Short Wave - Microbes: It's Complicated

Episode Date: February 5, 2025

For a long time, microbes like the ones in Yellowstone's hot springs were studied in isolation. Molecular ecologist Devaki Bhaya says we should be studying them in community. Here's why.Help shape the future of Short Wave by taking our survey: npr.org/shortwavesurveyPlus, if you liked this episode, check out our episode on the last universal common ancestor in the tree of life. Listen to every episode of Short Wave sponsor-free and support our work at NPR by signing up for Short Wave+ at plus.npr.org/shortwave.See pcm.adswizz.com for information about our collection and use of personal data for sponsorship and to manage your podcast sponsorship preferences.NPR Privacy Policy

Hey, shortwavers, some good news. You can help us shape the future of our show by completing a short anonymous survey. It's a chance to tell us what you like, what you don't, and what you want to hear more of. It's an awesome responsibility, but I trust you. And we want to hear from everyone, whether you're a day one listener or brand new. Just go to npr.org slash shortwave survey. We'll also put the link in our show notes. Thanks. Okay, on to the show. You're listening to Shortwave. from NPR. Ask any scientist what it's like to do fieldwork, you know, to venture into the real world and take samples of real things, and you'll get a lot of answers. For some, the environment is full of beauty and wonder and preciousness.

And for others, it's almost really like suddenly entering hell. This is Devaki Bahia. She's a molecular ecologist and researcher at Carnegie Science. And the environment she's describing is Yellowstone National Park in Wyoming. The first time she's saw, saw these geysers and hot springs, it was a bit of a shock.

It's barren, there's steam coming up, it smells of sulfur, there's boiling mud. I mean, it's what I would think of as being in hell, right? But then, she got closer and really looked into the hot springs. There's all these colors, beautiful colors, dark oranges, bright oranges, green, beans, olive greens. Devaki became fascinated by all of these tiny life forms, able to withstand these boiling hot conditions, life forms that are known in the biology world as extremophiles.

Microbial extremophiles, so microbes in really intense environments, have long been studied by scientists in isolation, where they take a sample, stick it under a microscope, and see what that microbe eats and what it produces. But for Devaki, that approach only gives us half the picture. It's great to study things in isolation because you can do a lot of manipulation, but you absolutely miss what they're doing with their friends and foes and cousins. How do they behave in a village?

Devaki wants to study the whole village. She wants to know how do microbes behave within their microbial community, and how do they form something greater than the sum of their problem? parts. When they work together, they make much more complex patterns. And so that's looking just as, you know, 100 devaquis, how do they behave? Now you talk about 100 devakis and everybody at Carnegie. And now you come up with things, the sexy term is emergent behavior, things you could not predict just by looking at how the 100 devahis behave. So today on the show, the microbe village, what microbes learn from each other, what they tell us about evolution,

and what we can learn from studying their tiny but mighty relationships. I'm Emily Kwong, and you're listening to Shortwave, the science podcast from NPR. Okay, Devaki, so let's start at the beginning, because I do want to understand, like, how you got to this place of studying microbes in community. What was your initial question? What did you want to figure out? Yeah, so the question which we sort of went off, on is how do populations behave. It's incredibly expensive to be sequencing genomes. So we took

all of the population and we got what is called a metag genome. So we got everybody who's there. Kind of like a hot spring census. And then, of course, you can get that DNA and then you have to kind of tease it apart and say, this genome belongs to this guy, this genome belongs to that guy. And now you try and figure out, well, how are they interacting? And the second layer of it is, okay, so you know who's there. Fine. What are they doing? That's when you use something called transcriptomics, which is to see, are they active? And when are they active? Are they active at night? Are they active at day? Are they active at noon? So it's filling in the gap from what an individual can do to what the whole community is doing, which I think is just incredibly

fascinating. Yeah. Okay. So you've taken this microbe census and you've started to look at which microbes are active at which times? And then what? Like, what are you finding out? So we resorted to something called comparative genomics. You look at the genome, you compare them and you see what's different. And the first thing that hit us was the fact that there seems to be these whole, let's call them modules that allow the cyanobacterium to suddenly do something it didn't do before. And that's what we call horizontal gene transfer. So something came in from somewhere else that suddenly gave these organisms an opportunity to go into a new niche, have a new ability. Right. And horizontal gene transfer is this idea that these microbes are just giving each other genes and in this case,

new functions. And you're saying you found horizontal gene transfer among these microbes in the hot springs, Right? So we think we know that at the lower temperatures, there's a lot more what's called genetic diversity. There's a lot more flexibility. There's lots more of this sort of scrambling of genomes. We see it less at the high temperatures, almost as if one can imagine the constraints are much higher. And there's less degrees of freedom of who can do what. But this is like thinking of evolution as a tree or as like a bush.

And this is like a bush. They're just changing and acquiring things, right? So it really puts the conventional view of evolution on his head. Yeah. So what's happening with microbes, they're not just operating on an individual level. Like they may act in a solitary way, but there's a lot of... Give and tech. My producer, Hannah Chin, calls this microbe mutual aid happening.

Absolutely, yeah. And specifically, these bacteria that you were studying, they were giving each other genes. They were in some kind of relationship with each other. Yes. Well, speaking of that, I'm very curious about this. Like, how do you then study a relationship? Is it like the difference between being an individual therapist versus a couple's therapist or a family therapist? Like, how do you do that? Yeah. So excellent question again. You can do it in one of two ways. One is what's called in situ, right? So you look at things as they're happening in the environment, right? You're leaning over the hot sprain with your face. collecting samples, not me sometimes actually a great number of fabulous postdocs and scientists. Sure, sure, sure, sure. You bend over and you collect samples, you freeze them away and you bring them back. But it's like a snapshot, right?

