Posts tagged diatoms

Antarctic epiblog: leaving McMurdo

Published by Jeff McQuaid on 26 November 2009 in Education and Microbial & Environmental Genomics.
Ice formation outside McMurdo Station

Ice formation outside McMurdo Station

After we took our samples out at the ice edge, we returned to McMurdo Station for several intense days of demobilization. We had to return all of the large drills, power equipment and camping gear, and spent a considerable time preparing our own gear for shipment back to the United States. Our samples and some of our critical gear will go by air transport to Port Huemene in California, and the rest will be shipped back to the US by icebreaker during the January sealift. In order to preserve the DNA and RNA of our plankton samples, we froze them in the field in liquid nitrogen: these samples will be air-shipped on dry ice to the J. Craig Venter Institute, where both DNA genetic code and RNA messages will be sequenced and decoded.

Mak in the Crary lab looking at some of Dawn's psychrophilic bactera

Mak in the Crary lab looking at some of Dawn's psychrophilic bactera

Mak Saito and his group will similarly take the phytoplankton protein samples back to the Woods Hole Oceanographic Institution and use a mass spectrometer to identify the protein fragments. The protein fragments . Mak’s group also had some success culturing psychrophilic bacteria: psychrophiles are organisms which live around the freezing point, though many of the mechanisms which allow them to survive are unknown. By

close-up of the Petri dish

close-up of the Petri dish

bringing back some live bacterial cultures to the laboratory, we will be able to grow them and study how both bacteria and larger phytoplankton can tolerate cycles of freezing and thawing, and also how the various proteins and enzymes in them remain flexible enough to function.

One student wrote in and asked if plants only grew in the sea ice and not on land. the best answer I can give is that the temperatures in the sea ice are relatively stable: at the ice-water interface, the temperature is a constant 28 degrees Fahrenheit (-1.8 Celsius). If organisms can adapt to

Antarctica and Mars have much in common

Antarctica and Mars have much in common

that environment, then conditions are relatively stable for life. In contrast, life on land is relatively harsh, and in one day the soil surface can go from warm and sunlit to being raked by freezing 50 mph winds. I understand that there is a type of moss which grows near the streams in the McMurdo Dry Valleys, and I understand that there are some lichens around Cape Royds, but other than that the conditions are too harsh for land plants: all of the plant activity is in the ocean, growing as phytoplankton!

Close-up of desert pavement in Antarctica: Winds are so strong that small grains are blown away, leaving only gravel to 'pave' the surface of the soil

Close-up of desert pavement in Antarctica: Winds are so strong that small grains are blown away, leaving only gravel to 'pave' the surface of the soil

This brings up a good point: we love to hear your questions and comments, particularly from students and the public. if you have been following this blog, and have and found it interesting, or want to know more about any of the topics covered here (polar biology, plankton, life in Antarctica), you can

Invite us to your classroom!

Invite us to your classroom!

leave us a message at the bottom of this blog page. For the educators and classrooms which have been following this blog, let us know if you would be interested in having one of our scientists visit and give a presentation on polar science to your class: we love to talk about our work, and would be thrilled with the opportunity to talk to your students.

So what lies ahead? Our frozen samples arrive next week, and starting in January I will extract the DNA and begin the long process of preparing the samples for sequencing. Collecting the samples was just the beginning, and we will be processing the samples and data for months to come - keep an eye on this website for periodic updates on our discoveries.

I’ll finish off this post with a picture I took of Castle Rock on our last night in Antarctica. While we were all eager to return home, we hadn’t seen the sun set once in three weeks, and it is moments of sublime beauty like this picture of Castle Rock glowing at midnight which keep polar biologists coming back year after year. Enjoy!

Castle Rock under the midnight sun

Castle Rock glowing under the midnight sun

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Station III: approaching the ice edge

Published by Jeff McQuaid on 22 November 2009 in Education and Microbial & Environmental Genomics.

As we were finishing up our work at Station II, we called MacOps, the radio command center for McMurdo Station, and got a 24 hour weather update: a high to the north of Ross Island was blocking a storm in the south, and we were caught in the middle. The prediction: snow, and lots of it. We had already been caught out on two other storms, and so this time we decided to speed up our activities and get to the next station, Station III, before the snow started falling and we got stuck. As we were rushing around to finish last minute experiments, we had some visitors drop by our camp:

Seven Emperor penguins toboggan up to us from the south. As they get close they stand up and start walking towards our camp

Seven Emperor penguins toboggan up to us from the south. As they got close they stood up and almost walked right into camp

The Emperor penguins get together and 'conference' about these strange red-jacketed aliens who have landed on their sea-ice.

