Preparing the Environment: Climate Special Part 1

In part 1 of our climate special, we revisit our oceans to look at the rocky atolls and reefs that are home to colourful world builders, coral!

Since the 1950’s the planet has lost half of its coral reefs due to degradation. With ocean temperatures rising and harmful environmental and human activities, how can we better protect essential ecosystems for communities and marine life alike?

Dr. Kaylee Byers sits down with Dr. Shayle Matsuda, a marine biologist looking into the effects of environmental stresses on coral reefs due to the climate crisis. And with the aid of genomic sequencing, Shayle wonders if we can utilize a clever symbiotic relationship found on these fascinating organisms to cultivate greater reef resilience into the future. Next, meet Ben Williams from the University of Exeter, who shares a unique acoustic invention to help restore reefs in Indonesia. And finally, researcher Madelyn Jones takes us through her work on the British Columbia coast to replenish the spiralling towers we call “kelp forests.”


00:05:37 - 00:11:58

Shayle Matsuda, struggling coral and the journey of becoming a coral saviour

00:18:36 - 00:22:06

Ben Williams, reef restoration using sound and preparing for our climate future

00:22:26 - 00:25:53

Maddy Jones, Kelpy Jungles and how to planet new ecosystems





Dr. Kaylee Byers: Meet Ben Williams. He’s in Makassar, Indonesia, along with a group of intrepid students. They’re on a mission.


Dr Ben Williams: We’re just in the car on the way to the docks now and then we’ll be heading out on the boat.


Dr. Kaylee Byers: And geared up with them, in the back of the car are hydrophones, a type of microphone that’s used underwater.


Dr. Ben Williams: Good to go. So, what are we doing today?


Researcher: So today we are going to go to the [source] (inaudible) to put six [hydrophones] and I will be doing a first quadrant there, which will be…

Read Transcript


Dr. Ben Williams: Should go well, let’s hope so.


Researcher: Yeah, let’s hope so.


Dr. Ben Williams: Awesome.


Dr. Kaylee Byers: Ben’s a marine biologist from the University College of London, and the team’s collecting sound from one of the most vulnerable ecosystems on our planet, coral reefs.


Dr. Ben Williams: Okay, so Jason is about to deploy the hydrophone for us on one of our sites. So when you’re ready, Jason in we go. Okay. He’s off.


Dr. Kaylee Byers: By collecting these electronic ears in coral reefs, it gives them essential information on how well a reef is functioning.


Dr. Ben Williams: Yeah, that sounds smart. It should be sort of more likely to be near the crest.


Dr. Kaylee Byers: I mean, as long as they can find the microphone later day one.


Dr. Ben Williams: No. Have you seen labels for the blocks at all? Are they? Yeah. Okay. Yeah, fingers crossed.


Dr. Kaylee Byers: Those microphones will sit for about a month and then they gather them up and review the sound that was collected.


Dr. Ben Williams: Okay. There’s the hydrophone. See you in a bit.


Dr. Kaylee Byers: Those recordings are uploaded into a custom artificial intelligence program, and it spits out that. The sound of a coral reef, sounds almost like a bonfire to me. This is the sound of a healthy reef, an active community of critters swimming, bubbling and snapping around amongst vibrant, colorful corals. But now they plug in a recording from another reef. That sound is a reef that’s floundering. You can still hear a faint crackle, but the richness of the sound fades. This reef’s in decline.


Dr. Ben Williams: And that’s important because, this soundscape is actually what attracts the juvenile fish and corals. They’re far more attracted to the sounds of a healthy reef than a degraded reef, and therefore attract that next generation of fish and corals to help bring it back to life.


Dr. Kaylee Byers: The decline of coral reef ecosystems has all sorts of knock-on consequences. So many people rely on them for food, they’re huge for the local economy. And finally…


Dr. Ben Williams: Barrier reefs, I’m sure everyone’s heard of that term, are really important for mitigating against storms and other freak weather events.


Dr. Kaylee Byers: They act as a shield for millions of people living along coastlines facing serious climate events. In many ways, there our underwater lifeline.

You’re listening to Nice Genes where we peek into the world of genomics, sponsored by Genome British Columbia. I’m your host, Dr. Kaylee Byers, your skipper for fishing out the big genomic story shaping our world.


Sailor: Aye mate.


Dr. Kaylee Byers: In our last episode, we dove down into some incredible stories about scientists studying the sounds of the planet’s ocean giants. Today we’re going to swim a little closer to shore, but unfortunately I have to start with some less than ideal news.


