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FALL 2010
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Feature: Environmental Sciences

Living Waters

Cornell researchers delve beneath the surface to protect the aquatic environment.
by Marissa Fessenden ’09
Living Waters

Dennis Kullis

Heartrending photographs of oil-soaked birds and stranded dolphins drove home the scale of the environmental and ecological disaster called the Deepwater Horizon oil spill. When the leak was capped in August, some may have breathed a sigh of relief, but the clean-up effort continues. The damage goes beyond what television and photographs are capable of showing. Cornell researchers are among those working to understand and mitigate the oil’s devastating effect. They are striving to save wildlife in realms difficult to capture on film, working for the whales and corals deep beneath the surface, studying marine viruses and microorganisms in our groundwater too tiny to see, and even enlisting bacteria to help break down the brown slicks of oil. They are joining in the fight to protect the world from humankind’s mistakes.

Christopher Clark
University Photography

Christopher Clark, director of the Bioacoustic Research Program, uses marine autonomous recording units to listen to marine life both close to and far from the Deepwater Horizon spill site.

Listening to the Ocean

In the ocean’s depths, where the light dwindles to near darkness, marine creatures rely on their sense of sound to envision their world. Far from silent, the sea is filled with a chorus of communication. Whales sing month-long serenades, shrimp click to hunt and socialize, fish boom and bark to mark territory, and lobsters rasp their carapaces to attract mates. Sounds like these intrigue the researchers who listen to them.

Christopher W. Clark is one of those researchers. As head of the Bioacoustic Research Program (BRP) at the Cornell Laboratory of Ornithology, Clark sees the biological world in a unique way. “We’re interested in the hows and the whys of life in all its different forms,” Clark says, “how animals make sounds, how they communicate, how they make a living, and why populations of animals behave the way they do and interact the way they do.” BRP researchers listen to the singing world, Clark explains, to gain insight into the behaviors of birds, bats, elephants, fish, insects, and whales.

As the Deepwater Horizon disaster unfolded in the Gulf of Mexico, scientists and citizens alike worried about the toll the oil would take on the marine ecosystem.

This past July, Clark’s team of researchers deployed 21 marine autonomous recording units (MARUs) along a path about 75 miles off the coast and stretching from Louisiana to Florida. The research is led by scientists from the National Oceanic and Atmospheric Administration (NOAA), in collaboration with Oregon State University and Scripps Institution of Oceanography, as part of a vast effort to understand the effects of the oil spill.

The MARUs are eavesdropping on the sounds of marine life, from dolphins and fish, to sperm whales hunting for deep-water squid. The units will be collecting data from sites both far from and close to the Deepwater Horizon wellhead. It is hoped that the distant sites will provide an approximate picture of the acoustic ecosystem before the spill, while sites close to the oil will reveal the extent of the disruption. The devices likely will hear much more than whales. After retrieval, the researchers will analyze the data collected from the units.

Originally inspired by some of the tools that the U.S. Navy uses to listen for Soviet submarines, the MARU technology was further developed by Clark’s team of engineers and scientists. “I call them pop-ups,” he says, “because they are placed on the ocean floor, and when they are finished recording they travel to the surface at about a meter per second and pop up when they reach the surface.” The MARUs currently in the Gulf will listen throughout the fall, and researchers will collect them at the end of this year’s hurricane season. Clark emphasizes the need to redeploy the devices and listen further to the creatures in the Gulf.

“Unfortunately, we have not as a society done a good job of paying attention to the Gulf of Mexico,” Clark says. “We do not have good baseline data on how that ecosystem works when it is healthy. We take an enormous amount from the Gulf in terms of resources, but we have not given back.”

Researchers are scrambling to understand what lives in the Gulf and what may need saving from plumes of oil. Clark explains that even decades of experience listening to the ocean might not give the BRP a good idea of the creatures threatened by the spill. “Every time we go to a new location we are surprised,” he says. When Clark deployed MARUs off Long Island and New York Harbor he was shocked to hear six species of whales within the first few hours of recording. “We heard blue, fin, humpback, minke, right, and sei whales. We have a population of fin whales just outside of New York Harbor, in an area visible from the top of the Statue of Liberty if you looked out into the ocean. And they are singing there all year long.”

As with any environmental conservation effort, researchers need to know what animals are there before they can figure out how to protect them. In Massachusetts Bay, a string of MARUs is part of the Right Whale Listening Network. The MARUs gather data that is then analyzed by researchers at the Lab of Ornithology. If the rare right whale is heard, ships are alerted and change their course to avoid harming the creature.

