those perforations, those drill holes, in fossils that we think were living in oxygenated environments? That would be an interesting test of the hypothesis that oxygen was an important cause of the rise of predation.

Oliver Strimpel: That's interesting. So both the evidence for a sudden change in environment and, indeed, the complementary question of whether there was even a burst of evolutionary activity that happened suddenly enough to reflect some such trigger seem to be open questions. And I wonder whether you would feel the same way about the Cambrian explosion. I mean, was that a really distinct, explosive evolutionary event that resulted from something environmental, or is that, again, a selection effect, something that doesn't really reflect what happened at the time?

Susannah Porter: You know, I have more confidence in the Cambrian explosion representing something really important. Something I've worked on is the earliest biomineralizing animals, and I think it's clear that there's really something important going on there. Skeletons obviously do have a good fossil record, right? And so when they show up in the fossil record, you can be pretty confident that that's approximately when those skeletons evolved. And what we see, looking at the early Cambrian, is mineralized skeletons evolving over and over again, independently, across the tree of animals. I don't see how you explain that as a preservation bias. That's real. That's telling us that something important happened at that time, and I think that it's predation. I think that we're seeing a repeat of the same ecological events that happened several hundred million years before in microbial ecosystems. We're seeing them in animals for the first time around the earliest Cambrian, latest Ediacaran. I mentioned the Ediacaran biota: they're soft-bodied, they are not making mineralized skeletons, and there's no evidence that they're being preyed on, that there's any other large creature taking bites out of them. And then, around the same time that we see these mineralized skeletons, we start seeing evidence of predation, and we see evidence of creatures that would be the predators. And sure enough, the skeletons themselves sure look like they evolved to function in defense. They are carapaces, sort of shields, which would cover the soft parts, or they're spines. One of my favorite creatures kind of looks like a barrel cactus; it's covered in spines. It seems like those really are functioning in defense. And we even see this when we look at the details of some of these mineralized skeletons. Some of them are well enough preserved that we can see the crystallites and how they're arranged, the microstructure of the skeletons, and these, again, seem to be adapted to defense against crushing. So everything, in my mind, is pointing toward the idea that part of the Cambrian explosion and the evolution of skeletons is the appearance of carnivores.

Oliver Strimpel: Do you have any theories as to why it took so long after that initial predation was sort of invented, if you like, in these microfossils, for it to appear again in these larger, more complex creatures in the Cambrian, and maybe coevolve with these mineralized outer shells or skeletons? Or, in even asking the question why it took so long, am I presupposing some kind of timescale that we have no right to presuppose?

Susannah Porter: I think it's fascinating that it's the same thing: an organism evolving to eat its relatives, and protists and animals have to do it in such different ways because of their sizes. Why did it take so long? There are two schools of thought. There are those who like the idea that these biological innovations are just waiting to happen, but there's some brake that's put on them, such that they can't. That's the idea that maybe low oxygen levels are the brake, and once that brake is released, once oxygen levels rise, then you have the ability to evolve creatures that are more active. They have fast metabolisms; they need oxygen to be able to be predators. And then, I guess, the other school of thought is that a rise in oxygen, or the release of whatever environmental variable, doesn't necessarily mean that these innovations are inevitable, and that there are contingent events that have to occur. I think when you see convergent evolution, similar characteristics evolving over and over again, that makes me lean toward the first school of thought, that these characters will evolve given the chance. And I think predation is one of those: eventually, given time, organisms will figure out how to eat each other.

Oliver Strimpel: What are you working on at the moment?

Susannah Porter: One thing I'm interested in is looking at patterns in the acquisition of mineralized skeletons. I did work earlier looking at carbonate skeletons in animals, documenting how many different times these skeletons evolved, when they evolved, and, when they did, what kind of mineralogy was selected, aragonite or calcite. There's a really interesting pattern there, where the mineralogy of the carbonate skeletons in animals corresponds to what seawater chemistry favored at the time. This includes other mineralized skeletons, like phosphatic and siliceous ones, but the earliest carbonate skeletons are all aragonite. And then in the later part of the early Cambrian and into the Ordovician, everybody who evolved a mineralized carbonate skeleton chose calcite, and then it switches back again to aragonite, and then it switches back again to calcite. So there are interesting patterns in skeletal mineralogy through time. I wanted to expand that work to look across all eukaryotes, and it's a pretty ambitious undertaking, because we're talking about more than 80 acquisitions of mineralized skeletons. But so far, I'm finding a really interesting pattern. Whereas in animals there's this big burst, with two-thirds of the animal groups that evolved mineralized skeletons doing so in the early Cambrian, with the protists you don't see signs of the Cambrian explosion at all. Their acquisitions are kind of randomly distributed throughout the Phanerozoic, the last 550 million years. And that suggests to me, again, that the acquisition of mineralized skeletons by animals in the early Cambrian really is an animal event. It reflects an ecological factor that affected only animals. If it were something like a change in ocean chemistry, you'd think that the protists might also record that somehow, and they don't.

Oliver Strimpel: Susannah Porter, thank you very much.

Susannah Porter: It was my pleasure, Oliver. Thank you so much.

Oliver Strimpel: For more about Geology Bites, as well as pictures and illustrations that support this podcast, you can go to geologybites.com.