Date: February 12, 2011
Title: Studying Extremophiles on Earth to Understand Life in Space
Podcaster: Adam Fuller
Organization: JHU Astrobiology Forum – http://astrobiology.jhu.edu
Description: With the Kepler Mission’s discovery of 4 potential Earth-sized planets orbiting in their host star’s habitability zones, the main question about life is no longer “Is there life out there somewhere?” Instead we must ask, “Exactly what sort of life could exist on these strange planets?” For today’s 365 Days Of Astronomy podcast, the JHU Astrobiology Forum’s Adam Fuller begin answering this question by speaking with Dr. Jocelyne DiRuggiero, an associate research professor in the Biology department at Johns Hopkins University, about her research with microorganisms here on Earth that live in environments so hellacious, they could easily be thought to be from another world.
Bio: Adam Fuller is a graduate student in the Planetary Sciences department at Johns Hopkins University in Baltimore, Maryland. For over a year now he has worked with Dan Richman and Veselin Kostov, both graduate students in the Physics & Astronomy department at JHU, to establish the JHU Astrobiology Forum, a cross-disciplinary group that promotes astrobiology research among undergraduates, graduates, and faculty at Hopkins and the surrounding research institutions. More information about the JHU Astrobiology Forum can be found at their website, http://astrobiology.jhu.edu.
Dr. Jocelyne DiRuggiero is an associate research professor in the Biology department at Johns Hopkins University. Her research focuses on how microorganisms evolve robust adaptive mechanisms in extreme environments. More information about her lab’s research can be found at its website, http://www.bio.jhu.edu/diruggiero/lab.
Today’s sponsor: This episode of “365 Days of Astronomy” is sponsored by Adrian Morgan (outerhoard.wordpress.com & @GoldHoarder on Twitter) in honour of my favourite episodes from previous years. These include August 15 2009, January 11 2010, and December 27 2010.
The search for life elsewhere in the Universe got a shot in the arm a week and a half ago with the Kepler Mission’s discovery of 4 potential Earth-sized planets orbiting in their host star’s habitability zones. Soon the question will no longer be “Is there life out there somewhere,” but instead, “Exactly what sort of life could exist on these strange planets?” To answer this new question, researchers must look at organisms here on Earth that survive and flourish under conditions so extreme as to be instantly lethal to humans. First discovered in the 1970s, these creatures, dubbed extremophiles, represent new and unexpected ways in which life evolves adaptive mechanisms for extreme environments. What we learn about Earth-bound extremophiles will greatly inform our search for life on other planets in the coming years.
Hi, my name is Adam Fuller, and I’m a graduate student in the Department of Earth and Planetary Science at Johns Hopkins University in Baltimore, Maryland. Along with Dan Richman and Veselin Kostov, I helped create the JHU Astrobiology Forum, a cross-disciplinary group that promotes astrobiology research among undergraduates, graduates, and faculty at Hopkins and the surrounding research institutions. As part of our group’s mission, this year we’re highlighting the cutting edge research being done by our faculty. For today’s podcast, I spoke with Dr. Jocelyne DiRuggiero from the Department of Biology about her research on extremophiles. What follows is an abridged version of our conversation. The full interview is available on the JHU Astrobiology Forum’s website, http://astrobiology.jhu.edu. And so we begin!
JDR: I am Jocelyne DiRuggiero. I am a professor in the Department of Biology at Johns Hopkins University. My research focuses on extremophiles. Extremophiles are microorganisms that live in places that we would feel very uncomfortable in. So, for example, a microorganism living in a deep sea hydrothermal vent, where the temperature is very, very high. Or they’re living in high salt environments—we’re talking about saturating salts such as the Great Salt Lake or the Dead Sea. Organisms that can live in acids, basically, very, very low pH. And also organisms that live in very dry environments. We know that water is essential for life, and when there is no water, it makes it’s really, really difficult for microorganisms to live.
