These dark sediments, recovered from more than 100 meters below the seafloor beneath 5,000 meters of water at the Peru Trench, contain methane hydrate (the white material here). It quickly fizzes away at room temperature and sea level. Photo by Leg 201 Shipboard Scientific Party; ©2007 Endeavors; click to enlarge.
Life Down Deep
by Jessica McCann
Go thousands of feet down to the bottom of the sea. Feel the cold, dark, weight of the ocean. Then tunnel down farther, deep below the seafloor, and find there an overwhelming abundance of life: countless single-celled organisms that live at extreme pressure and feed where most life would starve. The members of this microbial universe might be tiny, but they affect everything from nutrient cycling in the ocean to global climate change.
Life at the extreme
Andreas Teske studies Archaea, one of the three main “kingdoms” of life. The other two kingdoms are Eukaryotes — everything from plants to humans — and Bacteria. Bacteria and archaea live as single cells with simple structures, and, even with their microscopic size, make up at least one tenth of the weight of all life on Earth. Some scientists believe many of the harsh environmental conditions that foster microbial growth, such as the sediment found below the ocean floor, might resemble conditions on early Earth — or perhaps another planet. “These environments harbor extremely tough microorganisms that challenge our usual conception of where life can exist and under which conditions,” says Teske, associate professor of marine sciences. And these microbes are old. The microbial history of life on Earth accounts for 3.6 billion years. Animals have been around for only 600 million years.
Archaea are similar to bacteria in basic cell structure, but differ in numerous features of genome content, how their genes are expressed, and metabolism. “They are as different from bacteria as from all eukaryotes, such as animals and plants; they are a life form of their own,” Teske explains. Often called “extremophiles,” some archaea can live in habitats where most other life would perish — shallow pools nearly saturated with salt, the rim of a boiling-hot deep-ocean vent spewing sulfuric acid, or cold, oxygen-depleted mud at the bottom of the ocean.
Drilling for microbes
Teske’s team wants to identify the microbial species that are alive and kicking deep in the subsurface sediment. To do this, they first collect sediment cores from several feet below the ocean floor during two-month-long voyages aboard the JOIDES Resolution. (JOIDES stands for the Joint Oceanographic Institutions for Deep Earth Sampling). The Resolution is operated by the Integrated Ocean Drilling Program (IODP), a multinational group of scientists that conducts seagoing expeditions to study the history of Earth as recorded in sediments and rocks beneath the seafloor. And IODP includes subsurface microbiology in its mission.
The Resolution houses seven floors — nearly twelve thousand square feet — of laboratory space equipped for research in microbiology, geophysics, paleontology, and several other disciplines. Once the ship has reached the drill site, the Resolution can retrieve sediment from a depth of over five miles — just over nineteen Empire State Buildings stacked one on top of the other.
The Resolution at sunset. Photo courtesy Leg 201 Shipboard Scientific Party; click to enlarge.
Teske was on board the Resolution for Ocean Drilling Project Leg 201, during which scientists obtained cores from deep below the subsurface at a site off the coast of South America, known as the Peru Margin. The cores represent a vertically stratified record of life and geology in the deep-sea sediment. While often tens of feet long and packed with microbes, each sample contains limited material for the diverse needs of the scientists on board.
Before the cores are brought on deck, the seagoing scientists and IODP staff carefully plan how to divide samples between researchers and projects. Once the core arrives at the surface, it “has to be inspected and measured,” Teske says. “How much of it is actually sediment; how much is water? Core recovery is sometimes not complete.” The cores are often over-pressurized and in danger of exploding once they come to the surface, so the IODP lab staff drill little safety holes through the plastic core liner to let gases escape safely. In the meantime, the scientists stand by with their various tools and laboratory equipment, waiting to get their precious core samples.
Aboard the Resolution, one of Teske’s jobs was to carefully inspect each core for seawater contamination. Whenever the crew harvested a core, he used a syringe to take samples from its margin and center. Seawater contamination could render a sample useless, because scientists wouldn’t be able to discriminate between organisms that live in the seawater and those that can survive deep in the sediment.
Teske samples halfcores. Photo courtesy Leg 201 Shipboard Scientific Party; click to enlarge.
Naming names
The information that comes out of each sediment core is a molecular signature of what is growing in the subsurface sediment. Typically, scientists can use laboratory tests to identify and describe new bacterial and archaeal species after isolating and growing them in pure cultures. Since many of the subsurface extremophiles can’t grow at sea level or in a lab, Teske and other scientists rely on new tools to describe these species.
Teske’s team identifies organisms based on a molecule required for generating proteins in any cell — ribosomal RNA. It’s useful for classifying Archaea, Teske says, “and, in fact, for the entire tree of life that encompasses Bacteria, Archaea, and Eukaryotes.” Ribosomal RNA is essential for life, but every species has a few unique RNA sequence changes. So scientists are able to isolate total RNA from sediment samples, make copies of what ribosomal RNA is present, and then sequence each molecule, matching the different sequences with their parent species.
Teske and collaborators have published a study that categorizes deep-subsurface archaea based on their RNA sequences. In the past, scientists have used DNA to identify families of organisms that reside in extreme environments.
But DNA can be present in fossilized form, long after individual cells or whole species have died off. Only living cells can generate RNA, and so examining it gives scientists a snapshot of what is alive and active deep in the sediment.
Teske’s group also collaborated with German scientists who studied archaeal lipids in the sediment cores. Lipid components of cellular membranes are made only by active cells, and differ between species — another tool for putting together a complete census of deep-sea microbial life.
Tiny cells with a big impact
It’s good to know what’s living in the deep-sea sediments, but more useful to know what they do. While most life emits carbon dioxide as a waste product, some archaea in the subsurface emit methane instead. At the cold temperatures and extreme pressures where the subsurface microbes thrive, the methane remains solid and in the form of methane hydrate, says Mark Lever, a graduate student in Teske’s lab. But temperatures are rising across the globe. As the water near the bottom of the ocean begins to warm, the methane hydrate could effectively melt into its gaseous form, bubble up to the surface, and become part of the atmosphere.
Why should we care?
Because methane is a potent greenhouse gas, absorbing twenty times more energy from infrared radiation (think heat) than carbon dioxide does. If the solid methane in the deep subsurface begins to enter the atmosphere, a dangerous feedback loop may begin: melting and release of methane leads to more warming of the deep oceans, which leads to even greater methane gas release. Subsurface solid methane stores are far greater than Earth’s known coal and natural gas reserves, and could threaten the global climate, Lever explains. Scientists such as Teske believe that studying the microbial biosphere below the ocean floor will add to our current understanding of climate cycling and change.
Teske and his students have traveled the world’s oceans and seas examining life at the extreme. He insists, however, that you don’t have to go far to find microbes living where nothing else can. “When traveling, look at new or seemingly familiar corners of the world with a microbiologist’s eyes. Visit a smelly salt marsh. Look at hot springs. Each of them is a microbiological universe.”
Andreas Teske is an associate professor in the Department of Marine Sciences. He and collaborators Kai-Uwe Hinrichs of the Max Planck Institute, and Chris House and Jean Brenchley from Penn State, published their work describing subsurface microorganisms in Proceedings of the National Academy of Sciences.
