On June 14th, Emmett Smith (he/they) and Faith Jacobs (she/her) successfully extracted DNA from soil samples. This lab is located at the natural and heritage science research center in Skálanes, Iceland. To learn more, read Emmett’s blog post here, and follow us on Instagram!
Scroll down to see the best photo of Emmett hugging his lab notebook 😚
[Photos by Yujeong Lee]
We woke up to snow-covered mountains surrounding the fjord. Iceland is beautiful because of its contrasts, and the starkness of white snow on black rock is no exception. After marveling at the view through the window, it was time to get down to business.
Yesterday, Faith Jackobs ’18 joined us from Houston, TX to work with us for a week while we’re camped out here at Skalanes. Faith has been on a previous EPIC Advantage Iceland trip, and joined us in 2019 to help with our ancient DNA project. Today we tackled DNA Extraction from Icelandic Soils, a protocol that has been in development since 2017. We have never had much success getting the DNA out of the soils of Iceland, because the type of soils we collect (brown andisols) are very good at binding DNA, and not very good at releasing it! I spent a lot of time in the fall of 2019 attempting to improve the DNA extraction protocol, and stumbled across a winning recipe. The secret? Skim Milk!
In 2005, Hoshino and Matsumoto published the following paper: “Skim Milk Drastically Improves the Efficacy of DNA Extraction from Andisol, a Volcanic Ash Soil.” In this paper, skim milk was added to a DNA extraction protocol during the first, important bead-beading step. This step is where the DNA is removed from the soil, and removed from any organisms living in the soil. It typically involves 10 or more minutes of intense vibrations in a small tube containing specialty beads and a buffer that protects the DNA from any enzymes/cellular debris present in the sample. I decided to incorporate the skim milk into our method. Back at EC, I meticulously added 10 mg of powdered skim milk to all of the bead-beating tubes in our kit to prepare them for the protocol.
The other piece of the puzzle that fell into place was creating enough of a vibration that the bead-beating step could properly do its job. Charlie and I created a device we’re calling the “Porta-lyzer” – see my previous post for a video. It seems that, in combination, this device and the addition of the skim milk worked like a charm. We’ve gotten the best DNA extraction results ever here at Skalanes.
Need proof?
| 2017 | 2018 | 2019 | 2021 | |
| Average: | 4.2 | 27.2 | 52.7 | 66.83 |
| StDev: | 2.67 | 14.82 | 42.15 | 47.04 |
| StErr: | 1.20 | 4.28 | 12.17 | 10.79 |
Needless to say, I’m thrilled. We even collected DNA from the elusive Solo era A – which has only been out of the ice for ~20 years, and is always an era that gives us lots of trouble.
Now it’s time for a celebratory adult beverage and a walk out to see the puffins. Cheers!
To see a condensed video of Faith and I working on the extraction protocol, click here!
Sing it with us now … (https://www.youtube.com/watch?v=NrI-UBIB8Jk)
Ooga-chaka Ooga-Ooga
Ooga-chaka Ooga-Ooga
Ooga-chaka Ooga-Ooga
Ooga-chaka Ooga-Ooga
I can’t stop this feeling
Deep inside of me
Iceland, you just don’t realize
What you do to me
So much day-light
There is never night
Hiked a glacier
Everything’s all right
I’m hooked on a feeling
I’m high on believing
The beauty of this place
Terns aren’t sweet as candy
They dive-bomb all the time
Chicks got weighed and measured
Getting pooped on is just fine
We got bugs on stickers
But we don’t need no cure
Just keep flying Kia
We’ll get data for sure
Let’s play Euchre
Or some Carcassonne
Oh-oh, Iceland
Yeah, you turn me on
I’m hooked on a feeling
I’m high on believing
The beauty of this place
Did some camping
Spent some time alone
Oh-oh, Iceland
Yeah, you turn me on
I’m hooked on a feeling
I’m high on believing
The beauty of this place
I’m hooked on a feeling
And I’m high on believin’
The beauty of this place
I said I’m hooked on a feeling
And I’m high on believin’
The beauty of this place
Icelandic Field Studies 2018 is officially in the books. It was a great trip. It’s hard to believe we have been in country for 3 full weeks – things have gone by so fast. There were many firsts on this trip – it was the first trip to collect soil for aDNA extraction from an archaeological dig. The first measurement of tern eggs and hatchling weight in lupine vs. non-lupine environments. The first Earlham study of insect populations in lupine vs. non-lupine environments. The first structure-for-motion attempts from our drones. The first camping trips into the Skálanes hills. The first hikes in the Klauster hills. The first viewing of Iceland in the World Cup!
We had lots of similarities from previous years. We toured the Golden Circle to see historical and natural sites of interest. We hiked the volcanoes on Heimaey to test our elevation platforms. We spent quality time at Sólheimajökull, using our elevation platforms and drone to approximate the volume of its nose, as well as collecting soil for bacterial DNA extraction and measurement. We enjoyed our stay at Skálanes – what a beautiful and soul-filling place. We played many a game of Euchre, Carcassonne and Settlers of Catan.
