Nature Podcast 12 July 2007
Introduction
This is a transcript of the 12th July edition of the weekly Nature Podcast. Audio files for the current show and archive episodes can be accessed from the Nature Podcast index page (http://www.nature.com/nature/podcast), which also contains details on how to subscribe to the Nature Podcast for FREE, and has troubleshooting top-tips. Send us your feedback to mailto:podcast@nature.com.
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Chris Smith: This week while there could be trouble brewing at sea because climate change is triggering estuaries to alter the way they handle nitrogen.
Robinson Fulweiler: If this process that we measured here in this estuary is happening in other places, then that means that the sediments are actually able to produce large amounts of nitrogen and that could have pretty big consequences for offshore systems.
Chris Smith: So stormy waters ahead. Robinson Fulweiler who will be talking to you shortly. Also this week, with a powerful new toy for geneticists to play with.
Barry J. Dickson: We have generated a resource for systematically inactivating single genes in the fly in specific cells or tissues. So you can study much more complex phenomena that the whole animal does, not just single cells.
Chris Smith: And its not quite life on Mars, but this is a step in the right direction. The detection of the liquid of life on planets outside the Solar System.
Giovanna Tinetti: This is the first time that we can say with a little bit of security that we find water on an extra-solar planet.
Chris Smith: Giovanna Tinetti! She will be wetting our appetites with that discovery later on in the program. Hello, you are listening to the Nature Podcast. I am Chris Smith. First this week, to the place where rivers flow into the sea - estuaries. They're very important because they remove nitrogen compounds that have washed into rivers from farmland. The nitrogen gets turned back into gas by microbes and then floats off into the atmosphere. Without this filtering effects, the sea would receive a much greater dose of nitrogen which could have serious consequences for marine life, but now Robinson Fulweiler who has been studying the waters around Rhode Island has found that things might be about to change and it could be down to the climate. Nature 448, 180–182 (12 July 2007)
Robinson Fulweiler: We are interested in how nitrogen cycles in coastal marine systems because nitrogen comes into these systems through a variety of ways namely from people, waste water discharge or fertilizer runoff that kind of thing and there is a process called Denitrification and that's where bacteria actually can remove biologically usable forms of nitrogen and turn it into a gas and that's a cleansing mechanism that is sort of built in the estuary and in fact Denitrification is found in fresh water systems and on plants, so it's a very common process. So we set out to measure that and we noticed that their rates have become lower over time compared to late 1970s and the early 1990s.
Chris Smith: So Robinson, how are you measuring the amount of Denitrification that was going on? What was the sort of study model?
Robinson Fulweiler: We actually can collect sediments throughout the estuary and bring it back to the Graduate School of Oceanography where we do incubation and then we can actually collect water samples and from that water samples we can extract the dissolved gases and then on a membrane inlet mass spectrometer we can measure how the concentrations of gas and the water change over time.
Chris Smith: And what you found is that the amount of nitrogen that was liberated in the 70s was much greater than the amount that is being liberated today?
Robinson Fulweiler: Exactly! And then in the summer of 2006, we actually found the opposite process, so instead of having N2 gas liberated, the gas from the atmosphere which was dissolved in the water and then the bacteria was actually putting it into their biomass, that's called nitrogen fixation.
Chris Smith: So what's going on? You have had this decline year-on-year for a long while then suddenly it flips and does something strange? Why?
Robinson Fulweiler: Well our working hypothesis here is that the amount of organic matter that is reaching the sediments has declined over that same period. For an estuary which are relatively shallow, the phytoplankton or organic matter produced in the surface water falls to the bottom and that provides food for the bottom community and so what we can see is that standing crop of phytoplankton in this past 30 years has been declining steadily.
Chris Smith: And is that bottom community that liberates the nitrogen?
Robinson Fulweiler: Yes exactly!
Chris Smith: And so if you don't feed them, what's the consequence?
Robinson Fulweiler: It appears that when you do not give them the organic matter, then a new type of bacteria are becoming dominant and those are those nitrogen-fixing bacteria. So instead of having bacteria that actually cleanse the water off nitrogen we have bacteria that are taking nitrogen and bringing it into the system and if this process that we measured here in this estuary is happening in other places, then that means that the sediments who we once thought were these filters, are actually able to produce large amounts of nitrogen and that could have pretty big consequences for offshore system.
Chris Smith: Do you know what triggered this sudden change?