AF: Now, your research specifically focuses on what aspect of all that?
JDR: So we’re interested—really, the lab has two main topics. One of them has to do with the way those organisms respond to environmental stresses….So we’re interested in how these organisms respond to environmental stresses, how they can protect the macromolecules in their cells—in particular the genetic material which is essential for the cells to survive and multiply. We’re looking at extremophiles because they have very robust adaptations to extreme conditions, so this is a place where we can really dissect those processes. We’re particularly interested in DNA repair mechanisms but also stress response in general to the environment.
AF: What sort of extremophiles do you work with?
JDR: So right now in the lab we have two types of extremophiles. Some are called hyperthermophiles. They grow above 90°C. They typically grow in the absence of oxygen, and sometimes we need to add elemental sulfur so they don’t respirate oxygen. They produce found something that is called hydrogen sulfide, which is this very smelly gas. So that’s one group of organisms. And we’re looking at particular DNA repair proteins in these organisms. The other group of organisms we’re using are halophiles, and those grow in high salt conditions, so we have to put 4 molar salt, which is about 20% salt in the culture medium for them to grow. If we add some water it basically lyses the cell; they just pop open. They really cannot survive without very high salt.
AF: Okay, so even if—oh, that’s interesting—so the water, it has to have a very high salt content. Normally, how do cells react in, like, say, like a normal bacterium—
JDR: So, if you put a normal bacterium in very high salt, you have very high osmotic pressure—what’s called osmotic pressure is the pressure outside the cells due to the salt. What this does is it draws out the water from the cell into the medium, so the cells shrivel and dry. Those organisms resist a very high salt because they also accumulate very high salt inside the cells; they balance the very high osmotic pressure outside the cells by accumulating very high salt. Now, what is very interesting is that the salt in the environment is sodium chloride, the same salt we use for our table salt, but inside they accumulate potassium chloride to the same level. This means that all the macromolecules of the cells have to be adapted to function in very high salt, and usually if you put a protein in very high salt, it precipitates. So we have an adaptation: the proteins that stay in their soluble form at very high salt and function perfectly well in this environment.
AF: What sort of environments on Earth, what sort of places would you find extremophiles like these?
JDR: As I mentioned earlier, the Great Salt Lake. That’s where the organism we’re using most in the lab, called Halobacterium salinarum, and has been isolated. But you can also find them in the Dead Sea—any places with very high salt. So the high-temperature hyperthermophiles. Those are found in deep sea vents, deep-sea volcanoes. They’re also found in places like Yellowstone National Park. Every time you have a very high temperature in an aquatic environment, you’re going to find those microorganisms. There are a few places on the earth and also a few places where we can find them in shallow reefs. For example, there is an island in Italy called Volcano Island, and right off the beach you can find some of those very hot small vents and you can isolate those microorganisms from there.
AF: Would you say that these are evolutionary adaptations these organisms have gone through to adapt to their environment? Or are these reflective of some prehistoric condition that hasn’t changed for these organisms as they’ve stated in one spot?
JDR: This is actually a very good question, and it’s really comes back to the debate about the origin of life. There are several theories about this, but one that is quite predominant says that the first type of organisms were hyperthermophiles, because they evolved very well protected at the bottom of the ocean, so they were high-temperature organisms. And it makes sense in many ways because if you look at the tree of life, which is this tree that represents all the life on Earth and is based on molecular data, all the organisms that are close to the root of the tree, the deepest branches of the tree are occupied by hyperthermophiles. This brought the idea that early organisms were hyperthermophiles and from that evolved the rest of the organisms. The other argument in favor of this theory is that the Earth at the time was heavily bombarded; it was very unstable at the surface. If you can imagine that if you have a very deep environment, that might be a good place for life to evolve. But there are quite a few problems with this. One of them is that if you look at the adaptation that hyperthermophiles have evolved, they’re actually very sophisticated. For example, the membrane is quite different than all the other membranes of organisms we can find on Earth. They also have enzymes that are very specific to those organisms and also very sophisticated. This really contradicts the idea that those features were primitive features and actually support the idea that those evolved afterwards. We had very basic simple cells, and then as life multiplied and diversified, you had colonization of those niches with organisms that evolved adaptations to specifically survive in those environments.
