Environmental DNA: Seeing the Unseen

2021 marks 100 years since the discovery of insulin. This week, there’s exciting news for the millions of people living in the UK with Type 2 Diabetes who already are, or could become, reliant on injected insulin to control their blood sugar levels - a fully automated pump has been trialed in outpatients for the first time to great success. Charlotte Boughton, a leader on the study, from the University of Cambridge is joining us now... 

Adam - So Charlotte, why was this study done? Why is, you know, just manually injecting insulin, not enough. Why do we need the pump?

Charlotte - We've previously shown that a closed-loop system or an automated system can actually improve people's glucose control in those with Type Two diabetes when they are admitted to the hospital. And so in this study, we wanted to see if the same system can be safe and effective compared to people's usual insulin injections in the home setting, as you mentioned. And we did this study in people with Type Two diabetes who also have kidney failure and need dialysis, and that's because that's a time when diabetes can be particularly challenging to manage

Adam - What are people wearing? What does it look like when they put it on? And how does it work?

Charlotte - A closed-loop system comprises three separate parts or bits of kit. So people wear a glucose sensor, which is about the size of a two pound coin, and that's worn on the arm or stomach, and that measures the person's glucose levels in real-time. And that then communicates with an algorithm or a controller, which in our system is on an app on a normal Android smartphone. And the algorithm calculates the right amount of insulin and tells a small insulin pump, which is a light, slightly smaller than a mobile phone-sized pump that delivers the insulin to the person. And it repeats this cycle about every 10 minutes, constantly adjusting the insulin dose in response to the glucose levels. And the person doesn't need to do anything, they just need to be wearing the kit.

Adam - And how easily do people tolerate this? Because I imagine at least part of it is going to have to be, you know, at least under the skin

Charlotte - Young children who have Type One diabetes wear very similar technology to this, so it's been designed in a way that it's highly acceptable. So the sensor is inserted every 10 days and it's just a tiny little wire that sits under the skin. It doesn't hurt at all. And then that sticks on with a bit of adhesive. And similar to the pump people are used to doing insulin injections, where with a pump, you just need to change the needle every three days, rather than doing injections several times a day. So people really like wearing the device. It takes some getting used to but overall is pretty well tolerated.

Adam - And is that then the big advantage that it takes the thinking, I suppose, out of your head? You can't forget. You can't make a mistake.

Charlotte - Yeah, absolutely. So in this system, it's a fully automated system. For people with Type One diabetes, they use a slightly different system. But in this case, you can almost forget about your diabetes because you don't really need to do anything. You don't need to measure your glucose levels because that's done automatically and you don't need to calculate the right dose of insulin to give, and provided that you change over the devices every sort of few days, then actually the system will work and allow you to get on with your day to day activities.

Adam - Now, to me, that sounds brilliant. The thing I can forget about until something, say, goes wrong. So what if my phone dies or I were to forget it and I needed my insulin. What would happen then?

Charlotte - We rarely leave our phones places, but absolutely it's something that we have to think about when designing these systems. So if the phone's out of Bluetooth communication or the battery runs out, then the pump still gives insulin. It's just it won't give it in an automatic way. So you lose the brains behind the system, but you can still measure the glucose levels and the insulin is still given. So it's sort of a safety net really.

Adam - And it will be effective enough until they can get their phone, or recharge?

Charlotte - Exactly, until it's recharged, yeah.

Adam - That's why it's potentially great for the patient, but what about on the other side, the hospital system, the NHS? Are there benefits for them, for people using this system?

Charlotte - So our study that we've just done was quite small and too short to demonstrate any clear benefits to the NHS. So this would need a much larger and longer study to see if that can translate into improved long-term outcomes, which may have cost savings for the NHS in this population.

Adam - Okay, that makes sense. You mentioned earlier that there are previously pumps for Type One diabetes, and this has been developed for Type Two. Why is Type Two coming later? What's different about it that makes it harder to get a grip on?

Charlotte - It was more where the priorities lay. Some of this research started off in children because of the concern about the effect of high and low glucose levels in young children with Type One diabetes, where they can't often communicate that they've got high or low glucose levels. And these closed-loop systems are transforming the management of Type One diabetes. I think it's come later in Type Two diabetes because in Type One, people don't have any insulin, and so rely on insulin completely to manage that glucose. Whereas in Type Two diabetes, we do have other treatments, so diet and exercise and oral medications and other injections as well. So there are more options available.

Adam - What state are you in? Could you see this being rolled out more widely?

