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Chris Smith: This week watching water from s___e. We'll be hearing how a satellite is helping scientists to re-draw the hydrological cycle.

David Noone: What this shows is the way that water moves around in the climate system, particularly the atmosphere. We can differentiate between land and ocean sources, as well as importantly understanding cloud processes and how perhaps they might feed into climate and climate change.

Chris Smith: More from David Noone coming up shortly. Also, how bacteria make friends and influence each other, and they may even evolve in the process.

Paul Rainey: What we found here are two organisms that have never met before and yet, within a remarkably short s___e of time, one organism has in fact adapted to the presence of another.

Chris Smith: And is the scientific equivalent of a SWAT team the answer to conserving the Amazon?

Tom Hayden: The idea of this expedition is to get a group of very knowledgeable scientists into the area for a rapid survey so that they can go in and get a quick sense of what the area's actually like.

Chris Smith: Tom Hayden joins us later to describe what happened when he dropped into an isolated mountainous spot in the Peruvian Amazon. Hello, I'm Chris Smith and welcome to this week's Nature Podcast. First up this week, we're getting immersed in the hydrological cycle because scientists have flushed out new data on how water moves around the planet. David Noone and his team have used an infrared spectrometer mounted on an orbiting satellite to study the atmosphere for water vapour containing either hydrogen or its slightly heavier relative, deuterium. Because we know the isotopic composition of the ocean, using this technique water vapour coming from the sea can be distinguished from water that's taken a more circuitous route through the atmosphere, and this has given the team a much clearer picture of what the water cycle really involves. Nature 445, 528-532 (1 February 2007)

David Noone: We're really interested in understanding the movement of water through the atmosphere, that's movement from the region of evaporation where the water comes from, the transport of water through the atmosphere, and then ultimately the loss of water from the atmosphere by precipitation and condensation processes. Some of the things we're finding is, surprisingly, that a lot of water in the atmosphere, in the free troposphere, has come from overland masses, which is surprising in that the ocean is clearly very wet - yet it's over the land regions where we're seeing a lot of the water getting into the atmosphere.

Chris Smith: So where's that coming from then? Trees, plants, that kind of thing?

David Noone: It is in part. There's perhaps two ways that water can get into the free troposphere over the land. One is directly from the plant. The transportation of the plants in particular has a very unique isotope signal that we can differentiate from the ocean. What that means is that we can figure out what fraction of the water in the atmosphere has come from the ocean versus from, say, the plants. The implication there is actually quite important, that if we change the number of plants, particularly forests, say, over land masses, the way the water gets into the atmosphere will also likely change. It'll come more directly from the ocean perhaps than over the land surfaces out of the plant system.

Chris Smith: Are you already seeing any manifestations of deforestation in, say, the Amazon, the amount of trees that have been lost there in the last X number of years, are there any signs of that?

David Noone: Well, we don't actually see changes in the forests in our measurements at the moment. What we can say is that there is a substantial fraction, or non-trivial fraction at least, of the water that gets into the atmosphere through terrestrial processes. Based on our measurements now, we have a snapshot telling us how the atmosphere behaves presently. If we continue these measurements in a monitoring sense, we can actually understand exactly your question there, how does changes in the forest and the amount of forest change the hydrologic cycle?

Chris Smith: Now when I was at school, they used to show us the water cycle as this big circle with a cloud and some land and some sea. So given what you've now done, how would we have to rewrite that cycle and change it?

David Noone: Well, what we've learned is some of the starting and ending points for those arrows on that diagram, we now know a lot more information. One interesting result that we find is that the evaporation of rain falling beneath the clouds is important. Typically, in the tropics about 20% of the rain that falls from the bottom of clouds evaporates before it hits the ground. In some cases it's more like 50%. This is really quite interesting because it's telling us that the way the water is recycled by the cloud systems: I think an idea that comes to mind immediately is some kind of engine that continually uses the cycle of condensation within the cloud and evaporation below the cloud as efficiently moving energy and heat in the atmosphere. This actually prompts an exciting new direction for our studies, thinking about the role of water in the energy of the tropical climate, details of those cloud processes are important. It plays directly into the radiative balances of the Earth and certainly something that's changing with climate change. So understanding those cloud processes is key to understanding climate and climate change.

