Bonding Over Science Episode 2: Fungi: Friend or Foe?

In this episode of Bonding Over Science, host Dawn Stringer investigates the underground world of fungi. Scott Baker, fungal biotechnology scientist and microbiologist Davinia Salvachúa break down the importance of fungi to the environment. They also dispel fears that fungi could affect humans as depicted in the fictional series, "The Last of Us." Read the feature article on EMSL staff researchers and users who are conducting fungal research.

Transcript: 

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Dawn Stringer: In the last episode of Bonding Over Science, we discussed the health and environmental impacts of harmful algal blooms, and if this could turn into the fictional series “The Last of Us” in real life... spoiler alert... algae in the atmosphere won’t turn you into a zombie.  

On the other hand, this show has viewers curious if research on fungi shows a threat to spreading as depicted on a fictional show. 

Google recently announced “Can fungus control humans?” is a worldwide breakout search this year. 

I’m Dawn Stringer with Bonding Over Science, let’s dive into the underground world of fungi. 

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Dawn Stringer: The HBO series “The Last of Us” has taken the country by storm, posing the question if organisms like fungi could be harmful to humans.  

EMSL’s Functional and Systems Biology Science Area Leader Scott Baker is the self-proclaimed fun-guy of fungi, and he is the perfect person to tell us more about the relationship between his research and the imagined world of “The Last of Us.” 

Scott, thank you so much for joining me today on Bonding Over Science. 

Scott Baker: It's a pleasure, good to be here. 

Dawn Stringer: I want to ask you the hardest question of the day. Is it fungi (FUN-gee) or fungi (FUN-jai)

Scott Baker: Either one works, I go with fungi (FUN-jai). 

Dawn Stringer: Okay. You know, I usually say fungi (FUN-gee). 

Scott Baker: Yeah, well, I've been called a “fun guy,” that's a joke that's used quite often when people meet me. 

Dawn Stringer: Okay, so I'll stick with that one. So a big reason why I wanted to talk to you today was something that I saw from Google. They actually showed on their Instagram that “can fungus control humans?” is a worldwide breakout search for the year, which I’m sure we could credit to “The Last of Us,” right? 

 Scott Baker: Yes, absolutely. 

Dawn Stringer: So tell me, have you heard of “The Last of Us”? And if so, how did you hear about it? 

Scott Baker: I have heard of “The Last of Us.” I first heard about it from my son who played the video game and loved the video game, and as soon as the HBO series came out, we started watching it. Now we're a couple episodes behind because he's a busy high schooler and I'm also busy, I guess. And so we haven't had time to finish it out, but I've enjoyed it so far, actually. 

It's the other way around, we tend to control fungi more than they control us. I mean, there are some things that fungi do that can be bad, but for the most part, we have a long history of controlling fungi. 

Dawn Stringer: Now, what was it like bonding with your son over “The Last of Us,” and did it make him more interested in your field work? 

Scott Baker: Oh, it's always good when you can find common ground with your teenagers, and I think that he enjoys the fact that I study fungi so he could ask me questions about –  "Is this real? Is this a realistic thing or is this not a realistic thing?" So that was great. 

Dawn Stringer: What do you think of the depiction of this zombie fungus on the show? You kind of touched on it saying that we control fungi more than it controls us, but what do you think of this depiction? 

Scott Baker: You know, I think that it's important. Fungi for a long time have been important microbes in the lives of humans, but they haven't been recognized as much as some of some of the bacterial pathogens as really serious pathogens. So I think it's good, any press is good press. It increases people's awareness that fungi are all around us. 

It's coincident with the WHO [World Health Organization] coming out with a report on fungal pathogens of concern. Their first list was in October. So I think it is a good time to be a fungal biologist. As far as the depiction goes, I think some of the background has been really interesting and fairly accurate. I really don't think that fungi are going to infect us and control us and turn us into zombies. 

As I said, we've used fungi for our purposes for a long time for bread, alcohol—like beer and wine—but also in traditional Asian food production, such as soy sauce and saké. So like I said, it's been the other way around. We've really controlled the fungi to do our bidding. More recently, we've used fungi for production of citric acid. 