Charlotte - So we already do have similar systems being rolled out in Type One diabetes. And our study was a sort of early proof of concept study that this is potentially a treatment that could be rolled out more widely, particularly in a follow-up study that we're doing in people with Type Two diabetes who don't have kidney failure. And that will hopefully provide evidence to support wider adoption of this technology.

We normally think of volcanoes as unchangeable - we couldn't stop one erupting if we tried, and we have tried! - but it turns out that some environmental factors like high sea level can prevent volcanoes from erupting. Eva Higginbotham reports...

Eva - If you live in the UK, you may not think that often about the risks of volcanic eruptions, but the 800 million people around the globe who live within a hundred kilometres of an active volcano surely do. Others like geologist Chris Satow from Oxford Brookes University just really likes studying them.

Chris - The question we were trying to answer was "What effects does sea level change have on volcanic activity, in particular at volcanic ocean islands?" And we were able to discover that low sea levels are the times when the majority of eruptions are concentrated and at high sea levels, the high sea level itself has the effect of reducing the likelihood of eruptions. And we used the volcanic island of Santorini as our case study.

Eva - Scientists had previously seen that in places where there had been large ice sheets in the past covering volcanic areas, like Iceland for example, there had been a big increase in volcanic eruptions when that ice had been removed.

Chris - So it got us thinking that perhaps the same effect might occur in the oceans, but of course in the oceans, it's not ice that's being removed and added. It's water that's being removed and added as the sea level has risen and fallen over many tens and hundreds of thousands of years. And the sea level goes up and down globally by quite a substantial amount. So the difference between the sea level today and the sea level during the last ice age is around a hundred meters. That's a huge change in the sea level. That's essentially saying that the English Channel would be entirely dry and you could walk from England to France at that time. That's a huge amount of mass to remove from the surface of the Earth or the top of a volcano. And that gave us an idea that the sea level change might have some influence on the activity of the volcano.

Eva - But how do they know when eruptions happened anyway? David Pyle is another volcano enthusiastic this time from the University of Oxford.

David - So Santorini is a fantastic example of a volcano that shows what we'd call a layer cake. You can see different layers of rock making up the cliffs, and some of those layers of rock, they weather in different ways, they crumbled in different ways. They've got different colours and different patterns on the surfaces. And as a geologist, what we do is essentially work our way down through those layers.

Eva - By analysing these layers of pumice and ash and solid grey lava, geologists can come up with a relative time or stratigraphy of when eruptions took place, which is what they did for Santorini. The next step was comparing that timeline with the sea level record.

Chris - By taking samples of sediments from the bottom of the oceans, and these come in huge tubes - cores as we call them - which might be even up to a kilometre in length. And we know that the mud that's higher up in that core is very young. And the further down you go, the further back you go in time. And if you can process them, if you can split it up into its constituent parts, you start to find fossils and most useful fossils for us to work out what the sea level was, are fossils of these creatures called 'foraminifera', or 'forams' if you're on first name terms with them.

Eva - Forams are these microscopic sea creatures who live almost everywhere on Earth, and they produce these shelves using the materials from the seawater they live in, including oxygen. Like all elements, oxygen comes in different varieties, called isotopes. And luckily for scientists, the ratio of various oxygen isotopes in the foram shells reflect what the sea level was when they were alive.

Chris - So these little creatures are recording what the sea level has been at various points in the past into the composition of their shells. And then we can extract them from their fossilised mud, analyse them and look back through time at how the sea level has changed over hundreds of thousands of years.

Eva - Chris, David and their colleagues then used computer modeling to marry up the data on Santorini's eruption history with the established sea level record and found that, indeed, during times of low sea level, there were more eruptions and times of high sea level, there were fewer. So does this mean, contrary to what we normally think, that having high sea levels like we do now is kind of a good thing?

Chris - The truth is we don't quite know what's going to happen to all the magma that's being stored underneath the volcano, if it's not being erupted. So it could be of course, that the magma gets stored and then more magma gets added and more gets added and then over time. So it could be that in fact, you build up a much larger volume of magma underneath the volcano, which then in the future could results in a much larger eruption than would otherwise have been anticipated

Eva - Interestingly though because the sea level rises all over the world at the same time, does this suggest that in some ways, all the underwater volcanoes around the world are sort of linked?

David - If you allow the system to persist for long enough, then indeed you'd expect that volcanoes would come into sync or there'd be some sort of synchronisation or synchronicity between volcanic systems that are physically independent, but they're all kind of responding to the same external processes.

Eva - So just as everyone around the planet is likely to be affected by the changing climate due to global warming, it seems volcanoes may be going to experience a similar phenomenon.

