Episode 15: OceanOmics: eDNA to Guide Marine Protection

Turn seawater into a species map. In this episode of Oceanography, host Clark Marchese talks with OceanOmics director Dr. Michael Bunce about how eDNA (environmental DNA), DNA barcoding, and genomics reveal what’s living in the ocean—from microbes to megafauna—using just a few liters of water. We follow the journey from deck to lab, then into powerful, human-friendly AI dashboards that translate massive datasets into decisions about fisheries, marine protected areas, water quality, and climate resilience. We also explore citizen science with easy eDNA kits and how these data help detect invasive species and track ecosystem health over time. If you’re curious how OceanOmics is transforming biodiversity monitoring into actionable ocean intelligence, this conversation is your field guide.

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Episode Guest. Dr. Michael Bunce

Find more about  Dr. Michael Bunce here. 

Find all Dr. Bunce’s publications on Google Scholar

Learn more on the OceanOmics webpage and explore the OceanOmics Dashboard

Discover the work of the Minderoo Foundation on their website and on Instagram

Listen to the other PFM interview with a team of Minderoo scientists on the impacts of plastic on human health 

Episode Transcript  and more information on the Pine Forest Media website

Follow Pine Forest Media on Instagram @pineforestmedia

Hosted, produced, and edited by Clark Marchese 

Cover art by Jomiro Eming

Theme music by Nela Ruiz

Find some more Pine Forest Media podcasts below:

Listen to South Pole on Spotify or Apple Podcasts

Listen to Plastic Podcast on Spotify or Apple Podcasts

Listen to Something in the Water on Spotify or Apple Podcasts

Transcript:

Clark Marchese (00:11.47)

Hello there, and welcome back to another episode of Oceanography, the podcast that dives deep into the science of our seas, the latest in marine research, and the people working hard to better understand and protect our blue planet. And today we are Ocean Nancy Drew Detectives.

Clark Marchese (00:50.518)

Alright, hello oceanography listeners, I hope you are all doing well. I am Clark Marchese, your host, and today we are grabbing our magnifying glasses and thinking just like Nancy Drew. Or Sherlock Holmes if you prefer. Miss Marple, pick your poison. Horro. Because we have some pretty big mysteries to solve and we are going to need to see some things that are really deep bitty, teeny tiny small. Today we are going to be learning all about eDNA and putting the pieces together of this puzzle to solve the mystery of protecting our marine environment. Okay, maybe I'm taking this detective metaphor a little bit too far. Anyways, eDNA, environmental DNA, is what we're talking about today. Now, DNA you've probably heard of. That's the genetic code that holds all the information about what a living thing is. eDNA you can think of as a breadcrumb trail that organisms leave behind in their environment - skin cells, mucus, tiny fragments that end up in the water, sand, or even ice. And we have two more vocabulary words that we will need. One is DNA barcoding, which we have spoken about on the podcast before. This involves creating a Cliff Notes version of an organism's DNA and storing it in a database. So you can quickly cross-reference it to eDNA samples from the environment and find out who left the breadcrumb trail in your sample.

Secondly, we have genomics, and this is a big one. Genomics is the study of all the DNA in a living thing. So you zoom in on one piece of DNA, which you can think of as maybe a sentence describing an organism, and then you zoom out again to the genome, which can be thought of as an encyclopedia describing the same organism. Now, brilliant scientists have figured out how to map genomes from DNA samples, and once you have the genome, you can ask much bigger questions about how living things work, how they're related, and how to keep them healthy. So I hope that's enough context for now. We do have an expert coming on the show to explain it much better than I can. And this brilliant scientist we are going to speaking to is going to place all of these scientific concepts in the marine context for us. Our guest for today is Dr. and Professor Michael Bunce, who is the director of the Oceanomics program at the Minderoo Foundation.

Clark Marchese (03:14.444)

Now, oceanomics is a pun for ocean and genomics. And Michael's team uses eDNA to map biodiversity from microbes to megafauna and turn those data into real decision-making tools. Think early warnings for invasive species, tracking ecosystem health, and measuring how well marine protections are working. In this episode, we'll start on deck collecting just a few liters of seawater and following it to the lab, where those drops are transformed into a living snapshot of everything in the ocean around us. We'll explore how DNA barcoding and genomics work hand-in-hand to reveal what's thriving, what's struggling, and how those insights guide decisions about fisheries, water quality, and climate resilience. Then we'll dive into the digital side, the dashboards and AI tools that let scientists ask plain English questions of enormous data sets and even let the rest of us explore what they're finding.

We'll look at how all this data is reshaping policy and helping evaluate whether marine protected areas are actually working and not just existing on paper. And finally, we'll talk about the citizen scientists, the divers, boaters, and everyday ocean lovers who can now collect eDNA and help monitor their own blue backyards. That's just about all we have before we begin today, except for this very big and very exciting new announcement for the Oceanography Podcast.

Oceanography is now sponsored by the Monterey Bay Aquarium, inspiring conservation of the ocean through amazing live exhibits and global action. Together, we can create a world without plastic that's healthier for people and planet, advance climate solutions so everything we love can thrive, and choose sustainable seafood to protect the ocean, people, and ecosystems that depend on it. Because there's wonder in the ocean and caring for it helps us all. Now, they'll be helping us out for at least the next 12 weeks and their leadership in ocean science and public engagement makes them a perfect partner for this series, and we are thrilled to have them on board. Now, if you are enjoying this series so far, and you think that the science communication that we're doing here is important, the easiest thing you can do to help us reach more people is to rate the show and review oceanography on Apple Podcasts or wherever you're listening right now. It takes about two seconds to give us five stars, and it makes a huge difference for an indie network like Pine Force Media.