Chris Smith: David Noone from the University of Colorado, with a much clearer picture of what constitutes the hydrological cycle. In a second, we'll be parachuting into a remote part of the Amazon Rainforest, but first to the microscopic world of the bacterial biofilm. These are mixtures of microbes that co-exist in complex communities, but how they evolve and develop isn't well understood. To find out, Auckland University's Paul Rainey has simplified matters. He introduced two bacterial species that had never met and then fed them something that only one of the two could eat. To survive, the other species of bacteria, which were a type of Pseudomonas, had to depend on metabolites produced by the first, which was an Acinetobacter. Initially, these dependent bacteria kept their distance, but after a very short time things began to change. Nature 445, 533-536 (1 February 2007)

Paul Rainey: We've taken two organisms that we know will grow together on a surface. We provide these two bacteria, Acinetobacter and Pseudomonas putida, with a single carbon source, benzyl alcohol. Only Acinetobacter can utilise benzyl alcohol but it excretes benzoate, which can be utilised by Pseudomonas putida. So what we have here is a two-species community where the activities of one organism are required for the presence of another.

Chris Smith: And if you look at this down the microscope to see how the two are interacting spatially, what do you see?

Paul Rainey: Well, it's quite striking. If one looks at this over a series of 24-hour periods, the interactions change remarkably. What we see looking down the microscope after 24 hours are discrete colonies of Acinetobacter surrounded at some distance by diffuse cells of Pseudomonas putida. Now, this is something of a surprise because Pseudomonas putida, remember, is utterly dependent on Acinetobacter, so it would pay to be as close as possible to Acinetobacter and thus maximise the availability of carbon source. Now, as one looks in successive 24-hour periods, what one finds is a marked shift in the physical structure of this community. It changes so that the commensal grows as a mantle directly over the top of the host species, Acinetobacter.

Chris Smith: So why do you see that happening? Why initially is the Pseudomonas at a distance from the Acinetobacter, the host? And then over time it creeps up closer to it?

Paul Rainey: In the first instance, Pseudomonas putida has within its genome a propensity to detach and leave a surface in response to low-oxygen conditions. The growth of Acinetobacter decreases the oxygen in the immediate vicinity of the colonies and this causes Pseudomonas to leave, so even though we might think that it would be smart for Pseudomonas to grow over the top of Acinetobacter, it in fact leaves because of this oxygen-dependent detachment programme.

Chris Smith: So something pretty special's happening, which means that it must be evolving to gain the ability to get (a) a lot closer, and also to be able to tolerate very low oxygen tension in the vicinity of the host, the Acinetobacter.

Paul Rainey: Exactly. Now, what is happening, it's a single mutation, single nucleotide change, which results in Pseudomonas putida becoming more sticky on its outside. In fact, there seems to be some a__ociation or some attraction between this new outer-membrane glue, as a result of this mutation of Pseudomonas putida, and Acinetobacter, so in fact it adapts specifically to the presence of Acinetobacter and doesn't become more generally sticky to the surface. So we have an instance of adaptive evolution driven by very simple genetic changes, which results in one species forming a very different a__ociation, in this case with its host species.

Chris Smith: Paul Rainey with new insights into how the microbial communities in a biofilm evolve and develop.

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Chris Smith: On the way, how physicists have created a virtual atom on the equivalent of a computer chip enabling the quantum information in a single photon to be read and transmitted. First, though, it's time to join Nature's Alex Witze, who caught up Tom Hayden to hear how he dropped into the Peruvian jungle to rendezvous with a group of scientists who act, as Alex puts it, like the ecological equivalent of a SWAT team. Nature 445, 481-483 (1 February 2007)

Tom Hayden: The idea is that there are large parts of the Amazon jungle that are still essentially unexplored by scientists, so the idea of this expedition is to first of all identify areas that have not previously been studied and that have the potential for being areas of high numbers of endemic species that aren't found anywhere else and high levels of biodiversity, and also areas that have the potential politically to be protected or conserved in some way. And the idea is to get a group of very knowledgeable scientists into the area for a rapid survey so that they can go in and get a quick sense of what the area's actually like.

Alex Witze: So what kinds of animals did you see? I mean are a lot of these sort of charismatic megafauna, like jaguars and stuff like that? Is it lots and lots of frogs and insects?

Tom Hayden: Well, there are all kinds of insects, for sure. You can't go into the Amazon without getting bitten and scratched and jabbed by all sorts of things that'll make you swell up in interesting ways. But in terms of the charismatic megafauna, I actually famously saw a lot less than the biologists. It turns out that my childhood experiences as a cub scout weren't quite enough to make me silent in the jungle to see the jaguars and a lot of the monkeys, but fortunately the scientists were better at it than I was. They used techniques like camera trapping to document the presence of jaguars and tapirs and 12 different primate species.

Alex Witze: So a lot of the discussion about conservation in some of these remote areas has been how much and how to get the locals involved in sort of long-term conservation projects - not only realising the wealth of what they have there but how to preserve it. What kind of local involvement is there in this project in this area?