Sally Le Page has spent the last couple of weeks with Naked Scientist Phil Sansom digging deep into the exciting new world of environmental DNA, or eDNA for short. It's the same technology you might have heard being used during the pandemic to detect COVID DNA in sewage water. But, what actually is this technology? Sally spoke to Beth Clare from York University in Toronto...

Beth - Environmental DNA is any DNA you collect from an animal that you didn't get directly from that animal. So, some people would argue it has to be effectively naked DNA that's out of itself, floating around in the environment. Other people would say, well, it's just sort of anything. It’s bits of sloughed off cells and bits of hair that are out there that you collect, but you don't actually see the animal when you get them. You're just taking them out of some substance, like water or soil.

Sally - But, why would you want to get the DNA from the environment, the water, the soil, and not just take the DNA directly from the animal?

Beth - Well, because some animals are hard to find. So, it's a good non-invasive way of collecting things from an animal that you can't get, or you shouldn't get in contact with. So, it's a way of collecting things that doesn't cause you to interact specifically with the individual that you are targeting.

Sally - When you say you shouldn't get in contact with the animal, what are we talking about here?

Beth - Well, something that's really sensitive, something that is highly endangered. You don't want to interfere with it in any way that might cause harm or cause stress to that animal. It's a really good non-invasive technique.

Just 20 years ago, it would have taken months of work to get just one eDNA sample. Luckily, nowadays the process is so simple that even primary school kids are doing it. Sally Le Page met up with Kat Bruce, founder of NatureMetrics, to discover what animals had been visiting the river, Great Great Ouse, at Over in Cambridgeshire...

Kat - So we're going to collect an eDNA sample, so we are going to filter some water. And that filter will be sent back to the NatureMetrics lab and we will analyse it to see what species of animal we can find from the river.

Sally - It's so exciting. How do you collect eDNA? What are we going to be doing?

Kat - Over the years, we've designed this really simple kit. The first thing we ought to do is put gloves on. Again, this is to stop us from introducing our own DNA into the river. In reality, we actually are able to use human blockers in our analysis, and that really sort of reduces the amount of human DNA, because to be honest, this river is full of human DNA.

Sally - And out of this plastic bag with all of the different ingredients, I mean, that just looks like a sandwich bag to me. Have you just brought your packed lunch?

Kat - I have, this is a very sterile pack, so you can see it seals. So, we have to rip the top off to open it, take the top off this bag, reach down and scoop up some of the surface water. I'm going to hold it so the bags facing upstream and the water can just flow into it.

Sally - We now just basically have a very clean sandwich bag full of water.

Kat - I mean, so you can think of the water in here as a sort of soup of genetic material of all of the wildlife that's been in and around the river. So it will contain the DNA of the fish and things that are living in the river, but also a surprising amount of the land-based species that have been either drinking or swimming or whose DNA has been washed off the bank into the river as well. And then we've got a hundred mil syringe. We literally just go to use the syringe to pull up the water and then the syringe screws onto the filter housing with a filter membrane inside it, when we're dealing with eDNA, we're dealing with really tiny traces of DNA. That makes it very vulnerable to contamination either from ourselves or from sort of other things that we've brought in from the environment. So, the membrane is kept inside that housing.

Sally - It does just look like a plastic coin almost.

Kat - Yeah. It's about sort of twice the size of a 50 pence coin, I guess. So, then we just push the water through any traces of particles, sediments, DNA, cells, et cetera, that are all stuck inside the filter membrane now. So, we'll do this about 20 times. I think this is pretty much my last one and I'm just going to press the preservative liquid inside. I've got the cap on each end, he seems to have a yellowish colour on the inside.

Sally - That's the only thing that people have to post to your lab.

Kat - Exactly.

Sally - So we have just samples, potentially dozens of species just in like 10 minutes. That's just by sitting on a jetty and squirting some water through a glamorised water pistol with a filter on the end. That's it, that's it.

Kat - Yeah. Expedite that delivery back to the lab and see what we can find.

Sally - It was just unbelievably simple and because it's so simple, they can send these kits off to researchers wherever they are. They can stick them in their backpacks and they don't need a lab. And the company nature metrics is now working with the conservation organisation, the IUCN to sample water from around the globe to create eBioAtlas documenting all of the world's aquatic species.

Sally Le Page was very keen to find out what animals in the river Great Ouse were revealed by our DNA test with Kat Bruce from NatureMetrics...And Naked Scientist Phil Sansom, Eske Willerslev from the University of Cambridge, and Beth Clare from York University of Toronto weighed in...

Sally - We've got our sample, we popped it in the envelope. We mailed it to your lab. What happens in the lab?

