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Arctic microbiomes | Field Report

Sentinel North International PhD School | July 2-12, 2019

 

The Sentinel North International Ph.D School heads towards Nunavik in northern Quebec, a land of contrasts and thriving life. The team of 18 early career scientists and 12 world-class professors and experts will explore the subarctic ecosystems along the vast coast of the Hudson Bay as part of a unique experience aimed at studying the role of microbiomes in shaping arctic food webs, ecosystems services, and human health in the North.

To accomplish this endeavour, the participants will harness state of the art technology directly on-site. Deploying such advanced equipment as DNA sequencers in the North is a challenge in itself, made possible by the collaboration of many partners united at the Centre for Northern Studies research station in Whapmagoostui-Kuujjuarapik. Moreover, the proximity of the School's basecamp at the boundary of the Inuit and Cree territories is a boon that will naturally encourage knowledge-exchange through activities planned with the community.

Follow the one-of-a-kind journey of young scientists as they experiment hands-on in the fields of microbiology, molecular ecology, geochemistry, complex system networks, environmental optics/photonics, remote sensing, and health. As they'll be studying northern ecosystems at the microscopic scale, their surroundings will be reminiscent of the human point of view, the underlying social and cultural aspects and the fundamental role of microbiomes in the Arctic.
 

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Day 11 - Goodbye Center for Northern Studies!

July 12 - Carla Greco, Paola Ayala Borda, Isabelle Fournier, Audrey Picard-Lafond


For our action-packed final day in Whapmagoostui-Kuujjuarapik, we gathered together for the last presentations of the PhD school. This time, they were hosted by the students! Each group presented the work done over the past 10 days, covering everything from fieldwork and laboratory work, data analysis, and the eagerly awaited results of each work package. We were all impressed by the hard work and dedication put into each work package by both the students and mentors. Pierre (our resident photographer) followed these presentations with one of his own, sharing his favourite moments of the trip.

 

sentinel north international phd school on arctic microbiomes

Our star students ready for the London Live interview (photo : Paola Ayala Borda)

 

Between each presentation, we had the incredible opportunity to take part in a Nature Live, a science outreach program in front of a live audience at the Natural History Museum, London. With Jaz Millar (a PhD student at the NHM) and Alastair Hendry (our Nature Live host) holding the fort at the David Attenborough Studio, we were broadcast live to the studio. The talk covered topics such as the changing arctic, life at the CEN research station, and we even answered questions from the studio audience.

 

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

Left: Inukshuk (photo : Carla Greco).
Right : The beach of Kuujjuarapik offers an outstanding view on the Hudson Bay. Students enjoyed a walk in the middle of ice sculpture grounded on the beach, that appears to us like a landscape from another world (photos : Pierre Coupel)

 

The presentations were followed by a picnic on the Hudson Bay next to an Inukshuk (a stone structure traditionally used as a way marker by the Inuit). The beach was a breathtaking sight, with many of us seizing the opportunity for a photo shoot with the sea ice. This was also our last opportunity to eat the great cuisine of our incredible cooks Jacinthe and Cathie, which we will all miss back home!

 

sentinel north international phd school on arctic microbiomes

Some of us left a stamp of our passage by carving or drawing the pieces of wood used to build the tipi (photo : Pierre Coupel)

 

After the picnic it was time to return to the research station to collect our bags (and ensure nothing was forgotten in our rooms!) Our final goodbye to the CEN research station was to complete the tipi we had been working on all week. Once again under the watchful eye of Sidney Orr we built the structure for the tipi, ready for a future group to compete it. Blessed with clear skies (and no signs of fog!) we headed to the airport ready to fly back to Quebec City.

 

sentinel north international phd school on arctic microbiomes

The Stars of the North! Thanks everyone to have made this experience rich, both scientifically and culturally. We look forward to meet again in the North and beyond! (photo: Pierre Coupel)

 


Day 10 - Let’s talk about science

July 11 - Béatrice Choi, Carla Bautista, Florencia Bertoglio, Paul George, Sahan Jayasinghe
 

This morning, we arrived at the CEN conference center to find the room set up for a proper roundtable discussion. It was a good prelude to the activity we were going to do – a quick-fire series of debates and discussions. In true television fashion (think BBC’s Question Time), we were hosted by the incomparable Warwick Vincent, with a panel consisting of our work package mentors, and a lot of collaborators (all of us!). We covered a lot of topics in a record time. First, we discussed the inherent pitfalls and compromises in designing experiments and sampling regimes in remote locations. Some of our cohort come from the field of biomedical of research and have now gained a newfound appreciation for the limitations of replication and sampling imposed by working off the grid. At the same time, the field ecologists were reminded of the importance of maximizing data collection to make the most of our always exciting, sometimes difficult, and occasionally perilous excursions to the wilderness. We also discussed the importance of sharing our findings with government and policy-makers. So get out there and meet your mayor, councilor, and MP!

