Podcast: Pre-industrial plankton populations, European science, and ancient fungi

Host: Benjamin Thompson

Welcome back to the Nature Podcast. This week, we’ll be finding out how plankton populations have changed around the planet, taking a look at the future of European science…

Host: Shamini Bundell

And hearing about what is perhaps the oldest fossil fungus ever discovered. I’m Shamini Bundell.

Host: Benjamin Thompson

And I’m Benjamin Thompson.

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Shamini Bundell

If we want to fully understand the ongoing environmental impacts of climate change, one important thing to look at is how ecosystems have changed over time. The ocean is the Earth’s largest ecosystem, and it’s also one that keeps its own record of the past. Within the marine environment there floats a community of very small, very informative zooplankton – they’re called foraminifera. These single-celled drifters can be found remarkably preserved in ocean floor sediments, providing a microscopic record of their historical communities. Lucas Jonkers from MARUM – the Center for Marine Environmental Sciences at the University of Bremen in Germany – drew on mountains of data on these animals, from both before and after the Industrial Revolution. Reporter Geoff Marsh called him up and asked why it’s useful to know what the marine ecosystem was like before the Industrial Revolution.

Interviewee: Lucas Jonkers

At the moment, we observe changes in marine ecosystems and we say that they are in a direction that is consistent with global change, but we have no clue what these ecosystems looked like before human input, and so that makes it really difficult to say that the changes that we are seeing now are due to global change.

Interviewer: Geoff Marsh

Because presumably we’ve got lots of nice marine ecosystem data over the last sort of hundred years.

Interviewee: Lucas Jonkers

Well, it’s even less. I think it’s maybe since World War II. We need longer time periods.

Interviewer: Geoff Marsh

So, the way that you’re probing these historical marine ecosystems is by using these zooplankton, the foraminifera. Tell us why you use those and why do they make a useful organism.

Interviewee: Lucas Jonkers

These little plankton, they form a calcite or carbonate shell that is very well preserved in the sediment. We can look in the sediment and see exactly what their species community looked like at the time when the sediment was deposited.

Interviewer: Geoff Marsh

Listeners should probably just go on their computer or smartphones and just Google them because they’re really beautiful, aren’t they, but they’re microscopic almost.

Interviewee: Lucas Jonkers

They are.

Interviewer: Geoff Marsh

What do they look like?

Interviewee: Lucas Jonkers

Well, if you’re disrespectful, you’d say they look like little popcorn, but they can be very beautiful. I think it’s magic. They’re unicellular organisms and very, very simple, but their skeletons are very beautiful. They have globular chambers and when they’re alive they have spines that extend double their body size sometimes and this is what they use to catch food. They’ve got intricate shapes and beautiful colours, at least the living ones – the dead ones all look white.

Interviewer: Geoff Marsh

So, you’re looking at the foraminifera living in the ocean at the moment, seeing which species are there and then by looking at the old sediment that may have floated down 170 years ago, you’re comparing those two communities to see how the ecosystems have shifted post-industrialisation.

Interviewee: Lucas Jonkers

Exactly.

Interviewer: Geoff Marsh

You’re doing this at a global scale, right? That sounds like a massive job.

Interviewee: Lucas Jonkers

It is a massive job, but I didn’t do that work. The data compiled has been collected by generations of scientists over decades, so It is really a lot of work but I didn’t do it. I just put data together.

Interviewer: Geoff Marsh

We all stand on the shoulders of giants, Lucas.

Interviewee: Lucas Jonkers

Exactly. Yeah, I’m indebted to other people.

Interviewer: Geoff Marsh

Well, good on you for jumping in at the end and writing a Nature paper. So, when you compared these old communities to the current communities of these zooplankton, what sort of shifts came up in the data?

Interviewee: Lucas Jonkers

The first thing that we tried to do is to compare the modern communities with what’s directly on the seafloor below, and we saw that they are different. We saw that that difference is bigger in locations where the climate has been warming more. So, then we thought there might be a link with global change and then we looked at where in the sediment, where on the seafloor, do we find species communities that are most similar to what we find in the water. And then we found that in almost all cases, that the most similar sediment species community, the sort of pre-industrial community, was in a warmer area. So, this means that the modern communities represent a warmer species community than you find below them.

Interviewer: Geoff Marsh

I mean the ocean hasn’t just homogenously heated up across industrialisation has it – some parts of the ocean have got colder.

Interviewee: Lucas Jonkers

In those situations, we also saw that the planktonic foraminifera changed in a direction towards colder temperatures.

