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Geomicrobiology

Life on the rocks


Special Web sidebar: Digging up germs


To understand the possibilities for life on other planets, scientists are digging into ice on Antarctica, overturning rocks in the Mojave Desert and tapping hot springs in Idaho. Here on Earth, microorganisms are popping up in the strangest places. The challenge is identifying them.

“Microbes have been evolving on Earth for 3.8 billion years,” said Ed Delong of the Monterey Bay Aquarium Research Institute in Moss Landing, Calif. Delong spoke during a session titled “New Biology of Rocks” at the meeting of the American Association for the Advancement of Science (AAAS) in Boston on Feb. 14. “As a consequence of that long period of evolution, they have invaded almost every habitat that we can think of on Earth and some of those habitats are just now being recognized.”

Understanding the age-old relationship between microbes and the environment is the goal of scientists working in the field of geomicrobiology. The field became a distinguishable part of the earth sciences less than 30 years ago and has recently received recognition of astronomical proportions along with geobiology, a field that looks at the bigger picture of how biological and geological cycles relate.

“NASA’s interest in astrobiology stimulated the field of geobiology and geomicrobiology,” says William Ghiorse, a Cornell University microbiologist and one of three editors for Geomicrobiology Journal. “Most of what they are thinking about in terms of life on Mars or any other place are related to the processes of biogeochemistry and geomicrobiology that happen on Earth.” In the last three years, Ghiorse has seen an upswing in the number of submissions to his journal in part because of increased interest in studying life in extreme environments. “It is directly applicable to what you would find if looking for life elsewhere,” he says.

Discerning what’s life from what’s rock will be a tricky part of future planetary studies; even on Earth the task is far from simple. At the Boston meeting, scientists shared new ways of thinking about and identifying life.

To prevent scientists from missing any bizarre examples of life here or elsewhere in our solar system, geobiologist Ken Nealson of the University of Southern California is working on ways to detect what he calls living rocks. “When conditions get really tough on this planet, microbes move into rocks,” he said. Bacteria can eat pyrite for lunch and breath sulfur. “They are tough, tenacious and metabolically diverse. They eat anything and breathe anything.”

Often bacteria on Earth that have made rocks their home are buried under a layer of fungi, algae or lichen, Nealson says. When that organic carbon is gone, the rock’s metabolic community becomes very different. Slow geological processes are ideal for life that may not include the usual genetic features of DNA, RNA, ATP and protein lipids, he says. Therefore life as we know it may not be the best model for E.T.

The natural black tarnish into which these petroglyphs are carved has a mysterious history. Although the petroglyphs indicate signs of human touch, scientists are uncertain whether the varnish coating formaed from a chemical or biological process. Courtesy of Jim Staley, from Painted Rocks State Park, Ariz.

Indeed, these normal clues for life are not always available even on Earth. Such is the case for a peculiar varnish found on desert rocks. The varnish, less than a millimeter thick, is composed primarily of manganese and iron oxides. So far scientists are baffled as to how the varnish formed and why. On Earth the varnish comes in shades of black or red depending on its ratio of manganese to iron, and the dark coatings on the red rocks of Mars seen in spacecraft photos look suspiciously familiar.

Jim Staley of the University of Washington presented evidence at the Boston meeting of amino acids in the varnish. He says the acids link the process to a biological formation.

Most amino acids on Earth are an “L” configuration rather than “D,” but can change over time. For example scientists find different proportions of both L-aspartic acid and D-aspartic acid in lichen, bone and tissues that are hundreds of years old, with D-aspartic acid accruing over time and L-aspartic acid diminishing. Other amino acids such as alanine take longer to change.

Various combinations of amino acids are responsible for the construction of protein, a vital ingredient for life on Earth. Ordinarily proteins and bacteria are endowed with abundant L-configured amino acids and sulfur-containing amino acids, but Staley found none of those.
 

Nevertheless, when he and his colleagues analyzed the black, desert varnish from rocks in the Mojave Desert, they discovered three different kinds of D-amino acids that suggest the varnish is of biological origin. “These are the amino acids that remain and predominate after long periods of time, hundreds to thousands of years,” Staley says. Still, the results are inconclusive.

“If we are going to be looking at objects in the future from Mars, can we tell if this is a biological process by doing the right sorts of analysis on the material?” he asks. “If we can’t tell if it’s biological on Earth, we’re going to have big trouble looking at martian samples.”
 
Digging up germs

At the meeting of the American Association for the Advancement of Science (AAAS) in Boston on Feb. 14, scientists expressed concern over potential threats in digging up unidentified microbes. 

The potential for an Andromeda-like strain in the 21st century is theoretically possible, warned Abigail Salyers, president of the American Society for Microbiology. Microbes that have lived in areas without plants, animals or humans - such as on Mars, or in the subsurface of Earth - may yet have the potential to cause unknown diseases in those hosts. Such instances might occur if the bacteria evolved defense strategies against other organisms in their environment, for example amoeba. 

While Salyers is one of the first microbiologists to raise the issue of whether geological exploration on Earth might promote the risk of infectious diseases, the threat from microbes is not unfamiliar. "We're finding that just about every time humans do something to improve human life or exploit natural resources, everything from air conditioning to cancer chemotherapy, we're changing things in a way that gives new opportunity for microorganisms to infect people," Salyers said. 

She pointed to the example of a soil bacterium that had evolved to live inside amoebas, protozoa that usually eat and kill bacteria. Air conditioning in the 1970s, introduced the bacteria, Legionella pneumophila to the human lung and resulted in an outbreak of Legionnaires' disease. Bacteria that have evolved strategies to defend themselves against attacking prokaryotes and eukaryotes may have the ability to live in human and other hosts. "On Earth we know that there are a lot of prokaryotes and eukaryotes wherever we look." 

In terms of the significance of this threat Slayers says: "I think this is very unlikely, but once again it's a theoretical possibility that we might be exposing human beings at some point through geomicrobiology endeavors to organisms that might be able to cause disease in some of us." 

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Christina Reed


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