 

sentinel north international phd school on arctic microbiomes

We wrapped up all that's been seen and learned during the School in a big roundtable discussion (photo : Béatrice Choi)

 

After a short coffee break, Anne shared her experience in popularizing science with the general public. This would be a good primer for the rest of the day’s activities, as we would be introducing Whapmaoogstui-Kuujjuarapik’s citizens to some of their smallest neighbors. She presented how the Natural History Museum interacts with the public. We discussed the various tools at our disposal to present our work to the public, like this blog. Top tip: if you want to see more of our photos and videos from our experience, look for us on Sentinel North’s Twitter page.

Sahan and Audrey had the great opportunity to talk on the local Inuit and Cree radio stations to drum up interest for our outreach event at the Northern Store later that day. We set up our microscopes outside the Northern Store to show some of the microscopic life collected in the nearby lakes. Our zooplankton and benthic invertebrates proved to be popular, especially with the younger part of our crowd! We had to field a lot of questions from our curious audience over the course of the evening. It was a rewarding experience to interact with the local people in this unique way, especially as earlier in the day Noah, a Cree elder we had met during the week, came by to discuss his experiences balancing modern and traditional life, living off the land, and carving.

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

 

sentinel north international phd school on arctic microbiomes

Having the opportunity to do some science outreach with the local population sure was a highlight.
Left : Noah shows us his soapstone carvings (photo : Béatrice Choi)
Right : Showing local kids what lives in the nearby water (photos : Pierre Coupel)

 

A couple of exciting notes to round out the day: Sahan was excited to have his first experience in Tim Horton’s and was surprised to discover sweets from his favourite Sri Lankan cookies on sale in sunny Nunavik! Tonight is also our station manager Patrick Lacerte’s birthday. So on that note we’re off to the pub – bonne fête, Patrick!

 

sentinel north international phd school on arctic microbiomes

 

Happy B-Day Patrick and thank you again for welcoming us to the CEN research station! (Photo : Béatrice Choi)

 


Day 9 - The killers killing it

July 10 - Caroline Doose, Thomas Grevesse, Pascal Paradis, Maria Scheel
 

As every morning, we enjoy conversations among the international community of PhD students and mentors at the communal breakfast while loading ourselves with caffeine to take full benefit of the productive day to come. Over the course of the School, we formed four smaller teams. Each of them works on their own aspects of the mostly invisible, microbial life harvested around Whapmagoostui-Kuujjuarapik.

The work day started with high level lectures on the nitty-gritty of processing and visualization of genomic data. A very nerdy discussion from an outside perspective, but crucial to provide high quality and solid scientific data and evidence. Then, after 4 days of field measurements and sampling, exploring ponds, rivers, permafrost soils, microbial mats and other unforgiving environments, it is time for sample processing and data analysis. This is a great opportunity to put into practice all the knowledge and techniques that we have been introduced to in the last few days. As we experienced one more time today, science rarely goes as planned. After 2 days of relentless pipetting of what looked like thousands of samples, we discovered only too late that the cooler that was supposed to keep our experiments at a constant low temperature – and completely dark – had been left open all day long. Under these conditions, our samples were unusable and ruined...it was a big blow. Such are the ups and downs of scientists in action in the land of mosquitos and melting icebergs. Hopefully, we had great tiny creatures to observe in the microscope to cheer us up.

