Wednesday, February 19, 2014

Answers for Jacob Madonna

Dear Dr. Sokol
I'm an AP Biology student from Maplewood New Jersey. I'm in the same class as Jonah, Chris, Emma, Sarah, and Tim . I've been following your blog for the past month and i have a couple questions to ask you
1) You've been going to Antarctica for a couple years now. How do you set yourself goals regarding your research?
Hi Jacob,
Great questions! Setting goals for research in Antarctica is generally pretty easy because we have to have a fairly specific research plan outlined to get funded to do research down there in the first place.

It seems that for our research group, we have a wish-list of goals and a realistic-list of goals. Usually the wish-list involves collecting many more samples from many more sites than is practical.

For my first project, our goal was to conduct a fairly extensive survey of soil biodiversity across an 800 km stretch of the Transantarctic Mountians. This involved planning travel by helicopter to a bunch of different field sites. We had a pretty simple, but specific soil sampling field protocol that we followed at all every site, so that made field work pretty simple. The tricky part was getting to all the sites. We prioritized a list of sites that we really really wanted to go to, and a list of sites that we would like to go to if weather allowed and we had enough time. I think we ended up getting a variety of samples that represent the soil bacterial diversity in the Transantarctic Mountains pretty well.

For the past three years, I have been working with the Long Term Ecological Research (LTER) group. The main goal of this group is to maintain a long-term record of the ecology of the McMurdo Dry Valleys, and also conduct long-term field experiments so that we can understand ecological responses that occur over fairly long time scales (e.g., decades). The McMurdo LTER has been running for a long time (20+ years), so a lot of the work I do with the LTER is continuing to collect samples to continue the long term record of the geochemistry and biodiversity of soils in the McMurdo Dry Valleys.
2) How does climate change directly affect your research with microscopic organisms? 
This is a question that we are currently trying to answer, but probably won't have an answer for a while. We think that in the coming decades climate change will increase glacial melt, and thus increase the presence of liquid water in the Dry Valleys during the austral summer. We think this will affect the ecology of the Dry Valleys, but we're not exactly sure how. One of the broad hypotheses of the McMurdo LTER project is that there will be increased "connectivity among landscape units." For example, we think increased melt from the glaciers will increase the amount of water that percolates though the soil, mobilizing nutrients and micro-organisms in the soils.

The frequency of melt events and amount of melt water will have consequences for the types of organisms that dominate the stream channels and adjacent soils in the wetted margins. For example, past studies have shown that a shift in water availability in a stream channel can lead to a shift in the species composition of the diatom community. There tend to be more endemic, cold-adapted diatom species in cold, dry stream channels that only see liquid water periodically (not every year). We think these types of streams may be very sensitive to the anticipated increase in glacial melt.
3) Have you ever had to change the way you approached an experiment or research topic because of Antarctica's extreme climate
We try to keep our field work simple to avoid complications due to the extreme climate. Most of the field work I'm involved in just requires collecting ecological samples. We normally store samples by freezing them, so Antarctica is actually quite helpful in that we don't always need to worry about bringing coolers and ice out in the field with us.

The extreme climate does affect our access to field sites or ability to collect samples. That is, sometimes we have to sit and wait for winds to die down or fog to clear before we can get a helicopter ride to or from a field site. Sometimes it is too cold to collect water, or sometimes we can't collect a soil sample at a particular location because it is frozen solid in ice.

This season, extreme weather has prevented us from being able to ship our science samples from McMurdo back to the US. There is a large cargo vessel that visits McMurdo each year at the end of the season. At the end of each season most of our science samples are loaded onto this vessel and they are shipped back to the US. However, an extreme windstorm hit McMurdo as they were loading the vessel this year, and the boat had to leave before all of our science samples were loaded onto it. These types of situations happen when you work in an extreme place. Luckily for us, I think most of the our samples will be fine in a freezer for a year... we'll just have to wait.

