As of this writing, there are already 367 bacterial genomes completely sequenced in the NCBI Genome Project. More sequences get completed every week. The sheer amount of information accumulated is enough to make one boggle. Many of the sequenced organism are of pathogenic importance--some cause diseases in humans others in plants, etc. And then, there are those of ecological importance. Take for instance, ecological disasters. The damage to the marine wildlife by oil spills (such as the Exxon Valdez in 1989 and the Gulf War in 1991) extends way beyond the initial accident as heavier toxic petroleum products persist in the environment for long periods of time.
A variety of methods are used to clean up oil spills. Setting the oil on fire could burn it away. The spill can be contained by booms and collected by skimmers. Or dispersants can be added to break up the oil into small droplets so it can be easily dispersed in water. Yet another method is to introduce microbes to speed up the biodegradation of the spill. For eukaryotes, petroleum products are toxic to life. Not only can these chemicals attack the membranes of cells, but they also have adverse effects oxidative stress reduction, the cell cycle, and DNA damage repair. Benzene, for example, is strongly associated with leukemia in humans. But luckily for us, there are microorganisms with the ability to metabolize hydrocarbons in petroleum. Pseudomonas, Rhodocccous, Psychrobacter, and Bacillus species all have the ability to munch on oil for lunch.
In this month's issue of Nature Biotechnology, Schneiker et al. have published the sequence to Alcanivorax borkumensis, an oil-eating marine bacterium. In fact, not only is the Alcanivorax genus a group of bacteria that can metabolize petroleum-based products, but they prefer doing so. A. borkumensis is so picky that it doesn't even use sugars and amino acids--the staple diet of so many other known bacteria. In 1991, A. borkumensis was isolated from sea sediment at the Isle of Borkum (off the northwest coast of Germany in the North Sea) by Passeri et al. while they were screening for biosurfactants. Compared to other oil-eating bacteria from the soil or fresh water, A. borkumensis did not have toxic effects on other organisms.
With the A. borkumensis genome at our fingertips, what characteristics can we determine that make this organism so good at degrading petroleum products? The bacterium's ability to degrade alkane is encoded in a genomic island that has similarity with other unrelated oil-eating bacteria--hinting that A. borkumensis acquired the ability from some horizontal gene transfer in the past. Another important ability is emulsifying oil with water which are usually mediated by proteins called glycosyltransferases--this organism has several genes for this as well. Other important genes include those that are involved in biofilm formation (to separate oil into droplets to be easily digested) and DNA repair (since petroleum products can damage DNA).
So with this blueprint available, not only can we begin to understand how the microbial milieu in the oceans keep the waters from clogging up with oil spilled from natural processes--such as natural seeps in the sea floor--but also possibly engineering a "super bug" to help clean up human-made messes.
In this month's issue of Nature Biotechnology, 
