Nature, red in tooth and claw, is rife with organisms that eat their neighbors to get ahead. But in the systems studied by the theoretical ecologist Holly Moeller, an assistant professor of ecology, evolution and marine biology at the University of California, Santa Barbara, the consumed become part of the consumer in surprising ways.
Moeller primarily studies protists, a broad category of unicellular microorganisms like amoebas and paramecia that don’t fit within the familiar macroscopic categories of animals, plants and fungi. What most fascinates her is the ability of some protists to co-opt parts of the cells they prey upon. Armed with these still-functioning pieces of their prey, the protists can expand into new habitats and survive where they couldn’t before.
Watching them gives Moeller a distinctive view into the underlying structure of ecosystems today and the evolutionary forces that made them. The protists’ pilfering of organelles may seem bizarre, but the mitochondria in our own cells mark us as products of a related kind of metabolic acquisition by our ancient ancestors.
“In the broadest sense, these are questions about when and how organisms specialize, and how they can break that specialization by gaining access to something new,” she said. “To me, this work addresses questions about how organisms expand their ecological niche, how those acquisitions can be permanent, and what that means about how metabolism jumps across the tips of the branches of the trees of life.”
Quanta spoke with Moeller by telephone about her career, her research on acquired metabolism and theoretical ecology. The interview has been condensed and edited for clarity.
You’ve become well known in ecology and evolution circles for your work on “acquired metabolism.” Is that a term you came up with?
Not intentionally. It’s what I mean by parts of your metabolism that aren’t encoded in your own genome. You gain access to them in some way by associating with another species.
That encompasses some forms of symbiosis, but it’s more than that. It also includes things like the acquisition of chloroplasts, the eukaryotic organelles for photosynthesis, from ingested prey, and even horizontal gene transfer, where a single gene or a whole package of metabolic genes is plucked from one organism by another.
I’m trained as a community ecologist, so I’m very interested in the roles that organisms play in ecosystems and how those niches expand and contract within their lifetimes. The study of acquired metabolism felt like a natural fit with that, because it’s very much about how organisms can expand their niches.
Is what humans have with our gut bacteria acquired metabolism?
I think that’s a great example. So much of our ability to eat diverse food sources and metabolize them comes down to those bacteria. Some of the important vitamins and cofactors that we require, like vitamin K, are manufactured by microbes that live inside of our gut. We’re very reliant on these partnerships.
What led you into this line of research?
You know, bacteria often move through a process called “tumbling and running.” They follow some chemical cue toward a resource, but when the signal peters out, they stop, they spin and they go off in a random direction. I think this is true for many scientists too, including me. We’re often following our nose and chasing after things that we get excited about. And sometimes it leads us to unexpected places.
I was lucky. My parents both trained as scientists, and although neither of them worked as one while I was growing up, I knew that research was a career option. I also got very lucky in my undergraduate education at Rutgers University, in that I had professors who took an interest and connected me with a faculty member doing research on marine microbes. The scientist I first worked with, Paul Falkowski, has eclectic interests. But one of the things that he was studying at the time was how chloroplasts got spread around the tree of life.
This was where my interest in acquired metabolism got its start. I found it totally fascinating, this idea that something I learned about in textbooks as a feature of plants was actually something they got a couple billion years ago by ingesting a bacterium. And that this has happened multiple times. I started working with Paul and Matt Johnson, who was his postdoc at the time, on organisms that steal chloroplasts today and what they might tell us about this evolutionary process.
I love the idea that an organism can start out in life without a chloroplast, and then just pick one up.
Right? Imagine if we had a salad for lunch, and then suddenly our arms turned green! I live in Southern California right now — I could take a walk between classes and get all the energy I needed. Although I like eating lunch, so I’m not sure I would really relish that.
In many cases, these organisms that obtain chloroplasts become quite bound to doing photosynthesis. Some of the species that we work on would die if they couldn’t photosynthesize, so they can’t survive if they can’t find prey to steal chloroplasts from. It’s an evolutionary curiosity to me that they backed themselves into this corner.
Do these species have to keep stealing chloroplasts because they eventually break down?
Generally, yes. However, these chloroplast-stealing lineages vary in how good they are at maintaining the chloroplast. In this group of marine ciliates that we work on called Mesodinium, some lineages don’t steal chloroplasts at all. Some steal them and run them into the ground really fast. And others steal them but also steal functional nuclei from their prey, which means that they can make more chloroplasts.