Robinson Fulweiler: Well we think that this decline in the organic matter production is linked to climate change. So there is a couple of different hypothesis, one is that warmer waters allow increased grazing, so microscopic organisms that eat the phytoplankton could be around longer throughout the year and they also might be feeding more because the surface waters are warmer. The alternative hypothesis is that with warmer winters we have more cloudy days and a lot of research has shown that the onset of the winter spring phytoplankton bloom is triggered by the amount of light that they get, so if they are getting in less light then that could be a reason why we are not getting the sort of bloom that we used to get.
Chris Smith: Rhode Island University's Robinson Fulweiler who has found that lack of plankton leads to a switch in the microbial community towards organisms that add nitrogen compounds to water rather than taking them away. Well, from bacteria to flies now and Barry Dickson who has created a library of genetic constructs that can be used to turn off virtually any gene in the fruit fly genome. Previously, when a gene was knocked out to study its effects, the whole organism is affected, which made it difficult to work out what the gene was doing because there was so many other knock-on effects through out the body. The beauty of this new system is that it can be turned on and off just in specific cells and tissues, using a pretty messenger called Gal4. Nature 448, 151–156 (12 July 2007)
Barry J. Dickson: We have generated a resource for systematically inactivating single genes in the fly in specific cells or tissues and it uses something called an RNAi transgene, which expresses an agent, a double-stranded RNA that triggers degradation of another message RNA, so it specifically interferes with another gene. So the whole point of it is you can selectively disrupt the gene in single cells or single tissues in the intact organism and so you can study much more complex phenomena that the whole animal does, not just single cells.
Chris Smith: So how you basically got the entire genome of the fly represented in this big library you have put together?
Barry J. Dickson: Yes, with 88% of protein-coding genes.
Chris Smith: So if I had a gene, which I wanted to switch off in a particular tissue, you could do that?
Barry J. Dickson: You could do that. You could order from us now or through this the Vienna Drosophila RNAi Centre, The VDRC. You could order one of our lines, cross it to whatever reagent you have to drive the expression of it in your cells and your tissues and then look to see what the phenotype is.
Chris Smith: So say I was in receipt of one of your lines, how would I actually deploy that in a living fly in order to see what the fly would look like when I used it?
Barry J. Dickson: Right! You need to have a driver line, which will express something called Gal4. It's a yeast transcriptional activator in your cells, so you have to have that. Now you order from us a transgene that will respond to Gal4 to trigger RNAi then in those cells and it's only when you cross these two together that you get the RNAi effect.
Chris Smith: Can you turn it on and off at will, so that you can see a tissue at different times during this development?
Barry J. Dickson: Exactly! You can turn it on first of all in any cells in which you have one of these Gal4 lines and there are reagents available where you can also turn it off using a repressor of the Gal4 that is itself self-conditional.
Chris Smith: So, if I wanted to turn off one particular cluster of nerve cells, how am I going to do that? How do I make sure that this only works in just that specific cluster of nerve cells?
Barry J. Dickson: Right! That's basically your problem. So, you need to have a promoter fragment that would drive expressions specifically in those cells.
Chris Smith: So you've kind of solved half the problem, but I've still got a problem trying to work at how to make sure I can strain the effect of what you have invented, just to the tissue I wanted to study.
Barry J. Dickson: Correct, but you have been studying that tissue for years and you have lots of reagents to drive transgenes in those cells and in flies there is an enormous number of these Gal4 lines out there to target basically any tissue you want. So this has not been the limiting problem usually. What has been lacking is the way to systematically disrupt gene function in those cells.
Chris Smith: So what would you say the major power of this technology is? Where is its real strength lie?
Barry J. Dickson: Yeah, the major power of this is clearly in being able to systematically disrupt gene function in any tissue of interest. So now you can do genetic screens, where you target the gene inactivation to the cells that you think are most relevant for that particular function and so it will most powerfully be used in genetic screens where you can systemically go through the whole library or may be that's just a clause of genes that you are interested in and just screen those looking for new genes that have some relevance for the process you are interested in.
Chris Smith: Barry Dickson is at the IMP in Vienna.
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Chris Smith: Coming up shortly, we'll be exploring the importance of biodiversity to maintaining a productive ecosystem and finding out why 250 million years ago nearly every animal on Earth became extinct, but who were the survivors and why? First though to outer space and the first confirmed discovery of water on an extrasolar planet. Giovanna Tinetti has used the Spitzer space telescope to look at the distant planet HD189733b. Nature 448, 169–171 (12 July 2007)
Giovanna Tinetti: This is the first time that we can say with a little bit of security that we find water on an extrasolar planet.