Though his work reveals vital information about marine ecosystems, Clark never loses sight of the beauty of his job. “As scientists we analyze the songs of whales and extract all of these measurements, but when you sit down and listen, you aren’t thinking of measurements, numbers, tables, and histograms. You’re immersed in and overwhelmed by the experience of listening to the majestic symphony of these giant ocean animals.”

For more on the Right Whale Listening Network and to explore whale sounds, visit

Drew Harvell

Drew Harvell (shown here) says coral is a desperately understudied species, but now the sequenced coral genome will allow scientists to understand the genetics of immunity.

Climate Change and Corals

Coral reefs are called the rainforests of the ocean, home to the beautiful, the colorful, and the diverse. These ecosystems are built on the interaction between the tiny invertebrates that make the calcium carbonate structure of the coral and the algae that live within them. The algae use sunlight to photosynthesize, providing the coral polyps with carbohydrates, while the corals build a protected home for the algae.

Corals are extremely sensitive to the effects of climate change. Acidification caused by rising carbon dioxide levels and warmer ocean temperatures conspire to make corals more susceptible to disease. This vulnerability is one of the research foci of Drew Harvell, professor of ecology and evolutionary biology and the new associate director of the Cornell Center for a Sustainable Future.

Harvell’s work with gorgonian corals, or sea fans, follows the melanization response. Corals have specialized cells that identify pathogens and literally wall the disease off by laying down a barrier of melanin. The invading pathogen or fungus is trapped on the other side. A sick sea fan displays lesions of infected coral surrounded by a bright purple ring, visible evidence of the melanization response.

What Harvell does not yet know is exactly why warmer waters and acidification lower coral disease resistance. “We have made amazing advances in the past five years towards understanding how coral immunity works,” Harvell says, “but it is desperately understudied compared to other species. We just now have a coral genome sequenced that can allow us to understand the genetics of immunity.”

Even if we somehow manage to curtail carbon dioxide emissions, we are still committed to several decades of warmer climate. The best hope for coral reefs is to help them shore up their defense against pathogens by giving them as healthy an environment as possible.

“We think that excess nutrients in the seawater can weaken the immune system,” Harvell explains. “Zones of the ocean where there are excess nutrients—such as from fish farms or sewage runoff—can also be a source of new pathogens.” Local management strategies can reduce the pathogenic load and help protect the fragile coral ecosystems.

The Deepwater Horizon disaster in the Gulf is a source of concern for nearby coral reefs. “Even the change of the water chemistry associated with the oil dispersants could seriously compromise coral immunity,” Harvell says.

Ian Hewson

Ian Hewson studies ocean viruses' role in the elemental cycles of the earth.

The Ocean’s Tiniest Inhabitants

The ocean is teeming with a vast diversity of life, all the way down to the microscopic level. In a single milliliter of sea water there may be millions of zooplankton, algae, bacteria, and even smaller denizens of the deep: viruses.

“There are a lot of viruses out there,” says Ian Hewson, assistant professor of microbiology. “If you counted all of the viruses and stacked them up, they would reach to Alpha Centauri and back. The biomass of marine viruses is about equivalent to 30 million blue whales.”

Viruses and other microorganisms play a big role in the elemental cycles of the earth. They move inorganic elements like carbon, sulfur, and nitrogen in and out of the food chain. For example, cyanobacteria are like microscopic plants, sucking up carbon dioxide and making it accessible to other creatures. Viruses that infect cyanobacteria release the carbon into the ocean when they kill their hosts. This cycle helps to sequester excess carbon dioxide in the atmosphere, but marine viruses’ influence on our planet go much further. Infection rates of microscopic ocean life could have effects that researchers are only just beginning to realize.

Each virus is very specific, perhaps infecting only one or two different species. This means that viruses have a profound sway on the structure of microbial communities. Hewson has observed that terrestrial viruses can be found at sea, miles from where freshwater rivers mix with salt water and where runoff from terrestrial rainfall enters the ocean. These disturbances change marine virus populations and, in turn, the microbes that they infect.

“Every day there is a battle between the bacteria and the viruses killing them,” Hewson says. “There is constant turnover.”

To understand what the changing viral load may signify, Hewson filters ocean water samples down to the smallest creatures—viruses—and looks at the genetic material. The DNA reveals the viruses present and their role in elemental cycling. The RNA provides information about the proteins and enzymes the bacteria use to respond to viral threats.

Hewson has found that microorganisms and viruses are extremely important in the marine ecosystem.

Eugene Madsen
Jason Koski/University Photography

Eugene Madsen studies how microbes digest toxins in our environment.

