📷 Braulio Castillo
Journalist: Luming Cao
Luming: Welcome to SciSection. My name is Luming, and I'm your journalist for this episode. We're here today with Braulio Castillo—he is a PhD student in the Department of Ecology, Evolution, and Marine Biology at UC Santa Barbara, and he does research on marine microbes. Thank you for taking the time to meet with me, Braulio. So can you tell us about your background?
Braulio: I grew up in Tijuana, Mexico, and that's where I was raised. And then I did my middle school and high school in San Diego. So I would cross the border, which is actually kind of pretty common there. I think there's a lot of people who just cross the border every day to go to school. And I did that. Then I eventually did my undergrad in Ithaca, New York. That's where I studied microbiology, and I guess that's where I started getting more of a knowledge of microbes. And that's how I started getting into, I guess, the path where I'm on now. So then from Ithaca, I finished my degree, and then I went directly to a Ph.D. program here at UCSB. It’s fun. I chose my program very much based on my advisor, because I felt I got along very well with her. That's how I decided to make that transition to here instead of any other place that I could have gone.
Luming: Nice. Can you tell us about microbes? So let's start from the basics: what are microbes?
Braulio: Yeah, so microbes are single-celled organisms. There's a lot of things that could count as a microbe—so like bacteria, archaea, some kind of fungi, there’s some kind of single-cellular eukaryotes. So there's this idea of prokaryotes and eukaryotes. Eukaryotes have nuclei and prokaryotes tend to not have that. So there's bacteria, archaea, and eukaryotes, and archaea are more closely related to the eukaryotes. So the prokaryotes term is kind of paraphyletic, which means it's probably not the best to use, but it's a useful way to like differentiate between small single-celled organisms without nuclei and an eukaryote that would have a nucleus. When I really got interested in microbes, I guess, was when I started learning more about these differences and how these like bacteria and archaea versus eukaryotes work. So bacteria and archaea, and lots of microorganisms, these microrganisms are very metabolically diverse. So they're able to use a bunch of chemicals, and they're very versatile in their physiology. And they're able to metabolize a bunch of things that someone like eukaryote would not. So like you and I, we just eat oxygen, right? Versus like bacteria and archaea, they can use a bunch of different [things] like electron receptors, electron donors… And that allows them to survive in crazy different types of environments that are not possible for us. So these small single-celled organisms, they're so physiologically diverse, and we, the bigger cells, or not bigger cells, but like sometimes larger organisms, eukaryotes, we are physiologically less diverse. We only have one big reaction, like the oxygen reaction. But morphologically we are more diverse in that sense. It's an interesting spectrum of looking at biology that, when I started learning about microbial diversity, I really got interested in bacteria because of that, I think,
Luming: Why is that they are so versatile but they’re physiologically simple? Or like, why is it that...
Braulio: They would be able to do all that?
Luming: Yeah.
Braulio: I mean, I guess a part of it is just having a single cell, there's so much gene transfer, and there's so much like the generations—bacterial generation times are happening a lot more quickly. So there's a lot more opportunity, I guess, for evolution to happen and for different types of bacteria to adapt to different niches. And that allows them to start developing different proteins that will help them—that did help them—adapt to different environments. Even before, like the earth didn't have oxygen, right? Or the oxygen was so minimal. That was a different type of metabolism, there was a bunch of sulfur metabolizing organisms that were able to survive in that time. Then there was this jump to cyanobacteria, which produced a bunch of oxygen that change the atmosphere of our Earth, that was called the great oxidation event, and so that the bacteria were able to survive through all that. And they were able to adapt to all these different kinds of physiologies, versus we evolved into this oxygen atmosphere and we optimized our physiology for this atmosphere. But then we were able to evolve morphologically. I guess that's a different way that these organisms… that we bigger eukaryotes or whatever, like we're able to change physically versus these bacteria that had these single cells. They changed their protein in such a way that they were able to metabolize things physiologically. I mean, it's just an interesting spectrum of how evolution happened.
Luming: Yeah, that's really cool. So your lab has a focus on ecology. So can you talk about how microbes come into play in our macro scale ecosystem? And why are they so important?
Braulio: Yeah, so I mean, as I said, so they're very involved in physiology, right? Like their physiology is so diverse, and that allows them to participate in a bunch of biogeochemical cycles. So they can transform important elements like nitrogen, sulfur, carbon, and affect how much of it is available to other organisms. So there are types of bacteria that are in other organisms that fix nitrogen. And by fixing nitrogen, that means that it makes it available to other organisms, like biologically available. So if we didn't have these nitrogen fixers, then we wouldn't have any nitrogen available for us to consume. Or that was the case until we were able to chemically produce chemically fix nitrogen, but before that, bacteria were the ones who were like fixing nitrogen that made it available to us. So on the small scale, they're producing these chemicals in the environment. When you add it all up, these organisms are producing a bunch of chemicals that are important to the survival of other animals and us or a bunch of other organisms. So by looking at all this, or thinking about all this, they do end up affecting the environment, or like, they can affect what chemicals are available, and also how other things like carbon in the ocean, they can affect how much carbon is available to other organisms, or how much carbon gets sunk into the ocean. So in that sense, they can become pretty important, if that makes sense.