Dr. Ben Williams: We’re on track if we get two degrees warming, we are still set to lose over 90% of the world’s coral reefs, which is really tragic.


Dr. Kaylee Byers: It’s sometimes easy to get caught up in thinking about the spaces that we see every day. Mountains, fields, cities. The underwater landscape can seem like a mysterious frontier. It’s vast. Over two thirds of the earth’s surface is covered in water. And it’s deep, real deep. I’ve been down there, well partway at least, and it can really feel like you’re in a different world. One that we know less about than some of the planets in our solar system. In fact, there have been 12 people who have landed on the moon. And only three people that have been to the deepest part of our ocean, the Marianas Trench. But it’s not an alien world. It shares the same space we all call home. What happens up here is also affecting down there. We’re all connected. Coral reefs in decline are an indicator of our climate crisis. And scientists like Ben are preparing coral for the changing climate.


Dr. Ben Williams: The number one thing we need to do for coral reefs is tackle climate change. And what’s sad is that we kind of know how we can do it. We know all the solutions, we’ve been shouting about it for years. So I think we need to see progress in that direction.


Dr. Kaylee Byers: So when it comes to our reefs, what will it take for them to survive?

Bye.  Oh no, don’t put that. 

I want to introduce you to someone I think can give us a little hope for the future of coral.

Oh no, they exist forever now.


Dr. Shale Matsuda: Mm-hmm


Dr. Kaylee Byers: That’s Dr. Shale Matsuda. He’s a David H. Smith post-doctoral fellow at the Shedd Aquarium in Chicago.


Dr. Shale Matsuda: And there I am a coral reef researcher and I study how corals respond to climate change and what we can do to help them as far as interventions and risk analysis.


Dr. Kaylee Byers: How did you get to this place of being sort of a protector of corals?


Dr. Shale Matsuda: Oh, that’s a good question. So this wasn’t like a linear path for me at all. I didn’t come to coral reef for coral biology until my later twenties. So I’m from the Midwest, I’m from Chicago, and my only exposure to the ocean as a kid was the Shedd aquarium. And so for me, being able to be back there is really coming full circle. 

And so I didn’t actually learn to scuba dive until my late twenties. I’m really claustrophobic. And so I put it off for a long time, and nothing could’ve prepared me. The feeling of descending under the water for the first time, breathing out, watching my bubbles go up and it was down this entire wall of these brightly colored corals and it really just took my breath away.

Unfortunately, in that area there was a lot of garbage pollution. And so lots of plastic cutlery, plastic bags, things like that around the reef. And I have a background also in environmental science. And so I’ve been plugged into looking at humans’ impact on the environment for a very long time. But being in the reef environment for me was sort of this moment where everything kind of came together. Like the urgency of the climate change on the reef, the beauty of just being in the coral reef environment. 

And just you don’t have to spend too long underwater to really see exactly what we were saying before, how important these coral structures are to all of the other organisms that are swimming around there. And the joy that comes with it. The joy of seeing a thriving system, and then the sadness that comes when you dive on these degraded systems. But really knowing that there’s a real chance to make an impact right now, was sort the thing that tied it all together for me.


Dr. Kaylee Byers: What do things look like for our corals? Do we have estimates of how significant the declines have been for coral populations? What’s the state of corals? How upset are we currently?


Dr. Shale Matsuda: Yeah, corals are not doing so well. There’s been estimates that, for example, down in the Florida region that we’ve lost at least 50% of the coral reefs in the last half century and that the stats aren’t much better for other places in the world. So folks who have been studying coral reefs have actually been able to see this in real time. You go back to your favorite reef even five, 10 years later, and you can see the impact of climate change on these reef environments. You see dead corals, you see the whole structure looking different. 

If you go snorkeling on a reef, you might think, oh, what’s that big rock? Is that a plant over there? But they are animals. Part of what makes them so successful is that they have this really unique symbiosis, this partnership with the single celled dinoflagellate algae. Why those are so important is just like land plants, those algae photosynthesize and provide food for the coral. They provide actually most of the coral’s nutritional needs. 

When the temperature in the water rises or another sort of environmental perturbation happens, the coral stress response is to eject these symbiotic algae. Ejecting these algal symbionts. And if that stressor goes away, that population will then regrow, and the coral become healthy again and survive. The problem is when that heat stress, for example, goes too high or for too long, and then the corals are actually starving on the reef. And we get the name coral bleaching just from the way it visibly looks. So these colorful algae give the coral their color, and as they’re being ejected, you can see through the corals own clear tissues to the white skeleton. And so it literally looks like the corals like paling and becoming more white. So you’ll see these stark white corals out on the reef during one of these bleaching events.