Clark Marchese (05:37.336)

All right, I think that is all before we dive in. So grab your field notebook and get ready for my conversation with Professor Michael Bunce.

Clark Marchese (06:03.206)

Alright, it looks like we are recording. First of all, thank you so much for being here with us today. At the top of the show, I'd to ask you if you could just tell us a little bit about your journey as a scientist and what led you to your position now at the Minderoo Foundation.

Dr. Michael Bunce

Good morning, good afternoon everyone. Well, I grew up in Aotearoa, New Zealand. I grew up in sort of connecting with nature there and had an awesome high school teacher who connected me to biology very early on the piece and introduced me to evolutionary biology and the world of DNA. So that led me to an undergraduate degree in New Zealand looking at molecular biology and a PhD in medical sciences. And after that, after those studies were complete, I ended up at Oxford University studying ancient DNA and getting DNA out of sediment material. So ice cores and sediments from New Zealand are looking at past biodiversity. And that was the sort of first foray into getting DNA out of environmental samples. So fast forward a few years, and I'm now at the Minderoo Foundation running the Oceanomics and Ecosystem Intelligence program there, where we're sort of using those same sort of core techniques of getting DNA out of environmental samples to make better decisions for the ocean.

Clark Marchese

Though I do ask this question to everyone and quite often teachers do get mentioned. So shout out to all of the science teachers out there. And before we dig into the DNA part of today, maybe I can ask you to tell us a little bit more about what exactly the Minerva Foundation is, perhaps maybe its mission and also how the Oceanomics project fits under.

Dr. Michael Bunce

Yeah, thanks for the question. The Minderoo Foundation is, guess, a charitable organization. So we've got founders that have, I guess, dedicated to giving away their wealth and their lifetime. And one of its sort of three core pillars focuses on natural ecosystems and its mission there is ambitious, but simple at the same time as that is to, I guess, preserve and protect natural ecosystems for future generations. And it's...

Dr. Michael Bunce (08:04.962)

focus is primarily in the ocean. So our, one of our founders, Dr. Andrew Forrest, did his PhD in ocean conservation in 2019. And at the sort of end of his PhD, he to some degree sort of drunk the EDNA Kool-Aid, if you like, and understood that there was a technology out there that was able to, with the right investment, able to listen to nature much more effectively. And so he formed the Oceanomics program early in 2020. And that's the program that I now run as its director.

Clark Marchese

Okay, and I understand that the Minderoo Foundation does quite a lot of environmental research. Listeners who've been with Pine Forest Media for a while might remember that I interviewed a team of Minderoo scientists about plastics and human health on Plastic Podcast. I can make that episode on the show notes. But today we're talking about a separate project called Oceanomics. Maybe we can get kind of an elevator pitch to set a baseline about this project. When did it start? Why did it start? What problems is it trying to solve? And how?

Dr. Michael Bunce

Sure, where to start with that? measuring nature is really difficult. There's a lot of biology out there from microbes to megafauna. I guess the complex interplay of all those organisms in terms of the tree of life, in terms of the food webs that underpin them. So, know, historically through sort of catch and look approaches, we've able to go into the ocean and we can sort of measure what's easy to see and easy to catch.

We tend to sort of look at catch data and sharks and fish that we catch. do quite a bit of work on plankton material, but other aspects of that ecosystem are far harder to study. So, you know, the elevator pitch, I guess, if you like it is, is to develop a better way of sort of tapping into the life in the ocean that matters, to understand what makes it tick and to hopefully make better decisions regarding its sustainability and its future.

Clark Marchese (09:56.046)

Okay, and just to make sure we're on the same page, and please correct me if I'm off-baton anyway, but this oceanomics project is basically trying to catalog the DNA that's in the marine environment to get a better picture of marine biodiversity.

Dr. Michael Bunce

That's one aspect about it because all of the marine life out there has a genetic code. There's multiple levels to this. So that's one aspect of the program that we're absolutely focusing on. And that is to sequence the genetic blueprint of marine life. Now we can do that by just sequencing the barcode if you like. This is like barcodes on supermarket products that people buy. Whenever we scan something, we know what that product is. So that's called DNA barcoding. And then we've got genomics, which is sequencing all the secret herbs and spices that sit inside the rest of the product and get the entire genetic blueprint. Now those are two very different aspects of it and that's one aspect of what we're doing. But the more fundamental question is what are you going to do with that information? How are you going to use that ecosystem intelligence to make better decisions? So in terms of things like genomes where we can determine lifespan of organisms or age, sexual maturity from the genome, that's one key aspect.

But in the field of environmental DNA, if we know that new invasive species are coming into an area, or an area might be overfished from its DNA signatures in the water, we might be able to change management of those areas. And that is, I guess, one of the key investment and sort of opportunities and impact opportunities that we're trying to bring in is just to make better decisions with our oceans, because at the moment we're slowly running down that natural capital at a rate that's not sustainable.

