Turned on and off
Scientists study seasonal gene expression in phytoplankton
Posted November 11, 2011
The transition from one season to the next is associated with all sorts of changes, from budding flowers and bothersome allergies to longer days and hotter nights, as colder months give way to warmer ones.
One team of scientists is investigating how moving from late winter to spring to early summer in Antarctica affects a community of microscopic marine organisms called phytoplankton at the genetic level. The researchers hope the information that they collect for a third of the year that they’ll spend at Palmer Station will answer fundamental questions about what controls phytoplankton growth in the world’s oceans.
“What happens during that transition from winter to spring is that species actually change,” said Deneb Karentz , a marine biologist from the University of San Francisco and expert in phytoplankton ecology.
“We expect to see a difference in the dominance of certain species, and that’s another thing that’s going to be very interesting to look at in terms of the gene expression — what makes a species at a certain time more competitive in terms of its ability to survive in a changing environment,” Karentz added.
Phytoplankton are microscopic, free-floating organisms that form the foundation of the polar food web. Most phytoplankton are single-celled plants that have chlorophyll to capture sunlight, using photosynthesis to turn it into chemical energy. They consume carbon dioxide and release oxygen.
Karentz and her team, including co-principal investigator Joe Grzymski , a microbiologist from the Desert Research Institute , arrived at Palmer Station in August, at the end of the Southern Hemisphere winter. They’ll remain at the U.S. Antarctic Program’s smallest research station through November, as summer begins and phytoplankton erupt in brown-hued blooms near the ocean surface.
The location is particularly intriguing for the investigators because Palmer Station is located on the northwest end of the Antarctic Peninsula, which is one of the fastest warming places on the planet. Climate change is turning the environment subantarctic, from cold and dry to warmer and wet.
In 2009, scientists with a monitoring program called the Palmer Long Term Ecological Research project published a paper in the journal Science suggesting that the phytoplankton community is shifting from larger-celled organisms such as diatoms to smaller-celled organisms like flagellates because of climate change.
That has repercussions throughout the polar food web because larger marine organisms like krill, a shrimplike critter that’s a key prey for big animals such as penguins and seals, favor the larger diatoms. Meanwhile, another type of zooplankton — jellyfish-looking organisms called salps — seems to be edging krill out. Salps are indiscriminate filter feeders.
It’s within this dynamic context that Karentz and Grzymski hope to see how the phytoplankton community evolves as the cold and darkness of winter moves into the lengthening, light-filled days of spring and summer.
“With this project, we’re able to get into the mechanisms that organisms use to deal with various types of changes,” Grzymski said. “One of the things that we’ll just inherently be able to do with our project is figure out some of the gene-level adaptations that organisms that live down here have to have to survive.”
The researchers will use the latest gene-sequencing technology to discover what genes are being expressed as environmental conditions change. Genetic expression refers to which genes of an organism may be “turned on” or “turned off” under different environmental conditions.
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.
“We’re able to take samples directly from the environment in the midst of this highly dynamic period and sequence the genes that are operational and use those data to figure out which organisms are adapting,” Grzymski said.
Specifically, the team wants to capture the transcriptome of phytoplankton cells as they undergo their seasonal adaptations.
Remember that all genetic information for every organism is stored in its DNA, an important blueprint passed on from one generation to another.
DNA directs all of a cell’s activity by employing another chemical called RNA. When information from DNA needs to be used to make proteins or regulate other gene activity, the message is transcribed into RNA language. A messenger RNA (mRNA) carries information needed to direct cellular activity; this regulation is called gene expression.
In gene expression, when a gene is “turned on,” it’s being transcribed. The transcriptome that the scientists want to understand reflects the genes that are being actively expressed at any given time — a snapshot of activity.
The researchers will combine the genomic techniques with other measurements, from cell counts under the microscope to fluorescence methods, which will tell them something about the makeup and health of the phytoplankton they analyze.
“We can enhance all of that information with gene expression,” Grzymski said.
Weather and sea ice conditions have conspired to make sample collection difficult early in the season for the researchers and their students, who use inflated rubber boats called Zodiacs to travel away from the station for their work. Extensive sea ice around Palmer kept them out of the water, forcing the scientists to use unfiltered water piped into the station’s aquarium to collect some specimens.
Strong winds in late August and early September temporarily blew out the sea ice, which offered another wrinkle to the investigation of how the phytoplankton adjust to abrupt environmental changes.
“That’s something else that we want to try to map out: What happens when they get these big shifts in light intensity,” said Karentz, whose previous research at Palmer Station has involved studying the effects of ozone depletion on phytoplankton. (The annual ozone hole in Antarctica allows more damaging ultraviolet radiation to reach that part of the Southern Hemisphere.)
The team will remain at Palmer through November collecting samples and working in the station’s labs and aquaria. The scientists have also kept a busy outreach program through a website hosted by DRI that includes journals, videos and interviews with the station support staff.
They’ve also been in communication with Dilworth Middle School students in Sparks, Nev. Grzymski set up an iPad application so the students could follow the research team’s adventures, as well as had iPads donated to the school.
“It has been a nice aspect with some real-time communication and trying to let middle schoolers who are at that impressionable science age get excited about science in one way or another by being closer to the action, so to speak,” Grzymski said.