The Emperor penguins get together and seem to conference about the intentions of these strange red-jacketed aliens who have landed on the sea-ice.

Eventually they decide we aren't all that interesting, and they walk on, seemingly deep in thought

Eventually they decide we aren't all that interesting, and they walk off to the north

We continue with our packing, and soon we are able to hitch up our vehicles and sleds and continue heading west, out across the McMurdo Sound. At first the sea ice was similar to the day before: lots of cracks and pressure ridges where the plates collide, all of which need to be checked out before we can safely pass. About half way there though, the sea ice becomes smooth, and the cracks become so small that none if them are wide enough to present a possible danger.

Jeff Hoffman and Abigail Noble set up tents

Jeff Hoffman and Abigail Noble set up tents

We get to camp, and when we climbed on the roof of our research sled, we could actually see the open water of the Ross Sea Polynya about two miles to our north. It was an amazing, and heartening sight, and we were excited to start seeing changes in both planktonic organisms and in water chemistry. As before, we arranged our vehicles in a windbreak, hoping to block the winds from the south, and had a quick hot meal before we got down to the business of prepping filters, drilling holes and labeling our collection tubes.

Jeff McQuaid collects some cores, with the skies darkening to the north

Jeff McQuaid collects a core while the skies darken

We are almost falling into a routine: I start working with the Kovacs corer while Mak and Abigail prepare the winch and tripod for casting the Niskin bottles. This particular station is over 700 meters deep, so lowering and raising a bottle 2000 feet will take some time. We had been using a HotFinger to melt and widen holes in the ice, but one of the connectors broke, so now Mak isn’t able to circulate hot glycol through the coils. He and Matt end up using the one of the large drills, which take two people and are extremely heavy. I start pulling up a number of cores, and notice that there is less coloration that the previous site, which was less than the first station. We wonder if this is a trend as you move away from land, and consider whether we will have time to head back and take a few additional cores for comparasion. As we are talking about maybe using the snowmobiles to do this, we get seven more visitors, this time from the polynya to the north:

Seven Adelie penguins approach from the waddle up from the north

A group of Adelie penguins waddle up from the polynya just north of camp

These Adelie penguins are not even a quarter of the size of the Emperor penguins we had seen earlier in the day, and unlike the stately and seemingly introspective Emperors, the Adelie seemed comical, almost borderline ditzy. The walked around camp, looking at our equipment, and they seemed pretty oblivious as they horsed around before headed back out to the polynya.

Abigail adjusts the rope on the Niskin Bottle winch as the storm develops

Abigail adjusts the rope on the Niskin Bottle winch as the storm develops

The snow started to fall, and the winds picked up - it was time for another Antarctic storm! We were only partway through sampling, but we needed a few critical pieces of equipment, including a snowmobile sled and a portable rack: as our last sample, Jeff Hoffman and I wanted to get up to the ice edge and sample the open polynya water, and to do that we would need more portable gear. It was decided I would go back in a Pisten Bully with Matt and try to beat the storm, and come back in the morning with our equipment. So I got a night in town - and a chance to post another update to the blog! Tommorow Jeff Hoffman and I will continue our transect right up to the sea-ice edge, which should be spectacular - stay tuned!

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McMurdo Sound

Published by Jeff McQuaid on 19 November 2009 in Education and Microbial & Environmental Genomics.
Winching our Pisten Bully out of a deep snowdrift

Winching our Pisten Bully out of a deep snowdrift

It took another day for the storm to blow itself out, but by Tuesday the wind and driving snow had abated, and we drove our Pisten Bully back out to our temporary shelter near Cape Evans. It took several hours of digging to clear the snow away from our vehicles, but once we started driving away from the hut we quickly ran into another problem: the snow was so

Using a Kovacs drill to obtain an ice core

Jeff McQuaid using a Kovacs drill to obtain an ice core

deep that our sleds and vehicles would bog down in the snowdrifts. Often we would pull out the Pisten Bully, only to have the Sno-Cat get stuck and have to dig that out. An entire day went by digging vehicles out of the snow, and in the process we broke our sled hitch and winch. Eventually we were able to drag our research sled to suitable location for obtaining a sample of plankton, and we set up camp.

