A Hungry Microbe: This mutant strain of Alcanivorax borkumensis turns oil into bioplastic. Illustration by American Society for Microbiology

On April 15, five days before the explosion of the Deepwater Horizon, a group of European scientists made an eerily prescient announcement: they would be undertaking a global study of microbes that eat crude oil, both on land and in the ocean. "Petroleum-degrading bacterial communities harbor a considerable and hitherto unexploited potential," the head of the project, the German microbiologist Dietmar Pieper, explained at the time.

The "potential" to which Pieper was referring -- the idea of manipulating microbial life to better degrade oil pollution -- has been the subject of much buzz since the dawn of modern genetics in the late 1970s. After all, the reason our oceans are not black and sludgy is that many microbes eat hydrocarbons. The Gulf of Mexico has a particularly active suite of native oil-eaters, which chew through the equivalent of about two Exxon Valdez spills a year -- petroleum that seeps naturally into the Gulf from hundreds of rifts in its rocky basin.

To suggest, however, that such organic processes -- known as bioremediation -- might easily tidy up the current mess would be woefully inaccurate. The microbial feeding frenzy that inevitably follows an oil spill upsets the equilibrium of the ocean: blooms of bacteria, for example, deplete oxygen levels. And should heavy hydrocarbons settle onto the cold seafloor, blanketing one of the most diverse ecosystems on earth, the resulting tar field would persist indefinitely, like some sort of deep-sea parking lot.

Enter "enhanced bioremediation," or the directed use of microorganisms to restore damaged ecosystems, a controversial field some scientists believe is poised to define the future of environmental engineering. "Bioremediation holds great promise for some of our worst problems," says Terry Hazen, head of the ecology department at the Lawrence Berkeley National Laboratory in California. "There is no compound, man-made or natural, that microorganisms cannot degrade." Indeed, scientists have found microbes that will even turn hexavalent chromium -- the toxic substance implicated in the cancer clusters exposed by Erin Brockovitch -- into chromium III, a benign form of the element.

Scientists estimate that less than 1 percent of all microbial species have been identified so far. And in the ocean, microbes may represent 50 percent to 90 percent of all life. Manipulating such complex microbial systems, as ubiquitous as they are poorly understood, is akin to engineering the dark matter of biology. The challenge lies in manipulating one set of these players without disrupting a multitude of others. 
As part of the study announced in Germany this spring, academic and industrial researchers from nine different countries, mostly in Europe, will investigate bioremediation of polycyclic aromatic hydrocarbons, some of the most noxious compounds in petroleum. In the United States, by contrast, funding for bioremediation research has focused on acutely toxic industrial contaminants like chlorinated solvents. The BP disaster seems likely to draw attention back to where the field began.

The first organism to be patented, in 1981, was a novel strain of the bacteria Pseudomonas, engineered to do the oil-eating dirty work of four species in one. But to date, no oil spill has been successfully cleaned up using microbes cultured in the lab.

Part of the problem with using microbes for cleanup is that crude oil contains tens of thousands of different hydrocarbons, from simple gases such as methane to complex liquids like benzene. The organisms that eat these chemicals tend to be highly specialized. "They tackle a specific compound, and only that one," explains Andreas Teske, a marine microbiologist at the University of North Carolina at Chapel Hill. "In order to degrade a complete oil spill, you need a big community of specialized bacteria that act in concert."

The solution may lie in an ambitious new field called metagenomics, which involves analyzing the DNA of an entire microbial community in its natural environment. In 2004 the biologist J. Craig Venter ushered metagenomics onto the world stage when he set out to sequence every genome present in a water sample from the Sargasso Sea. In an ecosystem believed to support relatively little life, he discovered 1,800 species and 1.2 million previously unknown genes."With a tool like metagenomics, what you’re trying to understand is the full genetic content of all organisms in an environment," says David Valentine, a biogeochemist at the University of California, Santa Barbara, who, like Hazen, is running a metagenomic analysis of Gulf microbes.

If this knowledge is to lead to new technologies, their ultimate forms are difficult to divine. Dozens of companies have been marketing microbe-based remedies for the Gulf, but the Environmental Protection Agency says it is unlikely to endorse them, characterizing the field as immature. There is still a divide between those scientists who embrace the ambitious aims of meta-genomics -- sequencing large samples of DNA to seek out, for example, novel microbes or genes that may carry out important or unknown functions -- and those who favor a more targeted approach, studying genes and microbes already known to science.

The vision of Dietmar Pieper in Europe, like that of many scientists now at work in the Gulf, hinges on combining these two approaches. "I remember 20 years ago, the hope was that we would make a superbug that could do everything," he says, recalling how scientists quickly found that genetically engineered microbes rarely behave as expected in nature.

The most daunting forum of all, as the Gulf reminds us, is the open sea, complex and uncontained -- though Pieper sees its mastery on the distant horizon. "Everything in biology is moving so fast," he says. "Five years ago what we are doing now was impossible."