Chris Smith: So what has clinched it for you? What means that you can say with certainty there is water on this planet where previous publications couldn't do that?
Giovanna Tinetti: Well it's just a method we used that just seems to be more reliable. The other measurements were actually using the Hubble space telescope, unfortunately on a particular wavelength range where the spectrum could actually contain some problem with the measurements.
Chris Smith: So lot of electrical noise or lot of optical noise?
Giovanna Tinetti: Exactly! There was some noise in the instrument. So again there is this possibility that water was already there, but again you cannot say with being 100% sure and in our paper we are trying to explain why they couldn't have seen with that particular method and measure water, even if water were there.
Chris Smith: So what have you actually done to nail the problem and where have you found water?
Giovanna Tinetti: Well first of all we have found water on a so called hot Jupiter, which means a class of objects, which are giant planets that which are orbiting very close to their parent stars, so we are talking about gas giants that are very hot. We have measured the transit of the planet, so while the planet is passing in front of its parent's star in three different wavelengths in the infrared. Now if you look at the signature of water in the infrared, then you can find out that water has a very distinctive signature and so that's why by comparing this three different measurements you can say that water is there.
Chris Smith: So the only rational choice has to be water in the atmosphere of this hot Jupiter.
Giovanna Tinetti: It was already predicted in a certain sense by photochemical models. Chang Liang and Yuk Yung which are coauthors to this paper made this photochemical model a couple of years ago predicting that this sort of planet should have unknown negligible quantity of water in their atmosphere.
Chris Smith: So what would you say the bottom line is here? This is a proof of principle. This means you can prove you can now do it this way, therefore it should be possible to apply the same technique elsewhere in the universe.
Giovanna Tinetti: That's absolutely correct. Certainly this particular technique works perfectly for these types of objects. For other types of objects my work might not be the best method to use.
Chris Smith: So, you wouldn't find another example of the Earth for example.
Giovanna Tinetti: Well for another example of the Earth if you do some simulation and we did actually, it turns out that the atmosphere of an Earth's planet is more compact so it's a little bit more difficult to use this method to look for the signs of water, but again there are several type of objects out there, so at least we know that this method can be very useful for a part of those.
Chris Smith: UCL's Giovanna Tinetti who studied the extrasolar planet HD189733B using 3 infrared wavelengths chosen specifically to pick up the characteristic spectroscopic fingerprints of water. Well returning to Earth now, how significant is biodiversity to the big ecosystem picture. In other words, if you look at individual ecosystems in isolation, there are some species that seem to be redundant. It looks like we could even do without them, but that's a big mistake, because Andy Hector has now looked at the contribution of these different species as a whole rather than in isolation and found out that they are actually quite critical. Nature 448, 188–190 (12 July 2007)
Andy Hector: I am interested in whether biodiversity is important for how environments function and whether when we lose biodiversity, ecosystems might function less well. In the past, people have been interested in biodiversity for its own sake, but the ongoing loss of biodiversity, which is forecast to continue for at least the next century, protocologists in the 1990s thinking whether levels of biodiversity could get so low that they might have detrimental effects on this functioning of ecosystem.
Chris Smith: So what you'd would see is a sort of ecosystems collapse because this dense network of things all relying on each other just shrinks to a level where there aren't enough interconnections to sustain it.
Andy Hector: Yeah! Well collapse might be a bit dramatic, although it could occur I suppose in some cases, but it could also be the way of seeing a slow but ongoing erosion of biodiversity and that might not lead to collapse of whole ecosystems but it might gradually reduce the way that they function.
Chris Smith: So what have you actually done to try and get a handle on how these dense networks actually do interact with each other?
Andy Hector: We have done research looking at the relationship between biodiversity and ecosystem functioning, so things like how productive the ecosystems are and what we found is that productivity and so on is positively related to biodiversity, but generally in a sort of saturating way. What that implies is that some of the biodiversity in the system may be redundant as far as the way that the ecosystem functions.
Chris Smith: Is that sort of like an insurance policy? You know that you have got that level of safety, so if you lose a bit you still are going to cope okay.