 

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

Top left : Fieldwork sometimes doesn't go as planned (photo : Thomas Grevesse)
Bottom left : Drawing what's under the lens (photo : Caroline Doose)
Right : The analysis goes on and on and on (photo : Thomas Grevesse)

 

We switched gears in the evening, and went on with another type of learning. We were invited to the Whapmagoostui Cree First Nation Annual gathering, an event aimed at preserving the culture and traditions in a rapidly changing world. This was a great opportunity for us to exchange and learn about the traditional knowledge that has been existing for centuries about the systems we are studying and on local medicinal plants. We enjoyed a good rest along with traditional games and food, discovering more about the local way of life. As we were going back to the research station to get some well-deserved sleep, a surprise was waiting for us : our bus got stuck in the treacherous sands and heavy machinery had to come to our rescue. But don’t worry, mighty reader, we made it back safely and soundly. Another day of science in the North…

 

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

We had the honor to attend the Cree annual gathering in Whapmagoostui, and required heavy help to get back to the research center (photos : Marie-France Gévry)

 


Day 8 - Sailing the seas of data in the comfort of our new home

July 9 - Flora Amill, Emelia Chamberlain, Ligia Patricia Fonseca-Coelho, Flora Mazoyer, Klemens Weisleitner
 

Hello from the North!

Starting our days early at the CEN research station gives us the opportunity to have breakfast altogether and build both scientific connections and friendships. This morning's discussion was about establishing the plan for the day : data crunching. The backpacks and field equipment have been replaced by laptops, microscopes, and loads of coffee. The intensive 4 days of field work are over, which means that we have a whole lot of data to assemble and process. Hopefully we'll end up finding some meaning to it all, but this shall be told in upcoming field reports.

We did some last-minute laboratory work during the morning, but mostly all the adrenaline we got came from Excel files and sailing seas of data (with no life jackets). Even the usually peaceful Emelia screamed at her computer, which made everyone in the room laugh! At least, working indoors keeps us from being eaten alive by mosquitos, which are particularly inspired on a hot and sunny day such as today.

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

After 4 days of field work, it is now time to finish lab work and process our data (photos : Pierre Coupel)

 

In the afternoon, we met in the classroom for group lectures to help connect everything we've learned in the last few days. Topics ranged from anthropogenic concerns like oil spills and climate change, to aspects such as growth of cyanobacteria on early Earth and astrobiological missions to Jupiter´s moon Europa. It is truly amazing to explore the range of applications within the fields of molecular biology and microbial ecology.

 

sentinel north international phd school on arctic microbiomes

The CEN research station provides an inviting space for fruitful discussions (photos : Pierre Coupel)

 

After a long day of learning, we all gathered to the kitchen for dinner. Everyone is always happy during meals, maybe because the food is so great! Our cooks, Jacinthe and Cathie, are incredible and we always have delicious surprises which make us feel at home. Today also was Lígia’s birthday, so we got to see her happily eat her pasta and taking trips to speak over the phone with her family back in Portugal. Jacinthe even surprised her with a nice birthday cake! It has been a busy week for the cooks with a total of 4 birthdays to celebrate!

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

With great food and greater people, mealtimes are always welcome
(left photo : Pierre Coupel, right photo : Klemens Weisleitner)

 

During the night, part of the group was working while the others got to play pétanque. Then we all went to the Social Club to celebrate Ligia’s birthday with 8 dollars beers and dancing. Now we are back and queued up for the bathroom. Good night!

 

sentinel north international phd school on arctic microbiomes

CEN research station by night (photo : Klemens Weisleitner)

 


Day 7 - Extracting information from sediments

July 8 - Paula Ayala Borda, Isabelle Fournier, Carla Greco, Audrey Picard-Lafond
 

As days go by at the CEN research station, expeditions are adding up… and so are samples to process! Water and sediments from rivers, lakes and ponds that have been collected over the past few days have been brought to the lab and sorted during the week-end. The next step is finding out what’s in there, through DNA analysis. And how do you go from freshly harvested, raw sediments to a pure DNA tube? The solution lies in DNA extraction.

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

Left : The coolest lab view ever! (photo : Carla Greco)
Right : Small volumes require great attention (photo : Pascal Paradis)

 

DNA extraction, such is our mission on this foggy Monday morning. The first step is to use enzymes to break down the cells contained in the sediment, which will release the DNA. It must then be washed to rid it of debris (cells contain a whole lot of other things than just DNA). After three hours of sample processing, you go from a raw sediment sample to a pure, translucent solution of DNA! The process is long, but worthwhile when you have wonderful teammates, good music and a fantastic landscape to admire outside. We all wish our home labs had such refreshing views!