Tuesday, February 18, 2014

Answers for Jonah Williams

Dear Dr. Sokol,
It has been really fascinating to read about the research that you and your team are currently conducting in Antarctica. As a strong activist in the climate change world, I am very glad to see that you have been having success compiling all your work, and that your research will provide valuable information on climate change patterns in the antarctic. I recently finished some research on carbon sequestration in photoplankton and microalgae, and the quantification and change in biomass due to ocean warming patterns.
My question for you relates the the biotechnological procedures you are using to observe these microscopic organism you are studying.
1. What types of procedures are you using to manipulate the DNA in certain organisms you study to make it easier to view. (PCR? Plasmid vectors?)
Hi Jonah,
It sounds like you are doing some interesting work. I'm not a molecular or microbiologist, so in the projects that I have mainly been working on we are not manipulating DNA. Our objective has been to conduct a relatively broad survey of the diversity and types of microbes living in arid soils in the McMurdo Dry Valleys. Some of our collaborators at the University of Waikato in New Zealand have worked with MoBio to develop a protocol to extract DNA from soil samples with very low microbial biomass. We then run PCRs on the environmental DNA using general primer sets that target broad groups. For example, we used a primer that targeted a conservative region of 16S rDNA, which targets bacteria generally. If you are interested, you can email me and I can send you some citations, or you can find our recent paper here. The published data set is just fingerprinting based off of tRFLP, so our most recent publication is about diversity patterns over very broad spatial scales. We have sequenced a subset of the fingerprinted samples using pyrosequencing and we are currently analyzing that data set to figure out the types of bacteria that are making up the diversity patterns. There are papers identifying bacterial taxonomic groups in the McMurdo Dry Valleys, but our recent paper is the first to look over a very broad spatial scale (~ 800 kms).  
2. How extensive is you laboratory in terms of equipment? I understand that you are in Antarctica, but do you have all the equipment that you might find back home at Virginia Tech?
Crary Laboratory in McMurdo is pretty extensive, but there is not a lot of equipment for doing molecular work. When we do our work, we collect our samples in the field aseptically and we add a preservative to the soil, like Sucrose Lysis Buffer. Then we freeze the samples and ship them back to New Zealand or the US for molecular work. We have tried to extract DNA from soils in the lab at McMurdo, and it is certainly possible, but it's much easier just to do that back at the University.

That said, Crary does have a lot of basic lab equipment. There are drying ovens, muffle furnaces, fume hoods, laminar flow hoods, centrifuges, etc., so there is plenty of equipment for us to do basic soil geochemical analyses. Some research groups have pretty sophisticated setups that they require on site for their work, but our setup is pretty simple.
3. What types of methods are you employing in population measurement of micro-organism species? How do you quantify the movement of certain populations in response to climate change? 
That's an interesting question. I have been focusing more on community level measures of diversity than assessing specific population level dynamics. Most of the work we have done thus far has focused on the link between microbial biodiversity and environmental variation. In that work, we use patterns of community similarity to infer how well microbial communities are connected among Dry Valleys.

Overall, we haven't done a very good job of actually directly quantifying the movement of micro-organisms, but that is something that we have been trying to get funding to do. One of our collaborators in New Zealand did a really interesting study where they set up a pump that pumped a large volume of air through a filter, and they then sequenced the bacterial DNA that was on the filter. They sampled air at a high elevation and at a low elevation to characterize the microbial communities that are entrained in the air at different elevations, and found differences, but we need more samples to be able to sufficiently answer questions about how well different groups of micro-organisms are dispersing throughout the Dry Valleys.

Another group of collaborators associated with the McMurdo LTER focuses on nematodes, and they set up sediment traps in the Dry Valleys. They found some viable nematodes in the sediment traps, so we know that the nematodes can be dispersed by wind, but we are trying to get a better handle on how extensively they are dispersed by wind. Dr. Byron Adams at BYU has done some work looking at population level genetics to infer levels of dispersal among Dry Valleys, but that is still an ongoing area of research.
Thank you for you time! I am looking forward to what you have to say, and keep up the good work!
Stay warm!
- Jonah
Thanks for writing Jonah!