Interviewer: Geoff Marsh

Can we be sure that temperature is what’s affecting these communities because by definition almost plankton are these free-floating organisms that are kind of at the will of all sorts of variables and currents and whatnot. How confident are you that it is to do with temperature?

Interviewee: Lucas Jonkers

I am very, very confident about that. Previous studies have already demonstrated that the distribution of these foraminifera is primarily controlled by temperature, certainly on an ocean-scale, and this is also the way we can use fossil species assemblages to reconstruct temperature back in the past.

Interviewer: Geoff Marsh

Is this compositional shift benign because I understand that all sorts of plankton form the basis of the marine food chain, does it worry you?

Interviewee: Lucas Jonkers

Yes, it worries me that we are changing not only the physical state of the ocean but also the biological state of the ocean, but it’s very difficult, at the moment, to predict what those consequences exactly are. But we’re definitely changing ecological interaction networks and things in the food chain, and this puts all the studies that have a shorter timestamp into a longer-term perspective and so we now are sure that the ecosystems are different and I expect that they will keep on changing into states that we haven’t seen before.

Host: Shamini Bundell

That was Lucas Jonkers from MAREM at the University of Bremen chatting to Geoff Marsh.

Interviewer: Benjamin Thompson

The European elections begin tomorrow, giving EU citizens over the age of 18 the chance to vote on who will represent them in the European Parliament. This week, Nature is publishing a series of features, comment articles, and an editorial looking at science in Europe. Nature’s Richard Van Noorden has been overseeing the features, and he joined me in the studio where we started by chatting about how Europe is quite a different place since the last EU elections back in 2014, and about how this might be affecting science.

Interviewee: Richard Van Noorden

So, science has really benefitted from the growing integration of the European Union over the last few decades, so there’s a sense that any threats to a united Europe are threats also to scientific research. We have the parliamentary elections this week and anti-EU populist parties are expected to gain more of a foothold in the parliament. It doesn’t necessarily mean that they will be able to do much to change the EU’s direction, but we’ll see. So, we decided to write about where EU science is going in the next decade or so. Probably the main thing that everyone wants to know about is where is the next tranche of money going and what’s it going to be spent on because the European Union devotes an amazing amount of its budget to research and innovation.

Interviewer: Benjamin Thompson

Well, a lot of this funding comes from Horizon 2020, which is this big overarching kind of scheme for projects all over the EU. As its name suggests, it’s time is almost up – here we are in 2019. What’s due to be coming up to replace it in 2021?

Interviewee: Richard Van Noorden

Yeah, so although, at time of speaking, we don’t know what the parliament will look like, we do have a clue to what the next Horizon Europe, as it’s called, spending programme will look like. At the moment, it is going to be more money – €107 billion if you include a new European defence fund. There are some sort of key things that are still up for debate. One of the things that still has to be decided is whether this programme will open itself up more to countries outside of the EU. At the moment, there are also geographically nearby countries that can take part and there’s some argument about this because the countries that do best out of the current programme, well, some of them aren’t in the EU – Switzerland, Israel – so to bring in even more countries could be quite divisive.

Interviewer: Benjamin Thompson

So, still lots to decide about what Horizon Europe ends up being and how much funding it will provide, but what lessons do you think have been learnt from the outgoing Horizon 2020?

Interviewee: Richard Van Noorden

One of the problems that the European Union has is that the countries that joined the EU recently after 2004 – many of them former communist states – don’t do as well out of Horizon 2020 as the rich, western countries like Germany and France. They pay in about 9% of Horizon 2020 and they get back about 5%. Now, there’s two schools of thought on this. One is they should get more money and the other is that the Horizon framework programmes are based on excellence and if you can’t compete as effectively because your domestic governments are not interested in science then that’s too bad and it’s up to your governments to do better. Now, in Horizon Europe the same arguments continue, but the amount of money given to these EU-13 expressly to help them compete for money and be more successful, that’s tripled to €3 billion from €1 billion, and we’ll see how that goes because this debate is not going to go away and countries like Romania, Poland, Bulgaria just feel that they ought to be getting more out of this research programme than they are and they worry about brain drain and their best researchers going off to western Europe.

Interviewer: Benjamin Thompson

Well, finally Richard, on Horizon Europe – so far, we have avoided the B-word which is of course Brexit. What effect has this has on the Horizon Europe budget?

Interviewee: Richard Van Noorden

Yeah, well, basically, all these negotiations have been taking place assuming the UK isn’t there and if the UK pays in to take part, which British scientists really hope is going to happen, that will be extra on top. I mean British scientists, perhaps more than anyone, know how important the multinational programmes enabled by Horizon Europe will be and they’re all desperately hoping that they’re still part of it.

