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This article is part of ����APP’s Fossil Fuel Boom series, which explores how oil and gas extraction in the United States is affecting wildlife, habitat, and people. Read more stories .

In the inky black waters nearly a mile below the surface of the Gulf of Mexico, Erik Cordes came upon a disturbing scene. Sea fans, waving in the darkness, were coated in a sticky black substance. Corals were unusually pale, with tissue falling off the skeleton. It was two and a half years after the 2010 Deepwater Horizon oil-rig explosion, and Cordes, , and his colleagues were surveying the seafloor roughly seven miles from the site of that disaster. The samples they took confirmed that the black substance was oil from the BP spill.

When oil began billowing into the Gulf following the explosion, responders raced to protect the region’s most valued and visible resources: pristine beaches and already fragile coastal marshes. The first priority was to keep the oil from inundating the shoreline. Seabirds and sea turtles coated in gooey oil became the iconic images of the spill. Yet out of sight, far below the surface, much lesser-known organisms faced an uncertain outcome that is still unfolding in one of the country’s most heavily drilled oil fields. Cordes and a number of other marine scientists are working to assess the harm inflicted on these organisms, and what another disaster could mean for them. These deep-sea dwellers help recycle nutrients from the ocean depths to the surface and back. They also form the base of the food chain that humans, birds, and many other organisms rely on, so their welfare is critical to the entire Gulf ecosystem.

Despite being the biggest oil spill in our nation’s history, the Deepwater Horizon disaster barely slowed the forward march of energy development in the Gulf of Mexico. While the oil was gushing, the Obama administration issued a temporary moratorium on deep-water drilling operations there to determine the safety measures needed to prevent another spill. The government lifted the ban five months later and decided to create a new agency to oversee offshore drilling operations.

Today oil companies pump 1.3 million barrels of oil from the Gulf every day, down from 1.5 million in 2010. Some 20 percent of the oil and 5 percent of the natural gas produced in the United States comes from offshore federal waters, the vast majority of it from the Gulf. More than 5,700 active oil and gas leases operate there, covering roughly 31 million acres. Oil and gas production continues to move into waters that are increasingly deep and farther offshore. Now nearly 80 percent of the oil produced in the Gulf comes from deep-water oil fields 1,000 to 10,000 feet deep.

The vast oil and gas deposits buried beneath the seafloor that make this such a hotbed of energy development also form the foundation of that deep-water ecosystem. Oil and gas seep slowly into the ocean through faults and cracks in the seafloor, providing a feast for hydrocarbon-loving microbes. As they feed off the chemical energy, they release gases and carbon. Over time, giant mounds of calcium carbonate form over the fissures, providing the cement on which corals can settle, a fact that researchers only recently uncovered. So far they’ve found a rich array of life—rare black corals, gorgonian sea fans, anemones, brittle stars, and multitudes of fish and crustaceans—in these regions beyond the reach of sunlight, 650 or more feet beneath the surface.

Some of these creatures of the deep play a critical role in the global carbon cycle, recent research indicates. In a nightly parade, plankton, small fish, and shrimp migrate upward from the ocean depths to the surface layers to feed on the abundant food in what is known as the photosynthetic zone. By eating these carbon-rich organisms and then swimming back down before dawn, the migrating sea life pumps carbon throughout the ocean, the extent to which biologists are still unraveling.In addition, some shallow-water species of fish, shrimp, and squid migrate downward to feed on deep reefs each day, returning to the surface at night. In this way, bottom dwellers act as a key link for the whole Gulf ecosystem.

“We are onlybeginning to understand the ways in which the deep sea is connected to the rest of the ocean,” says Cordes. “It’s one of the last pristine habitats on earth, and we’re starting to cause damage to it before we’ve ever even seen it.”

Cordes and his team have made several return trips to the deep-sea site where he saw the oil-coated sea fans to document its recovery or demise. “Some look like they’re definitely getting worse and probably won’t recover,” he says. Other parts of the same reef suffered less severe harm and are getting healthier.

Corals may face the same fate. Effects on reproduction or slowly evolving cancers are going to be nearly impossible to measure or document, says Charles Fisher, a deep-sea biologist from Penn State and another lead investigator on the team. “We know so little about what’s normal for corals in the deep sea.”

Then there are microbes. When the oil hit the surface, these microscopic organisms broke it down faster than expected in the Gulf’s warm upper waters. It was a different story in the depths. Some of the crude fell to the seafloor in “oil snow blizzards,” says Samantha Joye, an oceanographer from the University of Georgia. In the ocean, detritus and fecal pellets—which scientists call “marine snow”—continually falls through the water column. During and after the spill oil glommed onto the detritus, forming sticky globs and strings that eventually settled on the seafloor. At this depth the microbes are less active and therefore don’t metabolize the oils. “The stuff is just sitting there,” says Joye. “It’s not getting degraded at all.”

But it doesn’t stay there. Bottom currents can stir up the residues, which then become re-suspended in the water column and poison the organisms that live there. Oil contains polycyclic aromatic hydrocarbons (PAHs), compounds that, at high enough concentrations, can be toxic to sea creatures. PAHs—known to cause cancer and to induce changes in human DNA—also accumulate in tissues and pass through the food chain.

Just as determining a human patient’s health requires reliable diagnostic tools, understanding the recovery of the Gulf’s deep-sea ecosystems will require long-term monitoring and manpower, and sufficient ships and cruise time—all in short supply. “Any species that you want to name, we don’t know how many there are and how vulnerable they are,” says Ian MacDonald, an oceanographer from Florida State University.

The Deepwater Horizon oil spill raised awareness about the value and fragility of the Gulf and led to critical research funding. In May 2010 BP committed $500 million over a decade to support independent research. The funding has made it possible for researchers to do real-time studies in the immediate aftermath of other pollution events, such as the blowout of the Hercules 265 drilling rig in the Gulf of Mexico this past July.

Given that energy experts say future spills in the Gulf are inevitable without more stringent drilling regulations, there’s no time to waste in discovering what’s at stake.