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.Learn more about sponsor message choices: podcastchoices.com/adchoicesNPR Privacy Policy
Chapter 1: What is the significance of studying microbes in community?
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Chapter 2: How do microbes behave in their environments?
We'll also put the link in our show notes. Thanks. Okay, on to the show. You're listening to shortwave.com. 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 Bahaya. 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.
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? Yeah.
But then she got closer and really looked into the hot springs.
There's all these colors, beautiful colors, dark oranges, bright oranges, greens, olive greens.
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Chapter 3: What are extremophiles and why are they important?
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 and... 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 parts?
When they work together, they make much more complex patterns. And so that's looking just as, you know, 100 Devakis, how do they behave? Now you talk about 100 Devakis and everybody at Carnegie, and now you come up with things differently. The sexy term is emergent behaviors, things you could not predict just by looking at how the hundred individuals 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.
On the Code Switch podcast, 40 years ago, the Philadelphia Police Department carried out a bombing that destroyed a black neighborhood on live TV. And yet the deadly events of that day have been largely forgotten.
There is now a historic marker because a group of middle school children were assigned to look at police brutality in their community. Listen to the Code Switch podcast from the NPR network.
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 do you want to figure out?
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Chapter 4: How does horizontal gene transfer affect microbial communities?
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 try and replicate them in the lab. So you're not getting snapshots. You're seeing it over time. You manipulate light. You manipulate light.
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 microbe 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.
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Chapter 5: What new insights does community study provide about evolution?
So one of these organisms is long and thin and 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? 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 hypothesis, right?
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?
Yeah.
Chapter 6: How do microbes demonstrate mutual aid in their relationships?
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.
I have to ask, 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 a famous poet, John Donne, who said, no man is an island. I love John Donne. 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, right? So anyway, to go back to the evolution of cyanobacteria, 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, 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 they're 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 such 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
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