Interviewer: Benjamin Thompson

Well, you’ve mentioned it in passing, Richard, but let’s investigate it a little bit more as well. One of the features is looking at an upcoming EU funding stream for defence-related research. What do we know about this one?

Interviewee: Richard Van Noorden

Yeah, the EU is going to drastically increase its spending on military research. We don’t know the final figure but it looks like there’s going to be a chunk of €13 billion. Perhaps €4 billion of that will be for research that universities and so on might hope to take part in and the rest is procurement and this is quite controversial.

Interviewer: Benjamin Thompson

Well, I there is this kind of pushback, why is the EU sort of going ahead with this?

Interviewee: Richard Van Noorden

The origins of this is political. Essentially, following increasing tensions on the EU’s borders, Jean Claude Juncker – the EU’s commission leader – sees defence as an opportunity, a way for the EU to assert itself in the wake of Trump’s election win and the Brexit vote. Now, some of this research funding has already been paid out as a pilot scheme and we had a look at where that’s gone, and interestingly, so far, university academics have not won very much. They’ve only won less than 2% of the €44 million allocated in the last 2 years. Most of it has gone to companies and organisations and that’s quite different from the Horizon 2020 programme we’ve been talking about where Higher Education institutions win perhaps just under half the spending. So, for some reason, academics are not winning as much money and some researchers are unaware of it but some are actually avoiding it and this campaign group called Researcher for Peace that has gathered more than 1,000 signatures against this fund. The largest share has come from Germany where more than 60 universities have signed voluntary agreements not to carry out military R&D.

Interviewer: Benjamin Thompson

Well, last one from me then, Richard. Of course, the elections haven’t happened yet, nor have the negotiations for the final research budget, but in this Europe special, Nature has been looking backwards and forwards at research in Europe. Where do we think it is right now?

Interviewee: Richard Van Noorden

Yeah, so, our editorial is pointing out that European science is in a really strong position. Europe’s share of the world’s science and science spending is dwindling because China’s is expanding so fast, but it’s still extremely highly cited, it’s still extremely influential and its system of collaborative research projects is essentially unique in the world – no other block of countries collaborates to this extent. We’re arguing that there should be more money for the European Research Council – the highly competitive basic science funding agency – but beyond that, we’re saying don’t forget the benefits of stable, multi-year funding, long-term planning, collaborative research and hold fast to those strengths, essentially, against populism, nationalism or any other forces that might be driving countries apart.

Interviewer: Benjamin Thompson

That was Richard Van Noorden, Features editor here at Nature. To read all of the articles in the Europe special, head over to go.nature.com/europe and that’s all lowercase.

Host: Shamini Bundell

Later in the show, we’ll be hearing about new research looking at the neurological effects of homelessness – that’s coming up in the News Chat. Now though, it’s time for the Research Highlights, read this week by Anna Nagle.

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Anna Nagle

Ebola may have faded from the headlines, but it remains a serious public health threat. The current outbreak in the Democratic Republic of the Congo has so far claimed over 1,000 lives, with over 100 new infections reported every week. When someone’s infected with Ebola, their immune system produces antibodies to fight the disease. New research has now charted how such antibodies respond to the infection and how they change over time. Researchers studied the immune response of four people who survived an Ebola infection during the 2014 outbreak in West Africa. The team discovered that one type of antibody surged just after infection, but over the subsequent months and years, the antibody response changed. Other protective antibody groups appeared over time, perhaps responding to pockets of the virus that were hiding out in the eyes or lymph nodes. Crucially, the disease itself didn’t reappear. The research could be useful in determining whether new vaccines against Ebola are likely to work, by testing whether they trigger the same antibodies that survivors of the disease developed over time. You can find that research in Cell.

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Anna Nagle

Here at Nature, there’s a constant battle over the office thermostat. It’s always too hot or too cold for someone. So, new work to develop a wearable air conditioning system naturally caught our eye. The scientists involved used thermoelectric materials as the basis of their system. These materials pump heat from one side of the device to another, creating a cool zone and a hot zone. By adding polymer sheets to their system, the team were able to create a patch that separated the hot and cool areas from each other, allowing the heat from the hot side to dissipate into the air. Thanks to the polymer and a flexible battery pack, the patch is stretchy enough to be embedded in items of clothing and can cool skin by 10ºC. The scientists say the ultimate goal would be to combine multiple patches together to create smart clothing that provides personal heating and cooling. Try that research on for size at Science Advances.

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Host: Shamini Bundell

Next up, reporter Nick Howe has been trying to find out more about the origin of fungi.

