Genome of potential bioremediation agent sequenced

Shewanella bacterium can remove toxic metals from environment

Rockville, MD. – Scientists at The Institute for Genomic Research (TIGR) and collaborators elsewhere have deciphered the genome of a metal ion-reducing bacterium, Shewanella oneidensis, that has great potential as a bioremediation agent to remove toxic metals from the environment.

The genome sequence sheds new light on the biochemical pathways by which the bacterium “reduces” and precipitates chromium, uranium and other toxic metals. The research offers what scientists call “a starting point” for defining the organism’s electron transport systems and metal-ion reducing capabilities.

In the course of the sequencing project, scientists also discovered a new bacterial phage (a virus that infects bacteria) that may provide a wedge for possible genetic manipulation of Shewanella to target it for specific bioremediation projects.

“This is a very important model organism for bioremediation research because of its unusual capacities to remove environmental pollutants under diverse conditions,” said John F. Heidelberg, a TIGR assistant investigator. “Shewanella is the first microbe we have sequenced that can function for metal bioremediation and also survive in both aerobic and oxygen-free environments.”

Heidelberg is the first author of the S. oneidensis genome paper, which was posted online this week by Nature Biotechnology and will appear in the journal’s November issue. In addition to fellow scientists at TIGR, Heidelberg’s collaborators included Kenneth H. Nealson of the University of Southern California; Eric J. Gaidos of the University of Hawaii; Terry Meyer of the University of Arizona; Alexandre Tsapin of the Jet Propulsion Laboratory; and James Scott of the Carnegie Institution of Washington.

The genome project –supported by the U.S. Department of Energy’s Office of Biological and Environmental Research through its Natural and Accelerated Bioremediation Research and Microbial Genome programs — is expected to provide a boost for a wide-ranging research effort to develop Shewanella’s potential for bioremediation.

Jim K. Frederickson, who heads the Shewanella Foundation – a consortium of researchers that is part of the Energy Department’s Genomes to Life program – says the whole genome sequence “provides an essential foundation for the systems-level analysis” that the Federation has started. “It is enabling scientists to make global gene expression and proteome measurements that would otherwise be difficult or impossible to understand how this versatile bacterium responds to the environment.”

S. oneidensis is a rod-shaped bacterium that is found in the sediments of lakes and rivers in many parts of the world. While it is a relatively common microbe, it has uncommon attributes. Those include its diverse capabilities for “respiration” – that is, the use of its complex electron-transport systems to reduce ions of metals such as chromium and uranium – thereby allowing bioremediation efforts that would remove those and other pollutants that are dissolved in water.

Chromium is a toxic metal, some forms of which have been related to cancer and other ailments, including severe digestive disorders. Groundwater pollution involving hexavalent chromium near Barstow, California, was the focus of a major environmental case in the early 1990s – a case that later was the basis for the film, “Erin Brockovitch.” Uranium is a radioactive element that is also harmful to humans who are exposed to it.

TIGR’s analysis of S. oneidensis found that its genome sequence contains nearly 5 million base pairs, with a large circular chromosome with 4,758 predicted genes and a smaller (plasmid) circle of DNA with 173 predicted genes. Researchers found that the genome has an unusually high number of cytochromes, which are enzymes associated with electron transport – the key to the microbe’s potential for bioremediation projects.

In order to maximine the bioremediation potential of S. oneidensis, some researchers say, the microbe might need to be genetically altered. Providing a potential tool to do that, the genome analysis discovered a lambda-like phage that scientists say “may provide an avenue for genetic manipulation of this group of microbes and allow the design of strains for specific bioremediation purposes.”

Claire M. Fraser, president and director of TIGR, was the senior author of the S. oneidensis genome paper. She said the sequencing project represents part of an ambitious TIGR research program to sequence the genomes of a wide range of environmental microbes. “We expect this genome sequence to lay the essential groundwork for future research into Shewanella’s great potential for bioremediation,” Fraser said.