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Life in the Antarctic: Protistan Biodiversity
From: Woods Hole Oceanographic Institution
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Rebecca Gast |
EDITOR'S INTRODUCTION |
When most people try to imagine life in the Antarctic, they envision a barren ice-covered landscape dotted by a few penguins and parka-clad scientists.  However, beneath the snow in the most extreme conditions, a whole system of life manages to flourish in the slush and icy waters of one of the Earth's most remote regions.
In this feature from the Woods Hole Oceanographic Institution, Rebecca Gast (right) discusses her research of the biodiversity of Antarctica's protists. These tiny, single-celled microorganisms make up the bulk of the primary production and food web in the Antarctic. Gast discusses her methodology in analyzing and identifying these microscopic organisms in such harsh conditions, her goals for this research and the importance of studying a community that has been found in nearly every environment on the planet. |
Question: What is the nature of your work, and how did your research lead you to the Antarctic? |
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| Mark Dennett (right) and Rebecca Gast (left) at the Ross Sea Ice Shelf, Bay of Whales, Antarctica. | |
Rebecca Gast: In my laboratory, we analyze the gene sequences of organisms within environmental samples to directly identify protists. Besides identification, the sequence variability allows us to develop detection methods that are quantitative, so that we can determine not only "who" is present in the environment, but also how many are there. |
What led me and my collaborators (Dr. David Caron of USC and Mark Dennett of WHOI) to the Antarctic was a desire to determine what protists were present in that extremely cold environment, with the goals of linking "genotype" (a name) with morphology (a face), and understanding how these organisms were able to adapt and thrive in the extreme cold. Many of the cultures of protists that we collected in the Antarctic will not grow at temperatures above ten degrees Celsius. Proteins and enzymes have high and low temperature limits where they don't function. An extremely cold environment can be just as difficult for cellular function as a high temperature one. |
Gast: The textbook definition would be that they are single-celled eukaryotes, but what does that mean? It means that they are very much like us, but instead of being composed of many cells, they are only composed of one. The basic structure of the cell is the same, there is a membrane bound nucleus, and organelles (like mitochondria and chloroplasts), unlike the bacteria that have neither (although bacteria are single cells). Examples of protists include amoebae, ciliates, dinoflagellates and diatoms, and they can play many different roles in the environment. Some are phototrophic (photosynthetic) whereas others are heterotrophic (they eat), and some are even mixotrophic (they can do both). Some protists are beneficial, like symbiotic algae, whereas others are harmful, like parasites that cause malaria. |
Q: In Antarctica, what role do protists play in their environments and in the food web? |
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| Microalgae, like the diatoms shown here, constitute the base of the food web in extreme cold-water environments. | |
Gast: The ocean is often idealized as a relatively warm body of water, probably due to our fascination with the upper hundred meters of water in tropical and temperate areas. In reality, the majority of the ocean is permanently at three degrees Celsius or less. Protists play fundamental roles in the production and processing of carbon in aquatic ecosystems, including the Antarctic. In fact, photosynthetic protists (microalgae) are the only primary producers in extreme cold-water environments. Microalgae constitute the base of the food web, and heterotrophic protists (such as ciliates and small flagellates) are responsible for processing a large fraction of that primary production as well as much of the bacterial biomass. The magnitude of the role that protists play is still controversial because conventional wisdom suggests that physiological function should or would be dramatically decreased at extremely low temperatures (less than five degrees Celsius). Much of the information on protistan activity at cold temperature comes from measurements made by in situ incubation experiments. These studies indicate an active protistan community exists, but there is still little information on the relative importance of individual species for processes within the food web. Therefore, the issue of psychrophilic adaptation is still largely unexamined, and the physiological consequences of growth at low temperatures are unknown. |
Q: What is the importance of studying the diversity within the protistan species? |
Gast: Protists in general form an important part of the aquatic microbial food web, but further information on what protists are actually present is highly desirable. Accurate identification of many protists (especially very small ones) is difficult using light microscopy, and has resulted in a "black box" approach to the ecology of protists. Protists are grouped together because of their size, but that has little to do with how they make a living in their environment. The inability to identify, accurately and easily, the protist taxa in a natural assemblage has a direct impact on our ability to determine their trophic mode and study their distribution in the environment. This, in turn affects our ability to understand and predict the ecological impact of changes to the system. |
Q: What methods do you use in the acquisition and analysis of protists in such extreme cold-water environments? |
Scientists aboard the Nathaniel B. Palmer collect samples in the extreme cold of the Ross Sea.
