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On a chilly September morning, 12 miles off the coast of Monterey Bay, California, the notoriously rocky research ship I’m on tosses about, causing seasickness for even the seasoned crew. But below us, all appears eerily quiet in the waters of Monterey Canyon, which plunges to depths of more than two miles. On giant screens inside the control room, we watch the ship’s robotic submersible make its 45-minute descent through the inky darkness. Nothing is visible aside from a steady drizzle of “marine snow,” nutrient-rich pellets of organic matter, gliding past like an upside-down snowstorm. The vehicle settles gently onto the soft, silty bottom 1,900 feet below us and cruises toward its destination: the skeleton of a 33-foot-long juvenile humpback whale. The research crew has come to study this “whale fall,” the term given to the sumptuous feast left behind when a whale dies and sinks to the seafloor.

Under the submersible’s marauding lights the scene takes on a ghoulish green hue. As it nears the whale fall, barren ground gives way to signs of life. Sea stars, sea urchins, and flatfish stud the bottom like quiet sentinels. A jellyfish pulses gracefully across the screen. A lone hagfish darts into the headlights and quickly races away, and in the distance a sablefish cruises by, seemingly oblivious to the glaring headlights. The vehicle sidles up to the oceanic graveyard, revealing a complete whale skeleton obscured by a tangle of seaweed.

“Can I play?” asks Shannon Johnson, a molecular ecologist from the Monterey Bay Aquarium Research Institute in Moss Landing, taking the pilot’s seat. “There they are,” she exclaims with the exuberance of a proud parent. “Hello, girls.” She’s referring to one of the more flamboyant inhabitants she’s here to collect—worms of the genus Osedax (Latin for “bone devourer”), which cover the bone like a shag carpet. While the peacock-plumed females are about the width of a nail and the length of a pinky finger, the males are mere microscopic threads inside the females’ egg sacs that seem to function as little more than sperm factories. A five-foot-long robotic arm deftly retrieves a rib blanketed with hundreds of Osedax, their iridescent tubes waving madly in the current. Minutes later, a second, less nimble arm, which the crew aptly calls Mongo, begins breaking the four-foot-long bone into manageable pieces. After a painstaking half-hour, Mongo snaps the worm-covered bone in two and clumsily drops the pieces into a treasure chest–sized “bio box” that hauls samples to the surface.

As the vehicle settles gently on the deck, Johnson hurries over, sticking her bare hand into the stinging cold seawater to inspect the bones covered in snotty green worms—less striking in the flesh than in their bigger-than-life visage onscreen. She also quickly processes sediment cores, slicing them into thin hockey puck–like samples used to study mud-dwelling microbes. While perhaps the least glamorous members of whale fall communities, these bacteria are the workhorses of the whole ecosystem. “Bacteria are the beginning and the end of the food chain,” says Johnson. “Everything has to live with or off of bacteria to survive.”

Whales roaming surface waters are supporting ecosystems far below that, until 1987, scientists didn’t even know existed. A diverse assortment of bacteria helps sustain these communities. Some provide nutrition to organisms in exchange for safe housing, while others become food for grazers like snails and crabs, which dine on the juicy bacterial mats and are, in turn, eaten by larger creatures. This life-after-death progression recycles carbon and disperses it throughout the ocean—some may even make its way back to the surface to provide nutrition for living whales.

Johnson is among a small cadre of researchers employing extreme—and sometimes unpleasant—measures to understand whale fall ecology. Some 70,000 whales die every year along migratory routes, usually from starvation, injury, or disease. Yet finding a whale fall in the abyssal depths of the ocean isn’t easy, since the animals sink at random and can be spaced many miles apart. Despite the challenges, researchers are continually making new discoveries about this environment and its inhabitants. Of the roughly 60 new species discovered so far, many may be uniquely adapted to whale falls. And further research will likely turn up hundreds more species, says Johnson. “We can’t understand how the ocean works if we don’t understand the little things,” she says. “We’ve barely scratched the surface.”

The death of a single whale brings a bonanza of nutrients to the barren waters of the deep sea, delivering an organic parcel equivalent to thousands of years’ worth of marine snow. When a whale, elephant seal, or any large animal falls, it supports a range of fauna, from tiny bacteria (and potentially even viruses) to mobile scavengers like sharks and hagfish, creating an ecosystem that can survive for decades. When a whale dies, the scavengers, including squat lobsters, sleeper sharks, and crabs, rip apart the flesh in a feeding frenzy that can last a decade—the “horror movie stage,” as marine biologist Adrian Glover, of London’s Natural History Museum, puts it. As bits of soft tissue rain down, bringing a pulse of nutrients, a motley entourage of opportunistic worms, mollusks, and crustaceans move in.

Once the whale is stripped bare, a dense community of anaerobic bacteria dines among the decaying bones. These “sulfate-reducing” bacteria release sulfides up to eight feet into the surrounding sediment, supporting a rich mix of bacteria, mussels, clams, and worms. Just as some animals derive energy from the hydrogen sulfide and methane leaking out of hydrothermal vents and cold seeps on the seabed, similar “sulfur-loving” organisms found at whale falls get their metabolic fix from the chemicals released by whalebones. Finally, the carcass acts as a sort of reef, providing habitat for filter feeders and worms such as Osedax, which excavate the lipid-laden bones. Bacteria either live inside Osedax and other organisms as symbionts, or they provide a feast for worms and snails. Fish, octopuses, and crabs move in to munch on the degraded whalebones, consuming worms and mussels along the way.

