Science Friday - The Unseen World Of Seaweeds | Should 'Dark Fungi' Species Get Names?

Episode Date: December 27, 2023

The Unseen World Of SeaweedsChances are you don’t give much thought to seaweed unless you’re at the beach, or perhaps when you’re considering a dinner menu. But the thousands of seaweed species around the world are a key part of our coastal ecosystems.Seaweeds photosynthesize, provide food and shelter for marine animals, stabilize the coastlines, and even contribute to making your ice cream creamier (through an ingredient called carrageenans, extracted from red seaweeds in the Rhodophyceae family). Increasingly, they’re also being investigated as a source of biofuels and as biological factories, due to their fast-growing nature.Dr. John Bothwell, a phycologist at Durham University in the UK, has written a book in praise of seaweeds. In Seaweeds of the World: A Guide To Every Order, he highlights beautiful, unusual, and important species from each of the three seaweed lineages—green, red, and brown. In this segment, he talks with SciFri’s Charles Bergquist about some of his favorite species, where the seaweeds fit into the web of life, and the importance of seaweeds to the global ecosystem.“Dark Fungi” Species Don’t Get Names. Should They?Scientists have collected DNA samples of thousands of new fungus species over the past several decades. These fragments of fungal DNA are found nearly everywhere—in soil, decomposing logs, water, and even in the air. Mycologists have enough data to place these new species within the fungal family tree, but haven’t collected physical samples of them or been able to grow them in a lab. This means that according to the International Code of Nomenclature for algae, fungi, and plants, these new species cannot receive scientific names.How can you understand a fungus that has no name? SciFri producer Shoshannah Buxbaum talks with fungal taxonomist Dr. David Hibbett, professor of biology at Clark University, about a proposal to give these “dark fungi” scientific names, and why naming living things might help us better protect the Earth’s biodiversity.Transcripts for each segment will be available the week after the show airs on sciencefriday.com. Subscribe to this podcast. Plus, to stay updated on all things science, sign up for Science Friday's newsletters.

I'm guessing most of you don't give much thought to seaweed, but you should. Seawoids do in the sea what trees do on land. If we didn't have seaweed along the coastline, the coastline would die. It's Wednesday, December 27th, and yes, it's Science Friday. I'm sci-fire producer Charles Bergquist. The thousands of seaweed species around the world are a key part of our coastal ecosystems, whether you think of them or not. We'll look at the world beneath the waves with an author of a guy,

with the author of a guide to the Seawoids of the World. But first, the mysterious world of dark fungi. Here's sci-fry producer Shoshana Bugsbaw. 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 Hibbitt, professor of biology at Clark University based in Worcester, Massachusetts. Dr. Hibbitt, welcome to Science Friday. Thank you. Happy to be here. Let's start with the very basics. What are dark fungi? So dark fungi are fungi that we know exist in the environment because we have DNA, C. 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. I always say fungi. Is it fungi or fungi? You know, there's no single right way to say this. I say fungi. I've learned it that way, but other people say fungi or fungi. I don't think it really matters.

Okay, so where exactly are scientists finding dark fungi? Are they hiding in the soil in my backyard somewhere? 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. Are they microscopic? Is that an appropriate way to think of them? So for sure, there's lots of fungi that are microscopic, and many are not culturalable, 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 macro fungi, things that make mushrooms and so on. You'd mentioned this earlier, but why is it that they can't be cultured? Why can't they be grown in a laboratory? 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. So how many new species are we talking about here?

Is it in the magnitude of like thousands or millions? 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 in a culture and so on. When did these dark fungi originally start turning up?

When did scientists start being able to use DNA sequencing to detect them? Well, it really took off in the late 1980s when a technique called the Plymary Chain Rube. 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.

What do we know, or do we know anything about the role that these fungi play in the ecosystems in which they were found? We know a lot about them. I mean, 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 relative.

are, which may include things that we do have cultures for, 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. 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, 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? 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, there are sort of 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 got 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. This is Science Friday from WMIC Studios. If you're just joining us, I'm talking with Dr. David Hibbitt about dark fungi. I mean, why is it so important to be able to name these fungi and sort of place them within the fungal family tree? 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 kind of 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 sort of 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.