Clark Marchese

Okay, so that's a lot of information. Let's pause to do a quick recap. We have DNA barcoding, where you can connect one species to a sample of DNA found in the ocean. So part of this project is interested in filling out our database of barcodes. Maybe I can draw an analogy to Blockbuster for people who remember what that experience was like. When you went to a Blockbuster, all of the DVD covers were kind of hidden in a case that had the Blockbuster logo on it and you didn't know...

Clark Marchese (11:59.992)

what was inside other than the way it was labeled on the shelf. And then you would go to the counter and you'd scan the barcode. And then of course the system knows what movie it is. So part of what your work is doing is to create a database so thorough that you can take any sample of DNA from the ocean and know what sea creature is sitting inside of that video box. And then secondly, you have genome sequencing and it takes one sample of DNA and tries to understand the entire species genetic code.

For example, think about humans. If you take one strand of hair, you can find the DNA sequence that is inside of it and know that it belongs to a human and not to a cat or a dog. But if you look at the whole set of DNA instructions, the complete genome from that hair, then you can ask many more questions about us humans as a species, our characteristics, how we develop and how we're related to one another. Now to get from a sample of DNA to understand the full genome is hugely technical and it takes quite a lot of time. We only had a first draft of our own human genome by about 2003 and we didn't finish filling in all the gaps until 2022. We have gotten a lot faster and now we have a pretty good understanding of the full genome for a good handful of animals and even some viruses and bacteria that are particularly relevant to us for certain reasons. But certainly we do not have the full genome for all the creatures in the sea. So those are the two steps and then you see in which ways you can use all of this information to draw larger conclusions about ecosystem health or trends emerging in the environment and also how we as humans can respond to protect it.

Dr. Michael Bunce

just better, more sustainable practices around the ocean from things like fisheries to whether invasive species get in there, whether water quality is improving, whether a river or ocean is, or a beach is safe to swim in. All of those things are possible using DNA technology and it's a new kid on the block and we're learning as we go along. But just sort of one sort of, guess, addition on there is that the ability to sequence all the genetic code of all the life in our oceans is a decadal mission, right?

Dr. Michael Bunce (14:08.756)

And you know, there's a lot of biology out there, especially when you put microbes into the mix. So over the last few years, the Oceanomics Center here has sequenced about 800 full genomes. And we're working with our partners at CSIRO, we're funding a project to sequence all of the marine fishes in Australia and marine vertebrates. And there's about five and a half thousand of them. And that's just from the barcoding perspective. So we can identify every DNA fragment we get out of water.

Clark Marchese

Okay yeah, I think we keep coming back to realize just how vast the oceans are and how much laughter is still to learn. This is a pretty big undertaking. Can I ask how long this program has been around?

Dr. Michael Bunce

Yeah, it kicked off in about 2020 and our Oceanomics Center started in about 2022. And that is a laboratory that has lots of machines in it that go ping and sequence lots and lots of DNA. So it's those thousands of environmental DNA samples and hundreds of genomes every year.

Clark Marchese

Okay. That's a really good context. And maybe we need just a little bit more of a scientific foundation. We often find ourselves encountering acronyms. So of course there's DNA and most people will have heard of this before, but maybe we can do a little bit more of a deeper dive into the concept of eDNA. Can you tell us what that one is?

Dr. Michael Bunce

So if we start right back at the beginning, of course, all organisms have DNA in their genetic code. And what some of the listeners might not realize that are not geneticists is that, you know, we are constantly shedding DNA off into the environment. So if you've ever watched one of the sort of forensic shows, sort of CSI, you know, when they go on swab door handles and crime scenes, that's picking up trace amounts of DNA in the environment. That's probably the form of DNA sort of testing that most people are familiar with.

Dr. Michael Bunce (15:55.234)

But when we realize that every single organism is shedding DNA into their environment and that we can capture that material and read the genetic code, we sort of open up a whole raft of new opportunities for listening to nature more effectively. So water is a fantastic place to start, right? Because all these fish and corals and marine microbes are constantly shedding off genetic breadcrumbs into that environment. And simply by filtering a few liters of sea water, we can sort of capture those genetic breadcrumbs. and we can analyze them in the laboratory to come up with a long list of what's in the sample. So, you know, to bring it into simple terms, all animals are shedding DNA into their environment and there lots of ways of capturing that DNA.

Clark Marchese

Can you paint a picture of what this kind of work looks like in the marine environment? How do you go about collecting data, for example, in the Oceanomics project?

Dr. Michael Bunce

to backtrack just a little bit, every single substrate has DNA in it. some work that they're doing is just filtering, you know, air, where has dust in it. And of course that dust contains genetic molecules in it as well. But primarily by far, and this is probably about 95 % of all environmental DNA studies have typically focused on water. That's fresh water or ocean water, because it's a really good sort of aggregator and mixing pot if you like. So all of the DNA is sloughing around in there and when we filter it we get to sort of enrich that. It's also we don't seem to get long-term preservation in water because the microbes in there are chewing it up. So typically sort of generalizing here because it will depend on temperature and all sorts of things that the DNA signatures are typically if you know hours old and from within about one to two kilometers give or take from where the DNA was deposited in the first place.