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Gast: Many of the sampling methods that we normally use to study protists in the temperate marine environment are also used in the extreme cold. Water is collected using Niskin bottles that are attached to a CTD (conductivity, temperature and depth) rosette. The ice samples are collected using a drill called a Sipre corer. It allows us to collect cores of ice about 10 centimeters in diameter, and up to several meters thick. What we refer to as slush is the layer of melted ice found below the snow surface, and this is collected using shovels (to remove the snow) and spoons or syringes. We performed our sampling in the Ross Sea from an icebreaker called the Nathaniel B. Palmer. To collect water when we're in the ice, the ship breaks a hole in the ice, and the CTD rosette is deployed through a door in the side of the ship. To collect ice and slush, we actually get off the ship onto the pack ice or individual ice floes. When working in the solid ice, the ship wedges itself into the ice and a gangplank is lowered so that we are able to simply walk off of the ship. When working on ice floes, scientists are lowered over the side of the ship on a personnel basket. |
The analysis of our samples is accomplished using a combination of enrichment culture and molecular methods. For the molecular work, we collect the cells by filtration (after melting the ice and slush), and then lyse them to recover their nucleic acids. Then we use PCR (polymerase chain reaction) to amplify either a fragment of, or the entire, small subunit ribosomal gene. This gene is present in all organisms, and we are able to specifically amplify the gene from eukaryotic microbes (protists) rather than bacteria. We generate clone libraries of the full-length genes, and use denaturing gradient gel electrophoresis (DGGE) to analyze the smaller amplified fragments of the ribosomal gene. DGGE separates DNA fragments based upon the melting of the double strands as they pass though an increasing concentration gradient of denaturant in the gel. This allows us to examine the overall diversity of the population based upon the relative number of individual bands and comparison with other samples' band patterns. Sequence analysis of both library clones and DGGE bands, along with comparison of DGGE patterns, allows us to determine which populations are most similar and to identify the dominant individuals in the natural sample. We are then able to go to our enrichment cultures to determine whether we have recovered these naturally dominant organisms and to target those for physiological studies. |
Enrichment cultures were started while we were onboard the ship, and the samples have been kept at less than four degrees Celsius at all times. Different types of substrates were used to enrich for different organisms (e.g., rice grains). All of our enrichment cultures are mixtures of different protists, along with bacteria. We recover cultures of just one type of organism by micropipetting the desired cells into separate incubation chambers. If the desired protists need to eat other organisms, we also must include a food source--either bacteria or algae. This is time-consuming work, and must all be accomplished at temperatures below four degrees Celsius so that our organisms don't die. Onboard the ship we worked in a cold room where the temperature was set at two degrees Celsius. Fortunately we now have a special microscope stage that keeps the sample very cold, and we can work in our laboratory rather than in a cold room. We have been successful in recovering both phototrophs and heterotrophs, many of which die rapidly at temperatures above ten degrees Celsisus. We are in the process of identifying the individual organisms by their morphology and by their ribosomal sequence. |
Q: What adaptations do protists have that allow them to survive the extreme environment of the Antarctic? |
Gast: That's the mystery, the million-dollar question, and one that we hope to be able to answer through studies of our cultures. |
Q: How does the structure and diversity of the protistan community allow them to flourish in such extreme conditions? |
Gast: Again, we don't know yet. What we have learned about the protistan community diversity is that those communities present in the same type of environment (e.g., water) are genetically more similar than ones from different environments (e.g., ice and water). Despite the similarities, there are still many unique bands in each sample, indicating that the overall diversity is quite significant. We are in the process of determining which organisms (sequences) are common to different samples, and checking our culture collection to see if these organisms are available for further physiological studies. |
Q: What obstacles do you face in your research? |
Gast: Time. We have so many interesting cultures that it is difficult to choose the ones to work with. That's why we've started with those that are dominant in the original samples. They were the ones playing the biggest ecological role in the samples when we collected them, so they can tell us the most about their "daily life" requirements and processes. |
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| David Caron is shown working with cultures at the microscope in the cold room onboard the Palmer. | |
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Q: What lessons can be learned from the protistan community that can be applied to life elsewhere on the planet? |
Gast: In terms of protists elsewhere on the planet, we are learning that we have most likely not adequately sampled or assessed the diversity of protists in most environments. Those organisms represented in culture collections are important and informative, but they do not necessarily correspond to the ones that were dominant or active in the original samples. Many of our Antarctic protist sequences are more similar to ribosomal sequences from other environmental samples rather than sequences from known organisms. The challenge now becomes identifying these unknown isolates and bringing them into culture so that we can learn more about their physiological requirements and trophic modes. I would also say that I've become convinced that microbes are some of the most adaptable organisms on the planet. They exist in almost every environment where we've looked for them--I'm still amazed by snow and ice algae. |
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