Yeah, there's just so much power in sort of naming a thing that's in the world, right? 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... That's a lot. 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, you know, the actual number of species of fungi on the planet is estimated to be maybe around 5 million or so. And if that's the case, then it means that we've named, you know, around 3,000. 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.

taxonomy is just 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? 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 could have lots of names for diverse groups of fungi that environmental molecular biologists have known have been around for a long time, but which you're not going to read about in most well, textbooks or ecology books and so on. Now, I think a lot of people are concerned that if we allow names, of organisms for which we only have environmental DNA sequences,

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 sort of abusive naming, high throughput naming of fungal species without the intervention of the experts who really know the groups. Next summer, there's this big international conference, and there's a proposal to, you know, 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 sort of grappling with as well? 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 sort of a secondary proposal that's being worked up to allow a modification of the 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. 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. Hibbitt, thank you so much for being on the show. This has been so fascinating. I really appreciate you taking time to be with us. My pleasure. Thank you. Dr. David Hibbitt is a professor of biology at Clark University based in Worcester, Massachusetts. I'm guessing most of you don't give much thought to seaweed, unless you're at the beach or cleaning a boat, or maybe when you're considering the dinner menu. But the thousands of seaweed species around the world

are a key part of our coastal ecosystems, whether you think of them or not. I hadn't given much thought to all the seaweed's under the waves, but then I saw a beautiful book that really grabbed my attention. Dr. John Bothwell is a phycologist, that's a scientist who specializes in algae and cyanobacteria. He's an associate professor in the Department of Biosciences at Durham University in the UK,

and he's author of the book, Seasweeds of the World, A Guide to Every Order. I asked him why he felt the need to write it. Because they're really important. They seeweeds do in the sea, and certainly along the coast, what trees do on land. If we didn't have seawoids on our coastline, the coastline would die. So this book is beautiful. Listeners can see some pictures on our website at sciencefrily.com slash seaweed. There are things that look like clusters of tiny green grapes.

There are pink feathery fronds. There are things that look almost like undersea mushroom caps. How many different kinds of seaweed are there? Thousands. The main division is between the three major kinds of seaweed, the reds, the greens, and the browns. But within each of those major groups, there are several thousand species. The reds are probably the most diverse, but they're also the hardest usually to find, because they tend to live under the bottom of the tide limit.

The browns are usually the ones with most people will be familiar because they tend to live in what we call the intertidal. So the part of the shore that is exposed when the tide goes out. When we talk about the greens, the reds and the brown seaweds, is it really that straightforward? If I see something that's red, it's a member of the red seaweeds? It's pretty much that straightforward. The colour does depend on a number of factors.

One of the reasons I think why people don't appreciate seaweed is they never see them at their best. They always see seaweed when they're dried out, or they've been left to dry out on the shoreline once the tide has gone out. It's like judging the beauty of a plant by looking at your compost heap or by looking at what's been cut down in a storm. In order to see the real beauty of these things, you actually want to go diving, you want to go offshore, you want to look at them in their actual environment when they're, underwater. Help me to work out the family tree here. Should I be thinking of seaweeds as something like, sort of like the grass on my lawn or more like the slime in my fish tank? People often talk about seaweeds as plants that live in the sea. It's actually the other way around. The land plants that we're familiar with are seaweeds that about

600 million years ago made the move onto land. So the seaweed came first, and the and the land plants are their descendants. The division between the slime in their aquarium and the grass in your lawn is actually a really smart thing to point out because there's two kinds of algae. And the sea weeds are a subdivision of the algae. Algae is a very broad term that means things that photosynthesize that grow in water. And the big division in the algae is between what we call the cyanobacteria

and between what we call the eukaryotic algae. The eukaryotes are basically things that you can see with a naked eye. Anything you can see pretty much is a eukaryote, it's not bacteria. So the division between the cytopacterial algae and the eukaryotic algae is a really important one. In general, the aquarium slime is the bacterial algae, and a lot of the phytoplankton will be the eukaryotic algae. So, seawoids are a division of, or three divisions, reds, greens and browns, of the eukaryotic algae. You mentioned landplants being seaweed that managed to crawl out onto the ground and live.

