Author Archives: Julie Bevilaqua

Field sequencing with a view

We conducted our extraction on Wednesday hunched over under an overcast sky, catching papers, tubes, and foil as they blew away in the wind, and layering our gloves in a futile attempt to keep our hands warm. By contrast, our last day in the field gave us a fortunate change in the weather—the skies cleared, the sun broke through, and the wind dissipated. Thursday opened as half of our group set out early to begin a sequencing run at our field site in Kerlingarfjöll, and the rest of us arrived shortly after, the rest of our gear in tow. We arrived just in time to watch Maggie load our flow cell with our DNA from Wednesday’s field extraction, and we gazed on as the data begin to roll in and NanoOK started to return our analysis.


With our sequencing run chugging along, we set up our “field lab” with a beautiful view. The top of our ridge was in full sun, and the light illuminated the snow packs on the surrounding mountains against the dark rock. Part of our group hiked back down into the valley, toward the glacial streams and their surrounding banks, to collect more samples. As they set out, we began preparing another round of field extractions. We used a modified PowerSoil kit protocol to extract DNA from the soil sample we used the day before—the same soil whose DNA we had begun sequencing in the morning. We also extracted from a newly collected sample from a similar site. When the rest of our group returned, we concentrated a water sample from a glacial stream with our InnovaPrep concentrating pipette—in a matter of minutes, we had concentrated a few hundred milliliters into around 1 mL, some of which we were able to use in our extraction protocol alongside our soils. We worked through the protocol, swapping out instruments plugged into the generator to give each one enough power, and using field substitutions for some of the equipment we’d normally use in the lab. Once we had worked through our protocol, we prepped our DNA for quantification in order to see which samples, if any, were going to be viable for sequencing—and to check for contamination in our blank, which is an even bigger threat in the field.


I don’t think I’ve ever held my breath so much or hoped so frantically that a blank would turn out clean as I did then—when our control didn’t show evidence of contamination, we felt comfortable moving ahead with our second field sequencing run of the day. We prepared the DNA library, like we did in the morning, using a newly developed kit for field sequencing, and we set up our MinION (wrapped in some felt, to stay warm!) to begin our run. After only about 30 minutes, we were able to look at the first analysis returned by the NanOK RT pipeline and get information about the bacteria in our sample in real time. After spending the summer running practice extractions and struggling to properly load flow cells, we were finally able to see our entire process laid out before us, in the field—from raw sample to analyzed data, in one shot. It was exhilarating and gratifying to see all of our efforts come together and give us information about our sample, and also about what experiments are possible in the field.

As we drove back to the lodge, we tried one final test, just for fun—keeping one of our MinION runs sequencing on our laps as we drove over the bumpy dirt and gravel roads. We laughed about the MinION’s “road test,” and we were able to keep our sequencing run going during the trip back from our field site. While our sequencers ran through the evening, we packed our field equipment back into its suitcases. We set out the next morning for the long drive back to Reykjavik, and we crossed the Mid-Atlantic Ridge again, from the Eurasian plate to the North American, another step on our way home.


Indian Tunnel and Buffalo Cave

Today our group went to two of the publicly accessible caves that Sarah, Elena, and Savannah had sampled from last year—Indian Tunnel and Buffalo Cave. Indian Tunnel is one of the most popular publicly accessible caves, and the inside is lit by a large skylight. Since our focus is on chemotrophic organisms, we avoided sampling near the skylight and went to the darker region of the cave. There, we found that one of the larger deposits that was sampled last year had disappeared, so we observed that the deposits can vary a lot from year to year. Since we hope to come back in the winter to study the variation between seasons, the indication that the deposits vary annually is an important piece of the puzzle as well.

buffalo cave

Next we went to Buffalo Cave, which had more abundant deposits than we had seen anywhere else. We were all a little in awe as we walked through the cave, stopping every few meters to point out another interesting feature. The variation in color, and particularly texture, was readily apparent in these samples: we observed smooth deposits that flaked off while we were sampling, and little branches deposits that looked like corals. We collected three kinds of samples, one of which was so abundant that we collected 9 vials of it—a promising chance to explore not just the population composition, but also the kinds of RNA and protein that are most abundant in the sample. This analysis will give us a better understanding of how the microbes in the deposits survive and the metabolic processes they’re employing. These samples should give us a lot to work with back in the lab to expand our understanding of these populations, how they survive, and how they’re affect patterns of mineralization.