 

sentinel north international phd school on arctic microbiomes

 

From a crude sample to a pure sample (photo : Audrey Picard-Lafond)

 

After working hard to finish the extractions during the morning, the weather cleared up and we had the chance to go on a scientific/touristic tour of the permafrost thaw lakes mentioned in previous posts. The helicopter view of this very characteristic environment is quite unique with the obscure water reminiscent of espresso shots. Since our window of opportunity for a clear helicopter ride was narrow, we could not land near those sites, but what you learn from field work is that if plan A doesn’t always work, plan B (or C, or D) is still pretty awesome.

 

sentinel north international phd school on arctic microbiomes

Last call for helicopter boarding (literally!) (photo : Denis Boudreau)

 

The day ended with a friendly competition of “unbarking trunks”, where the goal was to do the longest strip of bark. Béatrice and Paul won, but it was funny to see everyone at work. Those trunks will be the skeleton of the tipi to be built later this week.

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

Left : New world record in unbarking tree trunks? (photo : Pierre Coupel)
Right : The trunks are ready for tipi-building (photo : Marie-France Gévry)

 


Day 6 - A heli-jump to the wonders of the Sasapimakwananisikw River

July 7 - Béatrice Choi, Carla Bautista, Florencia Bertoglio, Paul George, Sahan Jayasinghe
 

Our prayers to the weather gods have been answered! Sunny skies and a balmy 24°C! Bad weather had prevented the helicopter from getting off the ground over the last two days. It must have been beginners’ luck, as this was our first ever chopper ride. We flew to the thermokarst lakes, also called “espresso lakes” due of their dark coloration. The coloration comes from the dissolved organic matter leaching off the nearby pulsas – hills made of permafrost peat. However, the nice weather has a downside : a swarm of biting insects! After landing, we received an initiation to arctic geology as we dug into a pulsa to touch permafrost. Paul – our soil guy – dug down to 60 cm, where the substrate was 1°C and hard as concrete.

sentinel north international phd school on arctic microbiomes

https://sentinellenord.ulaval.ca/sites/default/files/inline-images/day%206-2.jpg

Left : Warwick Vincent introduces the group to the boreal tundra
Right : The team discusses permafrost and pulsa formation (photos : Pierre Coupel)

 

Next, we ventured through the boggy valley of the Sasapimakwananisikw River (most commonly called SAS River) to study a thermokarst lake. We took turns boarding a dinghy and learned how to use a variety of field equipment. Carla and Florencia used a modified CTD probe to measure a range of environmental parameters. Béatrice used a Secchi disk to measure the depth of the lake's photozone. The dissolved organic matter in the water only allowed light to penetrate the top 47 cm. Sahan collected plankton at the top 1.5 m and found a notable northern variety of Daphnia pulex, which is triploid. Paul also collected water along the horizontal axis from a 2 m depth, where the water was completely anoxic.

 

sentinel north international phd school on arctic microbiomes

 

Daphnia pulex (100X) collected from a thermokarst lake. This variety is triploid, meaning that its cells contain three chromosomal copies, unlike diploid conspecifics from southern Québec (photo : Sahan Jayasinghe)

 

The wind picked up as we were doing our sampling, which gave us a reprieve from the insects – we even ate our lunch without our mosquito nets! We trekked back to the helicopter and were able to live out our action movie fantasies as the helicopter shuttled us back to Kuujjuarapik. We will analyse the microbiome of this amazing boreal-tundra system. We are excited to study the microorganisms from the anoxic zone, many of which are responsible for methane production. Methane has four-times greater global warming potential than CO2, so understanding its production is especially important in a context of increasing temperatures in Arctic thermokarst lakes.

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

Left : Paul and Alex Matveev collect water samples from a 2 m depth for microbiome analysis 
Right : Florencia Bertoglio, Paul George, Sahan Jayasinghe, Béatrice Choi, Warwick Vincent, and Carla Bautista happy after a good day’s fieldwork. (photos : Pierre Coupel)

 


Day 5 - Mosquito Killer Blog Post

July 6 - Caroline Doose, Thomas Grevesse, Pascal Paradis, Maria Scheel
 

Like every morning, the local meteo report gives us a heads-up of the (slightly hard to predict) upcoming weather. Today : rainy, cold and foggy in the morning, sunny in the evening. But as thorough scientists, we did not depend on predictions and took precautions to stay inside. Not only to avoid getting wet, but also (admittedly) for the sake of ditching possible mosquito swarms.