Pretty much. Should I be imagining them as something similar to a land plant with structures like roots and stems and leaves? Or is it completely different? Are we not at that stage yet? That's a really good question, actually. The morphology, the shape, characteristics of a seaweed and of a land plant are determined largely by the environment in which they find themselves. Seawyd are in the sea, landplands are on the land. They both face common challenges, though. They need to find nutrients. They need to reproduce

and they need to spread their propagules, their reproductive cells, a long distance. They need to spread their populations. But in the sea, the nutrients all around. you, they're in the water. And water is a very good carrier of things. It supports weight. And it will also support your offspring. When you produce your offspring, they'll be carried away on the tides and with the currents. And seaweeds have adapted to live in an aquatic environment. So they don't need much support because the water carries their weight. They don't need very specialized reproductive organs because the water will carry their offspring away from them. They don't need, you mentioned roots, they don't actually need roots, because roots are specialized structures that extract nutrients from the soil.

Seawoids don't take their nutrients from the soil, they take it from the water. So in fact, in seaweed, the thing that looks like a root, it's called a holdfast. It's just a device for attaching it to the rocks or to the sand. It doesn't actually absorb nutrients. Land plants, in the other hand, all the things we think of, the flowers, leaves, roots, the specialized structures of land plants, they all evolved after ancestors of land plants moved on to land. And they evolved afterwards because land poses particular problems. You have to absorb the nutrients in the soil, so you evolve roots.

You have to spread your offspring a long distance away, so you evolve seeds. You have to lift your leaves up to outcompete other plants to gather light, so you develop lignin and wood. again, seaweed, we don't have that because the water supports them. So really, really good question. Tell me about some of your favorite species. You must have ones that you specifically love. I do.

It's a very personal question. I got a couple. I have one from each of the major groups, one green, one red, and one ground. My favorite green, and I'm very biased here, is Ulva. Olver is the Greek word for sedge or grass. and it's probably the most common green seaweed. If you go down to any northern hemisphere, certainly, beach, you'll see a layer of green.

Looks like lettuce leaves on the shoreline. We call it sea lettuce. Ulva is my favorite green because my group sequenced the genome of Ulva. So we did a lot of work on Alva and my group currently works on it. It's a cousin to the land plants. So we can work out a lot of the fundamental evolution. biology that drove the divergence of land plants and green seaweeds by looking at over and comparing it to land plant models. My favorite brown seaweed is fucouseratus, which is serrated

rat, which is very common on the shorelines around, certainly the North Atlantic. That was the first seaweed I did experimental work on. And one of the nice things about fucosuratus is that the plants can be either male or female. So if you see a plant that has orange speckles at the tip, that's male. If they're green at the tip, that's female. And my favorite red is one called conjures Crispus, which is Karagin moss in Irish, which is a beautiful little branching seaweed that looks very, again, very common in the shorelines around where I live. You mentioned just now the male and female nature of some of these species. Talk to me a little bit about the reproductive cycle in these organisms. You ask easy questions. Seaweed reproduction is

very complicated. And we're not quite sure why. So it varies between the greens, the reds, and the browns. But as a simple overview, sea which tend to have at least two life cycle stages. And one of those life cycle stages is diploid, which means that it has two copies of every gene. The other of the life cycle stages is haploid, which means it only has one copy of every gene. Humans have one diploid generation, which is us, the forms that we see walking around. That's the diploid adult stage. We produce haploid gametes, our sperms and eggs. The sperm and egg fuse to form a diploid zygote that then grows up into the diploid adult again.

So we do produce haploid cells, but only for a very, very short stage of our life cycle. In a lot of seaweed species, that haploid stage can actually develop into a free-living organism. So it's as if we could produce a sperm or an egg, and the sperm and egg could independently, confusing could just grow up into another person. So there'd be an adult male walking around who was haploid, an adult female walking around who was haploid. So this, it's called this alternation of generations. And there are variations on that particular theme in the greens,

the reds and the browns. They each do it slightly differently. But this basic alternation of generations is very longstanding. And we're not entirely sure why it happens. What it does do is allow seaweed to grow without having to find a partner. And that's a very powerful technique, because if you are a species that is buffeted around by the currents and you produce your sperm or your eggs and they float off somewhere else where they can't find a partner to join with, you can still grow up to become an organism.

So it allows for much more mobility. We know there are some populations of seaweeds that reproduce sexually in one region of the ocean, but then reproduce asexually in other areas of the ocean. So we think this alternation of generations helps with the spread and survival of seaweeds in what is a very extreme environment. How specialized are these species with respect to their niches around the world? Are they sort of generally widespread or are there seawoids that you? you would only find in, I don't know, one specific African Bay or something?

