Hot-Water Worms May Use Bacteria as Shield

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To find out if this theory is correct, the scientists first need to characterize the chemistry of the vent environment and sequence a large amount of DNA from the bacterial community—the metagenome. Then they need to compare the sequence with what is already known from previously sequenced genes.

"The metagenome sequence will tell us what all the possible genes are that are encoded by these bacteria," said Cary's colleague Alison Murray, an earth scientist with the Desert Research Institute in Reno, Nevada. "This doesn't mean, however, that the bacteria are utilizing all of those genes in their everyday lives."

This leads to the second aspect of the project, called functional genomics, Murray said. The goal is to get a "gene expression profile," which tells the scientists what genes out of the full metagenome are actually crucial to surviving the vent environment.

"The gene-expression profile will have certain characteristics that tell us the specifics of how the community is generating their energy, what chemicals they use from the environment, what their carbon source is, how they tolerate the high-heat and metal-laden environment they inhabit," Murray said.

To do this, the researchers have collected samples of messenger RNA (mRNA) from the community of bacteria. The pool of mRNA acts as a sort of fingerprint of what the community was doing at the time of collection, Cary said.

Using DNA micro-arrays, the researchers will map this mRNA against the environment, which will ultimately provide information on what genes the microbes use to survive. Micro-arrays are bits of DNA from specific genes arranged robotically in a grid pattern on a glass slide.

With the micro-arrays built, the mRNA from the community is labeled with a fluorescent dye and then flooded onto the arrays. The labeled mRNA—which is associated with a specific bit of DNA—will seek out its DNA target. When looked at using a special micro-array reader, DNA that has representative mRNA in the sample will light up. "What lights up is being used," Cary said.

Murray added that "many of the probes will have no signal. Those indicate that, although the gene exists in the metagenome, it was not being expressed at the time we collected the samples."

If all goes well, within a few years Cary and his colleagues hope to make the complete data set available to the public to be "mined by scientists for years." Understanding these genes may lead to new drugs and speed up chemical reactions used in industry, for example.

Last Cruise?

Extreme 2004: Exploring the Deep Frontier was followed along via the Internet by more than 50,000 middle and high school students around the world. It was an opportunity for Cary, who first invited interactive student participation in 1999, to bring the excitement of real field science into the classroom.

"The more they see that what we do is exciting and fun, the more we will keep [them] engaged," Cary said. "These kids are the scientists of tomorrow—it is important for them to know that there is still so much we don't know and yet to be discovered."

For the first time in 15 years, Cary does not have a cruise planned for the current year. The submersible Alvin will be at its home in Woods Hole, Massachusetts, for a five- to six-month overhaul. Cary hopes that he'll be back out at sea in 2006.

"I will try my best to make that dream happen. Every time I go out, it is a gift and not something to be taken for granted," he said. "When we are out, we use every precious minute of bottom time to continue to work and discover all that we can in this most extreme of environments."

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