May 30, 2006

Essential organism -- from peat bogs -- involved in global climate change is finally isolated for study

round- and rod-shaped forms of methanogens
S. Zinder
This image shows the round- and rod-shaped forms of methanogens isolated from a peat bog.

Among the unusual life forms found in peat bogs are carnivorous pitcher plants and methanogens, methane-producing single-celled organisms that live in oxygen-free environments. But efforts to take methanogens from acidic peat bogs and then isolate and culture them in the laboratory under peat bog conditions have been unsuccessful -- until now.

In a recent article in Nature Online, Cornell researchers published their methods for creating an acidic culture medium that isolated methanogens and allowed the organisms to thrive in a test tube. This will allow researchers to study methane-producing organisms and to better understand how they function in peat bogs and how they might respond to global climate change.

Indeed, methanogens play an important role in global climate because they are the largest natural sources of atmospheric methane -- a heat-trapping greenhouse gas 21 times more potent than carbon dioxide. Northern peat bogs hold one-third of the carbon fixed in the world's soils, the same bogs that recycle and store carbon from atmospheric carbon dioxide.

Also, as a result of this work, the Department of Energy Joint Genome Institute said it plans to sequence the genome of the organism.

"Methanogens are ubiquitous in the peat at low [acidic] pH, but no methanogens capable of growing at low pH have been isolated," said Suzanna Braüer, a graduate student in Cornell's Department of Microbiology and the paper's lead author. "We've succeeded in isolating a culture."

"This will provide us with a lot of information that we can then take back to the bog and study what these organisms are doing there," said professor of microbiology Stephen Zinder, the paper's senior author.

Even though methanogens dominate bogs, researchers have been unable to take them from the bog and then grow them in the laboratory. Braüer, Zinder and their colleagues used an antibiotic called rifampicin that killed off the bacteria in the sample but spared the methanogens. The methane-producers belong to a kingdom called Archaea, separate from bacteria and not bothered by most antibiotics.

The researchers' next step was to duplicate natural peat-bog conditions as much as possible. Typically, growth mediums use sulfides to get rid of oxygen, which is toxic to methanogens. Braüer said the organisms were finicky, very difficult to grow and so sensitive to oxygen that cultures sometimes died when syringe needles were inserted repeatedly into the tops of test tubes to test for methane. It turned out the sulfides were killing the methanogens as well. Instead, the researchers used small doses of a titanium compound to remove oxygen from the medium.

In the end they struck the right balance, creating a growth medium with an acidic pH that also supported the methanogens. The organisms turned out to be the most acid-loving and salt-sensitive methanogens known. But when studied closely, researchers found that the remaining organisms came in two distinct shapes: long thin rods and round cocci.

The plot thickened.

"You don't need a Ph.D. in microbiology to see a culture of rods and cocci and think you have two different organisms," said Zinder. To the researchers' surprise, "they turned out to be the same organism."

It took a year of tests, including studying genetic sequences of Archaea provided from a clone library, before Braüer and colleagues ultimately hit upon a fluorescent probe that showed the rods and cocci had exactly the same sequence of ribosomal RNA.

"That's when we actually said, 'Aha! We do have the same organism,'" said Braüer. The researchers are not sure why the organism appears in two shapes.

Now that the methane-producing Archaea have been isolated, further study can begin that relates to peat bog systems, Archaea and climate.

"Peat lands are really important in global climate change," said Braüer. "They are important not only for carbon storage but methane emissions as well. It's a delicate balance that could shift."

Joseph Yavitt, associate professor in Cornell's Department of Natural Resources, was a co-author of the study. The work was supported by the National Science Foundation Microbial Observatories Program.