Interviewer: Nick Howe

Fungi, or fun-ji, or even fun-gee, if you’re that way inclined, are a huge group of organisms that are probably most familiar as mushrooms or mould. They’re involved in things like breaking down dead plants or animals or, if you’re like me, your uneaten bread from a week ago. This is all part of nutrient cycling, and some scientists believe that through processes like these, fungi may have been essential to making land suitable for the very first terrestrial plants and animals. Because of this, scientists are interested to find out how and when they evolved. The molecular evidence we have suggests that fungi may be around a billion years old, but currently the oldest fossil evidence we have is only half that age, from 450-470 million years ago. But that may be all about to change, as this week in Nature, Emmanuelle Javaux and her team present a fossil fungus that may be older than those previously found… much older.

Interviewee: Emmanuelle Javaux

In this new paper, we have found an abundance of microfossils that are new. These fossils, they come from rocks that are dated between 1 billion and 900 million years ago, so this means that fungi are older than we thought and the new thing about these papers is that we have found older evidence of fungi. They are now 500 million years older than the earliest reported fossils.

Interviewer: Nick Howe

The new fossil species is a multicellular organism called Ourasphaira giraldae. Its fossil was dug out of an area called the Brock Inlier in Northwest Canada. Emmanuelle and her team believe it’s the oldest fungal fossil to date. But with a 500-million-year jump in the fossil record and 1 billion years between us and it, could it not be something else, like algae for instance? How certain is it that it’s a fungus?

Interviewee: Emmanuelle Javaux

We are very sure that they are fungi because we combined different lines of evidence.

Interviewer: Nick Howe

Emmanuelle used three main lines of evidence to make the case that these are fungi. The first was how the fossils looked (the morphology).

Interviewee: Emmanuelle Javaux

So, these microfossils, they look like small spheres that we interpreted as fungal spores. These spheres are attached to filaments and these filaments have a ‘T’ shape and they branch at right angles.

Interviewer: Nick Howe

This branching appearance is common in fungi, so Emmanuelle believes this is a good indication that it’s a fungus. The second line of evidence was the structure of the cell walls.

Interviewee: Emmanuelle Javaux

So, we cut these fossils in sections and we looked at them with electron microscopy, and this allowed to show that the walls are made of two layers with different textures and possibly different compositions. We have an external amorphous layer and an internal layer that’s made of microfibrils like in the walls of fungi.

Interviewer: Nick Howe

Fungal cell walls typically have two layers with differing structure, so that’s another tick in the ‘it’s a fungus’ column. The third bit of evidence was the presence of chitin, a large molecule that’s a component of fungal cell walls.

Interviewee: Emmanuelle Javaux

So, to analyse the composition of the organic wall of these fossils, we used a technique called infrared spectroscopy, so we can analyse one microfossil at a time and then we get spectra that are indicative of the composition of the organism and compare it with known biopolymers, and the composition of this fossil is similar to the composition of chitin.

Interviewer: Nick Howe

So, according to Emmanuelle, this fossil looks like a fungus, it’s got a cell wall like a fungus and it has a similar composition to a fungus. Just one of these aspects would not be enough to declare Ourasphaira giraldae definitively a fungus but combined, Emmanuelle believes it makes a strong case. However, Christine Streullu-Derrien, who studies fossil fungi but wasn’t associated with this study, is not convinced.

Interviewee: Christine Streullu-Derrien

I cannot say for sure that it is a fungus with what they present.

Interviewer: Nick Howe

The main concern Christine has is with the detection of chitin.

Interviewee: Christine Streullu-Derrien

Chitin is known as being very highly biodegradable and so for me, it’s a bit difficult to think that you can have a signal so close to the modern chitin.

Interviewer: Nick Howe

With this fossil being 1 billion years old and chitin being so readily degraded, Christine thinks it’s unlikely there would be any chitin left to detect today. Without the detection of chitin, she thinks the remaining evidence is insufficient to conclude this is a fungus. More would need to be done to convince her.

Interviewee: Christine Streullu-Derrien

I think they should have done other chemical analyses because there are other chemical analyses that you can perform on this kind of preservation, so they could have tried other methods to compare if they get from the other methods the same results.

Interviewer: Nick Howe

If this fossil is confirmed to be a fungus, it could change our understanding of the story of the evolution of fungi. For one thing, it would mean that multicellularity in fungi emerged way before currently thought. It could also change our understanding of early terrestrial life. This new fossil certainly doesn’t have all the answers, but the question of the first fungi is one that Christine thinks it’s important to explore.