To everyone following along on this blog, thanks. We’ve had a really great time. We got to know each other better, and at one point or another we all had “Hooked on a Feeling” stuck in our heads (thanks, Dre!). We hope we’ve been able to share some of this experience with you – though you can’t fully experience Iceland without being here. The stark beauty and power of the landscape has a unique pull on the soul. If you are able to visit, please do so – and get off the beaten path for a day or two. Give yourself the gift of Icelandic solitude.
Signing off till next year,
Emi Smith (and the whole IFS crew)
Today was a combination of exploring, testing and traveling. This morning we briefed the group on what will take place the next few days that we spend working at the glacier Sólheimajökull. Then we packed up and checked out of the B&B Guesthouse after a lovely stay. A subset of us worked on the drones and elevation platforms, while others of us were took one last hike on the island. After boarding the ferry, we drove east on route 1 to Vik, our destination for the next few days.
I was able to hike a very fun steep path up to a cliff top where we got a fantastic view of the island. We had to use a rope to climb a steep slope of scree, but the views were worth it!
After hiking, we all got on the ferry to head back to Iceland.
We drove past Sólheimajökull on our way to Vik. This is the first major science stop. In the next few days, we will be hiking on the glacier itself to measure its elevation and calculate the volume of its snout. We will also be collecting soil samples from a variety of locations surrounding the glacier. DNA will be extracted from the soil and we will sequence it to determine what types of bacteria are living in each sample. This will tell us how Icelandic soils recover from glacial coverage over the years. I’m excited to begin!
Like any good amateur birder, I kept a list of all the birds we saw on our trip. Special shout out to Neil who made many sightings, as well as to Sage, Cait, Nic and Kellan for contributing to the list. Total count: 27 species!
Bird Date Location
Common Snipe 24 May Thingveller
Pink-footed Goose
Mallard Duck
Black-headed Gull
Pied Wagtail
Redwing
Oystercatcher 25 May Selfoss
Whooper Swan Geysir
Arctic Skua 26 May Solheimajokull
Arctic Tern 28 May Klauster
Eider Duck Jokulsarlon
Snow Bunting
Whimbrel or Dunlin
Pidgeon Elgisstadir
Canada Geese
Fullmar 29 May Skalanes
Puffin
Kittiwake
Ringed Plover 30 May
Grey Phalarope 31 May
Robin
Gyrfalcon
Greylag Goose
Harlequin Duck 2 June
Black-tailed Godwit
Whimbrel
Raven 4 June
Next year I want to see the gyrfalcon!!!! It was spotted by Nic and Kellan while flying the drone.
… but we did ford some rivers! I have no photographic evidence of our journey (because I was worried about dying) so use your imagination as I walk you through the day.
Goal: Drive to Egilsstaðir to get to the airport to pick up a rental car so Dan, Neil and I can visit an archaeological dig on Friday (excitement!!) and do some shopping since the food delivery to Skalanes was delayed.
Problem: It’s been raining here pretty solidly for the last few days. The three (3) rivers that one must cross to get to civilization are rising … and rising … and rising …
Oli (the owner and manager of Skalanes) arrives in his big 4×4 truck circa 9 am. Charlie and I hop in ASAP, since Oli says the rivers are nearing the point of unfordability. We approach the first river. The water is rushing madly down to the sea. It is easily 3x higher than yesterday. Oli puts the differential lock on so the rear wheels will have more power. We charge through the river. It’s pretty intense but we clear it. We zoom down the road to the second ford and cross it, with similar trepidation (and a larger drop off downstream). Then we approach the third and final ford, which is the largest and most dangerous. The waters are roaring down the mountain. Oli angles the truck well upstream of our exit point, throws on the differential lock and moves forward into the current. I feel the truck being pushed downstream – the water level is almost up to the windows! Charlie is ready with his window-breaking tool, and I’m planning how I will roll down the window and climb out as soon as the river thrusts us against the rocks we are quickly approaching. Can I grab my pack (which contains all my cash, ID, credit card and passport)? Nope, better not risk it … the truck is groaning and lurching and then, inches away from the rocks at the end of the ford, the nose of the truck rises out of the torrent onto the road and we’re safe. Water has made it into the floor of the truck but we escape the mad dash to the sea.