Dr. Michael Bunce (17:43.726)

So we don't have to be right on top of an animal to detect it, but we need to be in its vicinity. And I think from the early days, people are being very struck by just how much regional patterning we get in the environmental DNA. So of course all the water in our ocean is connected, but that doesn't mean it all looks the same in terms of the biological assemblages that sit within that. So what does a general sort of day look like for the oceanomics team? Well, it would involve, if they're out on a voyage, it'll involve filtering lots of water. So we drop down devices that literally take about a couple of liters of water and filter them over a fine membrane. And we're trying to capture all those genetic breadcrumbs that are floating around in the ocean. So we end up with a filter with a sort of scum on it, if you like. That is all the biology that's floating around there. And we take that back to the lab and we pull out the DNA molecules and separate it from all the other bits and pieces in there, the proteins, the fats, the other things that make up the cells and other bits of the biology in there. And once we've got a pure form of DNA, that's when we sort of get out the photocopy or put it into the machines that can generate the DNA data.

Clark Marchese

Okay, and do find yourself doing a lot of fieldwork these days?

Dr. Michael Bunce

I used to do a lot most of the time. I sit on a computer these days and help steer the ship around a little bit, Clark. But what the Minduru Foundation does is find partners really around the planet that are looking, you know, world leading scientists. And we fund them to do work in this area. So over the past few years, we've generated a lot of environmental DNA data and it with our own partners here in Western Australia.

Dr. Michael Bunce (19:16.386)

But increasingly we're reaching out to international partners who have got expertise in this area to build a larger community of practice and funding initiatives that can really make a difference in this area.

Clark Marchese

You know, we did have a brief call a couple of days before recording and I happen to know for a fact that you just saw a whale shark on the job. Can you tell us about that?

Dr. Michael Bunce

That actually happened about three weeks ago. So, yeah, I was filming, I was filming with the BBC. It's the first time I've ever seen a whale shark three weeks ago. So we've detected their DNA signatures and quite a few of the samples we've looked at. But the first time I dropped in the water then was about three weeks ago. So we were showcasing, you know, what you can do with DNA signatures gone beyond just actually detecting that it's there. So Dr. Luke Thomas sat at Australian Institute of Marine Science. is actually trying to identify genetic signatures, individuals from the environmental DNA. So you don't actually have to biopsy the animal to get a decent DNA signature. So yeah, we were doing a BBC documentary on how we sort of study megafauna. And that was pretty special. The other one that sticks out in my memory is going to the Cocos Keeling Island group, which is sort of right in the middle of the Indian Ocean, sort of closer to Asia than it is to Australia, still in Australian territory. And that's just some beautiful untouched coral reefs and fish up there that sort of shows you what the ocean looks like when we don't over bake it.

Clark Marchese (20:39.798)

It seems like most of the people I speak to on the show have like the coolest job ever. Well, once you have gone out to see these beautiful coral reefs and interacted with the whale sharks and you've taken your filter and you've gotten a biofilm net and you've collected the data, what happens then? How do you go about organizing all of that information?

Dr. Michael Bunce

So if we sort of start back at the DNA extract, there's sort of two ways that we can sort of analyze the DNA if you like from an environmental sample. We can actually sort of sequence the entire haystack in there. That's referred to as shotgun sequencing, where you just look at all the DNA in the sample. But right from the early days, we realized that that's really good for picking up the microbes, which are really abundant in the sample. But if you want to look for fish, they are, you know, tiny needles in a massive haystack.

So what the solution there to break the analogy is, is we use technique PCR, polymerase chain reaction. And people may have heard it in COVID, way to photocopy up the DNA. So what we're essentially doing to that haystack, it's got a couple of needles in it, we're putting a big magnet in there and drawing out the needles out of the haystack, the bits of DNA that can tell us what organisms are there. The vertebrates in an environmental DNA sample like seawater make up just a tiny, tiny fraction of the total DNA that's in there through that sort of Nobel Prize winning idea of photocopying DNA, we can massively enrich the DNA barcodes in that sample. So they're the two we can either sequence all the DNA or just sequence the barcodes. But to give you, guess, your listeners a little bit of a taste of the power of this is that we've done about 10,000 environmental DNA samples around Australian waters in the last few years. The average number of fish that we detect from a two litre water sample is about 62 species of fish from a two litre water sample. The highest number is over 200 species of fish. And you would struggle to find that using any other approach, right? These are deep sea fish, nocturnal fish, things that live in the sand column that are not all the things you'd go when you went snorkeling in a tropical reef environment. So it's a powerful lens. And of course, fish is only one tiny aspect of what makes those marine ecosystems tick. So we can sort of focus our

Dr. Michael Bunce (22:49.198)

PCR, you like, our photocopy onto different organisms. So we will have a test for fish, another one from remammals, another one for a cartilaginous fish, another one for corals, another one for insects and zooplankton and sponges. So we can sort of, I guess, splice together lots of kind of different sort of tests for different organisms. And that's what give us the tree of life that's in there, this sort of unprecedented window into all the biology in that sample. And that's the game changer when it comes to environmental DNA the ability to look at all the pieces of the tree of life and not just focus on one arm of it.

Clark Marchese

Yeah, okay, that makes sense. So I guess there would be certain information in a DNA sequence that can tell you sort of which category the organism falls into. But then how do you go about sorting and organizing such large amounts of data?

Dr. Michael Bunce

Yeah, well end up with a tremendous amount of data at the end of it. So typically when we process an EDNA sample we might end up with say 100,000 barcodes from different things from corals through to fish. And your questions could be highly variable from that. It might be trying to find endangered species, invasive species. It might be to find species that are outside of their known range. So what

Dr. Philip Bayer and the team here at Minderoo has been doing is developing large language models tool so you can literally ask a question of the genetic data. So show me all the IUCN listed endangered shark species in that sample. know, show me an invasive species that or show me this endangered species that's out so and it's known distribution. So you can literally sort of jump onto our oceanomics dashboard and this has got data from Australia's federal marine parks and you can ask it questions with it.