The metaphor I love is that the ones that don’t steal chloroplasts are like the well-behaved child who’s never stolen a car. Others steal the car for a joyride, crash it into a tree and abandon it. But there are some who steal the car but also the owner’s manual, and they build a mechanic’s shop to take good care of the stolen property.
There’s this whole spectrum, and because they’re closely related, we can ask: What are the evolutionary differences between these organisms that facilitated the transitions?
Do they ever inherit chloroplasts from their parent cells? If the cells divide to reproduce, don’t the chloroplasts get passed on as well?
Some of them do. In some lineages, when the cells divide, they split up the chloroplast allotment between them. To refresh and replenish their chloroplasts, they need to steal them by eating.
But the cells that keep the stolen nucleus — the stolen instruction manual — can make the chloroplasts divide along with the rest of the cell. The nuclei seem to be what they still need to eat for. When they catch a prey cell, they hang on to its chloroplasts, because why not? But it seems like really what is critical is that they pick up new nuclei.
How is it possible for the ciliates to get energy from someone else’s cellular machinery?
That’s a really interesting question. When some of the Mesodinium ciliates eat, they strip away most of the prey cell. Electron microscopy has shown that the chloroplasts are pretty intact, but they’re also still inside the relic cell membrane of the prey. And then the ciliate has a membrane of its own around all that, because the ciliate stuck the prey cell into a vacuole [membrane vesicle] when it ingested it.
We really don’t know how molecules are moving across this multi-membrane system. That’s something that we are trying to dig into now by following where proteins are going.
What evolutionary question is this work helping you answer?
When we teach photosynthesis in school, we mostly focus on the land plants, whose ancestors picked up chloroplasts 2 billion years ago, when they domesticated free-living cyanobacteria as endosymbionts.
But when we look at phytoplankton in the ocean and freshwater systems, the picture is much more complicated. We are often looking at organisms that have what’s called a secondary chloroplast, which means that sometime in their evolutionary history, they obtained a chloroplast from something else. Sometimes you even see evidence of tertiary chloroplasts, where organisms are getting chloroplasts that were taken from some third cell. These secondary and tertiary endosymbiosis events have taken place, we think, at least half a dozen times. And that’s given rise to the huge diversity of eukaryotic phytoplankton.
What does it look like to go from being something that’s heterotrophic to something that’s highly photosynthetic? What changes do you have to make in your physiology? Where can you survive? What natural selection gradients have to be in place? The study of Mesodinium gives us insights into what that transition looked like.
Does acquired metabolism help organisms get ahead?
In the paper that we published earlier this year, we looked at an organism that is becoming photosynthetic by hosting endosymbiotic algae. It’s both acquired metabolism and a symbiosis. You could pop open these freshwater ciliates called Paramecium bursaria and isolate the algae, and the algae would happily live and grow on their own.
These paramecia are like little fuzzy green blobs that whirl around in the petri dish. We started looking at how the competitive abilities of these organisms depended on the availability of light. If they’re getting energy from sunlight, then the more sunlight there is, the more energy they should get for growing. We thought that would extend to their ability to compete with other species.
I had an incredibly talented undergraduate student, Veronica Hsu, who tested that idea. We had this incubator with banks of lights and little flasks of cultures growing at different light levels. Every two days, Veronica took samples of the cultures and put little droplets of them in petri dishes. Then she counted the numbers of different types of ciliates in each droplet.
But even without doing an exact count, you could see within just a few weeks that all the white translucent non-photosynthetic ciliates were disappearing, while all the bright green paramecia were increasing. You could see the competition play out before your eyes.
Veronica showed that as the light increased, so too did the competitive ability of the organism that had acquired photosynthesis by hosting the algae. And then counting the cells allowed us to grasp the data behind this phenomenon.
So getting these cell counts and building a mathematical model of what was happening was an important part of this?
Yes, when we run these experiments, there’s a lot of counting. My colleague Caroline Tucker said when we were in grad school together, “You know, ecology is just the science of counting.” At the time, I was kind of resentful of her statement, but she wasn’t wrong.
There’s a part of me that will always think there’s no substitute for sitting with your study organism and falling in love with it a little bit in the lab or out in the field. Sitting in a dark room, staring through a microscope, you feel like you sense the personalities of these different species. Some of these paramecia are kind of silvery white and teardrop-shaped and very translucent because they don’t have any photosynthetic algae. When they’re in a brand-new flask with lots of bacterial resources, they kind of bumble around slowly, but then as the experiment goes on, it’s like you can see them get hungry before your eyes and they start swimming really fast. And you can make observations that then lead to additional findings.
