The Microscopic World Beneath Our Feet

IRA FLATOW: This is Science Friday. I’m Ira Flatow at the Sheldon Concert Hall in St. Louis.

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IRA FLATOW: How many of you are regular listeners to the show on Friday?

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IRA FLATOW: Thank you.

If you’re a regular listener, you know that one of my favorite topics is the microbiome, right? All that stuff that’s living in your gut, all that bacteria and the viruses and things like that. It’s one of my favorite topics. And we tend to focus on the human microbiome. We’re a navel gazing species, right? We like to look at our– literally.

In fact, there are studies that have looked specifically, and exclusively, at the microbiome in your belly button. It’s true, and they have found– guess how many types of bacteria they have found there on the average? Any guess? Five? Ten?

SPEAKER 1: 100.

IRA FLATOW: 100? Close– 67. 67 different types of bacteria living in there, and they change all the time. And we pass them around to one another. Things like that. Well, tonight– I know it’s kind interesting to think about.

Tonight we’re going to leave your bellybutton behind a little bit and investigate another incredibly important microbial habitat, and that is the soil. There’s a microbiome in the soil right down below our feet, and we’re going to learn to how to get your hands dirty in this one.

IRA FLATOW: Bo Adu-Oppong is a microbe hunter of sorts. She’s a PhD student in ecology, evolution and population biology at Washington University in St. Louis. Welcome to “Science Friday.”

BO ADU-OPPONG: Thank you.

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IRA FLATOW: So we talk about what’s living in our belly button all the time. What’s living in the soil?

BO ADU-OPPONG: Yeah. So we have these microbes that are able to decompose different materials in the soil. So decomposition is one of the fundamental ecosystem processes. It’s fundamental because it’s able to recycle the materials on this planet Earth. Without them, we would have dead bodies just lying all over the ground.

IRA FLATOW: I hate when that happens.

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Yeah, yeah. And so turning dead material back into the soil is a big function of the microbiome.

BO ADU-OPPONG: Yes. So if we think about decomposition and we think about some of the biogeochemical cycles, one important cycle that decomposition is really important in is the carbon cycle. So carbon first binds to oxygen in the atmosphere as carbon dioxide. And then plants use carbon dioxide to react with water in order to make oxygen and sugars, which is super important for us, of course. In order for us to live here on this planet, we need oxygen.

But also, the sugars that are made by the plants are kept in the plant cells and used in order to make their cell walls. What’s really important there is that as consumers, we actually eat the plants. And therefore, this carbon is again transferred from plants into consumers.

And then we die, again, because of decomposers, they come and save the day, essentially. They come in and help break down those organic molecules into inorganic molecules into carbon dioxide. And then that gets recycled back into the atmosphere.

IRA FLATOW: Yeah. And then the plants take it back up again.

BO ADU-OPPONG: Exactly.

IRA FLATOW: And more stuff out of it.

BO ADU-OPPONG: And make more stuff.

IRA FLATOW: Now I talk about we have a microbiome in us. And you’re talking about the microbiome that’s in the soil. Do the plants, do trees have their own microbiome living in them?

BO ADU-OPPONG: Yes. So if we think about the root system of plants, we think about them as an inverted gut. So our guts are inside of our bodies. But for a plant, their roots are inside of the soil. And so what we’ve discovered and what I study in my lab is I’m really interested in the bacteria that actually live inside of the roots of plants.

So most people look at the bacteria that are on side of the roots, on the rhizosphere. And most of the time, they study these bacteria that can break down nitrogen. So nitrogen forms these bonds with each other, and they form these really strong nitrogen bonds, three of them. And so these decomposers are able to break down the nitrogen bonds and allow ammonia to exist for the plants to use up again.

However, I’m really interested in the bacteria that are inside of their roots, because why are they there? So it could be used for the immunity of the plant, so to help make sure that other pathogens, other bacterial or fungal that could hurt the plants, don’t invade that system.

IRA FLATOW: That’s sort of like in people.

BO ADU-OPPONG: Yes, exactly.

IRA FLATOW: Our defense system uses all those microbes in our gut and our intestines to fight off disease. You don’t normally think about a plant having an internal disease or a defense mechanism.

BO ADU-OPPONG: Yeah. Plants do have an immune system just like humans. But what’s different for plants is because, of course, they don’t move around, they’re having to have cells all around their plant tissue in order to recognize bacteria. So they’re able to do it in a very different way from humans, because we have these human cells that are able to travel around our body and find things that are foreign to us. But for plants, they have to have that type of function within every single one of their cells.

IRA FLATOW: Wow. Yeah, they’re not moving very quickly, are they?

BO ADU-OPPONG: No.

IRA FLATOW: Now I understand that one of the things that you have studied in the past was something that actually feasts, eats the soil bacteria.

BO ADU-OPPONG: Yeah. So what decomposes bacteria, right?

IRA FLATOW: You need a balance. You’ve got to have a balance.

BO ADU-OPPONG: Exactly. So what I had studied during my undergraduate degree was Dictyostelium discoideum.

IRA FLATOW: What was that?

BO ADU-OPPONG: Dictyostelium discoideum.

IRA FLATOW: There will be a test at the end of this thing.