Dr. Kaylee Byers: Corals are essentially living in their own little communities with these algae. And when they’re stressed they can say, you know what? I can’t deal with you right now. I suggest you go elsewhere. But that doesn’t have to be permanent. They can rebuild that relationship unless it’s been too long or too stressed.


Dr. Shale Matsuda: Yeah, exactly. So if you’re out on the reef and you see these bright white corals, they’re still alive. Corals are animals, so they’re able to get some of their nutrition from eating plankton and things that are in the water around them. But when you see corals covered in like macroalgae is when you know that the coral unfortunately hasn’t survived.

While there are a lot of local stressors that are really unique to certain areas, for example, like runoff or pollution, coastal development, things like that, that are making it harder for corals in a local area to survive. The big culprit is climate change and ocean warming. Not only are we seeing more of these warming events happening on reefs around the world, we’re seeing them happen more severely so with higher temperatures and repeatedly. So how is a coral going to respond if it survived one year? But then if we keep hitting it time and time again with these different stressors, what’s the breaking point? But this is really going to depend on local actions and global actions as we relate to climate change.


Dr. Kaylee Byers: So to be a coral researcher is to be a coral activist, I guess that’s sort of hand in hand.


Dr. Shale Matsuda: Yeah, absolutely. And there’s a lot of folks who ask us all the time, how does it feel to study an organism that is dying right in front of your eyes?

[In the field] Oh yeah. Okay, let’s do it.

While it’s really heartbreaking, it is also some of the most motivational things you can have.

[In the field] All right. So we are going to head out to the reef right now where we’re going to dive down and tag some colonies of Montipora capitata, take some samples and some photographs that we’ll then bring back to the lab to assess for their algal symbiont community.


Dr. Kaylee Byers: Shale’s work takes him from ocean to ocean. He recently returned from a trip studying coral off the islands of Hawaii.


Dr. Shale Matsuda: [In the field] So something that’s great about this site is that it’s right here off the back of the research station, so we can go check on the corals, make sure they’re all clean and the tags are all visible really, really easily. 

All right, we’re going in now. Clear. Cool. Roll it in.


Dr. Kaylee Byers: Shale, you just returned from Hawaii. So can you tell us a little bit about what you were doing there?


Dr. Shale Matsuda: What I was doing out there is we were talking earlier about these algal symbionts that are really helpful and we were working together some preliminary data for some new experiments we’re setting up. And so sometimes we’re able to bring corals into a lab and see if we’re able to manipulate some of these symbiotic partnerships. But we’re also really curious to know what are the drivers that are in the natural environment that might do this? And so we’re really looking at just the light environment, the temperature environment.

If we are moving corals around as we do some restoration work for example, what do we need to think about? What do we need to think about in advance before we do that? If we take corals from a deeper area that might not have been exposed to as high temperatures, how will they do in these warmer, brighter environments and how might that affect those symbiotic partnerships? So one of these really key species in Hawaii, that’s one of the main reef builders, the rice coral associates with symbionts in two different genera, and one of those is more thermally tolerant. One of them is less thermally tolerant. With these corals that associate with kind of mixtures of both. That’s really what we’re trying to get at. Can these corals, if they’re in these different environments, sort of naturally switch their communities to more of this thermal tolerant one if it needed, or this other one, or not?

So, something that we’ve learned that’s really exciting, these corals have these algal symbiont partners and for a long time we thought that they were all one species. And what we’ve learned is that they are multiple different kinds of species, different types. And what we’ve seen on the reef is you’ll have two corals, exactly the same species touching each other right next to each other on a coral reef during a bleaching event. And one will completely bleach and the other will look completely healthy.

One of these reasons that we have found is that the algal symbiont itself, that these different species also have their own thermal tolerances. And we’re finding that those can elevate the thermal tolerance of these corals on the reef. What we’re able to do is by studying these corals that we are seeing naturally being more resistant to bleaching on the reef, we can start to get clues about what might be driving that. And then we can harness that for a lot of our restoration activities. 

So for example, if we are growing corals in coral nurseries where we propagate corals, we have these big PVC trees where we hang corals, kind of like Christmas ornaments on them in the open ocean, and let those get bigger. And as we are selecting which corals would be good candidates for those, we can use some of this information. What are their algal symbiont partners? Are they from a coral parent that we know is exhibited more stress resistance or resilience? And propagate those.


