Genetic sequencing at the end of the world

In the UK, we are experiencing something of a cold snap. And that got me thinking. Whilst it’s no effort for us humans to chuck on a coat and hat, that luxury isn’t afforded to pretty much every other living organism out there. I’d assume. So, when the temperature drops, it often falls on an organism’s genetics to keep them alive and kicking. So what does that look like, and how is our understanding of such genetics changing? Well, it's worth finding out, but there’s no point in half measures when looking into this kind of stuff. So that’s why I’m joined by the British Antarctic Survey’s Melody Clark...

Will - Melody, where are you right now?

Melody - I'm actually sat in an office in the Bonner Lab, which is the marine biology laboratory at Rothera research station, which is about halfway along the Antarctic peninsula.

Will - You are at the South Pole. Marvellous <laugh>. We've really outdone ourselves. What's the weather like there today?

Melody - It's very south poley actually. It's blowing about 40 knot winds and it's absolutely freezing. And that's a very good reason for staying inside. Thank you very much.

Will - I do not blame you at all for that, but it presumably means that certain organisms, particularly in the waters around you, have a bit of a problem when it comes to low temperatures.

Melody - They do, but it is actually much more stable in the water than it is on land. So where I am at rather at the moment, the water temperatures throughout the year vary between about minus 1.86 degrees Celsius, which is when seawater freezes, up to the giddy heights of plus one degree Celsius, which it reaches briefly in the summer. If you go to the other side of Antarctica to McMurdo, which is by the Ross Sea, which is permanently ice covered, the animals only experience about half a degree temperature difference in the year. But essentially all the animals in the sea live almost permanently below zero degrees, which is pretty cold. Contrasted with that is the variability of the environment. So we have 24 hour light in the summer, 24 hour dark in the winter and in the summer you get these huge phytoplankton blooms, which is the kind of green stuff, the algae and diatoms in the water between about November and February. And then also we have the sea ice here, which doubles the size of the continent every year.

Will - All of this put together it sounds like a not ideal set of conditions for organisms to survive. But you've been looking at a group in particular. Would you mind talking our audience through what this latest genetic study looked at?

Melody - We've been looking at the notothenioid fish, which are the dominant group in the Southern ocean. The project was to sequence the genomes of these animals, to identify the genes in them and really to develop a resource to start to understand how these animals survive in such extreme conditions. And we sequence 24 of these fish species. And the idea of that was to, if you want to look at cold adaptation, you want to sequence as many animals that live in the cold as possible. So you can identify species specific variation, but also you want to compare them as closely as possible to ones that don't live in the cold. So you can identify the difference between cold specific adaptation species, specific adaptation. And yes, those genomes are readily available to the whole community and anybody can look at them. And the important thing is that now we have this information for these fish, we can start to use techniques that we're using to investigate model organisms such as mice, rats, and zebra fish in more detail in these fish species.

Will - Is there a potential idea then that someone takes all of this genetic data and they can find a gene or a genome or a cluster that might be able to explain how certain fish manage to survive such cold temperatures?

Melody - Exactly. And with 24 genomes, that's a huge amount of data. So by making it publicly available, people can then go in and investigate their favourite gene, their particular pathway or maybe do some large scale studies to try and identify in general how these species have adapted to the cold. So there's a whole raft of possibilities that people can research into now that these sequences are publicly available.

Will - This is almost a call to arms then, isn't it? If someone's out there and has a favourite gene, which I love the idea of someone having a favourite gene, you can go out and get stuck into this. Taking this up to sort of a more phenotypic level, we know several of the adaptations as to how fish can survive the cold. Is it then a case of us trying to work backwards into seeing which genes are responsible?

Melody - Yeah, so we know some very common adaptations that have been known for a long time. So all of these fish have a particular sort of antifreeze. They wouldn't be able to survive without antifreeze in their body. And it's an antifreeze glycoprotein and that they all have it. Bizarrely this identical molecule also is present in the polar cod. And this is one of these quirks of evolution where nature comes up with the same answer to the same problem in completely different areas of the globe in a slightly different way. So it's an example of convergent evolution. So they all have this antifreeze molecule that they produce all year round to help them survive the cold. And there are also some more weird adaptations. So we have about 16 species of fish called ice fish. They're called ice fish because they look completely transparent and when you cut them, their blood runs clear. It's not red. So it doesn't have the haemoglobin molecule, the red molecule that we all have in our body that carries oxygen around. And so these fish survive without haemoglobin. They only carry about 3% of the oxygen that a normal fish would. And they managed to do that because it is so cold in the southern ocean and as you cool water down, the amount of oxygen it increases. So it's heavily oxygenated. So they survive in this environment because it's heavily oxygenated and also they really do nothing much at all. I mean, they are the ultimate couch potato. So if food comes past their nose, they'll eat it, but they don't really go hunting for food. And this is a very peculiar adaptation that's only been possible because it's so cold in this environment. And in terms of other adaptations, yes, then we really need to understand what the other ones are. These are the common ones we know about, but there are bound to be plenty of others.

Will - And as you say, some of these adaptations are only possible due to the cold nature of the environment. Which brings me to the inevitable topic, whenever anyone mentions Antarctica, which is climate change, how might the shift in climate affect these fish and the future studies on them?

Melody - Okay, well, I'm afraid to say for the ice fish, it's really not looking good because they don't have haemoglobin. As the waters warm up, the oxygen amount will get less and they are not able to make haemoglobin. They've completely deleted it from their genomes, which is one of the interesting genetic discoveries. In terms of the other fish, they really don't like being warmed up very much at all. And neither do the marine invertebrates. The marine invertebrates like sea cucumbers, sea stars and sea urchins. So it's not looking good for them in terms of their temperature tolerances, but also we don't know how that affects their reproduction, their immune system. And also when things warm up, you may get more diseases that affect these animals. We simply don't know. But I would say on balance it's not looking great, which is a rather depressing thing to say isn't it. But I mean, if we have the genomes of these animals, we should be able to understand a bit more about how they perform and how they survive. If that's a more promising note to end on.