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The Habitable Planet: A Systems Approach to Environmental Science 

Oceans Interview with Penny Chisholm

Interviewer: Tell me a bit about your position here.

PENNY: My name is Penny Chisholm and I’m a professor in the Civil and Environmental Engineering Department at MIT and also in the Biology Department at MIT and I co-direct the Earth System Initiative at MIT.

Interviewer: How did you first become interested in this field?

PENNY: I started being interested in biology in high school, but then got interested in mathematics and when I went to college, I studied mathematics for a while, but realized that it wasn’t quite as interesting as things that were alive so I switched and became a biology major. My advisor worked on plankton in lakes and so I did an independent research project on that and I found them to be very fascinating, these microbes that I didn’t know existed. That’s really how I got started and eventually moved into plankton in the oceans, which was a much bigger challenge.

Interviewer: You grew up near Lake Superior. Had you spent any time near the oceans growing up?

PENNY: No, in fact, I had never even seen an ocean until I was about 14 when we visited New Jersey. I really knew very little about oceans at all until I did a post-doc at Scripps Oceanographic Institution in La Jolla, California and that’s where I started going on cruises and really learned oceanography.

Interviewer: The first thing I want to ask you is if you could just give me an overview of the ocean system.

PENNY: What most people don’t realize is that the oceans are responsible for half of the photosynthesis on earth and they produce half of the oxygen that is produced through the photosynthetic mechanism. The organisms that do this are the microbes, the phytoplankton, in the oceans. We call them the invisible forest. They are the plants of the oceans and they are the base of the food web. If they weren’t there, there would be nothing else living in the oceans because they supply all of the organic carbon or sugars, if you think of it that way, for everything else that lives in the oceans.

The phytoplankton take in carbon dioxide from the atmosphere using solar energy and convert it to organic carbon, sugars, proteins, all of the material that life is made out of and that’s the material that the rest of the food web relies on. As they do that in photosynthesis, oxygen is evolved and also all the other organisms use that oxygen to breath. They’re central to the functioning of the ocean ecosystem. They’re very small. They range in diameter from less than one micron — a human hair is about a thousand microns wide so that’s a good reference point — so they range in diameter from about one micron to fifty microns. There are very small microbes that eat them and there are slightly larger organisms that are shrimp-like crustaceans that eat those smaller ones and up we go in the food web with larger and larger organisms, but it all starts with the phytoplankton.

Interviewer: I’ve heard you refer to the ocean as a machine. Can you elaborate a bit on that.

PENNY: We can think of the ocean ecosystem as a photosynthetic machine in a sense. A critical function of this machine is to steadily pump carbon dioxide from the atmosphere into the surface oceans and then export it to the deep ocean, and at the high pressures and cold temperatures of the deep ocean, that carbon dioxide is what’s called sequestered for hundreds of thousands of years. The deep ocean represents a very large reservoir of CO2 and that’s an important part of the global carbon cycle. The phytoplankton are at the heart of this pump; what they do is the CO2 in from the atmosphere into this complex food web where much of it is recycled and comes right back out again, but some of it stays as organic carbon in the form of aggregates, dead cells, fecal pellets from zooplankton. That settles down to the deep ocean through various density barriers that isolate the deep ocean from the surface and then down in the deep ocean it is then regenerated by bacterial activity into CO2. The net effect is that there’s a lot of CO2 coming in and a lot going out, but some fraction of that settles to the deep ocean and is held there for a long period of time.

Interviewer: For millions of years we weren’t burning a lot of CO2. Can you talk about how that worked in terms of balances and keeping CO2 under control.

PENNY: Before humans started mining fossil fuel, which is really just ancient photosynthetic product that has been sequestered in the earth for millions of years, the earth had a global carbon cycle that was coupled to the climate system in which the oceans played a very important role. This biological pump is central to that role. One way to think about it is that if there were no phytoplankton and if the pump didn’t exist, if the oceans suddenly went dead, which is not likely to happen, and the oceans all mixed top to bottom and all that CO2 in the deep ocean equilibrated with the atmosphere, the concentration of CO2 in the atmosphere would more than double. So that gives you an idea of how much the deep ocean plays a role in the global carbon inventory and how important the phytoplankton are in keeping that pumping downward to keep that CO2 in the deep part of the ocean. It’s all part of a very important complex, co-evolved system that maintains a balance in the whole CO2 system through these really important feedback mechanisms. What we’re concerned about now, having mined this fossil carbon and put it suddenly into the atmosphere, is that in the earth’s history there’s never been a change in CO2 that’s been this fast and that’s the major difference in the perturbation of the system now through human intervention and the natural cycles that the systems goes through. It’s unprecedented in the earth’s history to have carbon dioxide increase so fast in the atmosphere and the ocean system can’t keep up with that and so it’s accumulating in the atmosphere.