 

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

The daily weather in the North makes a huge difference (photos : Maria Scheel)

 

As other teams decided to go all out in some minor storm and rain, I rather took on the real laboratory work (says Thomas, the guy in the selfies, to the displeasure of his teammates, who were ACTUALLY working. Like EVERYBODY else. Really, Thomas.).

 

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

Thomas obviously enjoying the hard work of his team (photos : Thomas Grevesse)

 

Now seriously. Today, our team, the “Mosquito Killers”, started the day fresh (because caffeinated) with lectures and discussions on how to understand genetic material using computer science, also called “bioinformatics”. A short 101 on genetics : every organism has a genome, which is a sequence of base pairs that makes itself uniquely identifiable. Each base is represented by one of the 4 letters (ATGC) and as the average bacterial genome, made up of DNA, has roughly 2 Mio of these pairs, big computational power is crucial. For that, our mentor Jacques Corbeil shared his insights and knowledge enthusiastically. Over the last years, big progress was made in the field of genome sequencing, plainly converting them into biological and ecological knowledge. What a chance to learn from such a professional as Jacques, as well as all the other mentors and professors at the Sentinel North PhD School.

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

Left : Pipetting product into the tiny gel pockets takes a steady hand (photo : Thomas Grevesse)
Right : Invitrogen e-gel analysis with surprising new instant visualization of the gel bands excited everyone (photo : Klemens Weisleitner)

 

During the last few days, all the PhD students had collected biofilms (see earlier posts). It was time to investigate which bacteria were present in these mats. How did we do that? Switching from theory to practice, we swirled into our lab coats. After extracting the genetic material and cleaning the solution, we quantified how much pure DNA we got. This amount is usually not enough to do all the planned experiments, so we had to PCR-amplify it, or “copy paste” if you prefer. That worked surprisingly well to the satisfaction of our supervisors (and ours, too!). Now we are passing the torch of glory to the next team to use the new Nanopore sequencing technology and convert the genetic material to bits and bytes and dive deeper into the bacterial communities.

It is now 11:00pm and we will rest our battered bodies by the bonfire thanks to Patrick, the CEN station manager.

 


Day 4 - Delving into the world of microbial oceanography, from the river to the sea

July 5 - Flora Amill, Emelia Chamberlain, Ligia Patricia Fonseca-Coelho, Flora Mazoyer, Klemens Weisleitner
 

What a good day! Everything began so well! Mist, mosquitoes, and dogs followed us from the research station to the riverbank lined with beautiful Cree canoes. Together with our mentors Alison, Charles and Denis, our goal for the day was to collect two water samples and measure environmental parameters from three sites along a river gradient from up-river to the mouth of Hudson Bay. We hope to use this data to find out if the microbial community changes along this gradient. To accomplish our sampling mission effectively, the teams were split in two. The first expedition was accompanied by two local Cree guides, Richard and Eveline, who helped us navigate the waters of the Great Whale River (kudos to Genevieve for being a perfect captain in the second boat!) Marie-France accompanied us to the shore to help us shove off; and like that we were pushed out into the unknown. It was so peaceful with the fog, the calm river and… a young black bear on the coast.

 

sentinel north international phd school on arctic microbiomes

This denizen of the subarctic woods didn't seem to bother too much of us passing by (photo : Emelia Chamberlain)

 

But, as with all good field work, the tranquillity didn’t last. When pulling to shore to get a bit of leg stretching, one Flora fearlessly jumped into the river to prevent one boat from bumping into the other. But the river was deeper than she thought, and she had to carry on with wet trousers and socks! After this incident, we took a walk along the rocky riverbank. We got a beautiful view of a waterfall, but Emelia, an oceanographer with apparently no “land-legs” fell down several times, including on Ligia’s knees. But no fear, no pain! This is all in the name of science!

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

The riverbanks of the Great Whale River proved a healthy challenge (photos : Klemens Weisleitner)

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

Left : Flora and Flora in complete symbiosis (photo : Emelia Chamberlain)
Right : Ligia smiling, maybe because she kept slapping mosquitos off Klemens' head (photo : Klemens Weisleitner)

 

Eventually, however, we were back on the water to do the required measurements. We were drifting so much that we had some difficulties using the CTD and Ekman sediment grab. We eventually managed to adapt our techniques and to collect all of our measurements successfully, to the point where the crew was very (VERY!) excited when they hauled up a full grab of clay! Once the joy tempered down, we could hear Ligia and Klemens, who could never seem to agree on salinity levels read from the refractometer!