Dr. Kaylee Byers: How is that work going to help us prepare these corals for climate change?


Dr. Shale Matsuda: It’s easy for people to understand that yes, we should plant corals back onto the reef. Yes, this matters, but we also want to do it safely. And we want to be prepared before we have to make these decisions. When we talk about what’s going to happen to reefs down the line in 50 years, for example, that’s happening now in Florida.


Newscaster: Florida coral reefs are among the most damaged in the nation with as little as 2% remaining.


Dr. Shale Matsuda: Reefs are doing really, really bad and we need to act now. We need to take big risks, do big actions to save the functions of these coral reefs and folks are working on the ground. We’re moving corals further and further away, but what we want to know is kind of can we push the boundaries, push corals further than they would have to go? And that’s the work that I’m doing at Shedd, in a closed system, is by putting some corals in these different challenge environments, these different habitats, pushing them further than [we’re] considering doing at all right now. Just to get an idea, this is something we need to consider. Maybe the microbiome is completely stable and corals are happy being next to other corals from different oceans or in different ‘microbial soups’ that they’ve never seen before, but we don’t know yet.


Dr. Kaylee Byers: Is Florida a place where those decisions have to be made now?


Dr. Shale Matsuda: Yeah, so Florida has so much more coral diversity. You can swim out onto a reef right now and see lots of different species compared to Hawaii’s reefs for example in Kāne‘ohe Bay. However, the coral cover itself is much more spotty. It’s a coral over there, coral over there. And some of our iconic species down there that are the really big reef builders are moving towards functional extinction in the sense where they’re not reproducing naturally on the reefs anymore. 

Coral translocation, which is moving these corals for genetic rescue is, can we move corals into these environments that can then reproduce with these populations, kind of help them recover themselves in these areas. And so those are sort of the questions that we need to get at. We have to try. We have to try. 

There are folks who are doing work in reefs all over the world. We do a lot of work in the Caribbean, in the Florida Keys, previously in The Bahamas, field research out in French Polynesia, in island of Mo’orea, were able to really bridge these conversations between what we’re doing in the Pacific and the Atlantic.


Dr. Kaylee Byers: Coral reefs are scattered across the globe. Though they only make up around 1% of the ocean floor, a quarter of all marine life rely on them. And that’s partly why there’s a global effort to prepare them for our climate future. Which brings us back to our other beach comber scientist Ben Williams, on his adventures to use sound as a tool to rejuvenate reefs.

Can you tell us a little bit more about your project where you use sound and artificial intelligence to inform reef restoration?


Dr. Ben Williams: So our most recent investigation was a study that built on the back of work a colleague had done, Tim Lamont. Where I’d been fortunate to work with him. And we’d found that you can observe restoration of a reef, which is done at this project by actively restoring it by listening to what we call ‘soundscape’. So that’s the culmination of all the sounds on the reef, which is kind of a whooping and grunting from fishes. And then there’s the snapping shrimp noise in the background. All of these come together on a healthy thriving reef to produce this rich soundscape.

So we did this by manually listening and annotating, counting the fish sounds, but that took ages to do just a small amount of data. And so more recently I’ve been looking at using artificial intelligence, which we found can do a really good job at this for us. It does it way quicker. And so that was what’s really exciting about our most recent piece of work.


Dr. Kaylee Byers: And can you tell us also how those soundscapes ultimately help us prepare for climate change?


Dr. Ben Williams: Yeah, so I’m really interested in restoration because it can help us bring back habitats that have been lost and many of these are habitats that have had a kind of freak incident or damage over time, but this has since been removed. So where we are currently, this was bomb fishing, which was really prevalent in the region and it’s decimated reef. Bomb fishing, dynamite fishing as it’s called, is the practice where fishermen drop a stick of dynamite in the sea, which blows up a large area of reef, absolutely destroys everything nearby and of course kills all the fish which float up to the surface, really easy to pick off. So it’s a very quick effective way to catch loads of fish with low effort, but also a really quick and effective way to destroy a good chunk of reef.

So restoring reefs that have been bomb fished, and these are all rubble fields where waves and tides turn the rubble and that smothers any new coral. So these sites just generally don’t recover. So it’s disturbances like that the stress has been removed and so the reef can be repaired, are brilliant. But of course climate change is an ever growing issue and we can do all the restoration we want on sites where perhaps one stress is being removed, but doesn’t mean that climate change might not remove it in the future. But what we often say is we like to assume that we’ll be able to do that, right? We’ve got to be optimistic and think, yeah, we’ll get a grip on this. Let’s say we do that. Well, we want our way to be able to restore reef that have been lost through other means or perhaps might be lost through climate change, but in the future we might be able to go back and help these recover.