Interviewer: Is there stress in the ocean system or is it just the ocean system can’t keep up?

PENNY: It’s both. It’s both a stress and the system can’t keep up. The stress is that right now the PH of the oceans is increasing from the carbon dioxide from the burning of fossil fuel going into the oceans. It’s just that it doesn’t equilibrate fast enough to take it all out of the atmosphere so as it moves into the oceans. It shifts the PH and that is causing significant problems and dissolving coral reefs, etc. and that’s going to get worse. And then, in addition of course, the warming that is predicted due to the greenhouse effect of the CO2 in the atmosphere will change the physics of the oceans. The surface oceans are warming steadily, small amounts now, but that changes the physics and the global water patterns, which in turn will change the protoactivity of the phytoplankton in ways that we don’t really understand. And so the system — the state of the whole system — will change and it’s very difficult to predict.

Interviewer: Tell me what you were doing when you were part of the group that discovered Prochlorococcus.

PENNY: When I first started my research here at MIT, I was studying a group of phytoplankton called diatoms; they’re about 20 microns in diameter and they’re very important in the marine food web. We were studying their cell division cycle and in order to do that, we were using an instrument called the Flow Cytometer, which is a laser-based instrument with a laser focused on a flow cell so that the cells can go by the laser one cell at a time. We could stain the DNA in the cells and that allowed us to see which cells had replicated their DNA or not. This is an instrument that was developed for biomedical research, not for studying plankton in the oceans or whatever. So we started working with this instrument and we realized that it would be really useful for studying plankton in the oceans because they have properties that would show up in the laser and in fact, their pigments fluoresce — when you shine the laser on it, their pigments fluoresce distinctive colors. Rob Olson was a post-doc in my lab at that time. He’s a scientist at Woods Hole now and he was very talented with instrumentation and so we negotiated with a company to take one of their biomedical Flow Cytometers on a cruise, an oceanographic ship. Rob made this instrument work and we started studying a group of plankton called Synechococcus, which are interesting in that they fluoresce orange. Most plankton, if you shine blue light, fluoresce red, but this one fluoresces orange, and so you could separate them from all of the other cells in the system. We were studying this Synechococcus and as time went on, we started seeing some very, very tiny signals that were fluorescing red but scattering much less light than any known phytoplankton cell would scatter, which said that they were extremely small. We thought that it was electronic noise for a long time. But Rob persisted in looking at this and ultimately it started taking on characteristics that were alive and that it changed with depth in the oceans. So we started focusing on these little signals with the Flow Cytometer and ultimately were able to isolate the cells which turned out to be a very important component of the ocean ecosystem.

Interviewer: What was that moment like for you personally?

PENNY: Like most discoveries it really wasn’t a moment,. The discovery of Prochlorococcus was a slow realization; we started seeing these signals and ignored them and over time it was a slow realization that indeed this probably was something that was alive so I can’t really think of a particular moment, but I do remember when we realized that it really was something going on. Rob and one of my students were on a cruise going from Woods Hole to Africa and I started getting these email messages from the ship saying, this is what’s happening and that’s what’s happening and suddenly we all said, hmmm, this is really interesting. Even at the time when we realized that these were living cells that were smaller than anything else known and very abundant, we still didn’t appreciate the significance of it. I think because you get deeply immersed in it and you’re excited and you work on it, but you suddenly realize these cells are dominating the oceans and we didn’t know they were there until months ago. How our picture must’ve been warped. We get immersed in what we’re doing and we forget to step back and say ooh, wow, this is really important.

Interviewer: So why should we care about this tiny life form?

PENNY: Over time we’ve come to learn that Prochlorococcus is a very special phytoplankton because it’s filled with superlatives. It’s the smallest photosynthetic cell in the world as far as we know and it has the smallest genome of any photosynthetic cells so, with the smallest number of genes, it can convert solar energy, CO2, and inorganic compounds into organic carbon. I think of it as the minimal life form. It doesn’t rely on other organisms for organic carbon, it creates everything de novo and also, it turns out it’s the most efficient light absorber of all known photosynthetic cells, and we think it’s also the most efficient carbon fixer of these cells.It’s also the single most dominant — numerically dominant — phytoplankton group in the oceans. So it is very unusual in its position in the plankton world. I remember the moment that I decided I was going to devote the rest of my career to studying it and that was when we had studied it in the field and we had finally isolated it into culture and I realized that this was one cell that you could study at all dimensions of its life existence. Prochlorococcus provides us with a really useful model system for understanding micro ecology because we can study it from genome level, from the level of its 1,700 genes and how they come together and make this photosynthetic cell all the way up to the ocean basin level. That’s what we’re interested in understanding in biology and life sciences at all of those levels of organization from the single cell to the ecosystem that it’s embedded in, and this is a cell and a system where you could actually do that, which is not true of most of them.