Andy Hector: Yeah that's right. There is two ways of looking at redundancy, the sort of negative connotation of the word is that something you say, useless, but the positive side of it is that it may function like a backup system. So for example the space shuttle has a completely separated computer system, so that if the primary computer goes out the secondary one can kick in and obviously when you are talking about system that your existence depends on as ours depends on the planet then you would want that redundancy built in really. So what we have done with this new research is that go back to our old data and sort of say well, we have measured all these ways in which ecosystems function and we looked at them one at a time, but what we really wanted to do was to look at how biodiversity affected the functioning of the ecosystems as a whole to put all of these processes together in the same analysis. So what we did is we took 7 measurements of ecosystem services we had made in European Grassland Systems and an ecosystem service has some benefit that humans derive from the environment. So for each service at each field site, we then identified the set of species that affected each service and then all we really wanted to know was if the group or the sets of species that is important for one service is the same that is important for the other ecosystems services too.
Chris Smith: And what did you find. Do you find that there is a gross overlap between these different things or are each of these ecosystems highly individual?
Andy Hector: What we did first is to look at each pair of ecosystem services and to say how much the groups of species that affect each service overlap and what we found was that the proportion of species each pair of services shared in common was only about a fifth to a half.
Chris Smith: That's quite small, what about when you looked at more than just pairs.
Andy Hector: That's what we did next. We gradually worked our way through all possible combinations of all the ecosystem processes we had measured and simply tossed it up the number of species needed to provide any combination of two, any combination of three and so on and what we found was that as we took more ecosystem services into our analysis, we needed greater range of biodiversity to provide those services.
Chris Smith: Well that's called striking isn't it, so what this says in terms of the big picture is if you got an ecosystem on the scale of whole world, then its very, very rich and therefore in order to have the kind of outputs that we derive from it, we are going to have to maintain a very broad biodiversity because if we don't, then we are going to start losing things.
Andy Hector: Yeah! I guess the implications of the research are that in science, we often have to take a fairly reductionist view point, so we have to focus in on one aspect of the problem and what our new analysis suggests that by doing that we might have underestimated the levels of biodiversity needed to keep an ecosystem fully functional if you like.
Chris Smith: Zurich University's Andy Hector on why it's important to see the big picture especially when it comes to biodiversity.
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Chris Smith: And to finish this week, fire brimstone, a mass extinction, here is Kerri Smith.
Kerri Smith: It is a murder mystery on most massive of scales, 250 million years ago, at the end of the Permian period, almost all life on Earth went extinct, whether your land dwelling animal, a fish, and insects or even a plant, the chances are your species did not survive, but what could have been responsible for this great die off. Here in the studio with me, to hazard some guesses is Nick Lane of University College of London. He has written a feature about it for Nature. Hi Nick! Nature 448, 122–125 (12 July 2007)
Nick Lane: Hello!
Kerri Smith: I wonder if you can set the scene for us first of all what was the Earth actually like 250 million years ago.
Nick Lane: Well in the period building up to that, it had been certainly on land almost an iconic period. There had been giant dragonflies and things, giant millipedes, all kinds of gigantism in the period right before it, in the carboniferous times, which is unexplained actually, but is perhaps related to very high oxygen levels at that time and really a great abundance of life complicated, complex life on land. In the seas, these ecosystem seemed to be rather simpler and they were split roughly fifty-fifty between quite simple systems with things like brachiopods with shells, organisms and various stalked filter-feeders evolved so after and then more complex animals like trilobites and so on which had been around for 250 million, 300 million years at that point, but were beginning to die back for some reason which again is unknown.
Kerri Smith: And then all of a sudden 251 million years ago, something happened to kill off up to 96% of all these species that had then been alive. Now there are quite a few scientists turned detectives looking for the culprit of all of this. What kind of theories abound us to what could have possibly happened at this time.
Nick Lane: The single biggest idea now relates to volcanism at the time, one of the largest eruptions of basalt flowing across the surface of the ground was the Siberian traps and that was dated a few years ago to exactly the same time as the main extinction, so that seems to be the trigger that caused the death. The question then is what actually, why does volcanism of that kind cause death on this scale that it's actually seen. It could be for example, it throws a lot of ash and so on up into the atmosphere causing some kind of a volcanic winter equivalent to a nuclear winter, but that doesn't seem likely to have wiped out life for example in the seas necessarily or to account for the kinds of patterns that are actually seen. The more convincing interpretation relates to carbon dioxide pumped into the atmosphere, which could lead to global warming and again exactly how global warming kills everything off has been squabbled about and it suffices something which is very pertinent to our own times today.