That process is, you know, it was discovered in 1913. We've used fungi for production of enzymes to help us digest food, and I think that patent is 1896 for digestive enzymes. And then we're using fungi now to help us both degrade plant material so that we can get it into sugars and then fermenting it into biofuels, bioproducts, and potentially biomaterials. 

Dawn Stringer: Are there other industrial ways to use fungi? 

Scott Baker: I think people are starting to explore plastic deconstruction by microbial enzymes, including those of fungi. You know, fungi can degrade, like I said, plant biomass and other kinds of stuff in nature. When you see fungi growing on something, it's digesting. I would say we live in the fungal digestive tract as the fungi digest the world around them, whereas we ingest food and, you know, put it in our stomach. 

The fungi —the world —is their digestive tract. 

Dawn Stringer: Is it possible for it to lead to mind-altering behavior? 

Scott Baker: I'm not a medical professional, but I mean, certainly there are compounds produced by fungi that can be mind-altering. There is a theory that some weed contaminated by fungi that produced ergot had played a role in the Salem Witch trials. I'm not an expert again, but I think there's a little bit of debate, so there are a variety of mind-altering compounds and, you know, magic mushrooms, etc. are fairly well described. 

So yeah, the fungi can lead to produce compounds that can impact your cognitive processes. 

Dawn Stringer: Well, it seems like it's in more places than we may have realized. 

Scott Baker: Oh, absolutely. I just returned from a conference where they talked about using fungi as building materials. 

Dawn Stringer: Do you think this is something that is a positive impact to the environment, to use these for industrial purposes? 

Scott Baker: Absolutely. Absolutely. If we can, you know, move away from things that are land intensive or use a lot of resources to grow, like, I guess a cow for both meat and leather, then I think, you know, the more choices there are in the market that are economically viable, the better off we are. 

Dawn Stringer: Absolutely. Now, how does it form into the organism that it is? 

Scott Baker: Well, I mean, fungi are really cool because they have a whole bunch of different growth modes and lifestyles. So you know, you've got yeast that like [whose] growth is a single cell that just divides. You know, I tend to look at molds where they form these hyphae, which are these long tubes that kind of grow at their ends. 

Obviously, mushrooms or fruiting bodies of fungi is a little outside my expertise, but they like to grow. That’s all I could say. 

Dawn Stringer: Because they like to grow, is it possible for it to ever evolve into something that we see like in “The Last of Us”? I know it's a little dramatized on the TV show, but is that even a possibility? 

Scott Baker: I don't think we're going to have fungi controlling us and making us zombies. I think at worst, there are a number of diseases where, you know, fungi grow like any other microbe infection, because fungi are eukaryotes and have mitochondria and subcellular compartments that they can be a little harder to kill. So we need to continue to search for good anti-fungal drugs. 

I think that's where there needs to be effort that kind of matches what we have in antibiotics. But, you know, I'd see people getting sick, not turning into zombies. 

Dawn Stringer: How is EMSL helping you advance your research in fungi? 

Scott Baker: Well, you know, EMSL is an amazing user facility that has a lot of expertise and capabilities to understand the cell biology of fungi, to look at the molecular underpinnings of different kinds of metabolic pathways, to look at the structure of enzymes. So there's a lot of tools here that help myself and my colleagues understand how fungi fit into the different niches that they live in. 

And how can we then either understand how carbon is cycling in the environment, you know, with fungi in soil and associated with plants, or how can we then take these processes and turn them into biotechnological advances that can lead to fuels and products. So I think you have to have that fundamental knowledge that then you can use to engineer these organisms to do your bidding. 

So again, we want to be in control, and we have been for centuries. 

Dawn Stringer: So what kind of instruments here at EMSL are helping you with this research? 

Scott Baker: Wherever applicable, we use microscopes, mass spectrometry to look at proteins, metabolites, microscopes to look at subcellular compartments. We've started an initiative to look at the structure of fungal proteins where we don't necessarily know what the protein does, but maybe getting a structure of the protein would help us understand that in conjunction with other, you know, studies that we can do in genetics. 

So I think it's kind of limitless what we can do. If I haven't used an instrument, it's probably because it's on me that I don't necessarily know what it could offer. 

Dawn Stringer: Now, something I want you to leave us with before you go is what is something you wish people knew about fungi? 

