‘Dark Fungi’ Species Don’t Get Names. Should They?

CHARLES BERGQUIST: You may have heard of dark matter, but I bet you’ve never heard of dark fungi, not the mushrooms you found way at the back of the fridge but something a bit more mysterious. SciFri producer Shoshannah Buxbaum is here now to tell us more about it. Hey, Shoshannah.

SHOSHANNAH BUXBAUM: Hey, Charles. Yeah, the term dark fungi had me hooked as soon as I read about it. Basically, scientists kept collecting DNA samples of the new fungi species but have yet to grow them in a lab or collect a specimen. They haven’t, for example, picked up one of these dark fungi off a log in the forest.

As you can imagine, this has created some intriguing logistical and philosophical questions for mycologists. To learn more, I spoke with a fungal taxonomist, Dr. David Hibbett, professor of biology at Clark University based in Worcester, Massachusetts. Dr. Hibbett, welcome to Science Friday.

DAVID HIBBETT: Thank you. Happy to be here.

SHOSHANNAH BUXBAUM: Let’s start with the very basics. What are dark fungi?

DAVID HIBBETT: So dark fungi are fungi that we know exist in the environment because we have DNA sequences that indicate that they’re there. But we don’t have a specimen. We don’t have a culture. So we don’t have a physical organism in hand, but we know that the organisms are there because we can detect them using environmental molecular biology methods.

SHOSHANNAH BUXBAUM: I always say “fun-gi.” Is it “fun-gi” or “fun-ji”?

DAVID HIBBETT: There’s no single right way to say this. I say “fun-ji.” I’ve learned it that way. But other people say “fun-gee” or “fun-gi.” I don’t think it really matters.

SHOSHANNAH BUXBAUM: OK, so where exactly are scientists finding dark fungi? Are they hiding in the soil in my backyard somewhere?

DAVID HIBBETT: Oh, that’s an easy one. They’re finding them absolutely everywhere. So they’re finding them in all the places that we usually look for fungi, so forest soils, wood, places like that, leaves, roots. But they’re also finding them in places where we don’t usually go hunting for fungi, such as in freshwater and marine systems or samples from the air. Lots of places where mycologists have not traditionally gone hunting for fungi we’re finding out that there’s tons of fungi there because we can now use these molecular methods to detect.

SHOSHANNAH BUXBAUM: Are they microscopic? Is that an appropriate way to think of them?

DAVID HIBBETT: So for sure. There’s lots of fungi that are microscopic. And many are not culturable, or at least we haven’t been able to figure out a way to get them into culture yet. But plenty of the fungi that we discover using environmental molecular methods we think probably are related to macrofungi, things that make mushrooms and so on.

SHOSHANNAH BUXBAUM: You’d mentioned this earlier, but why is it that they can’t be cultured? Why can’t they be grown in a laboratory?

DAVID HIBBETT: Often we don’t know why we can’t grow fungi in the lab. Some are living in symbiosis with other organisms, like plants and so on, and so it kind of makes sense that it’s hard to come up with a simple culture medium that provides everything they need. But in many cases, we just haven’t figured out what it is that they need physiologically to be able to be supported. And that’s common for lots of different microbial organisms. There’s lots of unculturable biodiversity out there.

SHOSHANNAH BUXBAUM: So how many new species are we talking about here? Is it in the magnitude of like thousands or millions?

DAVID HIBBETT: It’s many thousands. It’s hundreds of thousands. And that’s something that environmental bioinformatics people like to try to quantify. But it’s absolutely the case that the rate at which new species of fungi are being discovered using molecular methods dramatically outpaces the rate at which new species are being described using traditional methods based on a specimen of culture and so on.

SHOSHANNAH BUXBAUM: When did these dark fungi originally start turning up? When did scientists start being able to use DNA sequencing to detect them?

DAVID HIBBETT: Well, it really took off in the late 1980s when a technique called the polymerase chain reaction came along. And this was a gene amplification method that let you make many copies of a gene from a very small amount of starting DNA and then sequence it. This is not really new.

It really took off in the mid, early 2000s. It was around 2009 that some of these new methods started to be picked up by fungal ecologists. And all of a sudden, you had studies that were pulling up tens of thousands or hundreds of thousands of sequences from a single sample, many of which were new and undescribed.

SHOSHANNAH BUXBAUM: What do we know? Or do we know anything about the role that these fungi play in the ecosystems in which they were found?

DAVID HIBBETT: We know a lot about them. It’s all inferential, but we can make lots of predictions about what these fungi are doing in the ecosystem, first of all, because we know where we collected them. We’ve got all the metadata. And we can also use the power of evolutionary biology to take those DNA sequences and put them, place them in the tree of life, see what their closest relatives are, which may include things that we do have cultures for that we– or we have whole genomes, or we know more about them.

And so we can make a lot of predictions about what these organisms are doing. We just can’t see them. And we can’t do direct experimentation because we can’t grow them.

