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Mapping the microbial world

INEEL scientists offer the first web-based database of some of the world's smallest, hardiest creatures.

Mammoth Hot Springs is one of the many homes in Yellowstone National Park to microorganisms that thrive in extreme environments. Click here for more photos.

Microbiology and Geographic Information Science—Scientists are cataloguing and mapping the life inside Yellowstone’s hot pools. Hardy microorganisms ranging from emerald-green bacteria to fire-red rock slime have long fascinated microbiologists with their ability to live in the scalding hot water at Yellowstone National Park, the acidic ore deposits of abandoned mines or the salt pools of the Great Salt Lake.

Up until now, though, microbiologists have had no central storehouse of information or method of searching for the microbes. This month, researchers at the U.S. Department of Energy’s Idaho National Engineering and Environmental Laboratory (INEEL) launched an experimental version of the Microbial Database and Map Server—an interactive web-based catalog and search program combined with geographic information systems (GIS) mapping software. They introduced the database this month in the journal Applied and Environmental Microbiology.

Research and commercial scientists prize microbes that survive in extreme environments. Scientists commandeer the resilient proteins and enzymes inside these bacteria to do work that no others can do. "If you want an enzyme that has tolerance for high salt, you go to the Salt Lake," said INEEL microbiologist Daphne Stoner. "If you want a high-temperature enzyme, you go to a hot spring."


Heat-tolerant enzymes are now used widely in household hot water detergents, in a common laboratory practice to copy DNA, and in other high-temperature food and industrial processes. For example, one microorganism found at Yellowstone builds an enzyme called xylanase that can bleach paper pulp while withstanding the heat of paper-making. An entire field called bioprospecting has developed around the search for natural enzymes with potential commercial or scientific value.

Bioprospectors are especially drawn to hot springs. But Stoner ran into difficulties several years ago when she tried to bioprospect for one extremophile. She needed bacteria that would thrive in hot and acidic water. "I went to Yellowstone and said, ‘Where are the springs with the characteristics that I need?’ They pointed to this whole bank of filing cabinets. I went through drawer by drawer by drawer, and thought, ‘There’s got to be a better way.’"

At the time though, there wasn’t. "You would be rummaging through the literature, calling up geologists, etc.," said Stoner. Some of the information was in published articles, some on individual computers, and some could only be found through word-of-mouth. Then Stoner talked to INEEL biologist and advisory scientist Ron Rope, who suggested creating a web-based database.

With the Microbial Database and Map Server, researchers will be able to go to one place to find the type, location, and characteristics of bacteria they want. The current version is a limited experimental prototype with just enough data to show that it works. It is supported by compatible Internet browsers, e.g. Internet Explorer. The INEEL researchers plan to modify and add to the prototype database and welcome comments from microbiologists who visit the site. In its full form, the database will include published, compiled and anecdotal data, and will extend far beyond Yellowstone.


The database will be like a microbial shopping guide. Say a scientist wants to find a microorganism that lives at a pH lower than 6 and a temperature over 40 degrees Celsius (104 degrees Fahrenheit). She can enter in her criteria and the map highlights all hot springs holding such bacteria. She can find out the names--genus and species--of the bacteria already isolated from each spring.

She can also look at individual pictures of each hot spring, find the GPS location, and read about the water or soil conditions (including temperature, pH, conductivity, texture, color and smell).

That’s not all. On a clickable, zoomable map, the researcher can find the roads to the spring and the lakes nearby. "We’ve put it together in map form—that’s the strength of the GIS technology," said Stoner. "This is live. You construct the map that you want to see." GIS specialists and software programmers at INEEL (Julie Brizzee, Randy Lee and Luke White) helped make the Microbial Database and Map Server far more than a simple catalog of microorganisms. They created a complex, interactive mapping platform with locations, conditions and pictures.


The web-based database for Yellowstone’s hot springs is the first of its kind for microorganisms. But its creators don’t plan on it being the last. "We want to go global," said Stoner, "so you can ask the big questions. ‘Can microorganisms become extinct?’ ‘Are they invasive?’" Stoner eventually wants to be able to compare microorganisms from the Arctic, (cold-tolerant psychrophiles or "the pink stuff on old snow") with those in the Antarctic. She wants to be able to contrast hot spring creatures from Japan with those in New Zealand.

In addition, the INEEL scientists want to expand the mapping capability into three dimensions. Bacterial populations change as the depth changes. A database with a depth component will help scientists working on underground bioremediation and subsurface ecology.

Even without three dimensions, the attempt to map Yellowstone’s microbes is a tremendous task. Yellowstone claims 10,000 "thermal features," from steaming geysers to small warm pools of mud. The geologist who created the database, Micah Geary, finds she has to search the literature for a certain hot spring and then enter information into the database paper by paper. "You have to do this for each spring. That’s why it’s a huge undertaking," said Stoner.

The microbial database is a needed tool for microbiologists worldwide, said Stoner. For all the counting, cataloguing and gawking done on the world’s largest wildlife, many of its smallest creatures aren't even on the map.

INEEL researchers who contributed to the Microbial Database and Map Server are Julie Brizzee, Micah Geary, Randy Lee, Ron Rope, Daphne Stoner and Luke White. It is funded by the INEEL's Laboratory Directed Research and Development Program.


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