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

We made it safely back to the research station after our river odyssey! Time to analyse all these samples now (photos : Klemens Weisleitner)

 

Learning new techniques is always an adventure. We learned the important lesson that we should never let a weight fall off the boat... or else never see it again. But despite the (minor) mishaps, it was an amazing day on the field, we learned a lot, laughed a lot and returned with a much needed boost of energy to analyse all of the water, phytoplankton and sediment samples in the lab during the evening!

 


Day 3 - Tech, mats and Cree sport!

July 4 - Raoul-Marie Couture, Marie-France Gévry
 

Our third day up North started with interesting lectures about the living cryosphere, to learn more about the great diversity of arctic and subarctic environments such as terrestrial, ice, freshwater and polar marine systems. We were then introduced to methods in microbiome science, beginning with a great talk by professor Denis Boudreau on the application of flow cytometry in phytoplankton studies. This talk made us realize how transdisciplinary work is powerful for the advancement of science, and made us eager to learn more about the newest technological developments.

 

sentinel north international phd school on arctic microbiomes

Chlorophyll a extraction and measurements in the lab (photo : Pierre Coupel)

 

We then did some lab work on the microbial mats harvested yesterday. We extracted and measured the chlorophyll a concentration using a fluorometer to quantify the primary pigments used by algae in photosynthesis.

 

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

Measuring oxygen consumption in microbial mats is a delicate operation (photos : Pierre Coupel)

 

We also used a small diameter Unisense oxygen microelectrode to measure dissolved oxygen concentrations in very thin microbial mats. The electrode was moved vertically by a motorized micromanipulator connected to a computer. Such precision allowed us to perform 20 measurements per millimeter, from the mat’s surface down to 12 millimeters below. We observed oxygen production due to photosynthesis in different vertical zones, followed by oxygen consumption due to respiration. We used a model that calculates rates of oxygen production and consumption to compare and contrast different types of mats. This is a delicate operation that shows us how active and complex very thin microbial mats can be. We hope to use that information along with genomic data to characterise the functioning of mats later in the week.

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

We had the honor to participate to the Cree gathering in Whapmagoostui (photos : Pierre Coupel)

 

In the evening we had the privilege to participate to the opening ceremony of the Cree gathering in a traditional tent, sharing stories and a feast with the community. One of the highlights of the day was certainly when some of us got initiated to Cree baseball, an extremely fun game that we can describe as an hybrid between baseball and dodgeball.

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

Going for the home run in our very first Cree baseball game (photos : Pierre Coupel)

 


Day 2 - Exploring freshwater microbial life and new technologies

July 3 - Vani Mohit, Anne D. Jungblut
 

After a good night sleep, we had a thought-provoking discussion about the importance of microbiomes in human health and bioremediation of contaminated soils. We found that microbiomes can have very specific habitats. For example, different species of Canadian berries can have very different types of microbiomes. But what actually is a microbiome? We had a heated discussion and agreed that a microbiome is defined by a group of microorganisms that are found in a habitat due to their ability to thrive under these conditions, and by their interactions. We plan to get back to that definition at the end of the school after learning more about the specifics of Arctic microbiomes.

We also explored the newest, cutting-edge DNA sequencing technologies that will make it possible for us to study microbial communities without having to grow them in the laboratory or using a microscope. This is a small revolution in itself, for it has been suggested that only 1% of bacteria can be grown in the lab. Combined with the possibilities of big data, these new technologies will allow us to determine the number of species and their function directly from the genomes. We are therefore hoping to characterise the diversity of microbiomes from lakes, permafrost and the ocean during the School.

During the afternoon, we also had a demonstration of the Ecochip, a device that measures the growth of microorganisms in the environment directly after collection, without the need to bring the sample back to our home institutions. This technology has lots of potential because many Arctic microorganisms will likely adapt to grow in cold conditions, and might not grow under different conditions.

 

sentinel north international phd school on arctic microbiomes

Lakes and ponds of the subarctic taiga are home to lots of microbial life (photo: Pierre Coupel)

 

Today was also our first day exploring microbiomes in the Arctic in situ. We ventured out into the taiga along the Hudson Bay in the search for microbiomes in some of the many freshwater ponds and lakes in the area. After a 30-minute long drive along a bumpy road, we found a lake which had millimetre- to centimetre-thick cyanobacteria-based biofilms. Cyanobacteria (also known as blue-green algae) are a very old group of microorganisms.

