Taking a Very Close Look at Life at the Limits

Local residents keep an eye on the project. Dr. Alison Murray, with an Emperor penguin posing obligingly in the background, on the sea ice during her last research visit to Antarctica. (photo by Lynda Goff, University of California at Santa Cruz)

It is perhaps one of Nature's little ironies that we "higher" forms of life prefer a middle ground when it comes to living conditions. It's the reason there's no urban sprawl in the deep Sahara-too hot; no fishing junkets to icy Antarctic seas-too cold; and no gift shops atop Mount Everest-too high. No, we're more than a bit like Goldilocks, who had to have things just right. However, the "lower" forms of life-those tiny microorganisms that are apparently so much simpler than we are-take an entirely different approach to life on this diverse planet, choosing to survive, even thrive, in some of the most extreme environments known: in the boiling sulfur springs of Yellowstone National Park; in the desiccating waters of the Great Salt Lake; in the super-hot, metal-laden waters surrounding deep sea vents; and in the sub-zero seas of Antarctica.

DRI's Dr. Alison Elizabeth Murray has the honor of studying some of these remarkable little extremists, and she is employing the latest tools of biotechnology and genomics to understanding their diversity, their adaptations, and their roles in the ecosystem. As part of the National Science Foundation's Life in Extreme Environments, or LExEn, Program, she's preparing to spend six weeks in Antarctica, where she'll collect planktonic microorganisms to optimize methods of looking at the diversity and patterns of gene expression of these organisms living in their natural environment, that is, in water at -1.8°C (29°F). They'll also be studied as they are subjected to scientist-induced stresses, such as changes in light, temperature, and nutrient levels.

Murray, secured by a rope, prepares to lower a Niskin bottle into the Antarctic Ocean to collect bacteria-bearing water. The bottle allows scientists to sample water at a specific depth while protecting the sample from contamination by water at other depths or by air. (Photo by Lynda Goff, University of California at Santa Cruz)

While it may be simpler to study cultured microorganisms in a laboratory rather than in a natural, and in this case harsh, environment, it's just not always possible. "Only one percent of these types of organisms have been successfully cultivated," explains Murray. "So, we know very little about how they survive these extremes." By looking at the microorganisms in situ, that is, in their actual environment, researchers not only bypass the problem of cultivating them, they also get a far more accurate picture of what reactions and adaptations enable them to live where they do.

It's these reactions, which can't literally be "seen" in such small organisms, that hold the key to understanding their survival techniques, and it's here, according to Murray, that the genomic approach comes in. "Molecular biology has revolutionized what we can learn about these microorganisms. We're utilizing technology that has largely been developed in biomedical research and learning to apply it to the environment." That means looking at the tiniest bits-the DNA and RNA-of these tiniest creatures and identifying which genes are being actively expressed under various conditions. That is, which genes are "turned on" to cope with, say, an increase in water temperature or a drop in available nutrients. The goal is to discover not just what a reaction to the environment is-like eliciting an immune response when exposed to a pathogen-but also how it happens-what bit of DNA codes your immune cells to respond that way. "We're trying to understand, on a gene expression level, what major patterns these microorganisms are using to live in these places."

Connect the dots... Microarrays appear as ordinary glass microscope slides, but after being exposed to RNA-bearing samples and scanned by a laser; they will show a colored dot pattern. For Murray's experiments, green dots could indicate that certain bacteria (and their genes) are present in surface waters and the red could represent those found at a 100 meter-depth below Antarctic sea ice. The yellow-orange colors would represent genes found at both sampling points. (Photo by Alison Murray)

To identify which genes are being expressed, Murray will construct DNA microarrays-something like microscope slides-packed with some 15,000 different microbial genes robotically arranged in a grid pattern. With the help of an existing library of Antarctic microbial DNA, these microarrays will allow the researchers to "match up" expressed genes from the collected Antarctic organisms with known genes on the slides. This matching process will show which genes are being used to help them survive in their frigid surroundings.

While understanding individual responses to environmental changes is key, Murray says the study will shed light on how the microbial communities as a whole fluctuate in changing conditions, as well as on the overall diversity of organisms that call the Antarctic seas home.

According to Murray, "The two big questions in microbial ecology are, 'Who's out there?' and 'What are they doing?'" She is already acquainted with some of who's out there, particularly a microorganism belonging to a class of creatures known as archaea. Just seven years ago, says Murray, researchers found that these particular organisms constitute as much as 25 percent of the biomass of the Antarctic surface waters at certain times of year, making up a significant fraction of the planktonic community. But, she explains, "we haven't been able to cultivate them, so we don't know much about their basic metabolic processes. Interestingly, we do know that their closest cultivated relative lives at 100°C (212°F)."

