Decoding A Sulfate-breathing Bug

The microbe, Desulfovibrio vulgaris, plays a role in a process called microbially-influenced corrosion (MIC), which has caused staggering economic losses in the petroleum industry and at other industrial sites around the world. Such corrosion is caused by bacteria acting together in a biofilm that covers metal pipelines or equipment.

The analysis of the microbe's genes is expected to help researchers find better ways to minimize such damage as well as to develop methods to use such microbes to help remediate metallic pollutants such as uranium and chromium.

Desulfovibrio is a model for the study of sulfate-reducing bacteria, which use hydrogen, organic acid, or alcohols as electron donors to "reduce" (that is, add electrons to) certain metals, including uranium. Other sequenced microbes that are capable of such reduction include Shewanella oneidensis and Geobacter sulfurreducens, both of which were sequenced at TIGR.

"This genome will be a valuable asset to the community of scientists around the world who are studying the sulfate-reducing bacteria and their role in corrosion," says John Heidelberg, the TIGR assistant investigator who led the sequencing project.

The study, to be published in the May 2004 issue of Nature Biotechnology and posted on the journal's website this week, was supported by the Microbial Genome Program of the U.S. Department of Energy's Office of Science.

In their analysis of the D. vulgaris genome, scientists found a network of c-type cytochromes – proteins which facilitate electron transfers and metal reduction during the organism's energy metabolism. The presence of those c-type cytochrome genes are thought to give D. vulgaris a significant capacity and flexibility to reduce metals.

The study also found that the relative arrangements of genes involved in energy transfer provides evidence that the microbe uses a process called hydrogen cycling to increase the efficiency of its energy metabolism.

"With the genome sequence, we have a frame in which our theories and data must function. We have yet to see the frame very clearly, but that is developing," says Judy D. Wall, a biochemist at the University of Missouri-Columbia who collaborated on the genome analysis.

Wall says that having the genome of D. vulgaris will help biochemists determine exactly how the microbe corrodes iron and perhaps develop better ways to prevent that damage. "Understanding how sulfate-reducing bacteria use substrates to make energy and how they position themselves in the environment …is fundamental to efforts to control the bacteria or use them for our purposes," she says. Gerrit Voordouw, a microbiologist at the University of Calgary in Canada and a collaborator on the project, is an expert on the organism. "Knowing the genomic sequence will allow detailed unraveling of the mechanism by which sulfate-reducing bacteria like D. vulgaris use metallic iron as electron donors," he says.

Voordouw adds that future microarray studies of D. vulgaris will make it possible to determine which of its genes are turned on or off when the microbe is growing on a metal surface and is involved in the corrosion process. "This knowledge is a prerequisite to devising more intelligent ways to prevent microbially induced corrosion."

In addition, the genome sequence – by defining genes of interest in the process of metal ion reduction and metal ion precipitation – is expected to help scientists find ways to use D. vulgaris or similar sulfate-reducing microbes to help clean up pollution by toxic metals near mines or similar sites.

Says Voordouw: "This is important to help combat the spread of toxic metal ions in the environment at mining sites."

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The Institute for Genomic Research (TIGR) is a not-for-profit research institute based in Rockville, Maryland. TIGR, which sequenced the first complete genome of a free-living organism in 1995, has been at the forefront of the genomic revolution since the institute was founded in 1992. TIGR conducts research involving the structural, functional, and comparative analysis of genomes and gene products in viruses, bacteria, archaea, and eukaryotes.