SHOSHANNAH BUXBAUM: Yeah, so this is just so much data that scientists are able to collect. And there’s just so many of these new fungi species. But the problem here is that taxonomists actually can’t name them. Is that right? So why is that? Why can’t you name any of these new species that are being discovered?

DAVID HIBBETT: Right. So this is a huge debate within the fungal taxonomy community and within the taxonomy community in general is whether or not you can formally name these organisms for which you have environmental DNA sequences but no physical specimen. Most people probably don’t know this, but there are rules or quasi-legal rules that govern how organisms are named, not just fungi but plants, and animals, and so on.

And the rules that apply to fungi specify that you have to have a physical specimen. And without that physical specimen, the rules prohibit you from assigning a formal name, like a Latin binomial. But a number of us are trying to change that. The rules for naming organisms, they are revised on a periodic basis. Every four years or so, we get a chance to change the rules. And a number of us are trying to change the rules so that we can name things based on DNA sequences, which would be a great advance for fungal biology.

SHOSHANNAH BUXBAUM: This is Science Friday from WNYC Studios. If you’re just joining us, I’m talking with Dr. David Hibbett about dark fungi. Why is it so important to be able to name these fungi and place them within the fungal family tree?

DAVID HIBBETT: Yeah, well, names are useful for communication. So any organism that we want to actually talk about, communicate about, it’s really handy to have a name as opposed to some machine-readable code or something like that. For conservation purposes, it’s really important to be able to name species. And for describing the biodiversity in a particular area, you have to be able to say how many species are there. So bringing all of these environmental sequences into the taxonomic workflow, into the mainstream of taxonomy, which is still based on specimens and cultures, it would really broaden our ability to communicate our understanding of the diversity of life.

SHOSHANNAH BUXBAUM: Yeah, there’s just so much power in naming a thing that’s in the world, right?

DAVID HIBBETT: Yeah. And when it comes to fungi, we’ve named quite a few species of fungi. There are about 150,000 or so named species right now. And that’s a big number. And we name about 2,000 species or a little over 2,000 species a year, which is real testament to–

SHOSHANNAH BUXBAUM: Wow. That’s a lot.

DAVID HIBBETT: It’s a lot, and it’s a testament to the hard work of fungal taxonomists, who are often doing this kind of work with limited funding. And they’re doing this work all over the world. However, the actual number of species of fungi on the planet is estimated to be maybe around five million or so.

And if that’s the case, then it means that we’ve named around 3% of the species that exist. And at the rate we’re going, it’s going to take us another 2,000 years to name all the species. So there’s a real need to accelerate and name more of the diversity of life that we know exists in a way that regular people, and legislators, and conservation biologists can talk about. And that’s to say with regular names.

SHOSHANNAH BUXBAUM: Taxonomy is one of the oldest disciplines within biology. So how big of a shift to the field would it be to allow the identification of fungi from these DNA sequences rather than where it stands now of just the physical samples?

DAVID HIBBETT: I think, conceptually, it would be a really big shift. As I mentioned, there are certain groups that are known mainly from environmental sequences. In those groups of organisms, it would be a big deal because now you can have lots of names for diverse groups of fungi that environmental molecular biologists have known have been around for a long time but what you’re not going to read about in most textbooks, or ecology books, and so on.

Now, I think a lot of people are concerned that if we allow naming of organisms for which we only have environmental DNA sequences that the floodgates will open, and tens of thousands or hundreds of thousands of new names will suddenly appear, just flood the literature. And it will create chaos.

The proposals that are under consideration right now for allowing naming of organisms based on DNA sequences only I think are set up in a way that would prevent that because we would require peer review. We would allow only certain journals, at least at first, to be the places where these names are proposed to give the community some time to work out the kinks, figure out how to do this right, and to prevent abusive naming, high-throughput naming of fungal species without the intervention of the experts who really know the groups.

SHOSHANNAH BUXBAUM: Next summer, there’s this big international conference, and there’s a proposal to change this classification system. And it doesn’t apply just to fungi. It would also apply to plants, too. Is this a similar issue that other biologists are also grappling with as well?

DAVID HIBBETT: Well, this is a problem that applies in all fields of biology, but it’s particularly acute in groups like fungi, or microscopic algae, or bacteria, where the organisms are tiny. They may be unculturable. And so they’re very hard to detect using the traditional methods.

So there is a proposal, as you mentioned, to modify the code of nomenclature for algae, fungi, and plants. There’s also a secondary proposal that’s being worked up to allow a modification part of the code that applies only to fungi. So there are a couple of avenues that might allow us to start assigning valid legitimate taxonomic names to organisms for which we have only DNA sequences.

SHOSHANNAH BUXBAUM: It’s definitely a lot of hard work ahead to try and figure out all of these issues we were just talking about. So Dr. Hibbett, thank you so much for being on the show. This has been so fascinating. I really appreciate you taking time to be with us.

DAVID HIBBETT: My pleasure. Thank you.

SHOSHANNAH BUXBAUM: Dr. David Hibbett is a professor of biology at Clark University based in Worcester, Massachusetts. For Science Friday, I’m Shoshannah Buxbaum.

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