SCIENCE & TECHNOLOGY EXTRA SALTY Humans would find a pond three times saltier than the ocean unpleasant, if not unbearable. But as this slice of the bacterial mat from such a pond's floor shows, a diverse community of microbes makes a living there.
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DEFINING LIFE'S LIMITS Biogeochemists hope to unearth how certain microbes live in seemingly inhospitable places AMANDA YARNELL, C&EN WASHINGTON
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hot spring. A remote rock more than a mile under Earth's surface. A bone-dry desert where it rains only once every few years. To us, such places may sound downright inhospitable. But for certain microbes—traditionally known as extremophiles—such locales can be a perfect place to live. So what are life's true limits? That question was pondered and discussed by biogeochemists who gathered in San Diego last month for the American Chemical Society's national meeting. Attendees of "Biogeochemistry at the Limits of Habitability," a symposium cosponsored by the Division of Geochemistry and the Biotechnology Secretariat, were reminded that what we humans consider extreme can be another organism's dream. "What we'd like to be able to do is accurately predict where life can—and cannot—
exist," Everett Shock, a professor of geological sciences and of chemistry and biochemistry at Arizona State University told C&EN. Biogeochemists could then predict where andunderwhat conditions life might be found on other planets or at other times in Earth's history addedJennifer Macalady an assistant professor ofgeoscience at Pennsylvania State University who coorganized the symposium with Shock. To kick off the symposium, Shock introduced a new theoretical framework for comparing diverse environments' potential for supporting life, which he developed with geochemist Melanie E. Holland of Geotek Ltd. in Daventry England. "Extreme values ofsome physicochemical variables can actually prevent life, but most 'extreme' physicochemical variables merely exact an energetic toll on organisms that inhabit that environment," Holland said in an interview For instance, microbes living at lowpH must pay the energetic price
to pump protons out of their cells or to keep them out in the first place. Shock and Holland challenged biogeochemists to define the "habitability" of socalled extreme environments, a quantity they define as the net energy available to an organism in an environment per unit time. "This requires that we try to quantify both the energy supply in a given environment and the energy demands that environment places on those who live there," Shock told C&EN. As a first step, biogeochemists must thoroughly characterize not only the physical conditions and chemistry of a given extreme environment but also the biochemical adaptations organisms have had to resort to in order to make that environment their home, he pointed out. A NUMBER OF speakers recounted thenattempts to characterize the energy supply available in various extreme environments. Barbara Sherwood Lollar, ageologist at the University of Toronto, is using isotope analysis techniques to characterize potential energy sources for life deep under Earth's surface. Just a decade ago, "it was thought that life only persisted down a couple hundred meters under Earth's surface," Sherwood Lollar said in an interview. In recent years, however, microbial communities have been discovered in underground mine sites that extend several kilometers under Earth's surface. "Debate has raged over what these microbes could be using as a food source," she said. Sherwood Lollar previously showed that billions-of-years-old crystalline rocks in these mines release hydrogen and hydrocarbon gases. She wondered whether the H 2 might be used as a food source by microbes. On the basis of stable isotope ratio measurements, Sherwood Lollar reported that deep-dwelling microbes are indeed rapidly consuming H 2 (and CO2) and producing CH 4 . "Microbes could harness a substantial amount of energy from this reaction," she told C&EN. Sherwood Lollar and her microbiological collaborators have shown that the microbes making their homes on these deep subsurface
Theory may help scientists seeking to know whether life could exist on other planets or on early Earth. 60
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rocks include ones related to hydrogenconsuming surface-dwellers. Anumber of other researchers spoke of their efforts to tease out what organisms living in extreme environments use as food. Kenneth M. Voglesonger, a postdoc at Arizona State University described his efforts to study the microbial colonization of nascent hydrothermal chimneys on the floor of the Pacific Ocean. Even though such just-formed chimneys spew superheated, highly acidic, mineral-rich water, a variety of microbes manage to live on their walls. On the basis of chemical analysis ofwater samples and the minerals found within the chimney as well as thermodynamic calculations, Voglesonger concluded that sulfate reduction would be an energetically favorable metabolic pathway for microbes living on newly formed chimneys. Microbiological analyses have confirmed that at least one type of microbe living there can reduce sulfate in vitro. If you believe your nose, you might think that the microbes inlfellowstone National Park's hot springs are also powered by sulfur metabolism. But in this case, the nose knows nothing, according toJohn R.
New Medicine Proposal
Spear, a senior research associate in Norman R. Pace's lab at the University of Colorado, Boulder. He measured several key chemical variables—including sulfate, hydrogen, oxygen, and methane concentra-
FOOD S E A R C H Chris Romanekof the Savannah River Ecology Lab collects samples of gas bubbling from a hot spring in eastern Siberia to analyze their chemical and isotopic composition.
tions; pH; and the reducing potential—in a number of hot springs in Yellowstone (Proc. Natl Acad. Sci USA 2005,102,2555). Thermodynamic modeling of these data indicates that H 2 oxidation is likely to be the main source of energy for organisms living in the pools, he reported. ANOTHER SPEAKER, Albert S. Colman of the Center of Marine Biotechnology at the University of Maryland Biotechnology Institute, in Baltimore, described his lab's attempts to study who lives on what in the volcanic hot spring pools of Uzon Caldera in far eastern Siberia. These pools boast high concentrations of carbon monoxide, hydrogen, methane, and hydrogen sulfide, all rich sources of chemical potential energy Colman reported results of genomic comparisons, microscopy experiments, and chemical analyses that suggest that CH4-forming microbes and COconsuming microbes in these pools share a symbiotic relationship: The CH4-forming microbes also generate CO that's used by the CO-consuming microbes, while the CO-consuming bugs make H 2 that the CH4-forming ones use to make methane.