Being able to combine laboratory experiments with mathematical models forces me to be really honest and explicit about what I think is going on. What do we mean by “acquisition” of metabolism? What resources is the cell getting by hosting photosynthesis? How exactly does that affect its competitive abilities?
Now we have a model that we know describes how acquired metabolism can change competitive ability. And that has implications not just for acquired photosynthesis, but for other acquisitions of metabolism as well. The exact details that we plug into the model might change depending on the system. But we have a framework to use.
We talked about competitive advantages that can come from acquired metabolism. But are there downsides to taking over someone else’s metabolism?
Definitely. There’s a theory that our mitochondria — another metabolic organelle that we acquired through endosymbiosis — are the reason we age.
Because of them, we’re engaged in aerobic metabolism, using oxygen to burn carbohydrates and other molecules for energy. But the reactive agents that mitochondria and chloroplasts produce might also be oxidizing and degrading our body’s DNA. These are dangerous things to put next to your genetic material.
One thing that we sometimes see in these organisms that steal chloroplasts is that they have a lot of protective antioxidant machinery, which helps them to handle taking on a chloroplast. Having a chloroplast can make it very dangerous to be in high-light settings. You can basically get sunburned. One cool thing demonstrated by Suzanne Strom, a scientist in Washington State at Western Washington University, is that when organisms eat cells with chloroplasts, they tend to digest them faster when there’s more light available. It could be because light helps you break down the chloroplast. But it could also be that this organism is thinking, “I’m playing with fire here; I’ve got to get rid of it.”
So this raises interesting questions about the types of environments that these organisms might have been living in when they first started hanging on to chloroplasts. I suspect it was probably a lower-light environment because if your digestion depends on light, lower light will slow it down and also reduce the harm that the chloroplasts might do. You can manage it a little bit more. And Mesodinium is certainly a low-light species. But that’s very anecdotal. We need a lot more evidence. But of course there are also things that retain chloroplasts that live in a high-light environment too.
I noticed on your Twitter that you’re doing a lot of tree-root counting. What does that have to do with this other work?
One of the things that I love about being a theoretical ecologist is that I can dabble in a lot of different systems.
That’s another aspect of acquired metabolism that we work on. So we’ve talked about stealing metabolic machinery from another organism. But there’s also metabolic mutualism — the acquisition of metabolism through this really intimate partnership between two organisms. The business of trees, as we all know, is photosynthesis. But to photosynthesize, trees need nutrients and water from the soil. And it turns out, especially in temperate ecosystems, that they gain access to these resources by partnering with fungi, ectomycorrhizal fungi. These are fungi that live mostly below ground, although sometimes they put up really delicious mushrooms, and also sometimes toxic ones. The fungi are in partnership with the trees. The fungi excel at harvesting nutrients from the soil, and the trees provide sugar from photosynthesis, so they can support each other.
This metabolic mutualism helps trees to survive in all kinds of different environmental conditions and expand their ecological niche. A tree can partner with certain fungi that are good for one environment, and with different fungi in a different environment. We think that this allows trees to make a living across a more diverse set of environmental conditions than if they were on their own.
There’s so much talk about the microbiome, but we forget that it must have been really difficult to get all those relationships with microbes going at the beginning.
Yeah, totally. As we’re getting better environmental data from sequencing, we’re seeing that pretty much everything has got some kind of microbiome, even if it lives on their outside. Who controlled whose evolution, you know? Maybe we just had to deal with the fact that our guts were going to get colonized by bugs and we made the best of it.
That’s why I think the study of acquired metabolism is so fascinating. You’re studying organisms that are making these acquisitions today. You get some insight into how they were handling that ecologically in the past, what the selection pressures were and so on.
I feel like theoretical ecology is exploding lately.
I think it’s very in vogue now.
I think that part of the rising interest in theory comes from the overwhelming amount of information that we have now. When you have piles and piles of data, you make sense of it by developing some unifying theories about it. And mathematical models are one way to approach that problem. I think that’s why there’s been more interest among our graduate students in these topics, or interest at universities in hiring theoretical ecologists. It kind of boils down to: We have massive data. And we’re ready.