Scott Baker: I think fungi have been intertwined with human life for centuries and oftentimes for our benefit. Of course, you know, there's times where fungi have caused plant disease or human disease and those are important to study, but I think that in the long run, fungi offer us limitless possibilities for helping us live a more sustainable existence in changing times. 

So fuels, chemicals, materials can be produced by fungi, and then fungi also play a really important role in the environment, cycling carbon and other elements, nutrients as they pass to the environment. So fungi are important for animals, plants, other fungi. They’re really interesting. 

Dawn Stringer: Where can our listeners go to learn more about your research? 

Scott Baker: Well, I occasionally tweet. @moldomics is my Twitter handle. They can check journal indexes for papers that I've coauthored with colleagues. And if they ever see me at a at a conference or in an airport, they should feel free to ask me about fungi. Tell me that I'm a really “fun guy.” 

Dawn Stringer: There you go. That's what we'll leave our listeners with. The fungi of fungi. You said it, not me. 

Scott Baker: Yeah, that's true. That's true. I brought that on myself. 

Dawn Stringer: Well, Scott, thank you so much for joining me today. 

Scott Baker: Thanks, Dawn. 

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Dawn Stringer: Now that we have some background on what fungi is and what it’s realistically capable of, I wanted to get a take from another expert on the topic.  

Davinia Salvachúa is another expert in the fungi world, and she’s also an EMSL user, meaning her research project was awarded funding to use EMSL resources to advance her research. I was excited to catch back up with her and get her take. 

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Dawn Stringer: Knowing your research area, I have to ask you if you've heard about “The Last of Us.” 

Davinia Salvachúa: I have heard about it. I first learned about it because of video games. My partner loves video games and I was exposed to “The Last of Us,” not only the first part, but the second one. 

Dawn Stringer: So as a scientist watching this show, how scientifically accurate is the concept? How dramatized is it in your perspective? 

Davinia Salvachúa: Well, it is highly dramatized, but that's what it says, right? That's an apocalyptic universe. But I really loved, like, especially the two first episodes they were mentioning more fungi. I think that at the end of the story, like, it moves more toward people like every apocalyptic story. But in the first two episodes, they were really giving some science insights. 

So they were talking about mycelium, they have the mycelium connect miles away. But in this case, it's not like in nature that mycelium connects with fungi far away and they feel that chemistry. But in this case, in the TV show is that oh, yeah mycelium can communicate one mile away and can wake up a zombie. 

So yeah, the outcome was different and for the relationship of these mycelium but then in terms of the fungi that was infecting people in the TV show, cordyceps, yeah, they are really taking that into account in nature, they infect insects and they modify their brain so they have a special behavior so they can continue reproducing. In these cases the same they would infect humans, they become infected and then yeah, their brain operates like a zombie. And then at the end is like in nature, we know that the fungi utilizes the insect as a substrate, as a carbon source. So here in the TV show when they get infected for a long time, it's the same thing. Like they basically eat the human. But again, like this very dramatic. 

Like we know that right now, fungi cannot grow at the high temperature of the human body. So that’s something at the moment that is not possible. 

Dawn Stringer: Well, what can the show, in addition to what you just told me, what can it teach us about fungi? 

Davinia Salvachúa: It’s teaching us that [it] is a smart organism. I still believe that fungi are very unknown organisms—they have a special kingdom. And as someone of my colleagues say here at NREL (National Renewable Energy Laboratory) is that they are, they look more like as squirrels and mammals than bacteria. And I kind of agree, they look like hyphae. 

They look like hyphae, so they look more like a squirrel. But there is still a lot we need to understand from these organisms. Like, of course, from the pathology point of view, we are studying a lot in plants like sources that humans utilize for food in some insects, but normally they also infect humans as we know in the skin. 

But those are probably in that for human health purposes, they are more studied than for other purposes. 

Dawn Stringer: What kind of purposes can fungi be used for? 

Davinia Salvachúa: So that is where my research comes and well, I am saying for human health, but fungi have been utilized forever. But right now, like more complex fungi, filamentous fungi, I think that there are still a lot of options for them that we need to continue exploring, and right now that is our fashion on how to delight fungi for food like instead of utilizing eating what we know as the fruiting body they are utilizing it as the proteins from the fungi and mimic meaty foods. 

Dawn Stringer: So you mentioned some of your research here at EMSL and how the different purposes of fungi is something that you look into. So tell me more about your research here and why it's important to society. 