Interviewee: Christine Streullu-Derrien

It is important to know the origin, to know it and understand how they have been able to reach the land and in what way they adapted for the colonisation of land and they are so important in land today. They are associated with plants, with animals, with Earth. They have so many roles in nature today so it is important to know the beginning of the story and we have a lot of gaps to fill.

Host: Shamini Bundell

That was Christine Streullu-Derrien from the Natural History Museum in London. You also heard from Emmanuelle Javaux who’s at the University of Liège in Belgium. You can find Emmanuelle’s paper over at nature.com.

Interviewer: Benjamin Thompson

Well, our show ends, as always, with the News Chat and I’m joined here in the studio by Flora Graham, Nature’s Briefing editor. Flora, hi!

Interviewee: Flora Graham

Hi.

Interviewer: Benjamin Thompson

For our first story today, we’re going to head over to California where researchers are about to start looking at some of the health effects of homelessness.

Interviewee: Flora Graham

That’s right. A new study that’s launching from the University of California, San Francisco is specifically looking at neurological disorders and how they seem to happen more quickly in older homeless people.

Interviewer: Benjamin Thompson

And what sort of things are the researchers going to be looking for?

Interviewee: Flora Graham

The study is going to look for signs of debilitating brain conditions, like dementia, in the frontal and temporal lobes, and it’s going to look at at least 20 homeless adults, and this ties into existing work which looks at the fact that homeless people seem to age almost in hyper-speed. So, conditions like strokes and falls and visual impairments – they seem to appear much younger in older adults who are homeless rather than in the general population.

Interviewer: Benjamin Thompson

So, I guess that homeless people face a number of factors that could contribute to neurological issues, and so this is the interplay that the researchers are looking at. What’s the homeless situation like in San Francisco where the researchers are based?

Interviewee: Flora Graham

Well, homelessness is on the rise in the United States in general, and the problem in California is particularly acute. In the San Francisco Bay area, over 28,000 people are homeless.

Interviewer: Benjamin Thompson

So, some quite staggering numbers then and as you say, this research has just started, but what are the kind of long-term goals then for the researchers?

Interviewee: Flora Graham

Of course, the goal is to help health outcomes improve for homeless people, specifically older homeless people, but also to ensure that the interventions are more efficient and hopefully save taxpayers some money.

Interviewer: Benjamin Thompson

What about those running the study? What are they saying?

Interviewee: Flora Graham

Well, it’s interesting to note that Serggio Lanata, the neurologist leading the research, says that neurological issues might have contributed to putting people on the street in the first place. He says that some of the patients he looks at, if they didn’t have strong family support, would have ended up homeless since no one could or would care for them.

Interviewer: Benjamin Thompson

Well, let’s move on to our second story, Flora, and we’re revisiting the CRISPR embryo editing news that broke in November last year and centred on the Chinese researcher, He Jiankui's, very controversial work. What’s the update on this one?

Interviewee: Flora Graham

Yes, it looks like China is going to be introducing new regulations to restrict gene editing in humans, and this seems to be a direct response to what happened with these CRISPR babies.

Interviewer: Benjamin Thompson

And what are the specifics of these regulations?

Interviewee: Flora GrahamSo, this is the country’s civil code, the overarching legal framework that governs non-criminal disputes like marriage, inheritance, personal rights, and a draft of the new civil code lists human genes and embryos in a section on personality rights to be protected. So, experiments on genes in adults or embryos that endanger human life or violate ethical norms can be seen as a violation of a person’s fundamental rights.

Interviewer: Benjamin Thompson

As I remember, no one was really sure at the time whether He had actually broken any laws. I guess this makes things clearer?

Interviewee: Flora Graham

That was definitely an outstanding question. The outcry was huge, the controversy was worldwide, but the question remained: was it illegal, what he actually did? Now, Zhang Peng, who’s a criminal-law scholar in China says that, “now the law makes clear that those who do research with human genes and embryos cannot endanger human health or violate ethics.”

Interviewer: Benjamin Thompson

Finally on this one, I imagine these regulations are meant to put off any other researchers who might be considering repeating similar embryo editing in the future?

Interviewee: Flora Graham

Indeed. If someone is looking to do this research in China, they could be strongly dissuaded by these new regulations. They would be responsible for any negative consequences once those babies were born and grow up.

Interviewer: Benjamin Thompson

Well, Flora, thank you for joining me today. Listeners, head over to nature.com/news for more on these stories, and head over to nature.com/briefing to sign up for a daily dose of science.

Host: Shamini Bundell

That’s all for this week’s show. If you’ve enjoyed it, please do spread the word. I’m Shamini Bundell.

Host: Benjamin Thompson

And I’m Benjamin Thompson. Thanks for listening.