Devaki Bhaya
Appearances
Short Wave
Microbes: It's Complicated
There's all these colors, beautiful colors, dark oranges, bright oranges, greens, olive greens.
Short Wave
Microbes: It's Complicated
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?
Short Wave
Microbes: It's Complicated
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.
Short Wave
Microbes: It's Complicated
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. 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.
Short Wave
Microbes: It's Complicated
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, OK, 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?
Short Wave
Microbes: It's Complicated
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.
Short Wave
Microbes: It's Complicated
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 that allow the cyanobacterium to suddenly do something it didn't do before. And that's what we call horizontal gene transfer.
Short Wave
Microbes: It's Complicated
So something came in from somewhere else. That suddenly gave these organisms opportunity to go into a new niche, have a new ability.
Short Wave
Microbes: It's Complicated
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...
Short Wave
Microbes: It's Complicated
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.
Short Wave
Microbes: It's Complicated
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 leaning over the hot spring with your face. Collecting samples directly. not me sometimes, actually a great number of fabulous postdocs and scientists.
Short Wave
Microbes: It's Complicated
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 nine 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, et cetera, right?
Short Wave
Microbes: It's Complicated
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.
Short Wave
Microbes: It's Complicated
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
Short Wave
Microbes: It's Complicated
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.
Short Wave
Microbes: It's Complicated
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.
Short Wave
Microbes: It's Complicated
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.
Short Wave
Microbes: It's Complicated
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?
Short Wave
Microbes: It's Complicated
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.
Short Wave
Microbes: It's Complicated
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.
Short Wave
Microbes: It's Complicated
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.
Short Wave
Microbes: It's Complicated
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.
Short Wave
Microbes: It's Complicated
Because we cannot study that in isolation, right? Pretty obviously.
Short Wave
Microbes: It's Complicated
It's such a meta thought that we want to study communities, but we need a community of scientists to do it. We need...
Short Wave
Microbes: It's Complicated
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
Short Wave
Microbes: It's Complicated
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.