Posts Tagged ‘bacteria’

UGA Skidaway Institute scientists study microbial chemical warfare

April 18, 2017

In the battlefield of the microbial ocean, scientists have known for some time that certain bacteria can exude chemicals that kill single-cell marine plants, known as phytoplankton. However, the identification of these chemical compounds and the reason why bacteria are producing these lethal compounds has been challenging.

Now, University of Georgia Skidaway Institute of Oceanography scientist Elizabeth Harvey is leading a team of researchers that has received a $904,200 grant from the National Science Foundation to fund a three-year study into the mechanisms that drive bacteria-phytoplankton dynamics.

Researcher Elizabeth Harvey examines a part of her phytoplankton collection.

Understanding these dynamics is important, as phytoplankton are essential contributors to all marine life. Phytoplankton form the base of the marine food chain, and, as plants, produce approximately half of the world’s oxygen.

“Bacteria that interact with phytoplankton and cause their mortality could potentially play a large role in influencing the abundance and distribution of phytoplankton in the world ocean,” Harvey said. “We are interested in understanding this process so we can better predict fisheries health and the general health of the ocean.”

This project is a continuation of research conducted by Harvey and co-team leader Kristen Whalen of Haverford College when they were post-doctoral fellows at Woods Hole Oceanographic Institution. They wanted to understand how one particular bacteria species impacted phytoplankton.

A microscopic view of a population of phytoplankton

“We added the bacteria to the phytoplankton and the phytoplankton died,” Harvey said. “So we became very interested in finding the mechanism that caused that mortality.”

They identified a particular compound, 2-heptyl-4-quinlone or HHQ, that was killing the phytoplankton. HHQ is well known in the medical field where it is associated with a bacterium that can cause lung infections, but it had not been seen before in the ocean. The team will conduct laboratory experiments to determine the environmental factors driving HHQ production in marine bacteria; establish a mechanism of how the chemical kills phytoplankton; and use field-based experiments to understand how HHQ influences the population dynamics of bacteria and phytoplankton.

“This project has the potential to significantly change our understanding of how bacteria and phytoplankton chemically communicate in the ocean.” Harvey said.
The project will also include a strong education component. The researchers will recruit undergraduate students, with an effort to target recruitment of traditionally under-represented groups, to participate in an intense summer learning experience with research, field-based exercises and some classroom work.

“The idea is for the students to return to their home institutions at the end of the summer, but to continue to work with us on this project,” Harvey said. “This will be a unique opportunity to offer students cross disciplinary training in ecology, chemistry, microbiology, physiology and oceanography.”

In addition to Harvey and Whalen, the research team includes David Rowley of the University of Rhode Island.

NOTE:  A complementary video with an interview with Dr. Harvey is available at http://www.skio.uga.edu/news/videos/

 

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Tiny but all-consuming marine organism focus of UGA Skidaway Institute study

February 8, 2017
Marc Frischer

Marc Frischer

Doliolids are tiny marine animals rarely seen by humans outside a research setting, yet they are key players in the marine ecosystem, particularly in the ocean’s highly productive tropical and subtropical continental margins, such as Georgia’s continental shelf. University of Georgia Skidaway Institute of Oceanography scientist Marc Frischer is leading a team of researchers investigating doliolids’ role as a predator in the marine food web.

Doliolids are small, barrel-shaped gelatinous organisms that can grow as large as ten millimeters, or about four tenths of an inch. They are not always present in large numbers, but when they bloom they can restructure the marine food web, consuming virtually all the algae and much of the smaller zooplankton.

A doliolid with a cluster of juvenile doliolids on its tail. Actual size is approximately three millimeters, or one eighth inch.

A doliolid with a cluster of juvenile doliolids on its tail. Actual size is approximately three millimeters, or one eighth inch.

“The goal of this particular study is to find out what the doliolids are eating quantitatively,” Frischer said. “This is so we can understand where they fit in the food web.”

Scientists know from laboratory experiments what doliolids are capable of eating, but they don’t know what they actually do eat in the wild. They are capable of eating organisms as small as bacteria all the way up to much larger organisms.