You may think that the rest of the day will be tame compared to this adventure. Incorrect. After picking up our car and getting some serendipitous shopping completed, Charlie and I head back toward Skalanes with myself at the wheel. I head into the mountain pass of route 93 from Egilsstaðir to Seyðisfjörður. The wind is gusting at 20 knots and the rain turns into snow as we crest the pass. We drive through intense pea-soup fog patches as we pass by snowpack, and it’s a good thing that all cars in Iceland are required to have their lights on 24 hours a day so we don’t strike each other in the fog. We finally descend into the valley, and drive past waterfalls which are being blown backwards and upwards by the strong winds. As we approach Skalanes, we know there is no way we can drive our SUV past the rivers (indeed, Oli hung the “Closed” chain over the road as we left). We now face a 4.5 km trek from the road to the house. We call in reinforcements and Dan, Neil and Jacob answer the call. We trudge into the east wind with our groceries. Where there was a road, there is now a series of deep, large puddles and quickly forming new rivers. In one location, the land immediately next to the trail has disappeared (even since Dan, Neil and Jacob walked out to the car) and is quickly being eroded away. The cold wind is blowing the rain directly into our faces. After about 45 minutes, we reach the house. We drag our soaking carcasses into the warm, dry lodge and jump into showers to warm up.
The rest of the day really pales into comparison – mostly because I was exhausted and just sat around by the fire. Shout out to my Marmot water-proof pants and North Face GorTex jacket – they kept me mostly dry!
Tomorrow I take Dan and Neil and drive to the dig site in Stöðvarfjörður. We’re hopeful that we can offer them our services to aid their excavation! http://icelandreview.com/news/2016/09/15/major-archaeological-find-iceland
P.S. Sage’s code is working!!!!!
Signing off for now,
Emi
We’re just about ready for departure. Three of us leave this afternoon for flights out of Chicago, and the rest of the crew departs early tomorrow morning: Earlham –> IND/DAY –> JFK (7 hour layover) –> KEF –> Reykjavik!
It’s been a very busy 1.5 weeks, but, ready or not, we will all be in Iceland in less than 48 hours. We can anticipate cloudy weather in the 40s and 50s. We’re looking forward to experiencing another place, expanding our horizons (culturally, scientifically, emotionally), eating fermented shark, implementing our algorithms and devices, going back to Skalanes, to run in Iceland, seeing birds (especially Puffins), geocaching, standing on a glacier (and possibly sledding down it), climbing a volcano or two, lounging in a hot spring, and trying to learn some of the language.
Our gear is packed.
Our daily plans have been formulated.
Our devices are primed and charged.
Our sense of adventure is fully present.
Our Spotify playlist has been populated. What more do we need?
See you in Iceland!
Our biology and soil team has begun a practice run of the sampling, DNA extraction, and MinION sequencing protocols so that we are prepared and familiar with the process before we get to Iceland. We started by collecting soil samples from various places around Earlham campus: The Heart, the Japanese garden by Stout, the horse barn, the rain garden by the Wellness Center, and a popular social gathering place back campus. We used Maria, one of our elevation platforms, to record the coordinates of each sample site, and as a placeholder for the soil temperature readings we will take in Iceland. We put the samples on ice to preserve the living organisms within, since we are trying to identify what kind of biotic activity takes place and varies at each site, both here at Earlham and eventually in Iceland on Sólheimajökull. Back at the lab, we extracted the DNA.
We also ran a gel electrophoresis and a Nano Drop to test the quality of the DNA. The former told us how long the strands were, and the latter told us how many nanograms per microliter of DNA we had in our samples. Both yielded positive results, meaning we have a good quality and quantity of DNA to put through the MinION.
We had some technical difficulties at first with this new tech, but we made it work eventually and are now working on setting up the nanopore. We are almost ready to sequence the DNA and find out what microorganisms are living all around us! We had a great win the other day with QGIS. Though we had a rocky start, we were finally able to georeference our first map! Enthusiastic cheers echoed through the Turing room, and we all celebrated with a trip to Dairy Queen.
We have received, from Oxford Nanopore, the MinION. (Min-ION, not one-eyed yellow minions, get it straight.) This device promises whole-genome sequencing of microbes, viruses and archaea from soil samples we will collect at the Solheimajokull glacier. This device is extremely small and portable, and one sequencing run can be done on a laptop in 6-8 hours. One flow cell can run up to 12 samples at a time, and while the samples are being sequenced, internet access will allow simultaneous queries of a database that will determine what species were in our sample. Thus, in REAL TIME, we can identify the composition of the soil microbiome. This is a drastic improvement over prior methods, which involved sending 16s rRNA samples to a company and waiting for 2-3 weeks for results. 
What kind of science are we doing with this device?
We will be collecting soil samples at the Solheimajokull glacier (near the town of Vik in Iceland). We want to obtain samples that have been “out of the freezer” i.e. not covered by the glacier for a specific number of years – 10, 20, 50, 75, 100, 150, 200, etc. We will compare the microbial populations present in these different soil samples and look at the type of soil and flora growing in these different locations. This will teach us how the land “recovers” once it is freed from a glacier.
This device will help us do this analysis on site and give us the data almost immediately. It’s really new, cool and exciting. We’re looking forward to learning about soil succession with the use of this device!
Blogger: Emi (Biology Professor and MinION hand modeler)