We first tested the ice thickness at our sample site using a standard ice drill – we needed three drill extensions, or drill flights, to get to the bottom of the sea ice, which meant using an awkward 100 inch drill. The ice were we were stationed turned out to be 78 inches thick. We then used a Kovacs Mark II coring drill to obtain a 4 inch diameter core of ice. The sea ice is remarkably consistent, until you approach the bottom layer, where diatoms and other phytoplankton have entrained themselves in the ice. By keeping to the

An inverted ice core showing the mass of phytoplankton growing on the bottom of the ice

An inverted ice core showing a layer of phytoplankton growing in the sea ice

underside of the ice, microscopic plankton are the first organisms to intercept light as it enters the ocean, but the plankton are still close enough to the unfrozen seawater to obtain dissolved nutrients and minerals. Living in the ice also protects the phytoplankton from grazing zooplankton like Antarctic krill. We took the core on the left, removed the brown layer containing the diatoms and other phytoplankton, and carefully preserved the cells in liquid nitrogen for sequencing at the J. Craig Venter Institute. These diatoms probably function very differently from diatoms living in the water, so sequencing their mRNA transcripts (or transcriptome) will tell us what kinds of proteins they make and how they function in a frozen environment.

Jeff Hoffman runs the filtration statoin inside our research sled

Jeff Hoffman runs the large steel filters for separating the phytoplankton by size

Once we have a clear hole in the ice we begin pumping seawater through a series of filter discs so we can separate the plankton based on their size. Our first filter is a 200 micron pre-filter on our sample tube - this keeps us from pulling zooplankton into our filters (we are mostly interested in the primary producers, the microscopic phytoplankton). The first filter is 3.0 microns, and intercepts the large eukaryotic phytoplankton. The second filter is 0.8 microns in size, and intercepts smaller picoplankton and some prokaryotic bacteria and archaea. The last

Mak Saito monitoring the winch and tripod

Mak Saito monitoring the winch and tripod. The wind picked up as the day progressed

filter is the 0.1 micron filter, and the organisms entrained here are almost exclusively prokaryotes. Before the seawater is returned below the sea ice, it is passed through a 50 kilodalton tangential flow filter: this last filter will remove and concentrate marine viruses, which may have a large effect on the function of the marine food web. In Antarctica, we are passing several hundred liters of water through the filters at each station, and usually in triplicate, which can take us most of the day.

Dawn's corner: culturing marine organisms and measuring particulate carbon

Dawn's corner: culturing marine organisms and measuring particulate carbon

On station, our group had different tasks to do: Jeff Hoffman worked the internal pumps and filters, while I took ice cores and kept the external machinery running. Mak Saito (pictured above) used a winch to deploy nansen bottles down through the water column and collect water from discrete depths: at our particular station, the water was 182 meters deep. The water Mak collected was passed along to Dawn (on right), where some of the water was filtered for particulate carbon analysis. Dawn also worked on culturing out organisms from the various samples as they arrived. The bulk of the water from the Nansen bottles went to Abigail Noble, where

Abigail in the clean room for trace metal analysis

Abigail in the clean room for trace metal analysis

she took them into her clean room for trace metal analysis. Because dissolved metal concentrations are so low in the ocean, all analyses have to be done in a controlled clean room: even a speck of dust could potentially alter her final concentrations. Abigail had a laminar flow vent leading into a plastic bubble-wrapped enclosure, and she even wore trace-metal clean slippers while inside. It was a sophisticated operation for a sled out on the sea ice!

We worked through the evening, and by midnight we were ready to wrap up our operation and head back to McMurdo Station. Mother nature had a different idea though: as we were leaving, the winds picked up, and began gusting over 50 knots, while the blowing snow caused the visibility to drop. McMurdo operations informed us that the weather had just deteriorated again, and was Condition 1, meaning no travel whatsoever. We were pinned down by yet another Antarctic storm!

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Out onto the ice

Published by Jeff McQuaid on 15 November 2009 in Education and Microbial & Environmental Genomics.
Our vehicle train leaves McMurdo Station under a bright blue sky

Our vehicle train heads out onto the sea ice under a bright blue sky (Photo JH)

It took an enormous amount of effort, but on Thursday we ventured out onto the sea ice with our train of sleds and snow machines. The tucker is our strongest (and slowest) vehicle, and it is pulling both our yellow research sled and a pair of snowmobiles. The red Pisten-Bully is pulling a second sled with several drums of diesel, a generator and assorted science gear. The weather was clear, cold and windy, with snow in the long-term forecast.

