Rewriting Life

Better Bugs for Oil Spills

Oil-eating bacteria offer new hope for bioremediation.

Scientists in Europe have sequenced the genome for an oil-eating bacterium, a move that could pave the way for faster and more efficient ways to clean up oil spills.

Hydrocarbon-eating cells could help clean up oil slicks by converting the alkanes in crude oil into storage polymers, shown here as white spots within the cell. (Credit: Heinrich Lünsdorf, German Research Centre for Biotechnology)

With a complete blueprint for Alcanivorax borkumensis, researchers hope to better understand the specialized physiological mechanisms that enable the bacteria to live almost exclusively on hydrocarbons, says Vitor Martins dos Santos of the Helmholtz Centre for Infection Research (formerly the German Research Centre for Biotechnology) in Braunschweig, Germany, who co-led the international project. The sequencing of the 2,755-gene organism is described in the journal Nature Biotechnology. The findings could reveal how to optimize the conditions for these bugs and thus enable them to help mop up the hundreds of millions of liters of oil that enter the sea each year, says Martins dos Santos.

The ability of some bacteria to metabolize oil has been well known for more than a century. But so far efforts to exploit these capabilities for remediation efforts have faltered. “It has been used in the past and was a complete failure,” says Victor de Lorenzo, deputy director of the National Center of Biotechnology in Madrid, Spain.

In one example, bacteria were used experimentally to try to help clean up the 11 million gallons of crude oil spewed out by the Exxon Valdez after it ran aground off the coast of Alaska in 1989. But it didn’t make any difference, says de Lorenzo.

The problem was not a lack of bacteria, he says. Indeed, though the oil-eating bacteria are not common in unpolluted environments, they are plentiful where there is oil; A. borkumensis makes up as much as 90 percent of microbial populations in oil spills. The challenge in using these bacteria to clean up oil lies in creating the right conditions for them to grow faster and metabolize oil more efficiently. Cleanup workers have started to do this: “Now it is standard practice to add nutrients like oil-soluble forms of nitrogen and phosphorus to oil spills,” says de Lorenzo. However, they still have no real understanding of what specific nutrients the bacteria need, says Martins dos Santos.

Because bacterial remediation methods have not succeeded, cleaning up oil spills still depends mainly on the laborious process of physically removing the oil using booms and introducing chemical dispersants to break up what remains. But such methods are less than ideal. Recovering oil physically is expensive, and the chemically dispersed oil that remains in the sea still poses a threat to the environment even if it is no longer visible on the surface.

But decoding the genome of organisms like A. borkumensis is going to make a difference, says Jan van Beilen, a microbiologist who studies the molecular genetics of oil-eating organisms at the Institute of Molecular Systems Biology in Zurich, Switzerland. The genomic information has revealed molecular transport mechanisms that enable the organism to scavenge nutrients from its environment. This should, in turn, help identify which forms of phosphorus and nitrogen would create the best conditions for the bacteria.

The research could also identify the plethora of genes that produce the oxidative enzymes the bacteria use to degrade the oil, which should make it easier to search for other organisms with similar capabilities.

And such organisms will be needed. A. borkumensis can only metabolize compounds of low molecular weight, and these make up only about 70 percent of crude oil. So the next step is to look for organisms that are specialized to consume the remaining high-molecular-weight compounds, says van Beilen.

Sequencing A. borkumensis is only the first step, says Martins dos Santos. But, he says, research is under way in the United States, Australia, and Japan to sequence other oil-eating bacteria.

In the meantime, Martins dos Santos and colleagues have already begun applying the knowledge gleaned from A. borkumensis’s genome. Working with the Alfred Wegener Institute in Bremerhaven, Germany, they are running pilot tests in tanks in the North Sea to see if they can improve the bacteria’s appetite. “We add these bacteria, add nutrients, and try to see how they react,” he says.

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