Answers for Kristin Renda

Dear Dr. Sokol,
Reading your blog, as well as other questions students like me have asked you has been very interesting. Like other students have posted before me, I am from Maplewood, NJ and it was my AP Enviro teacher who got me interested in the work you are doing. I just have a couple of questions about what life is like for you in Antarctica and how your research is being used.
1. Does the intense weather conditions ever interfere with you research?
Hi Kristin,
Weather does often interfere with our research. The 8 and a half hour flights from New Zealand to McMurdo, Antarctica are often influenced by weather. There is no control tower for the ice runway at McMurdo, so planes can only land if the weather is clear. If there is ice fog or visibility is low, then flights often have to turn around and go back to New Zealand.
LC130 plane on Ross Ice Shelf near McMurdo Station.
Because the landscape is so extreme, and because we don't want to build roads everywhere, the only practical way to get from McMurdo to our field research sites is by helicopter. The helicopters can't fly if visibility is low or of if it is too windy. Wind storms originating over the polar plateau are not uncommon, so we can have very clear, very windy days.
Helicopter landing at one of our field sites in Taylor Valley, Antarctica
2. What do you do for leisure?
At McMurdo Station, there are hiking trails around the station. A fun, short hike is to follow a trail to the top of Ob Hill, where you can get a view of the Ross Ice Shelf and McMurdo Station. If it's cold outside, I like to stay in and play music. The are guitars and other stringed instruments available for us to borrow. We also play board games and watch movies.

In the field, we can hike or play board games for fun. All in all, we usually don't have very much down time, unless we get stranded because of bad weather.
3. How do you think your research will benefit science?
That's a good question! The goal of my research is to understand the ecological processes that determine biodiversity. Two of the major drivers are (1) how well organisms move about the landscape, and (2) whether local habitat conditions favor some species over others. My research in general is to create computer models to understand how these processes influence diversity for different types of organisms (e.g., bacteria, nematodes, diatoms, etc.). In the Dry Valleys, we are trying to understand exactly which soil chemical properties are linked to soil bacterial diversity, and if the same rules apply everywhere in the Dry Valleys. We are using the data we collect to validate computer models that predict biodiversity. If our models work, we will be able to use computer models to predict how biodiversity will change in the future as the Dry Valley habitat changes for bacteria and other organisms (e.g., nematodes, diatoms, etc.).

Specific to Antarctic ecology, I hope that this work will help us determine the best way to measure biodiversity so that we can have some confidence that we will actually detect changes in the ecosystem when those changes happen.

More generally, I am comparing our biodiversity models for Antarctica against models we use in other ecosystems (e.g., the Everglades, temperate forests, urban ponds in Baltimore, etc.). I think it will be really interesting to find ecological processes that work the same way in ecosystems in Antarctica and Baltimore.
4. You said in your blog that ten years ago the glaciers were at a level that they melted to in just weeks. Do you think the lake levels will return to what they were before this recent melt, or do you think they can freeze back just as quickly as they melted?
In that post I was referring to the lakes. The lake levels in Taylor Valley dropped during a period of cooling in the 1990s. Then in one season (2001-2002), there was a lot of glacial melt. In that one season, the lake levels rose back to their previous level (recovered all the water that was lost over the previous 10 years). I think the lakes are dynamic, and rise and fall periodically. There is evidence that over the past century, the lakes have been rising. There are pictures from historic expeditions that show the lake levels were much lower in the 1910s. So the lake level decrease observed in the 1990s was an anomaly for the past century. The lake levels have been rising since I've been going to Antarctica (the past 4 years).
5. Will this recent melt affect your research in any way?
Yes. It will affect the logistics because we have semi-permanent field camps near the lakes that will need to be moved as the lakes rise. The US Antarctic Program has already had to move some huts and helicopter landing pads to uphill sites as the lakes have risen.