I was there at 9 in the morning, this is what the microbes were doing, right? And the way you do that is you can get their genes, you can get their activity through looking at what genes are active, etc. right? But what I would say is that we're moving into an age where we take individual guys and build what I call synthetic communities. So now you learn the rules in a way from what's happening in the environment. And now you're trying to replicate them in the lab. So you're not getting snapshots. You're seeing it over time. You manipulate light. You manipulate oxygen levels. Wait, you're making your own microbial communities. Yes. Yes. And we're starting to do that, and I'm terribly excited about that. I think it's going to have a lot of hiccups, a lot of bumps in the road. But I think that's the way to go. Yeah, and then you start playing with the microbial version of the Sims, you know, just like playing around with all the micro relationships.

So upon having studied these microbes in situ and now potentially experimenting with them in synthetic ways, what questions do you most want to answer with these synthetic microbial communities? Excellent, yeah. So we are starting kind of like scientists do one step at a time. I'm going back to this question of phototaxis, right? Two organisms that are very different in shape, in genome. When they come together, can I predict how they're going to move towards light? So let me give you a beautiful example.

Okay. So cyanobacteria are these microbes. They were often called erroneously. blue-green algae, but actually they're what's called prokaryotes. They don't have a nucleus. And what they have is the ability to do photosynthesis under all sorts of different conditions. Right, those beautiful blue-green colors you were talking about earlier in the hot springs. So one of these organisms is long and thin. It has certain pigments. It does photosynthesis as well. The other guy, the ones I sort of talk a lot about cyanobacteria, they're like little sausages.

So think of it as lasagna with sausages, right? The lasagna can move all over the place. They move fast, they move effectively. Cynobacteria are much more sort of motivated by light direction. So they're moving towards light. Now, if you put the lasagna and sausages together, how would they behave? Right? You wouldn't necessarily know, but you could make some hypothesis.

I feel like I said earlier you were playing microbial sims, but you're actually kind of playing microbial chef because these microbes are going to become so much more enmeshed with each other with the potential for horizontal gene transfer. Like what do microbes get up to when they all get together? Can I say this on NPR? One of the papers we wrote with a dear friend of mine, Daniel Fisher, we put in this word that bacteria really behave as quasi-sexual populations. And we thought... Wow, it is like the sim. they woo-hoo. But they're really doing a lot of exchange of genes and really leading to new behaviors,

you know, and that's sexuality, you know, biologically defined at least. And this is something you haven't touched on a lot. They're as communities, they're evolving, right? They're getting new functions. They're doing different things. But they do want to do something together and they're better together. I have to ask, you know, cyanobacteria. in addition to having much more exciting lives than I realized, like, wow, they're also pretty old.

I mean, these are ancient photosynthetic organisms that were around billions of years ago. In terms of the big picture, though, what does understanding the evolution of cyanobacteria and microbes tell us about evolution as a whole? Yeah, yeah, I would like to quote, you know, famous boy John Dunn, who said, no man is an island. I love John Dunn. I'd say no microbe is an island. And I honestly, I mean, it sounds cool, but I think it's really true and it changes the way we think about it. So anyway, to go back to the evolution of cyanabacteria, it is really spectacular. And I think it defeats my imagination for something to have been around three and a half billion years ago.

I mean, we've been around for 350,000 years and we're not doing such a great job. job at it. These guys have sort of hacked it over, you know, massive changes in the Earth's evolution. You know, just an incredible array of environments. Wherever you look, there's no place you haven't found them, you know, gold mines, thousands of feet below, you find microbes. So it is a microbial world and there's a quiet majority. And I feel like all of these new techniques give us the ability to probe that. But I think it wouldn't be a stretch to say that we need to study the idea of communal behavior. Because we cannot study that in isolation, right? Pretty obviously. Totally. Yeah. And I feel like that almost holds true for how science is done too, right? I know

other teams have used these analysis techniques you've developed for their research. So it's almost like you're doing, I don't know, horizontal gene transfer for your colleagues. And it kind of makes me think about how when one person is generous, the whole community benefits. It's a sort of meta thought that we want to study communities where we need a community of scientists to do it. We need microbiologists. We need people who are looking at protein structure. We need theoretic. And we need people out in the field doing this because we've all been doing it in our own way, sort of slightly siloed. And, you know, if you talk about dreams, that would be a dream. Then we take a few communities and we say, can we get our teams together to really get the big questions of the silent microbial majority.

Dr. Bahaia, thank you so much for talking to me. You're very welcome. If you liked this episode, you're going to love the one we did on. the last universal common ancestor in the tree of life, Luca. Check that out and make sure to never miss a new episode by following us on whichever podcast platform you're listening to. And if you're feeling right or Lee, leave us a review because it really helps the show. This episode was produced by Hannah Chin.

It was edited by our showrunner, Rebecca Ramirez, and fact-checked by Tyler Jones. Jimmy Keely was the audio engineer. Beth Donovan is our senior director and Colin Campbell is our senior vice president of podcasting strategy. I'm Emily Kwong. Thank you for listening to Shortwave, the science podcast from NPR.