Dr. Michael Bunce (24:33.324)

And that's a really big difference because the raw output of DNA has always been lots of ATCs and Gs, which has the accessibility of a brick, if you like, in terms of people just can't connect to it. So the challenge as a geneticist is to take this DNA code and make it accessible to people and to ask questions of it. And so you don't need to become a molecular biologist to use environmental DNA now. You just need to, if you can use ChatGTP, you can ask questions of environmental DNA data.

Clark Marchese

This is fascinating and I'm definitely going to play around with that tool and I will link it in the show notes for anyone who is interested in playing around with it as well. Really quickly, I have got a mention from our sponsor and this one is a little bit on theme today. This episode is brought to you by Monterey Bay Aquarium, a stunning showcase for the habitats of sea life in one of the world's richest marine regions. For over 40 years, the Monterey Bay Aquarium has led efforts to restore delicate ocean ecosystems through their Sea Otter Surrogacy Program, and expanding our knowledge of the natural marine world to help protect it for future generations. If Sea Otters got your attention, you got mine too, it's a pretty amazing program, and the first of its kind that involves rescuing, rearing, and returning Sea Otter pups to the wild. The ocean nourishes, humbles, and centers us. It unites communities and deepens our understanding of how we're all connected regardless of background or where we live. The aquarium's mission is simple, to inspire conservation of the ocean. Monterey Bay Aquarium creates extraordinary experiences that inspire awe and wonder, champion science-based solutions, and connect people across the planet to protect and restore the ocean. There's wonder in ocean life, and caring for it helps us all. Where the ocean flourishes, people thrive. Learn more at montereybayaquarium.org. All right, where were we?

As you were mentioning the different kinds of questions you can ask, I think that there's something that we can take a minute to really understand the power of data, especially data sets this large, because once you have access to it, the amounts of questions that you can answer or ask is just endless. We've also learned on the show a little bit about how certain species are moving around the ocean with the onset of climate change and how their migratory patterns might be a little bit different now than they used to be based on changing ocean conditions. And if you can, as you mentioned,

Clark Marchese (26:59.67)

identify whether or not a species is in a location it's normally found in, I guess there's a million questions you could ask about that, right? So this is a really valuable resource that you're creating. And, you know, we know the oceans are very vast, but we've also mentioned a couple of times that you're focused on kind of the Australian context or Australian waters. I know that the program is focusing on a couple of different local ecosystems in particular, such as the Great Barrier Reef or the Ningaloo Reef.

Can you speak a little bit about the importance of these specific ecosystems that you're looking into, why there was a choice to focus on them, and maybe some of the things that we've been able to learn?

Dr. Michael Bunce

Well, we're in late 2025 at the moment. And right at this time, we've got sort of three major events that are occurring in the water. So the Great Barrier Reef is bleaching as we speak at the moment. So there's big ecosystem change here. And for the first time we've got the, on Western Australia, we've got the Ningaloo Reef. That's also undergoing bleaching. So two big marine heat waves over there. And down in South Australia, they've had harmful algal blooms that are killing huge numbers of fish down that way.

And those are all examples of how our planet, our ocean is changing and how the biology is, I guess, having to respond to that. So under a changing climate, we're going to have winners and losers out of this. Some things will be very adaptable to a changing climate and other things can't get up and move and they might be the losers. So where we put our conservation dollars or which species are under risk of local or total extinction and those that are doing okay becomes really important to sort of, guess, prioritise which areas where we spend our money and the impacts that we're looking for there. So although we've got, I guess, a focus on Australia, that's where our philanthropy is based, the impact we're trying to have in the tools that we're developing are of use on oceanic scales and globally. So part of our, I guess, the mission of the foundation is to, again, think locally, but sort of act globally as well and develop communities of practice.

Dr. Michael Bunce (29:01.78)

across nations that are going to make better decisions because it's no use just looking after our patch of the ocean or other ones are burning.

Clark Marchese

Okay, that leads me kind of directly into my next question. Can you speak a little bit more into how the data from these regions connect to a larger picture of global ocean health?

Dr. Michael Bunce

Yeah, well, you know, we could probably start a bit further back and just talk about aquatic health rather than ocean health. So probably one of the largest and best environmental DNA data set center in the globe is in New Zealand. I was based over there and until about a year ago, trying to generate understanding how the rivers over there are responding to sort of intensive farming and pollution. And what we were trying to do over there was to try and find invasive species, to try and find rare species and develop indexes of ecosystem health. So.

That's kind of what we can do with this DNA toolkit. Most people sort of look at it and saying you can come up with a list of species. But in actual fact, we can take the DNA barcodes that we're finding and some of those barcodes are only found in pristine rivers. Some of them found in really degraded rivers or pristine waterways or seas and really degraded bits of the ocean. And so we can sort of develop indexes of all the sort of DNA barcodes that we find from microbes to sponges to everything else in between.

One of the real accessible parts of what we did in New Zealand was develop something called a Tiki index, which is just a score that says whether things, whether that river is in poor condition, whether it's in pristine condition, whether it's tracking upwards or tracking down. One of the core missions we've got is to sort of use that same approach and try and apply it to oceans, whether it's our estuaries or whether it's marine protected areas.