Acoustics. There’s kind of two elements to it. So the first is, as we kind of covered earlier, it can be really easy to get this data. So it’s as simple as jump in the water, place a hydrophone down, get back in the boat, move on to the next site. And we can record for a long period of time, so we can record for weeks, months if we want to duty cycle our recorders so we can put them on a sleep record cycle. And that can get us this long time series data that your traditional dive surveys, visually done by divers of counting fish and corals, can really struggle to do. Because as you can imagine, it’s expensive, it’s logistically challenging, you need highly trained divers. And of course they only ever capture a snapshot, perhaps 30 minutes for particular reef that they happen to be working on at any time. But the other element we want to look at it, we want to see if that soundscape on a restored reef is the same as a soundscape on a naturally healthy reef. So we want to be able to see that restored reefs are going to be able to exhibit this function and therefore attract that next generation of fish and corals to help bring it back to life.


Dr. Kaylee Byers: When they plug in the sound, it tells them which reef is doing fine, and which reef could benefit from a boost. Keeping an eye, or ear, on these reefs, is one critical step forward in preparing our planet for the effects of climate change. But how can we use genomics, the DNA of the coral itself, to make them more resilient to what’s to come?

You’re listening to Nice Genes, a podcast all about the fascinating world of genomics and the evolving science behind it, brought to you by Genome British Columbia. I’m Dr. Kaylee Byers, your host, and we want to get more people listening to the genomic stories that are shaping our world. So if you like Nice Genes, hip follow on Apple podcasts or wherever you get your shows. Keep that reef activity snap crackle and popping by inviting your fishy friends to flop on over and give it a listen.

In this episode, we’ve been globetrotting to corals around the world, but corals aren’t the only underwater ecosystem that are important. So I want to bring the conversation over here, to my home of British Columbia.


Maddy Jones: Hi, my name’s Maddy Jones.


Dr. Kaylee Byers: An expert on the big leafy greens we call kelp.


Maddy Jones: I am studying kelp, not just studying kelp and looking at what kelp is, although staring at kelp for many hours is a wonderful pastime.

[In the field] All right, so we’re sitting here in the pure silence, we’re going to get a couple pieces of data.


Dr. Kaylee Byers: Kelp is a very specific kind of seaweed. They can form these massive ecological towers swaying back and forth with a push and pull of the tides. Hopping on a boat with a research partner, Maddy is dotting around the coast, surveying for the perfect spots where kelp can be grown.


Maddy Jones: So the term that that is, is called ‘sea forestation’. And sea forestation is important because we’ve understood this practice on land for a long time and we reforest our forest all the time. However, we do not do that to the ocean. And there has been a reduction in kelp canopy since the extirpation of the sea otter on the BC coast. And a variety of other factors.

[In the field] Kind of when you’re putting together things for field study, you kind of have to get creative. So this is basically a GoPro on the end of a boat hook.

When I’m looking at sites, I look at a few different factors, temperature is one of them. 

[In the field] Let me just turn on this video. 

Lumens at a certain depths is another factor.


Dr. Kaylee Byers: By the way, lumens are a measurement of visible light.


Maddy Jones: They line up or if there’s just one limiting factor for kelp growth there. 

[In the field] You see it downwards and popping it in.

So the reason why I’m studying kelp is because well one, it’s beautiful. If you’ve seen kelp, it’s mesmerizing underwater. The other thing is that I really believe in the co- benefits of planting more kelp.

[In the field] Right now we’re around low tide.


Dr. Kaylee Byers: Kelp forests are one of the most diverse and productive ecosystems in the world. Just like coral, they’re keystone species, supporting all kinds of organisms. They can help pull carbon from our atmosphere.


Maddy Jones: Carbon sequestration. So taking carbon from the short term cycles up in the atmosphere and down into the long term cycles that are the biosphere and ideally the lithosphere, if that can reach the ocean floor.


Dr. Kaylee Byers: BC’s struggling salmon populations…


Maddy Jones: And kelp forests provide sanctuary and habitat for these fish as they are at different times of their life and as they travel through the ocean. And sea otters also rely on it for their young.


Dr. Kaylee Byers: And they can be food for the future.


Maddy Jones: It’s food security, kelp grows very quickly, but you can grow bivalve, so, oysters, clams, mussels, in bags next to kelp really effectively. And it will filter the water and it’s a garden that you don’t need to fertilize, you don’t need to feed really because it will feed itself through the water.