“What they are eating and how much are they eating from the smorgasbord that is available to them, that is the question,” Frischer said. “We are investigating how much of those different prey types they are really eating out there across the seasons.”

The project involves intensive field work, including 54 days of ship time on board UGA Skidaway Institute’s Research Vessel Savannah. During the cruises they conduct trawls using special plankton nets to collect the doliolids. They also collect water samples to understand the conditions where the doliolids thrive.

Graduate students Lauren Lamboley and Nick Castellane deploy a plankton net from the Research Vessel Savannah.

Graduate students Lauren Lamboley and Nick Castellane deploy a plankton net from the Research Vessel Savannah.

“We take the doliolids and the water samples back to the laboratory, and that is where the magic begins,” Tina Walters, Frischer’s laboratory manager said.

Because the animals are gelatinous and very delicate, the researchers cannot use classical microscopic techniques to dissect the animals and analyze their gut content. Instead they extract DNA from the animals’ gut and use sequence-based information to determine what the doliolid ate.

“We go through a process called quantitative PCR,” Walters said. “So even though we can’t see the prey in a doliolid’s gut, because the prey have unique DNA sequences, we can identify and quantify them using a molecular approach.”

The three-year project is funded by a $725,000 grant from the National Science Foundation and will run until February 2018. Frischer’s collaborator on the project is Deidre Gibson from Hampton University. Gibson received her Ph.D. from the University of Georgia in 2000, and did much of her graduate research at Skidaway Institute with Professor Gustav Paffenhöfer.  In addition to Walters, Savannah State University graduate student Lauren Lamboley is part of the team, along with a number of students at Hampton University. Several undergraduate research interns have also participated in the project, gaining hands-on research experience. Frischer is also working with the Institute for Interdisciplinary STEM Education at Georgia Southern University to engage K-12 teachers by inviting them to participate in the research cruises.

UGA Skidaway Institute scientists study role of sunlight on marine carbon dioxide production

July 21, 2016

Scientists at the University of Georgia Skidaway Institute of Oceanography have received a $527,000 grant from the National Science Foundation Chemical Oceanography Program to answer one of the long-standing questions about carbon in the ocean—the rate sunlight produces carbon dioxide from organic carbon molecules in the sea.

Jay Brandes, Leanne Powers and Aron Stubbins will use a new technique they developed to measure this process, which is known as photo-degradation.

Researchers Aron Stubbins (l) and Jay Brandes

Researchers Aron Stubbins (l) and Jay Brandes

The ocean is full of millions of different types of organic compounds. Some are consumed by bacteria, but many are not easily consumed and remain in the ocean for hundreds or thousands of years. However, near the surface, sunlight causes the breakdown of organic compounds and converts them into carbon dioxide through photo-degradation. Until recently, this process has been nearly impossible to measure directly in most of the ocean because the additional carbon dioxide produced per day is tiny compared to the existing high concentration of CO2 present in the sea.

Researcher Leanne Powers

Researcher Leanne Powers

Brandes described the problem as looking for a needle in a haystack.

“You might think this is not important because it is hard to measure, but that’s not true,” he said. “We’re talking about a process that takes place across the whole ocean. When you integrate that over such a vast area, it becomes a potentially very important process.”

The project became possible when the team developed a new technique to measure the change in CO2 concentration in a seawater sample. The concept was the brainchild of Powers, a Skidaway Institute post-doctoral research associate. The technique uses carbon 13, a rare, stable isotope of carbon that contains an extra neutron in its nucleus. Researchers will add a carbon 13 compound to a sample of seawater and then bombard the sample with light. The scientists will then use an instrument known as an isotope ratio mass spectrometer to measure the changes in CO2 concentration.

According to Brandes, this project will be breaking new ground in the field of chemical oceanography.

“We don’t know what the photo-degradation rates are in most of the ocean,” he said. “We are going to establish the first numbers for that.”

The team plans to take samples off the Georgia coast, as well as from Bermuda and Hawaii.

While they will continue to refine the carbon 13 technique, Brandes said it is now time to put that tool to work.

“It is now a matter of establishing what the numbers are in these different locations and trying to develop a global budget,” he said. “Just how much dissolved organic carbon is removed and converted to CO2 every year?”

