Last year, the UC Berkeley team joined with the Department of Energy's Joint Genome Institute to pluck out the genomes of the five dominant bacteria in a slime, or biofilm, responsible for acidic drainage from the mine. Now, they have gone further and, with the help of colleagues at the DOE's Oak Ridge National Laboratory, identified the proteins that go with these five organisms, their so-called proteomes.
The technique they used is the first successful leveraging of a community genome to obtain the complete complement of proteins produced by that community of organisms, said team leader Jill Banfield, professor of earth and planetary science and of environmental science, policy and management at UC Berkeley.
This technique not only tells her and her colleagues what genes are expressed as proteins in each bacteria, but also how much of each is produced - the key to understanding the role each bacterial species plays in the biofilm community.
"Genomes tell you about the genetic potential of organisms that are present in the environment, what organisms might be able to do," said Banfield, a scientist at Lawrence Berkeley National Laboratory. "But you can't tell whether they are doing it or not. We want to go beyond the level of 'Can they?' to 'Are they?,' and the way we do that is go after some measure of gene expression."
Banfield and her colleagues at UC Berkeley, Oak Ridge National Laboratory (ORNL), Lawrence Livermore National Laboratory and Xavier University in New Orleans report their findings in a paper appearing May 5 on the Science Express Web site, an advance online publication of the journal Science.
For some nine years, Banfield has been studying the microbial