Microbes: It's Complicated

For a long time, microbes like the ones in Yellowstone's hot springs were studied in isolation. Molecular ecologist Devaki Bhaya https://carnegiescience.edu/bio/dr-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/shortwavesurvey http://npr.org/shortwavesurvey Plus, if you liked this episode, check out https://www.npr.org/2025/01/17/1225172117/life-species-luca-ancestors 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 http://plus.npr.org/shortwave. See pcm.adswizz.com https://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 https://www.npr.org/about-npr/179878450/privacy-policy

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• 0:49Emily Kwong?

  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...

• 1:02Speaker 02

  It's almost really like suddenly entering hell.

• 1:05Emily Kwong?

  This is Devaki Bhaya. 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 saw these geysers and hot springs, it was a bit of a shock.

• 1:21Speaker 02

  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?

• 1:33Emily Kwong?

  But then she got closer and really looked into the hot springs.

• 1:39Speaker 02

  There's all these colors, beautiful colors, dark oranges, bright oranges, greens, olive greens.

• 1:50Emily Kwong?

  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.

• 2:20Speaker 02

  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. And how do they behave in a village?

• 2:35Emily Kwong?

  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 parts?

• 2:46Speaker 02

  When they work together, they make much more complex patterns. And so that's looking just as, you know, 100 Devaki's, how do they behave? Now you talk about 100 Devaki's and everybody at Carnegie. And now you come up with things, the sexy term is emergent behaviors, things you could not predict just by looking at how the 100 Devaki's behave.

• 3:15Emily Kwong?

  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 Short Wave, the science podcast from NPR.

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• 4:52Speaker 05

  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?

• 5:04Speaker 02

  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 metagenome. So we got everybody who's there.

• 5:21Speaker 05

  Kind of like a hot spring census.

• 5:22Speaker 02

  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.

• 6:00Speaker 05

  Yeah. Okay, so you've taken this microbe census and you've started to look at which microbes are active at which times.

• 6:08Speaker 05

  And then what? Like, what are you finding out?

• 6:10Speaker 02

  So we resorted to something called comparative genomics. Which is where 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 opportunity to...

• 6:45Speaker 02

  Go into a new niche, have a new ability.

• 6:48Emily Kwong?

  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?

• 7:02Speaker 02

  So we, and 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 its head.

• 7:39Emily Kwong?

  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

• 7:48Speaker 02

  Give and take.

• 7:49Emily Kwong?

  My producer Hannah Chen calls this microbe mutual aid.

• 7:52Speaker 02

  Yeah.

• 7:53Emily Kwong?

  Happening.

• 7:54Speaker 02

  Absolutely, yeah.

• 7:55Emily Kwong?

  And specifically, these bacteria that you were studying, they were giving each other genes. They were in some kind of relationship with each other.

• 8:02Speaker 02

  Yes.

• 8:02Emily Kwong?

  Well, speaking of that, I'm, 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 couples therapist? Or a family therapist? Like, what's, how do you do that?

• 8:15Speaker 02

  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?

• 8:27Emily Kwong?

  You, you leaning over the hot spring with your face.

• 8:30Speaker 02

  Collecting, collecting samples. Not me sometimes, actually a great number of fabulous postdocs and scientists.

• 8:37Emily Kwong?

  Sure, sure, sure, sure, sure.

• 8:38Speaker 02

  You bend over and you collect samples, you freeze them away and you bring them back.

• 8:42Emily Kwong?

  Okay.

• 8:43Speaker 02

  But it's like a snapshot, right? I was there at nine in the morning, this is what the microbes were doing, right? And, and the way you do that is you can get their genes, you can get their activities through looking at what genes are active. Et cetera, 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 their environment. And now you try and replicate them in the lab. So you're not getting snapshots, you're seeing it over time. You manipulate light, you manipulate oxygen levels.

• 9:20Emily Kwong?

  Wait, you're making your own microbial communities?

• 9:24Speaker 02

  Yes, yes. And we're starting to do that, and I'm terribly excited about that. I think it's gonna have a lot of hiccups, a lot of bumps in the road, but I think that's the way to go.

• 9:36Emily Kwong?

  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, 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?

• 9:58Speaker 02

  Excellent, yeah. So we're 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.

• 10:17Emily Kwong?

  Okay.

• 10:18Speaker 02

  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.

• 10:36Emily Kwong?

  Right, those beautiful blue-green colors you were talking about earlier in the hot springs.

• 10:41Speaker 02

  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. Cyanobacteria 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 hypotheses.

• 11:21Emily Kwong?

  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?

• 11:39Speaker 02

  Can I say this on NPR?

• 11:40Emily Kwong?

  Yeah.

• 11:41Speaker 02

  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-

• 11:49Emily Kwong?

  Wow, it is like The Sims, they woo-hoo.

• 11:52Speaker 02

  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 we 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.

• 12:18Emily Kwong?

  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?

• 12:44Speaker 02

  Yeah, yeah, I would like to quote, you know, famous boy John Donne, who said, "No man is an island."

• 12:50Emily Kwong?

  I love John Donne.

• 12:51Speaker 02

  I'd say no microbe is an island.

• 12:55Speaker 02

  And I honestly, I mean, it sounds cool, but I think it's really true and it changes the way we think about it, right? So, anyway, to go back to the evolution of cyanobacteria, yeah, 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 at it. But 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, it's, there's no place you haven't found them.

• 13:36Speaker 02

  You know, gold mines, thousands of feet below, you find microbes. So it is a microbial world and they're a quiet majority. And I feel like the, 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.

• 14:06Emily Kwong?

  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, it kind of makes me think about how when one person is generous, the whole community benefits.

• 14:29Speaker 02

  It's a sort of a meta thought that we want to study communities, but we need a community of scientists to do it. We need microbiologists, we need people who are looking at protein structure, we need theoreticians, 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, that we take a few communities and we say, can we get our teams together to really get at the big questions of this silent microbial majority?

• 15:03Emily Kwong?

  Dr. Bahia, thank you so much for talking to me.

• 15:06Speaker 02

  You're very welcome.

• 15:11Emily Kwong?

  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 writerly, 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 Short Wave, the science podcast from NPR.

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