The project is funded for three years. The team will also create an aquarium exhibit at the UGA Aquarium on the Skidaway Island campus to help student groups and the public understand river and ocean color.

VIDEO – The climate change issue you probably haven’t heard about

July 6, 2016

The soil in the Arctic holds a massive store of carbon. These remnants of plants and animals that lived tens of thousands of years ago have been locked in permafost, soil that is always frozen…until now.

UGA Skidaway Institute of Oceanography scientist Aron Stubbins is part of a team that travelled to Siberia to discover what happens to that carbon when the permafrost thaws.

 

Warming climate may release vast amounts of carbon from long-frozen Arctic soils

April 24, 2015

While climatologists are carefully watching carbon dioxide levels in the atmosphere, another group of scientists is exploring a massive storehouse of carbon that has the potential to significantly affect the climate change picture.

Aron Stubbins

Aron Stubbins

University of Georgia Skidaway Institute of Oceanography researcher Aron Stubbins is part of a team investigating how ancient carbon, locked away in Arctic permafrost for thousands of years, is now being transformed into carbon dioxide and released into the atmosphere. The results of the study were published in Geophysical Research Letters.

The Arctic contains a massive amount of carbon in the form of frozen soil—the remnants of plants and animals that died more than 20,000 years ago. Because this organic material was permanently frozen year-round, it did not undergo decomposition by bacteria the way organic material does in a warmer climate. Just like food in a home freezer, it has been locked away from the bacteria that would otherwise cause it to decay and be converted to carbon dioxide.

“However, if you allow your food to defrost, eventually bacteria will eat away at it, causing it to decompose and release carbon dioxide,” Stubbins said. “The same thing happens to permafrost when it thaws.”

Scientists estimate there is more than 10 times the amount of carbon in the Arctic soil than has been put into the atmosphere by burning fossil fuels since the start of the Industrial Revolution. To look at it another way, scientists estimate there is two and a half times more carbon locked away in the Arctic deep freezer than there is in the atmosphere today. Now, with a warming climate, that deep freezer is beginning to thaw and that long-frozen carbon is beginning to be released into the environment.

“The study we did was to look at what happens to that organic carbon when it is released,” Stubbins said. “Does it get converted to carbon dioxide or is it still going to be preserved in some other form?”

Stubbins and his colleagues conducted their fieldwork at Duvanni Yar in Siberia. There, the Kolyma River carves into a bank of permafrost, exposing the frozen organic material. This worked well for the scientists, as they were able to find streams that consisted of 100 percent thawed permafrost. The researchers measured the carbon concentration, how old the carbon was and what forms of carbon were present in the water. They bottled it with a sample of the local microbes. After two weeks, they measured the changes in the carbon concentration and composition and the amount of carbon dioxide that had been produced.

A bank of permafrost thaws near the Kolyma River in Siberia.

“We found that decomposition converted 60 percent of the carbon in the thawed permafrost to carbon dioxide in two weeks,” Stubbins said. “This shows the permafrost carbon is definitely in a form that can be used by the microbes.”

Lead author Robert Spencer of Florida State University added, “Interestingly, we also found that the unique composition of thawed permafrost carbon is what makes the material so attractive to microbes.”

The study also confirmed what the scientists had suspected: The carbon being used by the bacteria is at least 20,000 years old. This is significant because it means that carbon has not been a part of the global carbon cycle in the recent past.

“If you cut down a tree and burn it, you are simply returning the carbon in that tree to the atmosphere where the tree originally got it,” Stubbins said. “However, this is carbon that has been locked away in a deep-freeze storage for a long time.

“This is carbon that has been out of the active, natural system for tens of thousands of years. To reintroduce it into the contemporary system will have an effect.”

The carbon release has the potential to create what scientists call a positive feedback loop. This means as more carbon is released into the atmosphere, it would amplify climate warming. That, in turn, would cause more permafrost to thaw and release more carbon, causing the cycle to continue.

“Currently, this is not a process that shows up in future (Intergovernmental Panel on Climate Change) climate projections; in fact, permafrost is not even accounted for,” Spencer said.