Luming: Yeah. They're pretty invisible to us, but they do so much in our environment.
Braulio: Yeah, you wouldn't think about it just because you can't really see them. But they're all everywhere, right? So they're all actively… To survive, they're changing a bunch of chemicals, and by doing that they're affecting the environment. And I mean, they can affect chemicals that we need, but they can also like, do a bunch of stuff, you know. There's bacteria that are used to clean up oil spills. And then there's bacteria that can clean a bunch of other like toxic compounds. And they're just so diverse that they can do a bunch of things. And that's what's really cool about them, I think, like bacteria and archaea. Yeah,
Luming: So how do you first get interested in biology and microbiology? Did you always just have an interest in microbes?
Braulio: I liked science, and I really liked biology. Chemistry was also fun. But I had a really hard time with physics, so I was like, I can't do physics. And in a way, microbial ecology is really cool, because it just puts together a bunch of like different things in biology, especially like, there's biology, there's chemistry, and then ecology. Then microbial ecology itself, you can do a bunch of molecular work. So you can look at the DNA in a bunch of bacteria or their proteins or you can perform molecular analyses, but you can also do stuff in the field and you can see… I guess it to me was kind of the best of both worlds because you can do a bunch of stuff outside and a bunch of stuff inside, you know. So I when I was an undergrad, I kind of was part of a like a soil, carbon ecology kind of microbial ecology lab. So we got to go sometimes to like a meadow or something, and then we would take soil from there. And now, in the lab I'm in, we looked at bacteria and salt marshes, and also bacteria in the ocean. And they're just microorganisms in the ocean. And while we can go out, we can also do a bunch of molecular stuff inside. So like, it brings together a lot of different parts of research that I like. So that's, uh, yeah, yeah, that's how I ended up deciding that I liked it. And then when I started taking classes and learning more, and then getting inspired by the people who were teaching and showing me a bunch of different things that I never even thought about that was possible, like the spectrum of evolution of how microbes can become so physiologically diverse. It just, like, set me into this world of how cool it is that like microbes can do so many different things. And there's just so much to know about them that we don't know yet.
Luming: Yeah. So what are some projects you've been working on?
Braulio: Yeah, yeah. So one of the things we do are is we're looking at these… My advisor, a lot of her thesis was on the macroscopic aggregates of bacteria called pink berries. So it's these. It's basically a consortium of a bunch of different bacteria, sometimes some diatoms, and it's a little centimeter-wide little ball, I guess. It'd be cool if you could see it. But I mean, if you even like Google it, you would see. If we put pink berries, or Lizzy Wilbanks, you'll see that it's just the macroscopic aggregate, and they can be like, from a few millimeters to a centimeter big. And part of what I'm doing is trying to look at the physiology of that. So this aggregate, the two main components of it are a sulfur oxidizer and a sulfate reducer. And then there's a bunch of heterotrophs and a bunch of other organisms there. So the purple sulfur bacteria, which is the sulfur oxidizer and the sulfur reducer, they tend to not like oxygen that much. So other organisms in the community consume the oxygen on the outer shell of the sphere. And that allows these two organisms to survive in the environment. So it's kind of like, I mean, it's not like an organism, like, it's not an organism, but it kind of like these bacteria cooperate in order to survive together, which is pretty cool. You know, our cells are all cooperating to survive as a single organism, and these bacteria, they're not an eukaryote, but it's just cool to see how these bacteria cooperate. And what I'm doing is looking at different… I expose them to different conditions and try to track what organisms are active under what conditions within this community. So it's kind of just cool just because like, probing community interactions and how physiology and like environmental conditions affect each other is pretty cool.
Braulio: And then another thing. Last year, we went on a research cruise, a bunch of people at UCSB, and we are interested in how microbes are affecting marine snow. So marine snow is basically decaying organic matter that's falling in the ocean. So it's like fecal pellets or decay organisms, like just any decomposition. And you can see, there's videos of it online basically: looks like snow is falling in the ocean, even though it's just like decaying organic matter. So it's like carbon coming apart. So what we did was capture a bunch of it in traps. And we tested it. We did experiments of like, just different assays of what kind of chemical transformations are happening. And we're hoping to do genomic and imaging work to try to understand how microorganisms are interacting with marine snow and how these microorganisms then would be affecting, like the carbon cycle in the ocean in different conditions. Yeah. So those are just some things that work on which, I mean, it's cool because as I said, what I liked about it was I'm able to go to a salt marsh or on a research cruise and then also work on like, lab work and try to do molecular stuff and use this knowledge of molecular biology and microbiology that I was trained on as an undergrad.
