THE WAY for detailed studies of how a wide range of microbial communities are structured and how they function has been opened by new research.

The combination of mass spectrometry support from Oak Ridge National Laboratory (ORNL) researchers with extensive reconstruction of genomes from community genomic data at University of California, Berkeley was key to this work, said Jill Banfield, who led the project.

Gene exchange

Banfield is a professor in UC Berkeley's Department of Environmental Science, Policy and Management. "More important perhaps is the demonstration of our ability to simultaneously identify a large fraction of an organism's proteins and to distinguish them from proteins derived from quite closely related organisms," Banfield said.

Pink slime at the surface of water trickling through an old mine in California is proving to be the treasure for researchers in their quest to learn more about how bacterial communities exist in nature. Researchers from ORNL and UC Berkeley discovered that Leptosprillium group II bacteria in these streams are exchanging large blocks of genes.

This is the first observation of exchange of huge genomic blocks in a natural microbial community.

Important information

"Consequently, this provides important information about the conservation of genetic resources to enable life to survive and thrive," said ORNL's Bob Hettich, a co-author.

A letter published in a recent online edition of Nature shows that it is possible to follow what microorganisms are doing in their natural environment by identifying the range of proteins that they produce. The technique, utilized in a microbial community thriving in battery acid-like streams underground at Richmond Mine, California, combines recently developed ways to sequence microbial genes with methods to identify the range of proteins from specific microbial members, according to an ORNL press release.

ORNL mass spectrometry provided the ability to resolve and differentiate peptides that differ by as little as one amino acid. Nathan VerBerkmoes of the lab's Chemical Sciences Division was instrumental in designing the experiments and acquiring the mass spectrometry data.

"A key aspect of this paper is the ability to get proteome information on organisms that do not directly have complete genome sequencing information," he said.

"As a result we could study organisms related to those completely sequenced — such as the bacterial clades, or `cousins,' that are likely to exist in natural environments.

"This also might have implications into helping study human proteomics because not everyone's individual genome will be sequenced."

The pink microbial biofilm communities found in the mine runoff provide perfect research subjects because they have fewer organisms than most communities found in nature.

The reason, Hettich noted, is that the a pH of 0.8 is too extreme for most organisms to survive. In addition, the water from the mine often exceeds 120 degrees Fahrenheit. Because of their simpler makeup, the Banfield Laboratory established these communities as a model system in the mid-1990s.

— OUR BUREAU

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