“Moving forward, we need to find out how consistent our findings are and to work with a broader range of scientists to better predict how fast this process will happen,” Stubbins said.

In addition to Stubbins and Spencer, the research team included Paul Mann from Northumbria University, United Kingdom; Thorsten Dittmar from the University of Oldenburg, Germany; Timothy Eglinton and Cameron McIntyre from the Geological Institute, Zurich, Switzerland; Max Holmes from Woods Hole Research Center; and Nikita Zimov from the Far-Eastern Branch of the Russian Academy of Science.

UGA Skidaway Institute researchers complete ‘26 Hours on the Marsh’

July 30, 2014

Pitching a tent in the woods and fighting off mosquitos may not sound like logistics of a typical oceanography experiment, but that is how researchers at the University of Georgia Skidaway Institute of Oceanography completed an intensive, round-the-clock sampling regimen this month. The project, dubbed “26 Hours on the Marsh” was designed to investigate how salt marshes function and interact with their surrounding environment—specifically how bacteria consume and process carbon in the marsh.

The team set up a sampling station and an outdoor laboratory on a bluff overlooking the Groves Creek salt marsh on the UGA Skidaway Institute campus. The scientists collected and processed water samples from the salt marsh every two hours, beginning at 11 a.m. on July 16 and running through 1 p.m. July 17. By conducting the tests for a continuous 26 hours, the team can compare the samples collected during the day with those collected at night, as well as through two full tidal cycles.

The UGA Skidaway Institute team processes water samples at their outdoor laboratory. (l-r) Megan Thompson, John DeRosa (UGA Intern), Zachary Tait and Dylan Munn (UGA Intern.)

The UGA Skidaway Institute team processes water samples at their outdoor laboratory. (l-r) Megan Thompson, John DeRosa (UGA Intern), Zachary Tait and Dylan Munn (UGA Intern.)

“We wanted to be able to compare not only what is happening to the carbon throughout the tidal cycle, but also what the microbes are doing at high and low tides and also during the day and night,” said Zachary Tait, a UGA Skidaway Institute research technician. “So we had to have two high tides and two low tides and a day and night for each. That works out to about 26 hours.”

The research team ran more than 30 different tests on each sample. The samples will provide data to several ongoing research projects. A research team from the University of Tennessee also participated in the sampling program. Their primary focus was to identify the bacterial population using DNA and RNA analysis.

This sampling project is one of many the researchers conduct during the year. They use an automatic sampling system for most of the other activities. The automatic system collects a liter of water every two hours, and holds it to be collected and processed at the end of the 26-hour cycle. The team could not use the auto sampler this time for several reasons; the scientists needed to collect much more water in each sample than the auto sampler could handle and the auto sampler tends to produce bubbles in the water, so it is not effective for measuring dissolved gasses.

Megan Thompson supervises Dan Barrett (l) and John DeRosa, both UGA interns, as they process samples in a UGA Skidaway Institute laboratory.

Megan Thompson supervises Dan Barrett (l) and John DeRosa, both UGA interns, as they process samples in a UGA Skidaway Institute laboratory.

“The UT scientists wanted to conduct enzyme analysis as well as RNA and DNA tests on the samples, and for those, the samples must be very fresh,” said Megan Thompson, a UGA Skidaway Institute research technician. “You can’t just go out and pick them up the next day.”

About a dozen scientists and students were involved in the project, including Thompson, Tait, a group of undergraduate students completing summer internships at UGA’s Skidaway Institute and a similar group from UT. They split their time between the tent and outdoor laboratory on a bluff overlooking Groves Creek, and the UGA Skidaway Institute laboratories a mile away.

“It was an interesting experience, and I think it went very well,” said Thompson. “However, when we wrapped it up, we were all ready to just go home and sleep.”

“26 Hours on the Marsh” is supported by two grants from the National Science Foundation, totaling $1.7 million that represent larger, three-year, multi-institutional and multi-disciplinary research projects into salt marsh activity. These projects bring together faculty, students and staff from UGA’s Skidaway Institute, UT and Woods Hole Research Center. UGA Skidaway Institute scientists include principal investigator Jay Brandes; chemical oceanographers Aron Stubbins and Bill Savidge; physical oceanographers Dana Savidge, Catherine Edwards and Jack Blanton; and geologist Clark Alexander. Additional investigators include microbial ecologist Alison Buchan and chemical oceanographer Drew Steen, both from UT; as well as geochemist Robert Spencer from WHRC.

