Life in the cold and dark

Posted: April 15, 2008

Courtesy: Antarctic Sun

By Peter Rejcek

Alison Murray studies tiny critters with a potentially big role in the marine ecosystem of the Southern Ocean surrounding Antarctica.

Murray is interested in how bacterioplankton, the bacterial component of plankton communities, make their living in the Antarctic winter waters, when the long austral night presumably shuts down or slows many biological processes that rely on solar energy.

Murray and her colleagues, who include several international collaborators, as well as Joe Grzymski, a colleague at the Desert Research Institute, and Hugh Ducklow, principal investigator for the Palmer Long Term Ecological Research (PAL LTER) program, will head to Palmer Station in July, the middle of winter. From the U.S. Antarctic Program (USAP) research station, they will collect and analyze the marine microorganisms, which also include a form of life distinct from bacteria called archaea.

“The concept for the project is trying to understand what is unique about the organisms that are adapted to Antarctic winter,” explained Murray during a phone interview from her office at the Desert Research Institute in Reno, Nev.

An International Polar Year (IPY) project, the study will focus on one of the key themes of the two-year-long polar science campaign: life in the cold and dark. Murray’s proposal dovetails nicely with a series of field projects she conducted earlier this decade from Palmer Station to characterize bacterial diversity and study their gene expression under a program focusing on extreme environments.

Genetic expression studies what genes for an organism are “turned on” or “turned off” under different environmental conditions.

Grzymski explained: “If an organism is really stressed out, it ‘turns on’ stress-response genes and ‘turns off’ genes that detract from the stress response.

“Gene expression studies monitor what the cells are actually doing; it is one step beyond identifying the key players in the Antarctic winter and summer bacterioplankton communities,” he added.

For example, organisms that live in ice and subzero temperatures might need to “turn on” genes that encode ice-binding proteins during a particularly low-temperature day in the sea ice, while simultaneously down-regulating, or “turning off,” genes involved in growth and metabolism to deal with the stresses due to ice crystal formation, which can break cell walls.

The marine ecologists are particularly interested in figuring out how gene expression varies from season to season. From Murray’s previous work, they already know that composition and diversity of these microorganisms varies greatly from summer to winter.

Murray said the question then becomes, “What is different between the organisms that dominate the plankton during austral winter and summer?” The answer lies in genome sequences of these organisms.

Ducklow noted Murray’s previous work was instrumental in telling the researchers something about the composition of bacterial communities. It’s only in the last 10 years, he said, that researchers have been able to make such distinctions thanks to advances in molecular ecology and genomics, the study of genes that reveal biological diversity and the entire DNA sequence of an organism.

“We just worked on ‘bacteria’ without any real attention to which ones were doing what,” explained Ducklow, a marine ecologist and co-director of The Ecosystems Center at the Marine Biological Laboratory in Woods Hole, Mass. “With new genomic tools, we can really probe the composition of that community.”

Ducklow used the following analogy to explain the point further: Imagine walking in a forest. You see these things you know are trees, but you can’t tell one from the other — you can’t distinguish a pine tree from a birch, for example.

“That’s the way we were with bacteria until quite recently,” Ducklow said. “So now we’re able to see what the changes are, and also be able to start investigating processes of how they’re able to change over the season and from place to place.”

Murray helped solve that problem using a molecular biology tool called denaturing gradient gel electrophoresis. Basically, she developed a genetic barcode for the bacteria in the plankton community. Using samples collected over an entire year, her team was able to compare the genetic barcodes from summer and winter.

“There is really large turnover,” Murray said of the seasonal comparison. “The barcode completely changed over that annual cycle, more so than anywhere else I’ve worked.”

They also learned that bacterial diversity declines in summer, while the richest diversity occurs in winter. The finding is interesting because microorganisms are presumably more active in summer than winter, as they participate in various biological processes, such as the cycling of carbon and nitrogen. One might expect diversity to increase, not decrease, in the summer.