Interviewer: Is it important that there are so many Prochlorococcus and the number stays constant stay constant while other phytoplankton bloom and disappear?

PENNY: The interesting thing about Prochlorococcus is how stable it is in the deep blue ocean. That is, in the warmer waters of the open ocean, you find on average about 10 million cells per liter of seawater. There are some fluctuations in their numbers, but not dramatic and they double about once every one or two days so that means they’re eating as fast as they’re growing and they’re growing relatively fast for ocean phytoplankton in the middle of the ocean. So it’s a very stable system and yet very dynamic in how fast the cells are growing. We think that this system is playing an important role in regulating the stability of the ocean ecosystem and yet we really have no idea how to articulate that in any mechanistic way, but you can go out there year in and year out at the same time in the ocean, in the Atlantic and in the Pacific, and find these cells in their same abundance and they’re just cranking away doing their job whatever it is in the ocean system.

Interviewer: Do any short-term climate changes like an El Nino move them around in the oceans? Does that have any kind of impact on the health?

PENNY: Prochlorococcus are very passive in their behavior in the oceans. As far as we know so far they’re not modal, but even if they were, they’re so small they can’t change their position in the ocean relative to the water mass. So they move with the currents and we don’t have enough data to know whether any changes in the ocean temperature or currents or any of that has changed the Prochlorococcus’ population significantly. We certainly have no evidence that it has. Any time we go out there to study them, we find them very similar to the way they were the year before. They’re essentially like dissolved photosynthesis machines in the oceans and the information in their DNA, I think of it as dissolved information. The oceans are loaded with this genetic code instructing cells to go through photosynthesis and take up nutrients and do all of these living processes in the ocean.

Interviewer: Tell me a little about your lab – what its purpose is, when you established it, and the kinds of people you brought in to work there.

PENNY: The composition of my lab has evolved over the years. We started out as phytoplankton ecologists, but as we got committed to studying Prochlorococcus through all of these levels of organization, it’s now almost a miniature biology department within the lab in that we have students and post-docs with expertise all the way from genomics in molecular biology to global oceanography. It’s been really exciting for me at this point in my career to bring these teams of people together and watch them work together. I think of myself as a conductor of an orchestra and they’re all playing different instruments and they all have different expertise, but you put it together and it makes for really beautiful music. It requires lots of collaboration and coordination and peer to peer teaching and it’s just incredibly fun to watch. I think that they also enjoy that and it also minimizes any competition between people in the lab, which also makes it a lot more fun, so we stress cooperation. It’s like an ecosystem; everybody has their own role to play and together it works very well.

Interviewer: Tell me about the focus of your current work.

PENNY: In the last five years in our work on Prochlorococcus, largely through the work of Matt Sullivan and our collaboration with John Waterbury in Woods Hole, we have begun to work on viruses that infect Prochlorococcus. It turns out the oceans are teeming with viruses that infect microbial cells in the system, so it’s not surprising that there are viruses that infect Prochlorococcus. Matt has worked on isolating these and has built a culture collection of viruses in the lab and has isolated three of them and we’ve had their genome sequence. We now know the genetic information of three phage (viruses and phage are the same thing) that infect Prochlorococcus hosts so we can study that interaction at the molecular level. Matt has been working with Maureen Coleman, a graduate student in the lab, who has been studying the genetic composition of several Prochlorococcus strains and was able to identify signatures in their genomes that suggest that viruses actually are important in moving genetic information between host cells. It’s a very complex story and has changed our view of the role of viruses in the oceans that maybe it isn’t just that they’re there to kill Prochlorococcus but more that they do cause cell death, but they’re also moving genes around between different strains.We think that that’s very important in maintaining the metapopulation, the global Prochlorococcus population, because it maintains genetic diversity in this group of cells. I have started to think of it as some kind of a symbiosis more than a predator/prey relationship, which may be completely wrong, but they’ve been working on that story and figuring it out.

Interviewer: Did I read correctly that these viruses do not kill the host cells whereas some — was it P7 viruses — do kill their hosts? Can you talk a little bit about that?

PENNY: The viruses that we’ve studied do kill their hosts but we really only studied them in the lab and a limited number of them. But under the right circumstances, the virus injects its DNA into the host cell and takes over the host cellular machinery and turns it into a virus-producing machine and then it kills the cell and the viruses are released. But we know, and this is true in other systems too, we’re sure that we are going to find viruses that don’t kill the host and that are just carried along for generation after generation in the host until the time gets right and then they induce more virus formation. That’s one of the things that Matt and Maureen have been working on. These viruses have multiple ways of making a living out there depending on what the ecosystem is doing at a particular point in time.

Interviewer: And how it is that viruses are actually contributing to the numbers or population study?