Skidaway Institute intern wins research prize

July 16, 2014

Candy v wAn undergraduate student who conducted her research at the University of Georgia Skidaway Institute of Oceanography will attend a prestigious international science conference as a reward for winning the Outstanding Research Paper in the Savannah State University’s Bridge to Research program.

Candilianne Serrano Zayas’ paper was chosen from 10 others and tied for first place. She will attend the international science conference sponsored by the Association for the Sciences of Limnology and Oceanography meeting in Granada, Spain, in February 2015.

Zayas is a rising junior and biology major at the Universidad Metropolitana in San Juan, Puerto Rico. Her research project studied the microbiological community present in dolphins.

“One of the reasons this is important is because bottlenose dolphins are a marine sentinel species,” Zayas said. “This means that their health can be indicative of the health of the overall environment, which in the case of dolphins is our coastal waters.”

Zayas believes what made her project special was that it involved both field and lab work, and it created an interesting and important relationship between human health and animal health. “You don’t need to take a molecular biology class to understand how it works, so it makes it so much easier to explain to different audiences.”

Zayas worked in the lab of Skidaway Institute professor Marc Frischer, who praised her and her mentors.

“The combination of a good student, an appropriate project and, most importantly, a stellar mentor shoots these students to the stars,” Frischer said.

Zayas was mentored by SSU graduate student Kevin McKenzie, who is also a member of the Frischer research team. Zayas echoed Frischer’s praise. “Kevin took the time to explain it all to me, even two or three times, and he taught me everything I did on this project,” she said.

In the 2013, McKenzie mentored another REU student who also won this prestigious award. Kristopher Drummond, an SSU student and star football player for SSU, has continued the research he started and plans to continue his studies.

Zayas says she plans to complete her bachelor’s degree in Puerto Rico and then attend graduate school.

Zayas shared the first place honor with SSU student Darius Sanford, who worked at Gray’s Reef National Marine Sanctuary and who will also attend the ASLO meeting.

Launched in 2009, the SSU Bridge to Research in Marine Sciences program is a National Science Foundation-funded Research Experience for Undergraduates program. The SSU program has proven successful in inspiring under-represented student populations to pursue degrees and careers in science and technology-based research fields.

“African-Americans are greatly underrepresented in the ocean sciences,” SSU professor Tara Cox explained. “Of the 28 students who have completed the program, 20 are African-American.”

The seven-week 2014 Bridge to Research program began with field trips and classroom work covering research basics. The students then took a two-day research cruise on Skidaway Institute’s Research Vessel Savannah. They then were paired with a mentor at one of the participating organizations—Savannah State University, UGA Skidaway Institute of Oceanography, Gray’s Reef National Marine Sanctuary or Georgia Tech-Savannah. During this partnership, they conducted research and then presented it at a public forum.

Barrow — January 17

January 19, 2012

17 January 2012

We woke up a little late this morning after yesterday’s late night. Victoria and I met to go over plans for the day and to discuss the details of the experiment that we plan to start today. The experiment is a component of SSU graduate student Zac Tait’s thesis project. Zac couldn’t come this time because he is about to be a father. His daughter, who they will name Iris, is due on 4 February. Zac left me and Victoria with extensive notes and prepared all the supplies but we’ll run it.

The goal of this experiment, as in previous ones, is to test the hypothesis that Arctic Ocean bacteria can utilize the carbon locked up in the humic material that makes up the permafrost, but doing so will require them to acquire more nitrogen. The most abundant source of nitrogen in the water is found in the mineral form of nitrate (NO3). One of the major questions of our project is whether the release of the carbon stored in the permafrost will set-up increased competition for NO3 between the photosynthesizing autotrophs (phytoplankton) and the CO2 respiring heterotrophs (bacteria). The idea is that the more organic carbon that gets released into the ocean the more bacteria activity will occur.  However, that increase in activity will be at the expense of nitrate resources that the phytoplankton need in the spring (when the lights come back on) to grow.  If there is less nitrate available there will be less phytoplankton and therefore less fish, seals, whales etc that depend on a food web whose base is the phyotoplankton. So it’s somewhat of a counterintuitive idea; add more nutrients and get less out.