“Maybe the summer conditions are a little rougher on the bacterioplankton than we previously acknowledged,” Murray said. “I think [increased winter diversity] is counterintuitive and something we’re looking into.”

Microbes one key component of carbon, nitrogen cycles in the ocean

In the spring and summer, bacteria are involved in an incredible amount of metabolic activity, decomposing organic matter produced through photosynthesis by phytoplankton, and turning it back into carbon dioxide. Without the recycling activities of bacteria and zooplankton, the bulk organic matter would sink into the deep ocean, isolating the CO2 from the atmosphere.

“What’s opposing the sinking process is microbial respiration, which is turning the organic matter back into CO2 before it can sink out,” Ducklow explained. “Part of the system is trying to put it into the deep sea, while the other part is trying to burn it back out into the atmosphere.

“Bacteria represent one of the most important compartments at the basis of all food webs in marine ecosystems,” said Jean-Francois Ghiglione, a researcher at the Institution Centre National de la Recherche Scientifique in Paris. He is one of the international collaborators for the IPY project at Palmer Station.

“An estimated 20 to 50 percent of marine primary productivity is channeled through bacteria,” he added. “They respond clearly to environmental changes, and participate in all biogeochemical cycles. Therefore, they have many advantages to serve as a basis for any long-term oceanic observation systems.”

The scientists also want to learn more about how archaea are involved, particularly in the carbon and nitrogen cycles. Archaea are single-celled microorganisms that “look” like bacteria, but are actually more closely related to complex, multi-cellular organisms such as plants.

They were discovered in frigid coastal Antarctic waters by scientist Ed DeLong in 1994. In the mid-1990s, as a graduate student, Murray worked with DeLong at the University of California, Santa Barbara, doing some of the first molecular research on Southern Ocean microorganisms.

“At the time, it was quite surprising to see them down there because we didn’t know their global distribution, and they were commonly thought to inhabit extremely hot, salty, and often anoxic [lacking oxygen] environments,” Murray said. Now they know archaea are one of the most abundant single-celled organisms in the oceans, their sheer biomass accounting for upwards of 40 percent of the cells in the deep ocean.

However, distribution of archaea in the Southern Ocean is different from other marine environments, Murray said. “It’s one of the only places in the world where we find them in the surface waters.”

The seven-member science team will work from July through September collecting their samples and analyzing the organisms right at Palmer Station, including the genomic work. Ducklow’s graduate student Kristin Myers and technician Matthew Erickson also collected samples during this austral summer for comparison.

Though their tools are innovative, there’s nothing too high-tech about how they collect the bacteria and archaea. The technique will depend largely on the condition of the sea ice in the winter. Open ocean means the team can use Zodiacs, inflatable boats, to collect samples. The presence of sea ice will require team members to ski to designated sites and drill holes through the ice to reach the water.

“We have to be flexible because those conditions change at Palmer, and they’re not exactly predictable,” Murray said.

The scientists use big carboys, similar to what a homebrewer uses to make beer, to collect seawater, which can contain about 200,000 cells per milliliter. The team will work in an environmentally controlled room at the station, where the temperature will be that of seawater, about minus 1.8 degrees Celsius.

A filtration system squeezes out the water, leaving all the critters behind. “We get a kind of microbial soup,” Murray said.

The researchers will share that soup, using samples for different purposes “to crack the door open on processes rarely studied in the high latitude waters of the Southern Ocean,” Murray said, as they describe genomic diversity, gene and protein expression between summer and winter, as well as investigate the survival adaptations of wintertime bacterioplankton.

“It will be a busy day each time we go out,” she added. “You can’t quite understand the ecosystem ecology down there without having a seasonal perspective.”

And given the international flavor of the project, the scientists expect to learn something about how different programs operate.

“The IPY project is a wonderful opportunity to work together with our American colleagues, to share our experience, and get new insight on this extreme and very fragile environment,” Ghiglione said.

- Antarctic Sun-