It's called bioremediation. It has worked in the past.
from the Environmental Protection Agency: http://www.epa.gov/swertio1/download/citizens/bioremediation.pdf
EPA uses bioremediation because it takes advantage of natural processes. Polluted soil and groundwater can be cleaned at the site without having to move them somewhere else. If the right conditions exist or can be created underground, soil and groundwater can be cleaned without having to dig or pump it up at all. This allows cleanup workers to avoid contact with polluted soil and groundwater. It also prevents the release of harmful gases into the air. Because microbes change the harmful chemicals into water and harmless gases, few if any wastes are created.
Often bioremediation does not require as much equipment or labor as most other methods. Therefore, it is usually cheaper. Bioremediation has successfully cleaned up many polluted sites and is being used at 50 Superfund sites across the country.
Microorganisms have also been successfully applied during the removal of the Exxon Valdez oil spill. A number of microorganisms can utilize oil as a source of food, and many of them produce potent surface-active compounds that can emulsify oil in water and facilitate the removal of the oil. Unlike chemical surfactants, the microbial emulsifier is non-toxic and biodegradable. Also, "fertilizers" have been utilized to increase the growth rate of the indigenous population of bacteria that are able to degrade oil.
Use of microbes for bioremediation is not limited to detoxification of organic compounds. In many cases, selected microbes can also reduce the toxic cations of heavy metals (such as selenium) to the much less toxic and much less soluble elemental form. Thus, bioremediation of surface water with significant contamination by heavy metals can now be attempted.
They (oil workers) have a potential ally: microbes that have evolved an ability to break down oil that seeps from the ocean bottom. It gets devoured by a variety of bacteria, which eat it by chemically transforming its compounds into useful cellular constituents. "If it wasn't for the natural ability of bacteria to eat oil we would all be knee-deep in the stuff," says bioremediation expert Ken Lee of the Bedford Institute of Oceanography in Nova Scotia, Canada.
So could bugs help cleanse the gulf? A number of companies have tried to create bacteria that could break down oil on demand, but Lee and colleague Albert Venosa of the Environmental Protection Agency say that experiments have shown that novel bacteria, even if they show promise in the lab, cannot compete with bacteria already living on beaches and marshes. Experiments have shown that adding nutrients like nitrogen, phosphorus, and potassium to the beaches can speed up the ability of natural bacteria to break down oil. "What would've taken 5 or 6 years to accomplish can occur in a single summer," says Lee.
While adding such fertilizers has worked in small scale coastal experiments in which oil was purposefully spread on wetlands, experts don't know of examples from an actual spill. The challenge with wetland marshes is that the toxicity of the oil can kill plants before the microbes have a chance to get to work on the oil. "If that happens, you can lose the whole marsh," Lee says.
There is more good info at http://microsorb.org/