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

Gathering cyanobacteria-based biofilms (photos: Pierre Coupel)

 

Cyanobacteria evolved ca. 2.5 billion years ago and were the first organisms able to produce oxygen through photosynthesis. Many species are filamentous and form a matrix that serves as a habitat for many other bacteria, fungi, ciliates, other unicellular organisms and viruses. Samples were collected for further analysis and we also took measurements of important environmental parameters in the water column which influence the diversity and function of the microbial communities present in the biofilms.

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

sentinel north international phd school on arctic microbiomes

Fieldwork in the North during summer : bug net not optional (photos : Pierre Coupel)

 

Another highlight of the trip was that we found ancient, fossilized microbial biofilms next to the lakes of the modern communities. The fossilized microbial communities are called stromatolites, which are rocks formed by microbes some 1.8 to 2 million years ago. Whapmagoostui-Kuujjuarapik is located on a geological zone that is estimated to be more than 3 million years old, and formed when life on Earth was dominated by microbial life prior to the evolution of complex life, plants and animals.

 

sentinel north international phd school on arctic microbiomes

2 million years old stromatolites (photo : Pierre Coupel)

 


Day 1 - Discovering Whapmagoostui-Kuujjuarapik

July 2 - Marie-France Gévry, Pierre Coupel
 

The Sentinel North International PhD school on Arctic Microbiomes has started!

It all begun with a friendly kick-off meeting on July 1st, which gave us the opportunity to get to know each other a little bit. Despite the holiday (Canada Day!), we woke up early the next morning to fly up North to Whapmagoostui-Kuujjuarapik.

 

sentinel north international phd school on arctic microbiomes

All aboard! (photo : Pierre Coupel)

 

A 4-hour stop at La Grande because of the fog made us realize how arctic work is dependent upon weather conditions. When the skies finally cleared, we were able to reach our final destination and to discover the Centre for Northern Studies (CEN) research station, our home for the next 12 days.

There, professor and mentor Warwick Vincent welcomed us and gave us a highly promising taste of what’s to come. Whapmagoostui Band Chief Louisa M. Wynne did the same, welcoming us to her town. We then jumped into the thick of it with a first lecture on human microbiome by prof. André Marette.

 

sentinel north international phd school on arctic microbiomes

Whapmagoostui Band Chief Louisa M. Wynne (photo : Pierre Coupel)

 

After a delicious lunch prepared by the CEN’s cook (thanks Jacynthe!), we had the opportunity to participate in a tipi building experience. Under the supervision of Sidney Orr and other members of the Cree community, we went into the nearby mossy woods to harvest 14-foot black spruce trunks and branches. Equipped with axes, saws and lots of determination, we cut down the trees and used the trimmed bark and branches on the ground as an insulation mattress. An Elder also shared her knowledge of medicinal properties of plants, such as Labrador Tea and the local chewing-gum, the fir tree gum!

With the laboratory almost done setting up, we look forward to discover more about Arctic microbiomes in the following days!

 

sentinel north international phd school on arctic microbiomes

 

sentinel north international phd school on arctic microbiomes

 

sentinel north international phd school on arctic microbiomes

Tipi building workshop (photos : Pierre Coupel)

 


Departing soon!

As the School's participants, mentors and organizing crew are in transit to the place they'll be calling home for the next 10 days, here are some bits of info about the participants of this 5th edition.

 

33 people in the team, of which :


Learn more about the School's program and faculty.

sentinel north international phd school on arctic microbiomes

Sentinel North PhD School - Whapmagoostui-Kuujjuarapik Research Station

Left: Helicopter view of Whapmagoostui-Kuujjuarapik (photo: Denis Sarrazin)
Right: The CEN research station at Whapmagoostui-Kuujjuarapik (photo: Martin Fortier)

 


 

ABOUT THE SENTINEL NORTH INTERNATIONAL PH.D. SCHOOLS


As part of the Sentinel North training programs, the International Ph.D. Schools combine a practical approach in northern and/or highly technological environments with the opportunity to interact with high-profile scientists and experts. They provide international students with a chance to learn with world-class research infrastructure as well as specialists from various fields and domains.

This school is possible thanks to a key collaboration with the following partners: 


And funding from the Canada First Research Excellence Fund.

 

Text and photo editing by Jérôme St-Charles.