Luming: Yeah, so you kind of get a mix of fieldwork and working the lab. That's pretty cool.
Braulio: Yeah. I like it. It was fun.
Luming: What are some challenges you encountered when doing projects?
Braulio: I mean, there are technical challenges, like for imaging of these community interactions I was saying about. One of the bacteria is autofluorescent. So if I'm trying to use a bunch of dyes it kind of contrasts with it, so I'm trying too figure out something like bleaching it. I'm trying to figure out how to bleach these cells so that my dyes can come up. And I mean, that's just like, there's always technical problems like that in research. When I was first starting this project, I put layers of tissue onto slides. And everything was just falling off first, because you put it on slides, and then you put a bunch of solutions on it. But when I first started, the tissue was falling off, and I was freaking out. But then it just becomes a matter of being careful, and learning. I found a gel that could work for it. So in research, there's always small complications like that. And it can also be stressful. I guess, for example, like the research cruise I went on, I got very little sleep, but that's like everyone on the research cruise. And it's like, it was a new experience for me, right? Because, I mean, who ever gets to go on a research cruise as an undergrad? So as a grad student it was my first time and it was kind of stressful. I was like, will I get seasick? Will I not get seasick? Will I be okay? Will we have time to do all this? And I mean, we kind of did all the experiments we wanted to do, which was good. And I also didn't get seasick, which was great. Because otherwise I could not imagine having to do a bunch of like thinking and preparing stuff and having to deal with seasickness, because as is I was barely able to do everything. And there were other graduates on the cruise who were seasick. And they were basically out, llike they did as much as they could, but whenever they didn't work, they had to sleep and rest because it was hard. So research can be weird, but it was fun. It was a lot of fun.
Luming: Research cruise sounds really fun.
Braulio: It is fun. It's great. Just seeing the ocean.
Braulio: I remember our last day out. I was doing like some measurement at 5 am and a postdoc was like, “come out and look at the ocean with me just for like five minutes, you can take a break.” And like, it just looks so pretty, the ocean at 5 am. It just looks like it's glass. And it's just amazing.
Braulio: I don't know, it's just crazy. Like it was super stressful as an experience. So it was also like an amazing, like, very few and a once-in-a-lifetime maybe for me ,who knows.
Luming: Do you have a favorite microbe that we work with, or just any group of microbes that you think are super cool?
Braulio: I think cable bacteria are pretty cool. So they're basically filaments of bacteria. And they can transform sulfur. But it's a bunch of cells put together and they can just carry out interactions over a distance, which is just crazy. I don't know, just to be able to like do something on that scale. But also pictures of them are very pretty. So I just like both why they're different and because of how they look. I'm like, “They're cool! I like them.”
Luming: Yeah. So last question. Do you have any advice you could give to undergraduate students for exploring their interests?
Braulio: Yeah, I mean, undergrad, it's a stressful time, right? Just because there's so many classes and you're trying to get into research and I guess it's important to get into research eventually. I would say my first year of undergrad, I was just trying to get used to the whole college experience. And then after that, I started working in a lab and getting to know like, what it meant to do research even though I didn't … I don't know, it's just hard. But once I got into it, I liked it. And just, I feel what helped me a lot was just to talk to a lot of graduate students who were my TA's or just even people who I just met somehow randomly. It helps really much to make those connections and get to understand their perspective as a graduate student, what they were going through, whether I liked it, whether I thought it was for me or not. And just talking to them a lot helps me get a feel of what I might or might not be getting into. And then yeah, I just decided I liked it, or thought it would be okay. And then I found an advisor that works well for me. So for applying for graduate school, I think the advisor match is probably one of the most important things you know. And then when you're applying, which would be your last year of college or something afterwards, like if you decide to do something else in between or whatever. Really looking for someone who matches well with you. The advisor choice is probably the most important thing. So really paying attention to that I think is important. That would be I guess the biggest thing I could say,
Luming: Yeah, that's great advice.
Braulio: Yeah, that person will be, I mean, it will be the longest relationship I'll ever have, I guess, because it could be from five to seven years, right? I will have her until then, you know, so it's important. And they're your boss and your mentor. So yeah.
Luming: Yeah. That's great. And on that note, thank you so much for talking with me today. That is wonderful.
Braulio: It was nice to meet you. And it was also very nice to talk to you.
Luming: Yeah. Nice to meet you. And yeah, that's it for this episode of SciSection.