The researchers are eager to learn more, since it's a fairly safe assumption that such an abundant organism plays an important role in the functioning of the ocean ecosystem, perhaps freeing up nutrients that allow other creatures to survive. This particular group of archaea is also of interest because it lives in a seemingly backwards cycle, flourishing in the colder, darker parts of the Antarctic year and diminishing in the warmer, brighter summer months. "Our September trip, in the early part of the Antarctic spring, will coincide with this big population swing," she notes, "so we'll be able to look at the dynamics of that shift."

A Ride to Work. Murray will reach the tubeworms using the Woods Hole Oceanographic Institute's Alvin research submersible. (Photo by Rod Catanach, Woods Hole Oceanographic Institution)

Murray says the project will not only answer questions about what lives in these Antarctic waters and how the organisms survive so well, but will also result in genomic technology methods that can be used to study other organisms living in extreme environments. Ultimately, she'll be helping herself, as she prepares for another investigation set to begin in January 2002. In that project, headed by Dr. Craig Cary of the University of Delaware, Murray will use the same biotechnology techniques to study gene expression in a community of organisms living in yet another extreme environment-the mineral deposits surrounding deep-sea vents in the Pacific Ocean west of Costa Rica.

This time, the microorganisms have a partner in the form of a five-inch, tube-dwelling worm that shares a symbiotic relationship with the fleece ofbacteria that grow on its back.

Hot tail, cool head. Alvinella pompejana, or the Pompeii worm, survives th highly variable temperatures of its habitat with the help of the furry coat of bacteria growing along its back.

That Alvinella pompejana, or the Pompeii worm, gets by only with a little help from its friends is hardly surprising considering that it lives deep below the surface, withstanding tremendous pressure and living in virtual darkness. To make things even tougher, the water is laden with heavy metals and there are huge temperature disparities within its tiny living space: it's as hot as 80°C (117°F) where the worm's tail rests, and about 22°C (72°F) where the head emerges from its tube-shaped home.

Researchers know that the feathery bacteria covering the worm's back play a crucial role in allowing it to survive in such an environment, but precisely how the relationship works is still very much a mystery, as it is for many of the similar symbiotic associations being found in other extreme marine systems. "The lack of understanding comes in part from our inability to cultivate these creatures free from their hosts," explains Murray. "Even when we can cultivate them, it's unlikely that the responses we measure in the lab will truly represent what happens in the natural ecosystem."

To reach the community, Murray and her colleagues will use Alvin, a three-person research submersible owned by the Woods Hole Oceanographic Institution, that can dive as low as 13,124 feet below the ocean surface. Alvin became a vital tool in finding and investigating deep-sea lifeforms when, in 1977, researchers first discovered the giant tube worms and other extraordinary creatures living around vents off the Galapagos Islands. Alvin even lends its name to the Alvinellids, the class of small deep-sea worms to which the Pompeii worm belongs.

Antarctic samples will be analyzed in DRI lab in Reno. In her DRI lab in Reno, Murray plates E. Coli bacteria with genes cloned from Antarctic sea water. She brings all the samples she collects back to Reno for similar laboratory analytical treatment.

Murray's part of the project will look at the relationship of the Pompeii worm and its resident bacteria at the gene expression level and will be the closest look to date at how the components of such a system work together. "We'll look for what we're calling a core metabolism. Is there some core gene set, a theme of life in this community? It's exciting because this is the first time a project to sequence a 'metagenome' of a whole community has been funded."

While developing the technology to understand how life survives in the most inhospitable places is justification enough for this work, you can leave it to enterprising humans to come up with practical, even mundane, applications for what's discovered. Industry is quite interested in these little survivors, and most especially in the enzymes that help them function in their brutal habitats. The enzymes that remain active at cold temperatures could be used to develop detergents that work well in cold water. Heat-loving organisms have already yielded an enzyme that has made possible the common forensic use of DNA fingerprinting. The same enzyme is also used extensively in medical diagnosis and biological research. And enzymes from microorganisms that tolerate highly acidic, salty, or alkaline conditions have potential applications for improving animal feed, producing stonewashed denim, even extracting crude from oil wells.

Clearly there is far more than meets the eye, or microscope, when it comes to these little creatures. In Nature it seems, there's someone, or someplace, for everyone. These tiny extremists are happy inhabiting even the nastiest places on Earth. Perhaps what's really surprising is not that they can survive where they do, but that we "higher" forms of life may have so much to learn from them.

- Jackie Allen