Since natural whale falls are difficult to find, researchers must sink beached dead whales. To date scientists have sunk more than 25 whale falls and monitored about six natural ones. “Pebbles,” the one Johnson is studying today, washed up in April 2007—smelly and decaying—amid the stunning vista of the 18th green at Pebble Beach in sight of $2,000-a-night hotel rooms. Johnson received an urgent call from a whale-stranding network and mobilized her team. “Every time a dead animal washes up on the beach, I get like five phone calls,” she says. Donning hip waders, rubber gloves, and sweatshirts destined for the trash, the researchers often gut the whales, using machetes to remove the blubber, before they tow them to a drop spot. But towing and sinking a five-ton juvenile, let alone a 35-ton adult, is no small undertaking. When whales die, they quickly bloat up with decompositional gases, becoming buoyant, so it may take several tons of scrap metal, mostly from old train wheels, to weigh them down. (In nature, whales often sink immediately before gases build up. But those that do bloat float for days to weeks before washing ashore or being ripped apart by scavengers at sea and descending.)

Ashley Rowden, a marine ecologist at New Zealand’s National Institute of Water and Atmospheric Research, understands the inherent rigors of the science. On one occasion, Rowden’s team first had to acquire support from indigenous Maori, who prize the whales’ enormous jawbones. When a 40-ton sperm whale washed up in 2008, they raced against a thunderstorm in the notoriously turbulent Cook Strait. Wearing masks to avoid breathing in dangerous particles from the decaying animal, the crew endured several hours of frantic rope work before finally securing it to their vessel. “It was a bit like the old days,” says Rowden. “Every hand was needed on deck, and everyone was slipping all over the place because of the amount of blubber.” It then took more than 24 hours to tow the whale to sea. “We were all very glad when it finally made its way to the bottom.”

In 2007 and 2008 Glover, Thomas Dahlgren, a marine biologist at Sweden’s University of Gothenburg, and Craig Smith, a University of Hawaii at Manoa biological oceanographer, sank whalebones in frigid Antarctic waters, where whale fall fauna haven’t previously been studied. This past March they recovered some of the bones. To their delight, they found a new species of Osedax. Next they’ll deploy bones off the Antarctic Peninsula to gauge the fauna’s diversity and geographical distribution. “The Antarctic is one really fascinating piece of the puzzle,” says Smith. “It’s a big habitat with a long history of whales, and it is somewhat isolated from other regions. So I think we may find really unusual diversity there.”

So far the most exotic find has been the nearly 20 species of Osedax worms. In 2002 Johnson’s colleagues turned up the first two species on an unknown whale carcass in Monterey Canyon. Osedax have evolved a nightmarish feeding strategy. They have no eyes, mouths, or stomachs but possess elaborately branching root systems that tunnel into whale bones, whittling them into something that resembles Swiss cheese. From the marrow, the worms’ roots extract fats and oils, which bacteria living inside the roots break down. Never before had scientists found this sort of microbe living in a symbiotic relationship with another animal. It isn’t clear where the bacteria come from: Osedax don’t have them as larvae or seem to inherit them from their parents. “They’re somehow getting them from the environment, but we haven’t found them in the environment yet,” says Johnson. “They’re out there somewhere.”

Osedax evolved roughly 40 million years ago, about the same time scientists believe many whale species arose. To learn more about how specialized the worms are for life on whalebones, Johnson, led by Monterey Bay Aquarium evolutionary biologist Bob Vrijenhoek, planted cow bones near a study site. To their surprise, they found six of the eightOsedax species from nearby whale falls on the cow bones—though there were only a handful of worms; thousands can inhabit whalebones. So the giant, fatty whalebones may be the meal of choice, though preliminary data aren’t conclusive. The team also recently detected some 100 worms on an elephant seal carcass they sank, but it’s not yet clear how much biodiversity such bones can sustain. Whereas smaller cetaceans’ bones may decompose totally in three months, some whalebones may support fauna for 80 years.

Still, the discovery provides a provocative clue about how larvae find whalebones, since they may travel hundreds of miles before encountering another skeleton. “It’s a pretty risky life history strategy to float around in the ocean waiting for a dead whale, which are few and far between,” says Johnson. Scientists estimate that only one larva in thousands may successfully settle and reproduce. Studying more species will likely reveal a range of feeding strategies, Smith says, including generalists that feed on a variety of bones and specialists that feed only on whale carcasses.

Researchers are also trying to determine the relationship between whale fall organisms and those that thrive near deep-sea volcanoes. At least 12 species are common to both environments, including clams that rely on bacteria to mine sulfide seeps. “It’s quite reasonable that some of these clams may use whale falls as dispersal stepping stones,” says Smith.

As exotic and diverse as whale fall communities are proving to be, whaling in the 1800s and 1900s may have drastically reduced the number of carcasses that sank. “The decimation of whales during the last century also has consequences for an entire community of decomposer animals that live at the bottom of the ocean,” says Vrijenhoek.

Many whale species are rebounding as a result of the International Whaling Commission’s moratorium on commercial whaling, adopted in 1986, though humpbacks, fin, right, and blue whales are still well below their pre-whaling numbers (estimated to have been more than a million great whales). Biologists hope depleted populations will rebound to at least 50 percent of pre-whaling levels over the next few decades. Even if they do, Smith estimates 15 percent of whale fall specialist species may die out; there’s usually a lag between habitat loss and consequent extinction. In the North Atlantic, where many whale populations hover at 25 percent of pre-whaling levels, Smith estimates that about one-third of whale fall specialists may have already been wiped out. “Removal of whales from the ocean will cause the extinction not only of whales, but likely dozens to possibly hundreds of deep-sea species that appear to rely on whale fall communities to complete their life cycle,” explains Smith.

Despite the potential loss of species—some perhaps yet unknown—scientists expect to discover more connections between the behemoths above and their graveyards below. And, says Dahlgren, “For people looking for additional reasons to save the whales, this is one: a clear connection between the number of large-bodied whales and marine biodiversity.”