In previous experiments we found generally that this hypothesis is true, but that the carbon-rich humic material we collected directly from the tundra is used very slowly which makes the question hard to address given the practical constraints of our time here. Because our time is short and the temperatures are cold which slows everything down, we decided on a new twist for these experiments. This time, we are using humic material that has already been broken down some by exposure to sunlight. This process is called photo degradation. Photo degrading complex carbon molecules occurs naturally (It’s reasonable to expect that humics derived from melting permafrost will be exposed to sunlight on their trip to the ocean.) and it increases its availability to bacteria as a nutrient source. So, prior to the trip Zac exposed humics in a solar simulator for 0, 5 and 15 days resulting in increasingly degraded humic materials.  Amazingly, after 15 days of simulated exposure to sunlight the brown humic material was almost completely colorless. The carbon is still there but since it has been broken into smaller and less condensed molecules it doesn’t absorb as much light, thus it appears lighter in color.

Photo degraded humics used in our bioassay experiment

Our experimental design is relatively simple. We use 4 liter (1 gal) milk jugs (actually they are a special nontoxic plastic but they look like milk jugs) to incubate bacteria with the humics and allow them to grow.  Over the course of the week we’ll be here we take samples to watch the bacteria grow track the dynamics of the carbon and nitrogen. Our hypothesis will be supported if we see the bacteria grow and the carbon disappear in coordination with the disappearance of the NO3.

After 9 hours of filtering and rinsing we finally got the experiment set-up and running. We’ll sample it daily (or every other day) for the time we’re up here.

Zac’s experiment running

 

But the real excitement happened on the ice today. Because we are so concerned about the stability of the ice the UMIAQ crew went out to check our ice camp which we had left standing. When they got out there they realized that the ice was moving a lot and that large cracks were beginning to appear. The crew was scared enough that they just came back leaving the tent behind. But Brower thought they could get it and made a heroic trip back out with Tony and Glenn. They ripped the tents out of the ice leaving the stakes behind, quickly lashed it on two sleds, and hightailed it back jumping cracks with open water. We heard some of it on the radio. The whole situation has us pretty nervous and thinking very carefully about safety.

[Picture –

Brower and Glenn standing by the rescued tents.

Either way tomorrow we won’t go out.  We’ll re-group and re-evaluate.

Barrow — Jan 16

January 19, 2012

16 Jan 2012

Ice conditions are still unstable.  Our UMIAQ support team spent the morning doing reconnaissance of our intended sampling sites. After yesterday’s efforts they suggested that since it might be dangerous, it wasn’t a good idea for anyone on the science team to accompany them. Because the ice is still forming and the ocean is a powerful force, the ice can break-up pretty quickly. The team first scouted out our near shore site, but it was inaccessible due to a major crack between it and our ice trail. We use a trail cut through the ice to guide us on a safe snow machine run over it. They continued on to our second site located further out into the ocean and to the north. The ice in that area seems to be more stable. They liked what they saw and decided that it would be safe for us to set up camp there.

Brower Frantz, UMIAQ logistics leader proudly stands by the ice camp.

After making this decision the team came back, loaded up the camp gear (tents, generators, heaters, ice augers, etc) and went back out. This time Steven Baer from the Bronk group went with them to help orient the tents and make some basic measurements. Before starting we need to know the ice thickness, water depth, and usually how far light penetrates. In this case there basically isn’t any light but hey, we’re scientists. Measuring zero’s (or close to zero) can be just as important. Its data!

Meanwhile, back on the NARL campus where our labs are, there was a flurry of activity as we all checked and prepped our gear. Finally, around 3pm the camp was set-up and we were ready to go. I was pretty worried about how late it was getting, but because we have such a short time up here and the ice was deemed safe now we needed to push a little bit. Who knows if we’ll even get another chance given the dynamic condition of the ice.