Leaving tracks across the snow as we leave the sea ice road (Photo: AN)

Looking out the rear window as we leave the sea ice road and enter deep snow (Photo: AN)

Initially we followed the Cape Evans sea ice traverse out of town: this route is a flagged and reconnoitered sea ice ‘highway’, so we were able to travel at maximum speed without having to stop and check the thickness of the ice. (Note that ‘humming along’ in Sno-cat is going about 3 mph). After two and a half hours on the sea-ice highway, we turned off the traverse and cut fresh tracks across the snow towards Inaccessible Island. The island is a big hunk of basalt rising straight out of the Ross Sea, and as we rounded the tip of the island, we saw a line of Weddell seals stretching off into the distance, evidence of large cracks in the ice. We tested a number of possible routes through the area, but all of the cracks were too wide and thin to safely cross.

Warming hut at the Cape Evans wall

Warming hut behind Cape Evans (Photo: AN)

We followed our tracks back to the sea ice road and continued north, passing around the other side of Inaccessible and trying our luck north of some large grounded icebergs. Here there were fewerbseals, and sea ice was more uniform, but we still ran into several large cracks, and by the time we had surveyed our route, it was past nine in the evening, and we needed to consider setting up camp. The wind had picked up noticeably, so we decided to head back towards Cape Evans and get some shelter from the coming storm. We were located near the hut that Robert Scott built for his 1911 Terra Nova expedition to the South Pole, but spending the night in the area is discouraged, as the area is a world heratige site. McMurdo Operations alerted us to a warming hut located behind Cape Evans, sheltered from the continental wall by a glacier on one side and a large basalt wall on the other.

Dawn and Jeff wondering what is down in that dive hole (Photo AN)

Dawn and Jeff wondering what might live down in that dive hole (Photo AN)

The hut turned out to be a dive shack kept heated to prevent the dive hole from freezing over. This presented some hazards when walking around the hut - one of the first casualties was my camera, which tipped out of my pocket and is now somewhere on the bottom of the Ross Sea. Still though, it was far better than being camped out on the unprotected sea-ice and blasted by wind, so we brought in folding chairs, sleeping bags and a portable kitchen, prepared to hunker down while the storm passed.

The storm hits our warming hut

The storm hits our warming hut

And what a storm! I grew up in rural New Hampshire and lived in Siberia, so I’ve experienced my share of foul weather, but there is nothing like a Condition 1 Antarctic storm to give you new respect for the raw power of nature. The visibility progressively dropped and the sky darkened, and the snow began to fall. It became impossible to tell whether the snow was actually falling or just blowing off the glacier, and the hut shook in the gusts. We had good radio communications with McMurdo Station, so we were never in danger, but we were certainly not going anywhere anytime soon - Hut 12 was our new home.

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Ice diatoms!

Published by Jeff McQuaid on 10 November 2009 in Education and Microbial & Environmental Genomics.
Last-minute adjustments to our mobile science sled

Last-minute adjustments to our mobile science sled

Today has been a day of preparations, as tomorrow we hope to leave McMurdo Station and head out on the sea ice. Our mobile sled is almost ready for deployment: the carpenters who work for the US Antarctic Program are quite amazing, and our sled has filtration racks for separating different sizes of plankton, incubation chambers, and a mobile clean room for trace metal analyses. All of this in a 6 x 12 foot space! I’ll have more photographs in the posts to come, but it very much a sled of the 21st century.

Dawn and Abigail check out the row of Scott tents available for check-out at the Berg Field Center

We are also assembling our equipment list for camping on the ice, and the list is impressive: tents, coleman stoves, fuel, kitchen boxes, ice screws, shovels, jerry cans, carabiners, spare sleds, and a hurdy gurdy. Don’t ask me what that last thing is, I’ve been told it is a ‘fuel transfer unrelated to the musical instrument. The place to get all of these items is the Berg Field Center, which is a storehouse of mountaineering and back-country equipment available to all scientists doing Antarctic field work. For someone who likes mountaineering as much as I do, visiting the Berg Field Center is like letting loose a kid in a candy store - the place just oozes exploration.