[In the field] So yeah, there’s a low flow at climate there.


Dr. Kaylee Byers: The information Maddy’s collecting can help us know the world of kelp a little bit better. That information is critical to understanding the impacts of our climate crisis.


Maddy Jones: We also had a ‘heat dome’ here a few summers ago that you could smell the sea life dying on the shoreline for days and days and we had a huge wipe out, we are still trying to understand how much of an effect that had on our ecosystem here on the coast.

[In the field] Going to observe anything else. The water here is really clear.

So, looking at where we can put it because we need to put it in the water. We need to plant more in the water. We need more kelp in the water to help solve a whole slew of problems and crises that are affecting us on the BC coast, but also globally.


Dr. Kaylee Byers: What we can draw from Maddy’s work is a hopeful look at some of the ways we can rejuvenate these vital landscapes.


Maddy Jones: [In the field] We’re done. High five. Yeah, we’ve been out here for four hours. This is good. Let’s go turn the stove on and have some tea. I can’t feel my feet, can you? I can’t feel my hands either.

The last few days were kind of like an emotional rollercoaster for me before coming up here, wondering if I was capable of this, which is so funny to think because I teach a lot of this. And I always support my students going out into the field.


Dr. Kaylee Byers: Let’s return to coral. Can we finally crack its code? Back to Shale Matsuda. 

Can you tell us a little bit about how genomics plays into the work that you’re doing with corals?


Dr. Shale Matsuda: Being able to do DNA sequencing has totally changed the game just in our understanding of corals and their symbiotic partners, but also in how we’re understanding the responses to stress like climate change. So I’m using amplicon sequencing, so we’re just targeting smaller regions, not whole genome sequencing. Get an idea of who are the algal symbionts there, how diverse are these communities? How diverse are their microbial partners that are bacteria? And how are they changing in response to stressors? And then can we use that information to either help these corals by trying to manipulate these symbioses, or to sort help us understand who might do better. So for example, when there’s a natural bleaching event like the ones in Hawaii, and we saw these corals, of the same species touching each other on the reefs, one of them bleached, one of them didn’t bleach. What we found by sequencing their DNA is that those corals that did bleach all had this one type of algal symbiont, Cladocopium, the Cs symbionts, and the ones that didn’t bleach had Ds or Durusdinium symbionts. So for some coral species we’ll see that sort of natural shift to the thermally tolerant ones after a bleaching event. But in other ones, it seems like they’re not going to budge.


Dr. Kaylee Byers: Oh, stubborn.


Dr. Shale Matsuda: Yeah, exactly. But it’s in the same thing for the bacteria. The coral microbiome is all of the bacteria that are living inside and on the coral. You’ll find them in the coral’s mucus and the coral’s tissues themselves. There’s even bacteria in the coral skeleton. Bacteria’s a pretty new player in the coral world, only last couple decades have been really sequencing their DNA. And from that we can just take a tiny couple millimeters size biopsy of the coral tissue and see who’s there. Are there sort of these culprits to helping the coral survive these stressors, or that might actually lead to mortality. Then we can start to really learn the dynamics of the response to these stressors.


Dr. Kaylee Byers: Well, and I’m even curious about, let’s say you’ve got your adorable little coral polyp, and you go and you sample from one branch over here on the right side, and then you go and, you sample over here on the left side. Would you see different things? Could there be different dinoflagellates setting up shop?


Dr. Shale Matsuda: I’m so glad you asked. That’s been one of my favorite questions for years. And this is some work that I did in Hawaii that actually came out of this idea that we were trying to characterize these microbial communities across the entire colony with these tiny little genetic samples. If I take a sample over here and it’s these C symbionts, is that the whole picture?

So did this experiment where we went out in the reef and found these coral colonies, and I took 16 samples from all over trying to, basically capture the most differing micro habitats. So top of the branches, as deep in the colonies as you can go, the undersides, top of plates. All over these habitats. And what we found when we did DNA sequencing to identify what these symbiont communities were, is that yes, we’re finding different communities than we are on some of the deeper areas. What we’re trying to do right now is understanding how structural complexity may or may not play a role into a coral’s ability to host all these different communities that may help in a pinch.


Dr. Kaylee Byers: Corals contain multitudes, some more than others. That’s what I’m learning.


Dr. Shale Matsuda: Absolutely. And it’s what’s so exciting about them, but also so hard to study them.