AF: Can you tell me about some sort of experiment you’re working on right now in your lab?
JDR: We’re interested in this halophile that I was talking about, Halobacterium. In particular we want to understand how the organisms can go through periods of desiccation when the water evaporates and the organisms are trapped in the salt crystals, so there’s very little water. And when water comes about, they survive—they survive very well in the salt crystal, and then they start growing again. So, what are the metabolic changes that they undergo for those periods of desiccation? How do they resist desiccation? To do that, we don’t desiccate the cells. We actually irradiate them with ionizing radiation.
AF: You irradiate them?
JDR: We irradiate the cells with Cobalt-60, which is a proxy for desiccation. It’s much more reproducible, and we can very accurately dose the level of radiation. When you try to desiccate a culture, depending on the temperature outside—if it’s Baltimore in the summer, it’s still going to be very humid, so it’ll be very difficult to control. So, because there’s a very strong relationship between resistance to desiccation and resistance to radiation, and we know that the cellular damage in both conditions are very similar, we use radiation as a proxy. It’s much easier to do accurate dosing in a reproducible experiment. So we’re looking at how the cells are resisting to the irradiation and similarly to desiccation what we found is what desiccation and irradiation does to the cells is basically a very big oxidative stress. It oxidizes a lot of the macromolecules in the cells. So we’re trying to understand what is the difference between Halobacterium that can resist very well irradiation and desiccation and organisms like Pseudomonas that are very sensitive to both. So what is different in the cells that make one organism survive perfectly well and the other one basically dies. What we found is that all the enzymes that are typically present in the cells to fight the oxidative stress are not the most essential things in the cell. There are actually very small molecules that are able to scavenge, to basically take out those free radicals and then protect the cells. So the cell doesn’t get as much damage because it’s able to basically knock down all those reactive oxygen species before they cause too much damage, in particular to the proteins. We’re looking more in particular at the molecular pathways that control the production of small molecules.
AF: as far as how these extremophiles would evolve over time, would there need to be a change in the environment to spur genetic diversification of these extremophiles?
JDR: Well, microorganisms are absolutely fantastic. They can adapt to many different conditions and changing conditions in the environment. Even within a population of microorganisms that live in, say, a hydrothermal vent, you do have multiple variants and you have genetic changes happening all the time in these populations, random mutations that may have consequences on specific pathways of the metabolism or the way they use a specific energy source. So they’re constantly evolving all the time, and you have all those multiple variants in one population. If the conditions change to some extent, the dominant organisms might not be dominant anymore, but another part of the population that is better adapted will rise and then colonize this whole environment. What I’m saying is that microorganisms have a tremendous capacity to adapt. If there’s another niche that opens—for example, suddenly there’s an import of new carbon sources, you will find organisms that will be able to use those carbon sources and then colonize this niche. And it’s true for higher temperature and lower temperature—although we think there is a limit for the biochemistry that we know as far as temperature. But organisms in a population of hyperthermophiles are not all the same, and some might be able to grow at a lower temperature. So let’s say your thermal source decreases in temperature. Then you’re not going to have the same dominant organisms that you’re going to have otherwise.
And that concludes the abridged version of the interview. Again, if you’d like to hear the interview in its entirety, please visit http://astrobiology.jhu.edu. A big thanks goes to Dr. DiRuggiero for taking time out of her busy schedule to speak with us. And stay tuned for our next podcast when we speak with Dr. Naomi Levin of the Hopkins Planetary Science department about carbon isotopic fractionation and plants.
End of podcast:
365 Days of Astronomy
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