Dawn and Mak learn about drive belts

Dawn and Mak learn about drive belts and engine parts

In the afternoon our group attended a class on snowmobiles use and maintenance. Our research sled will be pulled by a Tucker Sno-Cat, and our lighter open-air equipment sleigh will be pulled by a Pisten Bully. Both of these machines are major workhorses in and around Antarctica, but they are slow: the Pisten Bully moves along at 6 mph. So for added flexibility we decided to bring along a pair of snowmobiles. With snowmobiles, we will be able to ride ahead and scout for hazard on the ice, as well as run back to McMurdo to pick up extra equipment or drop off samples. Driving a snowmobile is similar to riding a motorcycle, although the snowmobile doesn’t have any real gears, and snowmobiles reek of partially burned fuel (dirty two-stroke engines). As part of our training we ran a mogul course, and learned how to ride on ice and on slopes, and now I understand we are all certified ‘snow machine technicians’.

Diatoms growing in the ice

A layer of plankton growing in the sea ice

Hard to believe, but in between training sessions and lab set-up, Dawn has been able to have a look at some of the diatoms that Abigail and I brought back from our sea-ice training (see yesterday’s blog). On the right is a picture of a piece of ice from one of the holes we drilled when we were determining the thickness of the ice in cracks, and you can see that there is layer of ice discolored with pigment. These are microscopic plankton living in the ice, and for something non-mobile, living in the ice is ideal in some ways. Plankton embedded in the ice are protected from being eaten by krill and other grazing zooplankton, and ice plankton are also at the top of the water column, so they receive maximal sunlight. We transported our samples of ice back to the lab, and Dawn was able to put them under a light microscope with a camera attached and generate this picture:

Ice Diatoms: chain forming Fragilariopsis (center), ribbons of Amphiprora (squares with oval centers), and colonies of Nitzschia (long ovals growing end-to-end)

These are all diatoms, and not only could Dawn identify all of them without a guide, she could correctly spell them. Diatoms are glass shelled plankton famous for having some of the most beautiful patterned shapes in the ocean (see an SEM image here to get the idea). Diatoms play a vital role in the global carbon cycle, as the they remove large amounts of carbon dioxide from the atmosphere before dying and sinking to the bottom of the ocean. Large blooms of diatoms and other plankton may ultimately help remove much of the greenhouse gasses resulting from fossil fuel use, and is only one of many reasons why we are down here studying them.

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Why Antarctica, and why now?

Published by Jeff McQuaid on 28 October 2009 in Education and Microbial & Environmental Genomics.

So why are you going to Antarctica, and why are you going now? A very logical question… basically we are traveling to Antarctica to study microscopic marine plants known as phytoplankton. These organisms range in size from bacteria to diatoms to colonial algae, but all phytoplankton have two things in common: they are small enough to float in the water without sinking, and like all plants, they produce their own food using sunlight and carbon dioxide. They are so small that a cup of seawater may contain a million of them, and because they are at the base of the marine food chain, everything from shrimp to fish to whales depends on their existence as a food source. Phytoplankton are some of the most numerous creatures on earth, and ongoing climate research suggests that these microscopic plants will be the primary sink for absorbing and sequestering excess carbon dioxide greenhouse gasses.

If plankton are everywhere, then why go to Antarctica to study them? Well, it probably comes as no surprise that Antarctic plankton are some of the least studied of all the earth’s organisms, as simply getting to Antarctica is no small feat. But in addition to being one of the least studied environments, polar environments such as Antarctica are among the most endangered: ongoing climate change is affecting the polar regions faster than any other place on the planet, so there is some urgency to catalog what is there and how it is changing, and therefore establish a baseline of fundamental scientific knowledge.

To do this we will be using a number of tools developed for studying organisms which are too small to see. We will go out onto the sea ice and collect samples of water, and in addition to identifying the plankton using a microscope, we will try to identify them by reading and understanding their unique DNA signatures. We will be sequencing both the genes in the plankton, and also the genetic messages, or transcripts, that the plankton are producing. The transcripts are particularly interesting, as capturing them is like intercepting coded messages on what the plankton were doing at the time they were collected. At the same time, other members of our team will be analyzing the protein components of the plankton, and looking to see if the stories told between the DNA sequences and protein identifications match. In the end we hope to gather enough information to assemble a portrait of phytoplankton diversity and function in the Ross Sea.

To wind down this posting, here’s a montage of some of the diatoms we found on last year’s expedition. They really are beautiful!

Diatoms from last year's expedition (Dawn Moran, WHOI)

Diatoms from last year's expedition (Dawn Moran, WHOI)

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