Dr. Kaylee Byers: I want to ask you a question. Every once in a while, there’s some bits and pieces floating around about coral, and there’s one quote that sort of talks about coral being responsible for roughly half of the oxygen on our planet. There’s this quote from Eco Watch that says, “Coral reefs only cover 0.0025% of the ocean floor, and they generate half of earth oxygen.” Is that accurate? And I am worried that I’m now saying the thing out loud and then people are going to take that and be like, “It’s true.” Is it?


Dr. Shale Matsuda: Okay, so this is complicated and I am not going to get into the weeds on that answer. So the ocean produces about half of the oxygen on the planet. Yes. Half terrestrial, half comes from the ocean. And kind of half of what comes from the ocean is actually from a cyanobacteria. And that is producing this, it’s a huge oxygen producer. Those are definitely located in reef environments, but they’re also located in the ocean at large. So I can’t speak to the exact percent of oxygen production in a coral reef system, but that is a good question. But the ocean is very key element of oxygen production for us, for sure.


Dr. Kaylee Byers: Awesome. We should take better care of it. I will…


Dr. Shale Matsuda: Yes.


Dr. Kaylee Byers: I think that…


Dr. Shale Matsuda: Absolutely.


Dr. Kaylee Byers: That’s something we could say.


Dr. Shale Matsuda: So I actually had a really long conversation with my old advisor about this. It’s such an anecdotal bite that people, you hear sound bites, it’s sound bites everywhere. We want to talk about how that’s true, but it’s complicated. To what extent a breath of air that you were taking came from the ocean or not, is a complicated question for sure.


Dr. Kaylee Byers: So if we’re talking about the future of coral. I think it’s important that we explore the moment of their life cycle where it all happens. And for Shale it’s an exciting and valuable time for him and the team to do their work.


Dr. Shale Matsuda: Coral spawning, I think that’s a lot. I don’t know how deep we went into that, but I think that’s one of the coolest things out there.


Dr. Kaylee Byers: I mean, who doesn’t want to talk about coral sex?


Dr. Shale Matsuda: So yeah, so coral spawning on the reef is one of the coolest things you can ever see. So corals are not moving around, so they have to be able to find each other. What we see in Hawaii, for example, in the corals that we work on are the corals will package their eggs and sperm into these little bundles every summer in June and July. On the new moon at 8:45PM all of the corals in the bay from this one particular species will release these bundles in synchrony into the environment. And these little bundles, they kind of look like Dippin’ Dots, will float up to the surface.


Dr. Kaylee Byers: It sort of looks like it’s snowing underwater, but in the opposite direction.


Dr. Shale Matsuda: Yeah. It kind of feels like a snow globe a little bit, when you’re swimming around in that area. And around on the top of the surface, the wave action will slowly cause them to burst open. You’ll see a cloud of sperm and the eggs floating on the top. And after they fertilized, they develop into these little coral larvae. These tiny little minuscule jellybeans that will then sink down into the reef environment and settle down, form that first polyp that will then bud out to create the coral colony there and repeat the life cycle. And it’s also a really exciting life stage for us because it’s this life stage where we can really scale up some of our interventions. 

It’s kind of the not glamorous part of our job. So very often we will go out, we’ll put nets over these colonies during the day, set these coral nets up with a little like jar on the top so we can collect all of the gametes from a single colony that we know if it bleaches or doesn’t.

And then at night we get in these little boats, but very quickly the entire surface of the ocean is going to be covered in this slick of all of these little bundles as far as the eye can see. And what’s also really cool at that point is, you can imagine this is a feeding frenzy. This is all these lipids, these fats in the water. So all these other fish and organisms are coming out to feed on all these bundles as this is happening.

And what we have to do at that point is we jump in the water, so we get kind of covered in all this stuff and we have to go out there and collect those jars of all these gametes. And it is a lot of fats. And so we definitely smell like it when we come out of the water. And I have a friend who says that their cat gets really excited when they come home, from how we’re smelling. 

So we’re just skimming the surface and bringing these buckets of genetic material from all over the bay back into the lab to raise corals. Or even do selective breeding, where we collect bundles and we put a net around a colony so we can collect all the genetic material from a single bleaching resilient colony, breed those with different colonies, and then create then hundreds or thousands of baby corals.


Dr. Kaylee Byers: Yeah, okay. So, more to learn, but definitely stay out of the water at 8:45PM and let them do their thing.


Dr. Shale Matsuda: Exactly. Yeah, it’s really cool.


Dr. Kaylee Byers: So Shale, one of the overarching questions we have for this episode is how we can prepare our environment and ourselves for climate change. And what are some things that are being done that you feel can help us prepare for the climate future ahead of us?