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BO ADU-OPPONG: It’s a really cool organism. And this is one of the reasons why I really became a scientist. So I stumbled upon a discussion section in my undergraduate campus, and they were going over life cycles. And I said, whoa, what is this organism. So what happens is they first start out as single cells. So they eukaryotes, and they’re found in the protozoa family.

So what happens is that these single cells eat bacteria. And then when they start to starve, when there’s no more bacteria around, what happens is they send these signals to one another called cyclic AMP. So they say, hey, guys. We’re all hungry here. We should go somewhere else. So they all gather together and they form slugs. So again, they start out as single cells, and then they come together to form this slug.

And then they will travel a little bit, like centimeters, not very far. And then they will form a fruiting body. So what they do is this slug transform into a stalk. And then they have a sorus, which is on the top of the stalk. What’s really cool about this organism is that 80% of the slug of those cells will die in order to form that stalk. And then 20%, so only 20% of them will live on in the sorus.

And so in the sorus, you can find spores that are developed there. And that is essentially the next progeny for the next generation.

IRA FLATOW: Now I promised [? Leonius ?] that we had a hands-on, get yourself dirty experiment that we could perform. Tell us what we can do.

BO ADU-OPPONG: Yeah. So I’m part of the Young Scientist Program at Washington University. And what we are, we are a group of graduate students that go around and do science experiments with K through 12 students around St. Louis. So we work with public schools, we work with private schools. We just work with anyone who wants us.

And essentially, we do all these different fun activities. And we range all the way from ecology, which is what I do, all the way to anatomy and physiology. So we have all these different demonstrations.

So one demonstration or a demo that we did with the students just this past week at Vashon High School, where the students are actually part of this project called the Show Me Costa Rica Project, where they will be able to take an eight-day excursion to Costa Rica.

IRA FLATOW: Can I get in on that project?

BO ADU-OPPONG: Yeah.

IRA FLATOW: Eight days of Costa Rica.

BO ADU-OPPONG: It is. But essentially, we don’t want them to just think of it as a fun field trip. We want to teach them about biology. So again we were talking about the biogeochemical cycles, and we want to teach them how the cycles can happen in a fun and interactive way. So we made these Winogradsky columns. So what I did was I went to a pond out in Forest Park and collected soil there. And then we basically took the soil and put them in these columns.

You mix the bottom half of the column, or about a third of the column with paper, egg yolk and also chalk. And so these will serve as a substrate for the microbes to feed on. And then you pound the rest of the soil on the top and leave a little bit of water at the top of the column. And so what happens is once you close this column, it becomes a closed biogeochemical cycle.

And what will happen is you’ll see the stratification within the column. So you’ll have oxygen being more rich at the top of the column and oxygen being very poor at the bottom. And this creates basically bacteria that are able to live off of oxygen, so aerobic bacteria, will live at the top while you have anaerobes, bacteria that can only live in the absence of oxygen, living at the bottom.

IRA FLATOW: So you sort of have a layer cake.

BO ADU-OPPONG: A layering cake.

IRA FLATOW: And what’s the strata? What’s living where?

BO ADU-OPPONG: So the aerobic bacteria, so the bacteria that can live in the presence of oxygen, will be at the top. And the bacteria that can only live in the absence of oxygen will be living at the bottom.

IRA FLATOW: And kids are doing this.

BO ADU-OPPONG: And kids are doing this.

IRA FLATOW: Are they interested? Do they light up when you–

BO ADU-OPPONG: They loved it. One side note is that you will need to have a lot of paper napkins around, and also hand sanitizer. Because at first, we had gloves there. As you can see, the students had gloves. And then they said, oh, whatever. It’s soil. We can just grab it and go on our ways. And so they just loved the activity, and they found it really exciting.

IRA FLATOW: It is kind of cool. Step up close to the mic please, and ask your question.

AUDIENCE: Yes. So you were talking about microbials inside the actual plant. Can your research eventually lead to a point where we could have a new type of fungicide or insecticide that can protect our plants, our crops and things either at home or just in large-scale farms?

BO ADU-OPPONG: So that’s a very good question. So as a graduate student, that is something that I want to do next, as maybe during my postdoc or working with some industries. So part of my research is about is looking at the microbes that are inside the root and translating that to what the plant growth. So trying to understand if you have a certain microbial community in your root, do you grow faster? Do you grow more? Do you have more biomass just because you have a certain community structure there?

And so that could also lead to, is this microbial community stable? Is it stable over time? So if you were to perturb that microbial community with a pathogen, does it stay the same?

So it’s essentially in ecology, the stability hypothesis. And we try to understand, is that community stable even in the presence of a pathogen? And if it is, then we know that that pathogen can’t get into the community. If it’s unstable, then we know that that pathogen can perturb the microbial community, and then there will be things in flux. And so that’s the things that I really want to study as my next steps.

IRA FLATOW: If only you had a biochemical company located–

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In this city.

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Nah, never going to happen. Thank you, Bo. Thank you for taking time to be with us. Bo Adu-Oppong is a PhD student in ecology, evolution and population biology at Washington University.

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Thank you. And playing us through the break, Buckley and Walsh.

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MAN: Thank you.

IRA FLATOW: This is “Science Friday” from PRI.

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