Dr. Michael Bunce (30:42.91)

or areas that are overfished and not sustainable anymore. We hope to be able to shine a light on them by developing indexes for those areas, measure, you like, litmus test of ecosystem health in those areas. And that's where I think we can have a really tangible benefit, not only coming up with a list of taxor invasive and endangered species, but telling people whether that their local environment is getting better, is getting worse, or staying the same.

Clark Marchese

Okay, that makes sense. And that also again kind of leads me right into my next question, which was what to do with this type of information. Aside from giving a more detailed picture of what's going on in the marine environment, in that last example, it makes sense how it could inform local sustainable practices if we're thinking about one river system and how knowing which areas are quote worse off or better off can inform or prioritize funding or implement policies to avoid putting stressors on those certain areas. That totally makes sense locally, but in an ocean wide environment, is there anything that we can do to kind of use this information to support the conservation of specific ecosystems in such a vast global ocean?

Dr. Michael Bunce

Well, I would argue strongly we can. When we're trying to protect 30 % of our ocean, the 30 by 30 initiative, and this is what David Attenborough sort of called for in his recent film Ocean by David Attenborough. He asked us to sort of protect 30 % of the ocean because that's the number that we need for spillover so we can sustainably manage and harvest the other 70%. So I guess the question goes, well, how do you know how effective that's being? what the spillover effects are. So we're never going to get to the bottom of that if we don't measure ocean health and what's going on there. So the most obvious one, of course, under 30 by 30 is overfishing, right? We go in, you know, this is not universal because some marine protected areas are indeed fished, but it's simplest form. If you have fished and unfished areas, how much can we fish the fished areas relative to the unfished areas to make decisions about...

Dr. Michael Bunce (32:46.222)

quotas and sustainability of specific species within that fisheries. So not just as I guess on oceanic scale as saying which areas should we protect? is the unique biodiversity? What is the value in locking that away and not using it as its source populations? And of the areas we do go into, we still got to sustainably manage them. We can't just have open season on the 70 % of oceans and for example our high seas and saying well, have at it, right? Because we will fish ourselves into local extinctions where we can no longer generate sustainable livelihoods from those areas. So I think the challenges with the ocean are many and they are tied to measuring things to make good decisions because without that, you're flying blind.

Clark Marchese

You know, by the time this episode comes out, will have somewhat recently had an episode about marine protected areas. And I think that last effort gives a really concrete explanation of how the data that you were collecting can have a conversation with the decisions being made about marine protected areas. Not only in identifying the ecosystems which are under the most stress, but also to measure the effectiveness of the MPAs or the marine protected areas. Because what I also learned was that once these areas are drawn on a map, all of the different things that go into maintaining them and collecting data to see if anything needs to change. So I think there's a really good conversation that's being had between the type of data that you're creating and the decisions that are being made.

Dr. Michael Bunce

Yeah, you got it, Clark. Just to sort of inject on that is there's a concept referred to as paper parks, which is just you draw a line on the map and you let it go. And of course, that means you're not policing who's going into those areas or actually understanding how that marine ecosystem is actually even changing. You know, it's quite expensive to put boats out there and go and collect information. So, you know, one key aspect of that is how we can use emerging technologies, remote sensing satellites, environmental DNA collected by people who are on the water out there to collect information.

Dr. Michael Bunce (34:42.998)

and do it in a cost effective way. So, you know, I spent quite a lot of time at the science policy interface in New Zealand. you know, one of the sort of hard realities for a scientist in there is that of course there's competing, you know, do you want to build a new hospital or put a protection in for a new marine protected areas? What you can't do in conservation biology is just sort of just pile a whole pile of money into it and not understand what you're getting for that investment. And it seems really sort of harsh and brutal, but politicians is held accountable for where they invest it and what outcomes they're getting from that. So if we don't measure the efficacy of those marine protected areas or the efficacy of sustainably managing fisheries or protecting port environments or local beaches or water quality, it's very hard to answer that question. You know, what are we getting for that level of investment? Are we using the information? Are we making good decisions with it? And fundamentally, that's what we're trying to produce in

We need a toolkit of approaches to do this. And we would argue here and many others will as well that we're bringing quite a powerful tool to that party for measuring biodiversity in the form of environmental DNA, but it is not the only tool we're going to need to effectively measuring at scale. What we do know is that we can't spend more on measuring it than the benefit that it gives us, right? So we can't put divers in the water, spend expensive research vessels to every single square kilometer of ocean. We will spend more than what we're trying to protect. So how we do this thing cost effectively, how we prioritize it is just vital.

Clark Marchese

Yeah, that makes total sense. And I'm curious, have you seen that any of this data has led to a beneficial conservation decision or positive newsworthy policy, either in Australia or internationally that you can share with us?

