DNA Decoding Reveals Secrets Of Iron-Breathing Microbe, UMass Amherst Researcher Says

AMHERST, Mass. — The publication of the complete genetic sequencing and analysis of the Geobacter sulfurreducens bacterium in this week’s issue of Science signifies a quantum leap for research on the inner workings of the iron-breathing microbes and their potential for bioremediation of radioactive waste and generating electricity, says University of Massachusetts Amherst microbiologist Derek Lovley, one of the co-authors of the study.

According to Lovley, the sequencing project led by Barbara Methe of The Institute for Genomic Research (TIGR) "changes the whole way we do biology" by allowing researchers to create computer models based on the genetic information of the Geobacter. "This is like a 10-year jump forward," he says. "It’s really brought genomics to UMass."

Methe, who began her work decoding the bacterium as a postdoctoral researcher in Lovley’s lab, is the lead author of the Science article. For Lovley, who discovered the Geobacter in 1987, the results of the genome analysis have been something of a revelation.

"There were quite a few surprises," he says. "We though it was a pretty simple organism, but there is a greater complexity in its metabolic mechanisms and how it responds to its environment."

For example, Lovley and his colleagues originally thought Geobacter was incapable of movement, leaving them puzzled over how the microbes were able to locate the underground metals that provide their nourishment. "We’d never seen it swim in the lab," he says, but when the team began decoding DNA of Geobacter, "One of the first things we could see was the gene for a flagella," the whip-like structure that bacteria use to move. Using that knowledge, the scientists were able to replicate the proper laboratory conditions for Geobacter to develop a flagella.

The researchers tied that finding to the discovery of the microbe’s ability to detect the underground sources of iron oxide on which it relies. "It’s very rare to see one organism just take over an like Geobacter does in the subsurface," says Lovley. From the genome sequence, it’s now becoming clear how this organism has been so successful living in these environments. It’s totally changed our ideas about Geobacter."

In another example of the bacterium’s adaptability, Lovley says the researchers identified a gene for processing oxygen, an unusual capacity for an organism previously thought to be anaerobic. After further study, the team found that Geobacter can use oxygen in low concentrations — less than 25 percent of normal air levels. That ability, says Lovley, allows the organism to adapt to influxes of oxygen resulting from rainwater filtering through subsurface areas. "To be able to use oxygen at low levels is a very smart thing to do," he says.

The research team also found that Geobacter has a very high number of genes devoted to sensing changes in its surroundings, says Lovely. "It’s highly tuned to the environment and might be a good organism for the developing of biosensors to detect various chemicals."

The U.S. Department of Energy, which funded the genome project, is keenly interested in Geobacter because of the microbe’s potential for bioremediation of radioactive metals in groundwater by reducing their ions in a chemical process that allows them to solidify into more easily removable forms. The same process also creates small electrical charges that could someday serve as an alternative energy source.

Lovley says the gene sequencing also lays the groundwork for a more far-reaching study under the aegis of DOE’s $103 million Genomes to Life program. Last year, Lovley was awarded an $8.9 million, three-year grant to decode and analyze more than 600 pairs of base genes in microbes that have potential for uranium bioremediation of soil and electricity production. UMass Amherst is the only public university in the country to serve as a project leader in the effort. The other project leaders are Harvard University Medical School and the Oak Ridge, Lawrence Berkeley, and Sandia national laboratories.

Derek Lovely can be reached at 413/545-9651 or dlovley@microbio.umass.edu.

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