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Quantifying the energy demands that a given environment places on its residents is a far bigger challenge than quantifying that environment's energy supply, Shock pointed out. The first step is to identify adaptations that allow organisms to live under extreme conditions such as low pH or high pressure. At the meeting, Sabrina
Tachdjian, a graduate student in Robert M. Kelly's lab at North Carolina State University, reported her efforts to use microarray profiling to study adaptations required for living at low pH. Sulfolobus solfataricus is a thermophilic archaeon that thrives in highly acidic environments. Tachdjian used a tiny DNA chip arrayed with all of the genes
BIOTECHNOLOGY
Extreme Microbes Are Explored For Industrially Useful Enzymes
E
characterization of a cold-tolerant xynzymes from microbes that live at lanase from an Antarctic bacterium. Xylife's edges are beginning to find lanases are used in the baking industry use in demanding industrial to improve the texture of bread dough. processes, according to work presented Unlike currently used xylanases, Gerat last month's American Chemical Sociday's cold-tolerant enzyme shows high ety national meeting in San Diego. catalytic efficiency at the coot temperaBecause of their exquisite regio- and tures used for dough handling but can stereoselectivity, enzymes already find be rapidly inactivated during baking. wide synthetic use in the food, detergent, Heat-stable xylanases are also of inpaper, fine chemicals, and pharmaceuticals industries. But enzymes from organisms that live at extremes of temperature or pH may be better suited to the often-harsh conditions of such industrial processes, according to Garo Antranikian of Technical University Hamburg-Harburg, in Germany, one of several scientists who discussed their efforts to harness extremophilic organisms for industrially useful enzyme catalysts in a symposium organized by the HOT SPOT Mathur (second from left) and his Biotechnology Secretariat. team, including Diversa CEO Jay M. Short (second from right), inspect microbial samples Antranikian reported that collected from geyser runoff in Siberia. he has isolated a lipase from a heat-loving bacterium that dustrial interest. San Diego-based Diveris likely to find industrial use. Lipases, sa introduced a heat-stable xylanase for which hydrolyze the fatty acid ester use in the paper-processing industry bonds of fats and oils, are currently used last summer. At the meeting, Eric J. in fine chemicals synthesis and in fat Mathur, Diversa's vice president for sciand oil processing. He pointed out that entific affairs and molecular diversity, the thermostable lipase has the advanrecounted the discovery of this enzyme tage of being able to tolerate elevated from an uncultured microorganism livtemperatures (up to 80 °C), at which ing in a volcanic hot spring in Uzon many fats are more soluble. The therCaldera, in far eastern Siberia. "We mostable lipase—which also tolerates a looked here because the conditions broad pH range and boasts high regiosematched those required for chemical tectivity—has been patented by Denbleaching of wood pulp—high temperamark-based Novozymes, he told C&EN. ture and high pH," Mathur told C&EN. Enzymes adapted to a cold environDiversa's xylanase uses nearly a third ment may also be industrially useful, acless chlorine dioxide than commercial cording to Charles Gerday of the Univerchemical bleaching methods and is cursity of Liege, in Belgium. Gerday rently in large-scale mill trials, he added. described biochemical and structural
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in 5. solfataricus to assess which genes were turned on or offwhen the organism experienced a sudden drop in pH. Tachdjian found that most changes in gene expression occurred within the first 30 minutes after the pH dropped. She reported that acidification appears to result in a general slowdown in cellular metabolism as well as an increase in production of a variety ofwhat are likely lipid-producing and membrane proteins, including one involved in pumping protons out of the cell. "We now need to do some biochemical experiments to follow up on the hypotheses generated by microarray data," Tachdjian toldC&EN. Michael P. Thelen of Lawrence Livermore National Laboratory described efforts by a team led byjillian F. Banfield of the University of California, Berkeley, to take the next step: measuring protein production directly Previously, Banfield's lab reported the genome sequences of the two dominant members of a community of microbes that live in highly acidic, metal-rich water produced when pyrite-rich rocks are oxidized upon exposure to air and water. Now, Banfield's team has used mass spectrometry to quantify how much of what proteins these microbes produce. Banfield hopes that biochemical analysis of the most abundant proteins will reveal how these organisms persist at such low pH. Also at the meeting, UC Berkeley's Ronald Amundson described attempts to determine the minimum amount of water required to support microbial photosynthesis—work carried out by postdoc Kimberley A. Warren-Rhodes at UC Berkeley and the National Aeronautics & Space Administration's Ames Research Center in Moffet Field, Calif. Warren-Rhodes surveyed for photosynthetic microorganisms in Chile's Atacama Desert, one of the driest spots on Earth. Where rainfall is absent, these microbes are rare and those that do exist may have found away to harness the water in fog to power photosynthesis, she said. In an interview, Shock admitted that it remains challenging to accurately define both the energy supply available in a given extreme environment and the energy demands that it places on the organisms that live there. What's more, an abundant energy supply may not be the only requirement for life in some locations—certain nutrients maybe limiting, for example. Despite these potential limitations, "our theoretical framework may help scientists who wish to determine whether life could exist under particular conditions—for instance, on other planets or on early Earth," he added. •
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