The lake level rise may affect some of our soil research plots, but most of the plots are quite far from the lake edge, for now. However, we anticipate that more water in the landscape will affect the Dry Valley ecosystem in general. We anticipate that with increased melt, streams will become wider, and there may be new or larger water tracks in the landscape. More wet soil will probably mean more active microbial life in the soils.

Thanks for the questions!

Answers for Chris Kearns-McCoy

Hi Chris, sorry I'm taking so long to respond. My schedule has been pretty hectic lately...
1. How do you relate to other scientists doing research elsewhere in Antarctica? For instance, are there techniques and methods that you can benefit from that come from say, the research being done in places like Lake Vostok? Even though dry valleys and submerged lakes are clearly different, they are both undisturbed environments requiring great caution, and I was wondering if some of the concerns are the same?
Great question. I'll answer this as best I can, but I am not involved in any of the subglacial lake projects. You may have read about WISSARD, which is a project where researchers are studying subglacial Lake Whillans. One of the really innovative aspects of the WISSARD project is their sterile drilling method. By avoiding contamination of the subglacial lake, with microbes and chemicals from above, they can be sure that the samples they collect represent subglacial life and the subglacial environment. Some of the scientists involved in this project consult with research groups from other countries, like Russia and South Korea, so that those countries may also develop sterile drilling methods. This is about the extent of my knowledge on that topic.

In our studies of Dry Valley soils, we work closely with microbiologists at the University of Waikato, New Zealand to understand how environmental factors, such as extreme soil chemistry, temperatures, and dispersal by wind, influence microbial diversity in arid soils.
2. As the climate warms and glacial melts in the Dry Valleys become more frequent, how do you expect the organisms you are studying to respond? Will more and more become active, or are there some that are suited to this cold that will die out?
This is a great question! This is the central question for the McMurdo Long Term Ecological Research Program! Based on observations we have made over the past few decades, and general climate projections, we anticipate increased glacial melt over the coming decades. Glacial melt water is the main source of water in the Dry Valleys, so an increase in glacial melt will be the main driver of ecological change in the Dry Valley ecosystem. We are just beginning to understand how different types life will respond to an increased presence of melt water. Overall, we hypothesize that the increased flow of water will increase the connectivity of the ecosystem. In other words, there will be more liquid water flowing through Dry Valley soils, which will be moving and mixing nutrients and microorganisms. This can be over very small scales, for example, microbes may not be able to access nutrients that are only micrometers away in dry soils, but saturating soil with water can give microbes access to nearby nutrients. At larger scales, water may mobilize nutrients and microbes and move them down stream channels over distances of 100s of meters to a few kilometers, or from stream channels into lakes. Some previous studies suggest that species that are adapted to the cold and dry antarctic climate, such as diatoms that are native to the Dry Valleys,  may lose out to more generalist species, but we're not entirely sure if this is true for all the types of organisms in the Dry Valleys.
3. What kind of infrastructure exists in Antarctica. If someone had a serious medical problem while doing research, are there sufficient resources nearby? If not, how would they be evacuated? I would imagine there are procedures in place, but I was curious as to what they are.
The infrastructure at McMurdo Station is quite extensive. There are dorms and a science lab and many buildings for support staff, equipment, and resources. There is a medical building with limited resources, but people are medevaced on the first available flight to New Zealand if a real emergency occurs.
View of McMurdo Station, Antarctica from the top of Ob Hill
McMurdo - the blue building is the cafeteria, the brown buildings at the top right are dorms, and the building with the red roof in the lower left is the medical building.
Crary Lab in McMurdo
Our lab space in Crary Lab at McMurdo Station

Tuesday, February 4, 2014

More answers to come...

Thanks for all the questions this season! I will answer all of them eventually, so keep an eye out for more posts here on the main page.