The ride out was relatively uneventful. The ice was remarkably smooth compared to our previous trips.  As was explained to me, when the ice first forms it is relatively flat and it only gets jumbled up later as storms, wind, currents, and tides push it around. Flat ice generally means that it is new ice.  That is what was worrying everybody. We know the ice is still forming and moving a lot. Hopefully it won’t move while we’re on it! After about 30 min of driving we made it to our camp. Having well established sampling routines by now, this is our 6th expedition, we all got to work unloading our gear and starting to sample. The Yager group occupies their own tent (the smaller one) while the Frischer and Bronk group occupy the larger one.

Ice Camp 16 January 2012

In the Frischer tent I got started right away making measurements of the water column. We are using a new instrument that lets us measure depth, temperature, salinity, oxygen, chlorophyll, pH, and turbidity. It’s a pretty nice instrument but a bit delicate and the computer software is not straightforward. We transported it as if it was a delicate infant wrapped in blankets with warm water bottles and hand warmers to make sure it didn’t freeze on the way out. I think we overdid it! When I unwrapped it in the tent it was positively hot. The instrument worked well and we got a good look at the water conditions. As expected the water temperatures was -1.8 deg C, salinity was around 33 PSU (normal for the Arctic coastal ocean), there was almost no chlorophyll in the water (no light no algae in the water). Most importantly the water column was well mixed which means that we could sample at one depth and be reasonably assured that it would be representative of the whole water column. We decided to sample at 2 meters below the bottom of the ice.

Graph of water data from the MANTA, Eureka Environmental

After I was finished measuring the water the Bronk group got rolling. They rinse and fill what seem like a million small bottles to which they add a very small amount of nutrients enriched in their stable isotope concentrations. Stable isotopes are non-radioactive form of elements (atoms) that are slightly heavier than the normal form. For example, the normal atomic weight of Carbon is 12 (meaning it has 12 protons) while the stable isotopic form has a weight of 13. We refer to it as 13C.  Because 13C  is slightly heavier than 12C, it can be measured on a mass spectrometer. By measuring how much of it goes into cells during an incubation, the rate of uptake can be calculated. The Bronk group is making some of the first ever measurements of nutrient uptake rates by microbes in this region of the Arctic coastal ocean.

The process went pretty smoothly but since it was so cold, even in the tent, the pipettes which they were using to inject the stable isotope into the samples were freezing and slowing the process.

Dr. Debbie Bronk injects stable isotope labeled nutrients into seawater.

Meanwhile in the other tent the Yager group were having even more problems with freezing. They are collecting water samples to make measurements of the carbon chemistry and general activity of the microbes, so it is especially important that their samples do not freeze and are not exposed to the atmosphere which can contaminate the dissolved gas content of the seawater. Unfortunately, their samples were freezing.  However, after getting them off the ice floor of the tent and placing them into a seawater bath (a cooler filled with seawater) they seem to have solved the problem and were able to collect most of the samples they needed.

Dr Tish Yager and Colin Willams collecting water.

When the Bronk group was finished it was our turn.  Our sampling is probably the most straightforward, but we need to collect a lot of water.  We’re collecting enough water so that we can extract DNA and RNA from the bacteria in it.  We collect about 140 liters (about 40 gal or 310 lbs). Using a specially designed submersible pump we collected water in seven 20 liter carboys wrapped in neoprene and then place them in a cooler of snow. Believe it or not, the snow actually keeps the water from freezing. But, as simple as it sounds, we had our problems too. The generator that was running our pump ran out of gas.  Actually, the generator had a gas leak so it’s lucky it just ran out of gas and didn’t explode. But, because of excellent planning on the part of the UMIAQ team we had two generators on site. However, that meant the Yager group was without lights in their tent. We solved that problem by moving two snow machines so they pointed at the tent and the headlights provided enough light.