Davinia Salvachúa: In my case, I am working with very specific organisms. They are called white rot fungi. This group of organisms is really good at degrading lignin, and lignin is the most recalcitrant polymer in plants. And this means that it is very difficult to degrade these polymers. So these group of organisms, these fungi, they have evolved to do this in nature. 

In fact, that is one of my favorite papers. It was published in Science in 2012. And they also said that one of the main hypotheses for the Carboniferous Period to end was that white rot fungi evolved to degrade lignin at the time. So that was one of the reasons about why carbon accumulation in our planet decreased. 

So that was a very important event in our planet. But what is even truly fascinating to me is that after 300 million years, these organisms are still the most efficient in nature doing that. So when we think of carbon cycling, all the turnover of wood in the forests, this is where the fungi are key for that purpose. Of course there are other organisms but for lignin degradation these are key. So in my project with EMSL, we are really trying to understand how that happens inside the fungi, because even in my thesis we were trying to understand how they break down the lignin, which are the mechanisms to break it down. But we never cared about what happens inside the fungi, what they are feeling. 

So that is basically what we are trying to understand now. So eventually we could utilize these organisms as bio catalyst to convert carbon from lignin to biochemicals, biofuels, or value other projects. 

Dawn Stringer: What kind of tools do you use at EMSL that has helped you advanced your research? 

Davinia Salvachúa: So most of the instruments we have been utilizing are related to omics. So basically what we are trained to understand—like to understand what the fungi feel—we are utilizing transcriptomics to see that gene expression and how that changes if they are eating this component versus this component. So we can see what happens at the gene level. Also proteomics, so we can see what happens at the protein level. And then the product of that is metabolites. So we are also doing metabolomics—in this case is NMR [nuclear magnetic resonance] metabolomics—to understand that. 

Dawn Stringer: What's so important about understanding each level of what you're looking at. 

Davinia Salvachúa: So you can have a whole picture of the whole process because many times like a gene can be activated but is not going to produce the protein. So the protein is a confirmation of what the gene is doing. But this doesn't mean that transcriptomics isn’t also very important because some of those increases in the suppression of genes, they do not always have to end up on a protein. 

They can be transcription factors. They are going to be more involved in the regulation of the whole network. So I think that integrating transcriptomics, proteomics, and then ultimately metabolomics, that's going to give you a better picture of what is happening in the whole network. 

Dawn Stringer: So what are your hopes for the future with the research that you're doing here at EMSL? 

Davinia Salvachúa: I think there are many possibilities because it is true that now we are focusing on how these fungi degrade lignin, and then what happens inside the fungi. But I think at the end of the day, what we are also doing is understanding overall the metabolism of the fungi. So then we can utilize this information to develop other types of technologies, or to modify these organisms genetically. 

So all this information is going to give us information about the regulation of all these processes. So then we can utilize that for other purposes. 

Dawn Stringer: Well, that's about all the questions that I had today. Is there anything else, any other information that you want to leave us with? 

Davinia Salvachua: I think that I would recommend to watch the TV show. It’s very different compared to other apocalyptic stories. But I think it is a good relationship between fungi and humans and I think that that really brought my curiosity and attention to the issue. 

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Dawn Stringer: While there may be some scientifically accurate points in “The Last of Us,” it’s safe to say we aren’t anywhere close to facing a zombie apocalypse. Who knew fungi could be good for us and the environment in several ways!  

Turns out.... we’re a lot more like fungi than we thought.  

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Dawn Stringer: We don’t have time to cover it all, so don’t forget to check out EMSL-DOT-PNNL-DOT-GOV for a full article on this topic featuring the two researchers I spoke with today. And don’t forget to follow us on all social media platforms for the latest and greatest news coming from EMSL! 

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Dawn Stringer: EMSL is a DOE Office of Science national user facility that accelerates scientific discovery and pioneers new capabilities to understand biological and environmental processes across temporal and spatial scales. EMSL leads the scientific community toward a predictive understanding of complex biological and environmental systems to enable sustainable solutions to the nation’s energy and environmental challenges. If you’re interested in working with EMSL, learn more at EMSL.PNNL.GOV, that’s E-M-S-L-DOT-P-N-N-L-DOT-G-O-V. 

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