Author Archives: Maggie Weng

Cold day at Hveravellir

Wednesday dawned cloudy and, you guessed it, cold at Hveravellir. We huddled over our morning breakfast of toast with jam, cold cuts, and fermented shark (hákarl) while contemplating how this could possibly be August. Nevertheless, we packed up the trucks and headed off into the day. Half of our group journeyed up to Kerlingarfjoll to sample streams, ices and sediment for further analysis while the other half stayed behind for a practical test of our field extraction protocol. We set up our remote extraction on a yoga mat far from signs of habitation. Our only sources of power were the gas-powered portable generator and the car engine, which we hooked up to an electrical inverter.

Due to complications with the CP Select, we were not able to use the concentrator pipet for our extraction protocol. Instead, we extracted from soils and biofilms collected at Kerlingarfjoll the day before: one sample from the bank of a glacial outwash stream, one soil sample further away from the water source, and one soil from the trailhead at the top of the valley. We hoped to compare the yield from each of these samples to understand what would be most promising for our field sequencing and analysis run. To extract, we used the Qiagen PowerSoil kit combined with the Terralyzer to lyse cells instead of a traditional vortex.
The first thing we discovered is that it is possible to stretch latex gloves over warm wool ones to retain feeling in one’s hands. The second thing we discovered is that doing so gives one far less dexterity. Faced with the choice between dropping bits of Kerlingarfjoll all over Hveravellir and losing feeling in our fingers, we opted for the latter but climbed gratefully into the warm car whenever we needed engine power.
After about one-and-a-half hours, we looked triumphantly at the microcentrifuge tubes filled with 30 microliters of clear liquid. Had we managed to isolate the code for life itself? That question would require more work. We took a break to warm up, during which time I confirmed that none of my toes had frostbite and found a bag of grapes in the truck’s backseat, which gave us the fortification to continue. Back to the yoga mat we went, now pulling out the Qubit to ascertain our DNA concentrations. Then we had our answer: we had managed to get DNA from all of our samples, the most from the soil near the trailhead and the least from the soil on the bank of the stream. Moving forward, we hoped to sequence our results from sample x in the field, as well as completing a field extraction, sequencing, and NanoOK analysis all in the same day.

Laguna Tebenquiche

Today, the roads to El Tatio were unfortunately still closed, but we were able to visit Laguna Tebenquiche. After a dramatic interlude in which muddy roads nearly bested our spirits, we finally made it to the laguna and it was beautiful! We weren’t able to definitively visually identify any stromatolite domes but we did see some interesting biofilms and mats. We also identified several regions of interest for further study, including an evaporate playa completely encrusted with halite, which contained several small pools of water supporting what could be distinct microbial mat communities and populations of what we believe to be Ephydra fly larvae. Surprisingly, although the pools were geographically close to one another, the mats within varied in pigmentation and the pools also varied slightly in pH, though stayed within the 6-7 range. Along the western edge of Tebenquiche proper we also noticed hardy salt-resistant plants growing, as well as the occasional bird which seemed to be consuming biofilms that were plentiful at the edge of the lake. This is exciting because these microbial biofilms would appear to be supporting a larger ecological community, or at least could be incorporated into one. A few meters from the lakeshore, we also noticed thin mud crusts with gas bubble formations that suggest microbial mediation of gas production. All in all, it was a successful reconnaissance of Tebenquiche which points to areas of further study in microbiology, especially pertaining to the lake’s biofilms and their interaction with halite crusts and salty conditions—although Tebenquiche is not a perfect Mars analog due to the concentrated presence of halite rather than silica.


Methods Testing

Weather conspired against us today! The roads to Salar de Atacama and El Tatio were both closed due to heavy and unusual weather, rainfall that turned into snow at one point during the morning. We made use of our time by performing extractions on a test sample using Purelyse, Omnilyse, Terralyzer and a Quick DNA kit (tissue version) to determine which would be most successful in the field. We tested the success of our extractions using the Qubit, and we determined that our most successful method was the Terralyzer. Guess it will be joining us in the field! We also simulated a field extraction and sequencing using a Zymo community standard and the RAD002 sequencing library on the MinION.


Arriving in the Atacama

Well here we are in Chile! We’re planning to look at silica sinters at the Mars analog environment of El Tatio, whose formations resemble silica formations in the Columbia Hills. Columbia Hills was previously explored by the Spirit rover and is now a candidate for the landing site of the Mars 2020 rover, whose mission goals include the collection of samples for transport back to Earth. Hopefully these samples will contain biomarkers, or ancient organic molecules, with which scientists will be able to study the formation and function of any life on Mars. Studying biomarkers and the DNA of ancient and current microbial communities at El Tatio will help us understand how life may function in these environments, and what to look for should a rover have the opportunity to collect samples from Columbia Hills or a similar location. We also hope to test the MinION sequencer in the field, on flow cells that are now 8 months old and which Mark has irradiated to the level that the sequencer would receive en route to Mars. It did manage to sequence successfully in the lab, which is a good sign! Now it’s time to put it through its paces. Lastly, we hope to visit the Salar de Atacama, which contain microbialites and microbial mats with diverse and well-preserved communities. These microbialites trap minerals and precipitate sediment, leaving biomarkers in the rock as clues to their existence. Studying these microbialite communities will help to gain a greater understanding of how microbes and the geologic environment interact and influence each other, and what clues this may leave in a martian environment.