Dr. Shale Matsuda: So most of what we’re doing for reefs right now is that preparation. It’s very much like a Band-Aid. You kind of mentioned it earlier, but we have to address climate change if we’re going to save coral reefs. But we can do a lot of things to help corals survive until we are collectively as a society ready to take the action needed to do that.

And so in the local environment, if you live on a coral reef or an area that is adjacent to coral reefs, being aware of any sort of pollution, of runoff, whether it’s from urban environments or from agriculture, just what is flowing through our systems into the reef environment is really important.

Whether you’re anywhere, being knowledgeable about voting, about who’s making decisions, who’s making environmental decisions, and that you can do from anywhere. But also, just I should say by elevating these issues to the forefront. For scientists, a lot of this work for us also comes to making sure that in our own communities are in Congress, we are making these connections and being resources of information to make sure that these issues and topics are even on the radars of people who are actually making a lot of these decisions.

I talk to a lot of people who don’t live on coral reefs. People who have never seen corals before. And this is a really hard thing to think about. Anything we can do to curb climate change in our everyday lives is obviously important. Bringing science into our daily lives will help us start thinking about these issues in more complex ways and helping us take action. But also what I tell people out here is actually focusing on the environment in your local area can make more of a difference to the environment than, just what can I do every time I’m on vacation on a coral reef.

Studying corals just as an organism themselves are just incredibly fascinating. And I could just go into the weeds about their biology and ecology. However, as we all know, they’re also being really threatened right now. And it’s both a really critical time for corals, but also a really exciting time to be in this field because we have so many people who are working together.

[In the field] Sounds good. We’re good. Cool.

To come up with really new innovative and key solutions in a really fast time and really in scalable way.


Researcher: Two, one, done. 29.


Dr. Shale Matsuda: None of this is done alone in the basement by yourself. It is a huge, dynamic, diverse community that are all coming together to work on these problems in a really exciting way.


Dr. Kaylee Byers: Dr. Shale Matsuda, thank you so much for taking us on a little bit of a coral journey and your own journey as well. It was really nice getting to chat with you.


Dr. Shale Matsuda: Great to be here. Thank you.


Dr. Kaylee Byers: I think what I took away from speaking with Shale, Ben and Maddy is that, there’s hope. Often we can hear about what’s happening in the world like to coral or kelp and feel, honestly, overwhelmed. Devastated, frankly. But there’re tons of passionate people pouring over field recordings and genomics information, and those efforts are affecting meaningful change. Scientists like the folks you heard today are thinking of climate solutions at all levels. Not just looking at what’s in front of us, but what’s happening beneath the surface.


Maddy Jones: Oh my God, a sea otter. I don’t know if everyone knows the story about sea otters on the BC coast, but we basically killed every single one of them for their pelts. Now you kind of see them coming back more and more and they’ve got such a relationship with kelp. Kelp needs the otters to eat the urchins so that they aren’t completely devastated by these urchins and cause basically like an underwater desert. And when I’m teaching and I see kids just being so jaded about this climate crisis that has been put on their shoulders, you have to hold on to those little glimmers of hope. And otters, that kind of beacon of hope for at least me.


Dr. Kaylee Byers: My guests for today have been coral reef biologist and post-doctoral fellow with the Shedd Aquarium, Dr. Shale Matsuda. And marine biologist, Dr. Ben William from the University College of London. Special thanks to Maddy Jones from Genome British Columbia, for taking us to our Wild West Coast and kelpy jungles.

You’ve been listening to Nice Genes, a podcast brought to you by Genome British Columbia. If you like this episode, go check out some of our previous ones wherever you listen from. And share the episode by hydro-phoning a friend. You can also DM the show on Twitter by going to @genomebc, and we also have learn-a-long activity sheets in the show description.

Down the road, we’re going to ask a bold question. Instead of preparing for a future of climate change, can we actually fix the damage that’s already been done? So stay tuned for part two of this episode, Repairing the Environment. It’s coming at you in a couple of weeks.

On our next episode, join us where we are on the front lines of the never ending race to spot diseases, both past and present.


Dr. Birgitta Evengård: Permafrost is frozen ground. So what’s frozen there, could be viruses that are 30,000 years old and 15,000 years old. Whatever is in there is Pandora’s Box. But whether it’s a pathogenic one for humans, et cetera, we have absolutely no idea.


Dr. Kaylee Byers: And before you go, it would really kelp the podcast if you gave us a review. Thanks for joining us.





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