The answer is a bit of both. There are some species that are what we call cosmopolitan, so spread worldwide. There are some species that fill very, very narrow niches. One of the problems with seaweed is we talked already about their simplicity. And so just to give a comparison, we often talk about multicellular organisms as being simple or complex. And that can be defined by the number of different types of cell that an organism can produce. Humans produce a couple of hundred different cell types, red blood cells, various kinds of white blood cells, neurons, etc. A land plant will usually produce maybe 50 different types of cell.

Most seaweed only produce half a dozen types of cell at most. So they're very, very simple. that allows them an awful lot of plasticity. So they grow very well in most places. And the clue is in the name. They're called weeds. They grow like weeds. But it also actually makes them kind of hard to differentiate

because when we identify two different plants, we'll often look at a particular structure on the plant, the flower, for example, or the leaf shape. It's a lot harder to do that with seawoids. So a lot of seaweed species are very difficult to tell apart, which means that we are probably underestimated. the number of species that are there. There's a lot of what we call cryptic diversity.

Cryptic diversity is where you have two things that look the same, but are actually different species. There are certainly cosmopolitan species, but we are only just really starting to get into a proper species-level description of exactly which species are filling, which niches. Sea which are extremely diverse, but so are the people and cultures that study them and use them. These things are spread worldwide,

and particularly in island cultures, seawoids are much more important to island cultures than they are to inland cultures for obvious reasons. So there's a lot of cultural interpretation and cultural importance to different seawoods, and I think it's really important to recognize that seawoids do mean different kinds of different cultures, and the diversity of seawoids is increasingly being matched

by the diversity of people who are studying these things. You're listening to Science Friday from WNYC Studios. I'm talking with Dr. John Bothwell about the wonderful world of seaweed. Let's talk a little bit about uses beyond the obvious animal habitat and food. Part of your day job is working in biofuels. They're biomass. They can be burned just like any other biomass. So humans have been burning plant-like material for thousands of years, and dried seaweed will burn as well as wood.

There's a lot of interest now in using seaweed as biofuels or as biotechnology precursors or as feed. There are initiatives certainly in Alaska. There's a lot of kelp farming going in Alaska. The giant kelps of California have been used for decades and worldwide, particularly places like Indonesia, increasingly in Africa. People are growing these things to see if we can use them as a feedstock. They do have advantages. One of them is, we talked earlier about the lack of specialized structures in seawoids. Specialized structures take a long time to make.

Trees grow quite slowly. Seawbage, on the other hand, don't have to make the specialized structures, which means they grow really fast. Seawood will grow two, three, four, five times faster than landfants. So they're very productive. It's one of the reasons why people are interested in them, and certainly at kelp farms. They're just a very, very fast-growing form of biomass. So there's a lot of potential there to grow biomass offshore.

And, of course, one of the problems with certainly a lot of the global north is there's a lot of pressure for land. There's more people. We're running out of land to grow stuff on. One answer to that is to start moving some of our production offshore. So, yep, there's potential. This is fascinating. And it's obviously something you care a great deal about. Talk to me a little bit more about why people should care about seaweed.

Well, the best way I can explain it is go to the shore sometime, go to the coast, and stand on the beach and turn around and look behind you. So look back at the land. What you'll see on most shorelines is dunes, grass on the dunes. You'll see behind that grass on the shoreline. You'll see trees in the distance. So you'll see see all of these plants that are keeping your environment alive. Now turn back around and look out at the sea and you won't see anything. You'll just see this flat horizon. You'll see the water lying there. But underneath that flat sea is just as much life as was behind you when you were looking back at the land. We can't see the seawoids. They're all underwater. A couple of miles offshore, there'll be kelp forest, there'll be red, there'll be asparagopsis, they'll be older, there'll be colerper, there'll be all sorts of species that you can't see.

But it's there doing its job, looking after the coastline and looking after you. Dr. John Bothwell is author of the book Seaweeds of the World. You can see some images from the book on our website at ScienceFriiday.com slash seaweed. He's also an associate professor in the Department of Biosciences at Durham University in the UK. Thanks for taking time to talk with me today. It's a pleasure. Thank you very much. And that's it for today. tomorrow we'll talk with the editors of the anthology,

the best American Science and Nature Writing, 2023, about what makes a truly great science story. Thanks for listening. We'll see you soon. Hey there, folks. Ira here. I'm counting down the minutes on what has been another long year and reminding you that this is your last chance to make a donation for 2023. We still have that dollar-for-dollar donation match in effect,

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