Kat - It goes in the oven which heats it up to about 56 degrees for a few hours. And that just bursts open any cells that are still intact and releases the DNA into solution. Then we need to make millions of copies of the DNA of the particular group of animals or organisms that we're wanting to survey. And that gives us enough to be able to sequence.

Sally - So, you're only making the copies of the animals you care about?

Kat - Yes, exactly. Otherwise, if we just sequenced the DNA as it is in the sample, it would really just be dominated by bacteria and things. So, once we've done that, it goes onto the DNA sequencer. At the end you have a data file which has 30 million lines of As, Ts, Cs, and Gs. And of course that doesn't mean very much to most people. So, it then goes through a computational process, which sort of summaries that information. And then it runs each unique sequence against a reference library of known DNA sequences of species. And that lets us put the names onto the species that we've found.

Sally - And the big question is what did we find in the Great Ouse?

Kat - So, it takes a few weeks to analyse a sample from beginning to end for meta barcoding. So, in this case I've got some results from last summer when I actually came down here with a group of citizen scientists.

Sally - In true Blue Peter style here's some we made earlier!

Kat - Absolutely. And in total, so we did a vertebrate analysis on the samples and in total, we've got 23 species. Most of these are fish. So, 14 of the 23 species are fish, things like roach, perch... quite a bit of human in there as well. It was a busy day on the paddle boards! But then, you know, even things that are much lower level things like spined loach, this is quite an important species in this area, actually it's really hard to survey because it just sits around at the bottom of the river and is not sampled with electrofishing.

Sally - That's incredible. And looking down the list, we got a whole bunch of fish. You've got your dace, roach, chub, but we've also got super exciting things like water voles. They are incredibly rare now in the UK and very hard to spot.

Kat - Yeah, absolutely. They are a protected species. A lot of effort goes into trying to survey and confirm the presence of water vole.

Sally - Just looking around, we're not even in a particularly quiet part of the river, there's boats going past, we've had lots of dog walkers. I can see the reeds, but I never guess that we've got water voles that we've got all of these fish species. We can't see down to the bottom of the river and they're just there and you can tell with their DNA.

Kat - Yeah. And what we really want is people to go, oh my gosh, now we know that these species are here, we're going to come in and look for them and get interested in them and then come to these places with more of a sense of what the place is and what you're sharing, what other species you're sharing the places with.

Phil - Sally, I've never even seen a water vole.

Sally - I've only seen one. And I was incredibly excited when I first saw them. They are, of course, Ratty from Wind in the Willows and their population has dropped. They're so hard to see and they were in the water.

Phil - Is that in line with your predictions, you think?

Eske - I think it's pretty well what you would expect from this.

Beth - Nobody is ever going to look at water or air or soil again once we start talking about what's in it, because these things are just soups. It's just everything that's been through leaves behind a trace of itself. And what eDNA is doing is letting us look at those traces, unlocking that little mysterious door. And as you said, see what's invisible.

Phil Sansom and Sally Le Page spoke with Eske Willerslev from University of Cambridge and Beth Clare from York University, Toronto about the future of eDNA...

Phil - Can you give me an idea of the limits of this?

Eske - I think the biggest limitation right now is, you can say, reference material or reference sequences because if you take an insect out, right, you can identify, in many cases you can say this is this species of insect. With environmental DNA, whether you are doing metabarcoding, or shotgun, you're relying on databases, you're relying on somebody else having sequenced that species before. And if they haven't done that, you're kind of in a situation where you can say, well, this is an insect, but I don't know exactly what insect I'm dealing with. Of course these databases are exponentially growing. So people are sequencing more and more and more. So, my prediction would be within that 10-year period, we will really have that reference. But at the moment it is a limitation.

Sally - And if we can get to the point where we've got a reference genome for every species on the planet and we can get genomes from animals without even seeing them, that's just going to revolutionise everything!

Beth - It already is. You've got entire groups of people now using eDNA in the water. Everybody from research scientists to conservation management organisations that are using that substance to help them track and monitor populations for different applications.

Sally - Just like what Kat's doing with the aquatic surveys around the world!

Beth - Exactly. It's become a commercial industry. It's a research industry. It's a management and regulatory industry. All of these different sectors have taken up eDNA as a way of doing their jobs more efficiently and understanding all of those factors, which make that possible is what we really need to do to push that field forward. And if we can push it into other realms, terrestrial life, through air and soil, the most unusual sources like honey, tracking eDNA and different things like that, that have been used allows you to really expand this field in a way that I don't think anybody could've predicted 10 years ago. So, Eske’s ten-year prediction for genomes from substances: I'll give him five.

Sally - Wow, five years. That will be very exciting.

Eske - It's really just the imagination that are the limits of how you can use it.