Skimmers, scoops and thousands of kilometers of booms cannot compare with bacteria and other microbes when it comes to removing oil. The microorganisms that naturally inhabit the Gulf of Mexico are the only real defense against the Deepwater Horizon spill. As researchers study how the microbes are cleaning up the mess, they remain wary of how these saviors could also choke marine life, too.

That natural microbes are better than human mop-up efforts may come as a surprise, considering that for decades, genetic engineers have touted the creation of an oil-gobbling superbug—the first patent issued for a genetically modified organism was for such a hydrocarbon-chewing microbe. But such microbes “are not effective for the most part,” says marine microbiologist Jay Grimes of the University of Southern Mississippi.

Engineered microbes come up short in part because no single organism, no matter how much it is enhanced, can beat the strength of a community of individual organisms, each with its own hydrocarbon-consuming specialty. In “every ocean we look at, from the Antarctic to the Arctic, there are oil-degrading bacteria,” says microbiologist Ronald M. Atlas of the University of Louisville, who evaluated genetically engineered microbes and other cleanup ideas in the wake of the Exxon Valdez spill. “Petroleum has thousands of compounds. It’s complex, and the communities that feed on it are complex. A superbug fails because it competes with this community that is adapted to the environment.”

If you can’t beat them, why not join them? Encouraging these bugs to work harder is theoretically possible through the use of fertilizers, such as iron, nitrogen and phosphorus. In fact, such an approach accelerated microbial activity in the sediment along the Alaska coast after the Valdez disaster. “We saw a three to five times increase in rate of biodegradation,” Atlas recalls.

The technique, however, is not likely to pay off in the Gulf. “In the ocean, how do you keep the nutrients with the oil?” asks microbial ecologist Kenneth Lee, director of the Center for Offshore Oil, Gas and Energy Research with Fisheries and Oceans Canada. He notes that “you don’t see bioremediation in the open ocean.” Even fertilizing onshore could prove problematic. Lee tried tilling oil-soaked wetlands in Nova Scotia where there was limited oxygen to increase microbial activity. “That didn’t work. We had large erosion as a result,” he says.

Chemical dispersants, which break up the slick, are perhaps the only way to boost microbial activity in the Gulf. “If the oil is in very small droplets, microbial degradation is much quicker,” says Lee, who has been measuring oil droplets to determine the effectiveness of dispersants.

Microbial consumption of oil, however, works best near the warm surface waters. “Metabolism slows by about a factor of two or three for every 10 degrees Celsius you drop in temperature,” notes biogeochemist David Valentine of the University of California, Santa Barbara, who is studying the microbial response to the oil spill. Breakdown of oil in deep waters, he remarks, “is going to happen very slowly because the temperature is so low.”

Unfortunately, that’s exactly where some of the Deepwater Horizon crude seems to be ending up. Researchers “saw the oil at 800 to 1,400 meters depth,” says microbial ecologist Andreas P. Teske of the University of North Carolina at Chapel Hill. His graduate student Luke McKay was on the research vessel Pelican, which first reported such subsurface plumes. Microbial activity is the only process to break down oil at depth. (At the surface, physical processes such as evaporation and waves help to eliminate oil from water.)

Microbes chomping on a spill the size of the Deepwater Horizon catastrophe come with a dark side. While eating the oil, the microbes consume the oxygen in the water, potentially asphyxiating aerobic organisms. Measurements of oxygen depletion weeks after the spill detected as much as a 30 percent drop in the Gulf of Mexico seawater. Although this amount of depletion has little impact on mobile marine life, scientists worry about anoxic effects down deep, where mixing with oxygen-rich surface waters is minimal. That spells bad news for the speedy breakdown of oil as well as for coral and other sessile deepwater life. Already dead sea cucumbers from the seafloor have bobbed to the surface, which could be a sign of a developing dead zone as much as an indication of oil toxicity itself.

Understanding how the microbes will work and how long they will take will require a better understanding of the amount of crude out there. Such predictions are “a function of size, and we don’t know size,” says microbial geochemist Samantha B. Joye of the University of Georgia. “We can’t begin to make any kind of calculation of potential oxygen demand or anything else.” Over time, that estimated amount has grown from an initial 1,000 barrels of oil per day to as much as 60,000 per day as of mid-June.

Whatever the case, that oil will linger in the environment for a long time. The microbes break down hydrocarbons in “weeks to months to years,” Atlas explains. Nature provides a solution, albeit a slow one.