Finally we were all done and got all our gear and samples loaded back onto the sleds.  It was unbelievably cold and windy and we were all tired and ready to get back. The trip started off smoothly until I managed to get my sled stuck. It’s really tricky pulling a very heavily loaded sled. I had to slow down over a series of small ridges because the person in front of me slowed, and that was all it took for the snow machine to sink a little too much into some soft snow and lose traction. With all of us helping we disconnected the sled and managed to lift the back end of the snow machine out of snow, enough to get it moving. Then we were able to push the sled back to some more level ice and reconnect it to the snow machine. It was exhausting! But the fun wasn’t quite over. As we started moving again Debbie, in an effort to make it over the hole I had dug with the snow machine, went a little too fast over the area and bumped into Rachel and Jenna who were on the snow machine in front of them. No real harm though. Jenna fell off the snow machine but it was into soft snow and she wasn’t hurt. The brand new snow machine Deb was driving suffered a cosmetic crack in its fairing. Without further incident we all made it back safely to campus and quickly rushed our samples to our respective labs for processing.

Victoria and I spent the next 5 hours in our cold room filtering all that water we had collected. We had hoped to start another humic addition bioassay that is a component of Zac Tait’s thesis research, but it was just too late so we decided we’d do that first thing in the morning. After all the filtering was done, our samples put away safely, and all our gear cleaned-up it was time for some well deserved rest. I felt weary and frozen to the bone but pleased with the progress we had made.

Even though the sun won’t shine, tomorrow is a new day.

Day 2 in Barrow

January 18, 2012

Marc Frischer continues his account of his and Victoria Baylor’s research trip to Barrow, Alaska.

15 January 2012

Today we again woke up early and began setting up our labs. Actually day and night are surprisingly similar around here.

Good morning, Barrrow!

Victoria spent most of the day setting up our molecular lab in the BARC building. It is in this lab that we will extract RNA, DNA, and preserve other samples from the bacteria we collect from the Arctic Ocean. One of the questions we are addressing in this project is whether Arctic bacteria are competing with Arctic phytoplankton for nutrients (specifically nitrogen) and whether when more organic carbon from melting permafrost reaches the Arctic coastal ocean if this competition is intensified. We suspect that an intensified competition between bacteria and phytoplankton (algae) for nitrogen will lead to a less productive Arctic food web in a future warmer Arctic ocean. One way to address this question is to measure how actively bacteria are using the most prevalent form of nitrogen in these waters, nitrate (NO3). By looking for this gene and measuring how active it is, we are learning about how this critical nutrient cycling function is controlled.

Victoria setting up lab in BARC.

While  Victoria was setting up the lab I was setting-up the lab (walk in freezer) where we will be filtering water and conducting a bioassay experiment (more on that later). I also spent some time making sure our sampling gear was organized and functional. The pump we use to collect the water from under the ice had seized but luckily with the help of Lance Bennett (part of the CPS team) we got it running. We also brought with us a relatively new instrument to measure water conditions that I am not too familiar with. Initially I couldn’t manage to get the instrument to communicate with its hand held computer, but after a long struggle I finally got it to work. Hopefully I’ll be able to remember everything when we are actually out on the ice.  It’s a cool instrument though, it measures water depth, temperature, salinity, pH, turbidity and the concentrations of chlorophyll and dissolved oxygen all in real time.

Eureka Manta water quality instrument

While we were setting-up, our logistics team accompanied by Steven Baer (VIMS) as a representative of the science team was scouting our sampling sites. For those of you who may not be familiar with our sampling plans, when the ocean is frozen the way we sample is to set-up a camp on the ice, drill holes, and collect water through them. To safely do this we need to be on well secured and thick ice. This time of year the ice is pretty dynamic as it is still forming and major storms can move it around quite a lot. In advance of our trip this year we had identified several possible sampling locations that were consistent with our science needs, but they need to be checked every day. So this morning the UMIAQ team checked. Unfortunately its seems as our original site developed a major crack in the ice and is moving so we had to switch to a different site a few miles northward where the ice appears to be thicker and is more securely grounded (frozen to land). However, even there the ice seems to be moving a lot. So the camp didn’t get set-up and the plan is to revaluate tomorrow morning. That means we wait, but it’s much better to be safe than to risk everything. If there is one thing I have learned during this project it is to be patient and to trust the support we are getting from our local logistic support team.

We’ll just have to see what tomorrow brings. The weather is predicted to be pretty mild.

[Picture- weather forecast for 16 January 2012]