Several other projects–from whale carcasses to wastewater sludge–are under way or already complete, promising a huge volume of novel genetic data. A recent project at the University of California, Berkeley, for example, identified three new organisms living in the highly acidic environment of abandoned mines. (Bacteria covering the floors of these mines convert iron into acid, which can then pollute nearby streams.) “They are close to the size of viruses and may be the smallest organisms ever discovered,” says Brett Baker, a research scientist at UC Berkeley, who worked on the project with Jill Banfield, also at UC Berkeley. These organisms may give clues to other life forms adapted to extreme environments, such as Mars.
The next hurdle in metagenomics will be trying to find the function of many of the newly identified genes: unlike cellulases in termites, most genes have little structural similarity to genes of well-studied organisms, making it difficult to infer their function. In a sample of water from the Sargasso Sea collected by genomics pioneer Craig Venter, the two most common and likely most important gene families are totally unique: scientists have no idea what they do. “In some ways, it’s crude to focus on enormous mountains in the genomic landscape,” says Hugenholtz. “But it does immediately draw attention to interesting avenues to pursue.” Structural studies are now under way to try to figure out these proteins’ function.
Metagenomics projects may eventually be able to shed light on these unknown genes. “We can look at representations of genes of unknown function in similar environments, compare them to environments that lack a particular function, and then triangulate,” says Bristow. And metagenomic signatures could one day be used as a fingerprint to identify certain environments, he adds. They “could be used as a way of identifying places you might want to drill for oil or look for minerals or contamination of some kind,” he says. “Just seeing the genes might tell you what’s happening there.”
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