Microbes in the Groundwater

Below the surface of a gently sloping forested hill above the Hudson River, billions upon billions of living creatures are busy at work, breaking down pollutants and purifying the soil and groundwater. This site is one of more than 2,000 in the Northeast contaminated by coal-tar waste from an old coal gasification plant.

For over 16 years, Eugene Madsen, MS ’81, PhD ’85, professor of microbiology, has studied how microorganisms are able to digest toxic compounds like naphthalene, the key pollutant at the South Glens Falls site.

This method of pollution management is known as natural attenuation. For sites that pose no immediate health or ecosystem threat, it is the best strategy to combat contamination. Understanding the process is necessary for effective management, and Madsen’s site is shedding light on the key players.

“When a tree falls in a forest, microorganisms are there,” Madsen explains. “The tree disappears and nutrients within its biomass are converted to inorganic compounds. If that didn’t happen, all of those nutrients in the fallen tree would not become available to the next generation of trees.”

The same process happens to organic pollutants like coal-tar waste and oil, says Madsen. “Unquestionably for the bulk of the oil recently spilled in the Gulf of Mexico, natural attenuation is going to be the major means by which the contamination is eliminated.”

These ecosystem services are performed by tiny, overlooked heroes who purify the water we drink and the land we cultivate.

“It is a longstanding mystery,” Madsen says. “We know that microorganisms are responsible for the cycling of nutrients in soil, in groundwater, in oceans, in sediment, and in sewage. They are everywhere, but only rarely have we deciphered the identities of ecologically important microorganisms.”

One gram of soil contains approximately one billion microbial cells and perhaps greater than 10,000 bacterial species, but determining which ones are active, consuming and recycling nutrients, detoxifying pollutants, is a huge challenge. Madsen used a stable isotope of carbon—carbon 13—to figure out which was digesting the naphthalene. He was able to isolate and characterize Polaromonas naphthalenivorans, a bacterium that can now be properly acknowledged as an environmental hero.

P. naphthalenivorans is only one of many. As pollutants are broken down, other microorganisms snatch up the leftovers. “As the pollutants are metabolized,” Madsen says, “microbial processes are likely to change the carbon cycle as well as components in the nitrogen and sulfur cycles. Everything is connected.”

Gary Harman
Rob Way

Gary Harman (left) and Thomas Bourne have developed an oil absorbent called OilMaster from recycled dairy cow manure.

Eco-friendly Oil Absorbents

Much of the oil from the Deepwater Horizon disaster has been skimmed or burned from the ocean’s surface, but the remainder is still wreaking a toll on the beaches and wetlands surrounding the Gulf of Mexico. Once the oil reaches the reeds at the border of the wetlands, or wave and tidal action emulsifies the slicks into microscopic droplets, mechanical, large-scale cleanup efforts are largely useless.

Gary Harman, professor of plant biology at the New York State Agricultural Experiment Station in Geneva, has helped to develop a product from recycled dairy cow manure called OilMaster, a successful ecologically friendly oil absorbent.

“The OilMaster concept came about because we were interested in the chemistry of lignins,” Harman explains. “Lignins are extremely effective because they have hydrophobic and hydrophylic groups, so they take up either oil or water.”

When cows consume plant material, they digest the cellulose and leave the lignin. “For OilMaster’s purposes, a cow’s digestive tract is a lignin factory, exposing the lignin while leaving the cellular structure. The result is material that is essentially little sacks—the empty cells—that soak up oil,” Harman says.

The OilMaster product is manufactured by Terrenew, a company headquartered at the Cornell Agriculture and Food Technology Park, with production facilities in Seneca Falls. The CEO of the company is Thomas Bourne, and Harman serves as the Chief Scientific Officer.

Terrenew’s OilMaster can be made into booms that will soak up oil before it reaches the marshes, or scattered as loose material to bind oil and makes it less harmful.

But absorption is only one aspect of the product’s abilities. Because OilMaster is derived from dairy cow manure, and although it has been treated to remove pathogens, the microbial activity of the product can break down the captured oil. The large surface area of the product makes it an ideal habitat for the oil-degrading biofilms formed by microorganisms.

“We need to look more in depth at the microbial interactions and learn how to enhance the bioremedial abilities and oil degradation,” Harman says. “It is extremely promising. Without adding any additional microorganisms, we already see 20 to 30 percent degradation within a week.”

The product is manufactured in several forms, as granular absorbents and as pads. Harman is currently securing funding to develop a version that could be used to clean up oil spills.

“We’re now ready to go to the next phase, which is large–scale production of our products,” Harman says.