Kerri Smith: Well! Whichever of that theory is, I suppose, turns out to be true it is looking out in a pretty scary place. Let us look on the bright side for a minute, 96% of things died that means we've got you know roughly 4% of species actually managing to survive that extinction and eventually re-conquer the Earth. What made these lucky few so resilient?
Nick Lane: Well! it's a very interesting characteristic that they all seem to share in common which is related to the way in which they breathe and there is two other factors I didn't just mention. Now one of them is that the volcanic traps exploded through coal fields and so would have produced a lot more methane. That way perhaps far more than could have been produced from the bottom of the sea, and the other factor is that model suggest that oxygen levels have been falling from this high point in the carboniferous period 50 million years before to an extreme low point at the end of the Permian. Now it is difficult to argue that the low oxygen levels in themselves cause the extinction but in that context, that we were fairly sure that the oxygen levels had really troughed at a low point really in the whole history of the last 500 million years. Yet the animals that survived, all seem to have sophisticated respiratory systems, they are all good at breathing, they all have gills if they are in the sea or they have quite a sophisticated diaphragm for example, nasal bones to cut off the nose from the mouth and so on which enables breathing and eating through different cavities inside, so they were all sophisticated breathers.
Kerri Smith: So the consensus from all of this seems to be then that more complex life forms were surviving to a much better degree than simpler forms. What were some these creatures have actually looked like?
Nick Lane: Well on land the iconic survivor was Lystrosaurus, which was cynodonts which is one of the earliest ancestors of today's mammals. That was a moderately large animal about the size of a badger all there about, perhaps a little larger. It had a kind of a barrel chest and rather a squat face. It may have been a burrower. There are examples of fossil burrows with the Lystrosaurus at the end of it, so no body is quite certain, but it looks as if its breathing was related to being a burrower. Otherwise the Archegosaurus evolved around about that time. They were the ancestors of today's crocodiles; they were the ancestors of the dinosaurs as well and so as crocodiles and the birds of today's survivors from that period. They also have an air sac system for breathing. It's a very sophisticated way of structuring the lungs. As we breathe, we breathe air in and then have to blow it out again and so you have dead end in the mammalian lung. Within the bird lungs they have a continuous throughflow, it is almost like a one-way system, and that's a very efficient way of breathing. And again exactly when they evolved is uncertain, but right at the end of the Permian, right at the beginning of the Triassic, during this period it might well be that this air sac system of breathing was what enabled to them to survive the conditions and enables you know geese and so on to migrate to very high altitudes today.
Kerri Smith: So among the survivors, mammals with squat faces and barrel chests; it sounds a bit like some of my relatives. Looking to the future, now how often do these kind of mass extinctions happen? Should we be scared, we are going to be in the middle of one soon?
Nick Lane: Well one of the most interesting aspects of the Permian extinction is how similar many of the factors are to what's happening today with global warming. I have mentioned pumping methane into the atmosphere and pumping carbon dioxide into the atmosphere, perhaps one of the reasons why that was so is because the volcanoes exploded through coal fields leading to really rather high levels of carbon dioxide and methane. But it seems that the problems is less, the overall magnitude than the speed of change and this is a problem which inflicts us today is not, I mean, the overall carbon dioxide levels were much higher than they are today but the speed of change was rather comparable. The other aspect, which is really very relevant to us today, is the way in which the ocean system and the atmospheric systems tend to work in concerts. So once you have falling oxygen levels and rising carbon dioxide levels and so on and you have some degree of global warming, then it tends to perpetuate itself because oxygen solubility in water for example is less as temperatures rise, metabolic rates also go up as temperatures rise, so in the oceans you have a situation whereby a lot of animals are effectively suffocating even just as a result of a small rise in temperature and that's happening today there being plenty of studies showing that fish population for example changed over time according to oxygen solubility in the water which is related to the global temperature of a particular year.
Chris Smith: UCL's Nick Lane talking with Kerri Smith and you can read Nick's feature in this week's edition of Nature. Well that's it for this week's podcast, but do join me next time when I'll be getting stuck into a gecko and spide adhesive. For more science in the meantime, you can also join me for this week's edition of the naked scientist, in which we find out what causes out of body experiences? Why yawns are contagious? What triggers epilepsy and the basis of bipolar disorder. There is also news that jelly fish might hold the key to looking young and beautiful even if you do smell slightly dubious. That's the naked scientist podcast and it's free from the http://www.nakedscientist.com. Production this week is by Azi Khatiri and I am Chris Smith. Thanks for listening, see you next time.
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