Dr. Michael Bunce (36:26.956)

Yeah, and you know, I, lent on an example of New Zealand before. We are changing how we are managing rivers in New Zealand using this technology, because in the past when we were going out, sort of collecting insects from streams, it taking six months and five years to find where the patterns were changing. Now we can rapidly do that in a matter of weeks. You know, we can actually look at all of the rivers in New Zealand every year. In the marine environment, we've done things like detect an invasive species early so they can start eradication campaigns or understand the impact of that invasive species on the receiving environment to get proportionality into the response? Should we mobilize everything to eradicate that or is it just going to simply coexist with some of the other taxa that are there or is it going to drive something to extinction? We're already seeing that in terms of assessing river quality invasive species is the obvious one. Efficacy of marine protected areas is another clear one that's in there what's inside the marine protected area compared to what's outside of it. So those are sort of some tangible examples. But what we're really missing in the field is, is, you know, all of the monitoring is based on changes over time. And as the new kid on the block, environmental DNA, is still struggling with not having data sets that are, that are many years, if not decade or on, to be able to see changes over time and to understand how quickly an area is degrading. So the real kicker for us is to be able to generate that temporal and spatial data. feed it into models and say at our current rate of decline, this area is going to be at risk of extinction of these fish or it's not going to be commercially viable anymore in five years time at its current burn rate. So how we turn information into useful intelligence for decision makers is one of the key challenges we're trying to address.

Clark Marchese

Yeah, and I think as you were speaking, it kind of makes total sense that you could really benefit from having a clearer picture of how these things are changing over time. So I guess other than continuing to fund these efforts, as someone who does spend a lot of time at the science policy interface, if there was one large piece of policy you could change or that you could make tomorrow at the snap of your fingers, what might it be?

Dr. Michael Bunce (38:36.44)

And at a big picture that would be, yeah, you know, it's an old adage that you can't manage what you don't measure. So if we don't, if we're not collecting samples and engaging lots of different people to collect samples, again, we're flying blind. So if I had one option, there is, put decent monitoring programs in place, put a triage layer in place for our oceans. So we're running a biodiversity hospital at the moment in our oceans and we don't have a triage department out the front of it. to know which areas are hurting the most and need to be sent for intensive surgery and which can kind of quite happily wait till next week when we've got a bit more time on our hands. So that lack of prioritization, that lack of triage in there means that areas are getting degraded really quickly and we're not paying attention to them. And other areas we continue to invest money into when they might be doing fine and that resource could be spent better elsewhere.

Clark Marchese

There is a whole lot of ocean out there. And I understand that there is an increasing initiative to make use of citizen science in this project. So can you tell us about how the public or the average person can roll up their sleeves and be a part of that triage unit?

Dr. Michael Bunce

Yeah, this is a key point of environmental DNA is that anyone can take a sample. So the work that we're doing on a global stage now, but very much started in New Zealand with some of our commercial partners, Wilder Lab in here, is developing very easy to use eDNA kits. So these are simple syringes that you, with a filter attached to the end of it, that you escort a water sample through, and then you put preservative on that filter, and then you can send it off to a lab that will get processed.

That entire process takes about sort of seven to 10 days to get an answer back. So if you took a water sample from your local ocean in a couple of weeks, you get a big tree of life of all the biology that's in there. So we know that sending out research boats is expensive and research teams out that area. And we know that local people are increasingly asking what they can do to look after their backyard, their blue backyard a bit more effectively. So there's a really clear pathway here that if we could get local people to take samples for us by filtering some water.

Dr. Michael Bunce (40:39.784)

sending them in, we can develop that triage layout because we can take lots of samples in lots of places. So some of the work that we've done, we're funding quite a few initiatives trying to, I guess, get people to take a ride to the DNA site, if you like, and think about what they can do locally. So one example is the project that we've got with UNESCO, which is in charge of all the World Heritage sites around the globe. And so there's marine World Heritage sites. So we're working together with UNESCO. to look at 25 of the marine world heritage sites and taking samples four times a year over multiple years to start really bringing this monitoring tool into play. We're working with Citizens of the Sea, which uses yachty communities that are traveling the ocean and they collect environmental DNA samples off the back of their boat. We're also doing some work with Conservation International, as well as traditional owners here in Australia and in New Zealand that have got interest in their backyard.

Now we don't tell these groups where they should sample. They sample in places that mean something to them. And hopefully once they get the information back in a timely manner, they can say, well, what are we going to do next? How do we restore that if the river system or estuary is bad? What can we practically do? Who can we talk to about doing more monitoring to steer it in the right direction? And that's probably one of the most satisfying things slightly later in my science career. Clark is moving away from off just one end of the participation spectrum, which is just informing people about what you found to move towards the other end of it where you're empowering and collaborating with communities to collect more. I don't know, maybe I'm just getting sort of older. We actually need people to engage in this mission, not just writing more science papers, but getting them to tell their stories at local places and why it means something to them.

Clark Marchese

I really like that approach for a number of reasons. mean, obviously there's the efficiency aspect of it. You know, if people are already enjoying the ocean and they can simply and easily collect data, then that's great. But it's also nice that they're collecting data about places that mean something to them, places that they're invested in. And then also when we were speaking earlier about how politicians need to be able to sort of see the value for their investment because they're held accountable, they can kind of make an easier

Clark Marchese (42:54.062)

for their investment when the public already cares about the ocean and is aware of the importance of the ocean and the importance of collecting the science. So I guess any opportunity we have for public engagement should be made the most of.

Dr. Michael Bunce

I agree. It's about connecting people to nature fundamentally, right? And we could argue that when we lack that connection to nature, we act unsustainably because we're just not listening well and responding to what it's telling us. yeah, that is one aspect, getting a sort of a bottom-up approach to the science as well as a top-down approach of saying, is what the science tells us, and this is what people are asking for.

Clark Marchese

Well, looking to the future, what do you hope for the future of this oceanomics program? Perhaps in the next 5 to 10 years?

