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!