Tom Hayden: Well, that is a critical part of the programme and of conservation generally. People are finally realising that you can't just declare an area a protected park and leave it alone and hope for the best. So the team I was with focuses very heavily, right from the planning stages, on collaborating with the local government, of course, but also with a large number of non-governmental organisations such as conservation groups, as well as with the groups who live in the area, who oftentimes live off of the resources of the area, and their participation is what's going to make or break any conservation in the long term. So they work in collaboration with local scientists, they solicit the help of local communities to get their input on, you know, what's important to them, what they would like to see protected, as well as what resources they use and how that resource use might be made sustainable into the future.

Alex Witze: So tell us a little bit about the market though, I understand that at the local market you can get all sorts of endangered and threatened species and things that really ought to be protected but aren't. What sorts of things did you see for sale there?

Tom Hayden: The scene in the market is remarkable. There are large, large numbers of people who have been settled into the area with very little rational economic development, so they're busy trying to make a living from the jungle any way they can, and that includes everything from harvesting palm fruits and various medicinal saps and barks and that sort of thing, through to harvesting the animals that live in the area. There's lots of bush meat for sale, peccaries and tapirs, and that sort of thing, all of which are present in considerable bounty in the market in Pucallpa today but without protection will disappear, just as they have in other parts of the Amazon.

Alex Witze: So it sounds like there's a lot of work that's still to be done. What's been the outcome then of this rapid biological survey that you talk about in your piece? Have they had much success in getting the area declared protected, reserved, in any sense of the word?

Tom Hayden: They have had actually quite remarkable success. Over the last six years they've managed to get something on the order of 9 million hectares of land in Peru, Bolivia and Ecuador, into official protected status, and an equal area is on its way because of their work. Nine million hectares is about the size of the island of Ireland plus Scotland put together.

Alex Witze: It sounds like a really remarkable place, Tom, do you yourself have any plans to go back?

Tom Hayden: Well, at this point, the only way in is, especially to the highland areas, by helicopter, and in this case by Peruvian National Police helicopter, and that is not a resource to which I have ready access, so I think for me it was a once-in-a-lifetime experience, but hopefully if some of the conservation efforts work out, it will be an experience that people in future generations will be able to have.

Robert Schoelkopf: What we're trying to do is build integrated circuits which behave like single atoms interacting with single photons and the goal in the long term is to use those atoms and photons to store information quantum mechanically, transmit it from place to place, and do information processing in a quantum-mechanical way.

Chris Smith: So if you can use an atom to do it already, why do you need a chip? Why can't we just use ions or atoms to do this?

Robert Schoelkopf: Right. So the goal there is to make rather complex circuits or logic devices that are composed of these individual, quantum-size pieces, these artificial atoms are 'qubits', and you could use real atoms, but it's rather difficult to make complex arrangements of real atoms and wire them up and couple them together - so a nice thing is if you can bring the sort of quantum properties that an atom has to something which already looks like a computer, i.e. it's an integrated circuit.

Chris Smith: So how have you done it?

Robert Schoelkopf: Well, what we do is we make an integrated circuit that behaves like a single atom which talks to a single photon trapped in a cavity - basically light bouncing back and forth between mirrors. But we do this all in the microwave domain so our light is just a signature cell-phone frequency that's bouncing back and forth.

Chris Smith: But the wavelength of the microwave is quite long, it's about 10 or 12 centimetres, isn't it, so doesn't this mean your virtual cavity or your cavity has to be quite big?

Robert Schoelkopf: Yeah, so it's a large cavity which has to be of the order of the wavelength long, so, yes, several centimetres long, but because we're at this frequency and because we use some superconducting wires, we're able to confine it into a long skinny tube essentially, much like a wire, and that has some advantages. It means that we can pin this photon down and we can sort of wire it from place to place on a chip if we'd like to, and also that we can confine it in a very small volume which makes it interact rather strongly with our artificial atom.

Chris Smith: And presumably that means you can also get down to the nitty gritty of what the individual photons are doing which has been a challenge before, hasn't it?

Robert Schoelkopf: Yeah, that's right. So it's not unusual in a physics lab to measure individual quanta of visible light but the ability to measure an individual quantum of microwaves is not something which is routine or has ever really been done, and what we report in this article is that we can couple a device we call a qubit, a little superconducting artificial atom, to the microwave photons inside this cavity and thereby actually resolve the individual number of microwave photons and measure them off.

Chris Smith: So in other words this is how you're getting the information back out in order to do the next step in the calculation chain if this were a computer, for example?

Robert Schoelkopf: Yeah, so for example, to use this in a computer, you'd like to take the state of the atom and convert it into a state of a certain number of photons inside the cavity and then you could transport that information from one end of the cavity to the other with the photon, and then write it back into another qubit: that would be like doing a remote operation between qubits that could, as you say, be separated by several centimetres.

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