Big Craters and the Highway Flow

On Friday, Elena, Kate, and I joined more of the FINESSE team in a trip to Big Craters, where there is a large ridge of basalt lava flow that NASA’s BASALT team has previously studied. We hiked along a high ridge to access the sample site, where we saw some incredible views of the surrounding park and the nearby spatter cones, which are mounds of lava that form around a main channel. We climbed up the lava flow to find the site previously sampled by the BASALT team, where we took samples for DNA, RNA, and protein analysis of unaltered basalt lava. Unaltered basalt is dark black in color, while the color of altered basalt lava is often changed because of chemical reactions. Lava that has already flowed out and cooled can be altered via oxidation, making turn a rust-red color, or through reactions with hot gases released later in the flow. We weren’t able to access the site for altered basalt that had already been sampled, so we trekked back along the ridge to prepare for the afternoon. 

highway flow

We then went on to the Highway flow—named because it sits directly across the highway from the Visitor’s Center. Shannon, one of the FINESSE project leads, took us along the flow, which is steep and jagged, with crevices throughout, making it hard to navigate without a guide. Before we entered the main body of the flow, we stopped to take in the rugged expanse, which Shannon told us is often referred to as Mordor (it’s a fitting name). After scrambling through the lava rocks, we found two sites—one of altered basalt that had been sampled before by the BASALT team, and another of unaltered lava that was nearby. The unaltered basalt was particularly tough to sample—it’s incredibly dense and hard, but we managed to break off enough for our analysis before setting off out of the flow and toward the highway again. The two samples from the Highway flow will give us a great means of comparing the microbial populations in the altered and unaltered basalt, and since the NASA team has sampled here before, we’ll be able to compare our results to their findings as well. We’ll have a great set of samples to work with when we get back to the lab. We’re rapidly filling the cryoshipper to take them all home.


Arco Tunnel

arco tunnel

On our first day of field work, we went out to Arco Tunnel, one of the longest lava tubes at Craters. Arco Tunnel is of interest to us because it’s no longer accessible to the public, so there’s less risk of contamination, and there’s no light inside, so we can focus in on non-phototrophic microbes. We were fortunate to have a great guide from the National Parks Service, two interns from the Bureau of Land Management, and Kate with us—Arco Tunnel is difficult to navigate, and we definitely needed help to avoid getting lost! After crawling and scrambling throughout the day, we found some great sample locations and collected from 11 different sites throughout the cave. Temperature and humidity also varied widely throughout the cave, from around 10 ºC (~50 ºF) to 18.8 ºC (~66 ºF) in a room closer to the surface. Hopefully this contextual data will help us in our analysis, both to understand gradients within Arco Tunnel and to compare to the sites from our other field days. It’s amazing to see the diversity of colors and textures that exist in the caves, from white crystalline mineral deposits on the ground to yellow biofilms clinging to stalactites on the ceiling. The range of microenvironments we observed in the cave likely helps facilitate some of this diversity, but it’s incredible that despite no access to light and very few sign of other life, so many populations of microbes have found their own way to survive in the cave. We’re excited to see what results we get from sequencing these samples so that we can understand who is surviving there, and how!

Heading to Idaho

julie and elena

Elena and I are traveling to Idaho to study extremophiles at Craters of the Moon National Monument and Preserve, which is often used as a Martian and lunar analog environment. We’re heading there with NASA’s FINESSE and BASALT teams, which come every year to study the lava flows on the surface and the lava tubes, which are caves carved out by lava flow. Much of the surface of the Moon and other bodies in the solar system is marked by volcanic activity, so Craters is a great place to expand our understanding of these features on Earth in order to be better equipped to work with them in space. Elena and I are looking to study mineral deposits in the lava tubes because subsurface environments are considered one of the important places to look for life on Mars, since they provide more protection from radiation than the surface environment. Since many of the mineral deposits are formed by microbes, we will take samples to sequence later so that we can get a sense of the microbial populations and activity in the lava tubes. We’ll also be joined in the field by our collaborator Kate Craft, from the Applied Physics Lab at Johns Hopkins. Together we’ll be collecting organically clean samples—samples without contamination from outside organic molecules, like those that might be on our instruments or gloves—to look for biosignatures that may have been preserved in some of the deposits. By comparing our sets of results, we’ll be able to target the same questions through multiple kinds of analysis, which will give us a much bigger picture of life in the harsh conditions of lava tubes!