Dr. Michael Bunce

five to 10 years. So in five to 10 years, we would have, you know, I think in about a year's time, after the work that Siro is doing, we will have have, you know, all the fishes of Australia sequenced. And that means that, you know, in terms of their barcodes, so very rarely will we get a DNA fragment out of the ocean that we don't know what it belongs to. That means we've scanned every product in the supermarket for its barcode and we can identify every single product. Nothing slips through the cracks in terms of its barcoding. In 10 years time, You know, we'll probably have all the fishes, the whole genome of them sequenced and understanding more about how long they live, when they become sexually mature and how to age fish from DNA markers, methylation markers on the fish that can tell how old a structure is. So I think we're to be making really much better decisions if we get the toolkit right. So I think we're laying down a really solid foundation at the moment. I'm quite excited and very optimistic actually that that

Dr. Michael Bunce (44:33.93)

We're putting this toolkit together and we're going to use the right tool for the right job at the right time and make better decisions about what work needs to be done and what can be delayed and how to prioritise. And I think people are going to slightly start to click that the same environmental DNA sample taken at a local beach can be used for many things. Biosecurity. can screen whether there's new species in there. Endangered species can be detected and reported up to IUCN Red List. It can be used for fisheries management. It can be used for water quality, for swimming, whether it's getting better or worse. It can be used for sustainable power generations, wind and wave generation out there. so five to 10 years, I think even in the next couple of years, we're going to see better information come into play and to put some tough decisions in front of decision makers with some solid evidence behind it. because the worst thing we can do at the moment is just not measure anything because the downside to that, you know, well the consequence of that is we just keep doing what we did last year. And so we're on the sort of downward sort of biodiversity spiral at the moment and we need to turn that around and that's only going come from better information.

Clark Marchese

Well, we will have to do a follow-up episode of the Oceanomics program in 10 years, or even sooner, because I really enjoyed this. I have two final questions for you, the first of which is, is there anything that we didn't talk about today that we'd be kicking ourselves if we forgot to mention?

Dr. Michael Bunce

Yeah, just to reflect back on a conversation over the last little while, it's the interweaving of environmental DNA data with other data. satellites are zooming around our planet. They are not going to tell us the species of bacteria in our oceans or where the fish are. But the information coming off them and other remote sensing, such as boys, sea surface temperature, et cetera, when we combine that together with environmental DNA, we have the ability of bringing in that triage department.

Dr. Michael Bunce (46:26.998)

So what I'm most excited about is interweaving environmental DNA data with other remote sensing data to develop a better triage layer. So if we can calibrate from the colors being measured in our oceans, if we can calibrate some of those colors based on DNA evidence, if we can use those satellites to understand where fishing boats are going and where they're not going anymore, that areas that might be fished out. So I would really like to see better interweaving of data sets. But this gets pretty gnarly and complex pretty quickly as satellite data even by itself is tremendously complex and so is genetic data. So we're sort of creating a whole new field of the interface between that. But I think that's really where the power is because then we have the ability of that triage layer working at the scale that it needs to work at. As you've pointed out, oceans are big place. We can't be in all the places all the time doing all the things. So how we make better decisions and prioritize different areas. That's probably the one area, Clark, that I'm most excited about that we probably hasn't touched on is that kind of whole toolkit for the triage layer and really importance of satellites and genetic data in tandem because I think that's where there's going to be some big gains.

Clark Marchese

I'll be very eager to watch this space and I am walking away from this conversation feeling very equipped, I think is the right word, because you've told us about all these different toolkits that we have and I just can't wait to watch us use them. My last question for you is where can listeners find you and follow the work that you're doing?

Dr. Michael Bunce

Yeah, you can Google, Minderoo Oceanomics, but the Minderoo Oceanomics dashboard is a cool place to go exploring. Yeah. I just, you know, reach out to some environmental DNA people close to you. said, anyone can take an environmental DNA sample. Well, sort of heart got filled the other day when I heard stories about people gifting a DNA kit to one of their relatives for a Christmas or a birthday present, I think it was, and they were going to go and explore what was in their blue backyard.

Dr. Michael Bunce (48:18.158)

I think that's a really cool thing to sort of reach out to. So if you want to know more about it, Oceanomics phase is a number of eDNA service providers that are popping up. There'll be one close to you. So yeah, go out and start exploring.

Clark Marchese

I'll be sure to include links to all of those things and to everything else we discussed today in the episode description. And this is the part where I say thank you so much for giving us your time today. Thank you for teaching us all about the Oceanomics project. And also thank you for your really important work in this space.

Dr. Michael Bunce

Thanks Clark, cheers.

Clark Marchese (48:59.736)

You've been listening to Oceanography. Special thanks to the Minderoo Foundation for making this episode possible and to the Monterey Bay Aquarium for sponsoring the episode. Just a reminder to anyone who's interested in helping us reach more people and share scientific research like this, sharing it with someone you know or a five star rating or written review on Apple podcasts or wherever you're listening are among the easiest and most effective ways to help us and reach more people. Oceanography is a Pine Forest Media production.

You can find more information about the network in the episode description. Cover art for the show was done by Jumero Emming, and the music you're listening to was done by Nila Ruiz. This show was hosted and edited by me, Clark MacCasey, and you can find more information about Pine Forest Media and our other science podcasts at pineforestpaws.com or follow us on social media at Pine Forest Media. All right, that is all I have for you today. Thank you so much for being here with us and I will see you. Right back here again next week.