PENNY: If Prochlorococcus is doubling every two days, then they have to be being killed every two days. There are three factors in the death of Prochlorococcus. They could be killed by a virus, they could be eaten by a small protozoan, or there is a thing called spontaneous cell death that we know very little about, but probably plays a role. They just die. To be honest, we don’t know the relative importance of those three factors; at any point in time, at any place, it’s likely they change in relative importance. But the viruses are, we think, a significant source of mortality in the system.

Interviewer: Do you go out on the research vessels? What’s life like on a cruise

PENNY: I don’t go out that much. I haven’t for five years or so. Once the boat has left the dock, I love to go out, but the preparation for going out drives me crazy and it’s extremely hard work, non-stop. But there’s a sense of excitement that is incredibly motivating, not to mention being out in the middle of the ocean seeing lots of beautiful wildlife and sampling for our favorite phytoplankton. And if we have Flow Cytometer on board, it’s incredibly exciting because we can take samples from different depths and run them through the Flow Cytometer and we can count the number of Prochlorococcus at the different depths and right away get a picture of what the population looks like. But more often than not, we don’t have the Cytometerand so we go blind and we go by our previous knowledge in understanding what depths to sample and we bring the samples back. Each cruise you basically start with a stripped-down ship in terms of the laboratory part of the ship and you build a lab from scratch every time, haul all of your equipment in and build it to your custom design for your cruise and off you go and get the samples you need from different stations and bring back what you need and then do the work in the lab.

Interviewer: You mentioned that the genomics part of this whole story is the most exciting. Can you talk about that and talk about why it’s so important?

PENNY: About five years ago, we were fortunate enough to have a strain of Prochlorococcus sequenced by the Department of Energy. They have a place called the Joint Genome Institute, which was very important in the human genome projects sequencing the DNA of humans. After that project was finished, there was a lot of sequencing power and they turned that toward sequencing microbes. When we got our first sequence of the first strain of Prochlorococcus, it really changed the way we thought about this organism because suddenly we could see the 1,700 genes that contained all of the information that enabled it to get through its day out in the middle of the ocean. The challenge, of course, is decoding that and about half of those genes, we don’t know what they do, but some of them we do. The most interesting thing that came out of it was as we sequenced more and more strains that were very closely related, we learned that they had important genetic differences. By looking at the genes that they share, it tells you what is the core of Prochlorococcus and then by looking at the ones that they don’t share, it tells you what makes one strain ecologically unique relative to another, ultimately it tells you that, once we are able to decode some of this information. There have already been many things that we’ve learned that make sense in terms of mapping the genetic composition onto the distribution of these different ecotypes in the ocean ecosystem.

Interviewer: If you could have a final about the importance this of Prochlorococcus, what would you say? Why is it so important? Why is it something that we would benefit knowing about?

PENNY: I think there are two dimensions to the significance of Prochlorococcus. One is the role it plays in the biosphere. If the oceans are responsible for half of the photosynthesis on earth and Prochlorococcus are a significant fraction of that, that makes this one particular group of organisms that we didn’t even know existed until 15 years ago an important photosynthesizer on a global scale. It is extremely important that we appreciate that these “invincible” cells are playing this role in the biosphere. But the other more philosophical thing is that it’s incredibly humbling to realize that we didn’t know this cell existed until 15 years ago and we had models of the ocean processes and models of the earth and we thought we understood this pretty well. We always think we understand it pretty well and then along comes something that just completely changes the way we think about these systems. Prochlorococcus is just one of the surprises. We’re going to have many, many, many more. We do have many discoveries like that every year in science telling us oh, boy, we really don’t understand how this system works. So for me, it’s a constant reminder that we really don’t understand these systems and if we continue to play with them and perturb them — meaning the human impact on the global ecosystem — in ways that are stressing the system without understanding how it works, then I think that any hope for a sustainable use of the earth’s resources by humans is greatly diminished. That’s what Prochlorococcus is to me — a constant reminder that nature has surprises in store for us.

Interviewer: What do you hope to do- in the future with your work? What is your goal?

PENNY: When I was a graduate student back in the 60s, E-coli, Escherichia coli, was a microorganism the studies of which revolutionized our understanding of molecular biology. It was the model system upon which molecular biology was built. That corresponded with the discovery of the structure of DNA and so there was this explosion in molecular biology and this one microbe was studied intensively. That’s how people really understood how these systems worked at the molecular level. My hope for Prochlorococcus is that my students will go out and study and bring it to their own labs and we will have a lot of people focusing and understanding this one organism and that it will serve as a model system for what I call systems biology, that is, the study of one organism from the molecular level to the entire ecosystem that it’s embedded in. That really hasn’t been done yet so that’s really my goal for this organism.

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The Habitable Planet: A Systems Approach to Environmental Science