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International Polar Year:
Bacterioplankton genomic adaptations to Antarctic winter

Alison Murray

Blogs: Alison Murray (lead PI)

July 10-17 | July 17-31 | August 1-11 | August 10-17 | August 20-30


July 10-17. Travel to Chile and Crossing Drake Passage

Week 1: All the hustle and bustle of getting things ready for this expedition are finally put to rest once we’re in the hands of the TSA and American Airlines. Travels for our team were all uneventful all the way to Punta Arenas. The same was not true for the other science team, led by Art DeVries, who are also going to Palmer Station - they had delays, lost baggage, and lost team members which finally coalesced in Punta Arenas on the LM Gould the morning of the day we departed.

We spent a day and a half in Punta Arenas prior to boarding the ship. Those hours are easily consumed by walking around town, revisiting favorite watering and dining holes (Santinos, Lomits, Olijoes, La Luna), shopping for last minute supplies (chocolate, more chocolate, and other confectionaries), and rubbing the toe of Magellan in the town square which is supposed to impart good luck and a safe crossing of the Drake Passage.

Finally, we departed Punta Arenas ~ 2:00 pm on July 13th after deciding to load the “tin can” or more formally, the Landing Craft – a relatively new member of the fleet which has been used on only a few occasions in the Palmer Station region. This boat should be able to handle waters with more ice than the zodiacs. It will also hold more bottles of seawater – which might come in handy for our sampling needs. The caveats are that we can only use it when the Gould is in port – for safety/rescue reasons you need a boat of equal or superior capacity for rescue.

The days being short meant that we only had ~ 2 hrs of daylight in the Straits of Magellan before darkness subsided. The first 30 hrs of the transit were uneventful in terms of weather and swell. This changed as we entered the Drake the following evening ~ 11:00 pm. We entered ~ 10 ft. seas and rocked, pitched, and rolled for the next 20 hrs through the polar front. That day – Tuesday – was spent horizontally by several of us – not to say anything about the sea legs of most on board, it was just a tad challenging to stand upright. Many came out of cabins though for the 9:00 pm showing of the third and fourth episodes of the Flight of the Concordes (HBO series in which a cult following is rapidly expanding).

The following 24 hrs across the Drake were amazingly calm. No wind and minimal swell accompanied the greeting to Antarctica provided by stunning views of Smith Island in the early afternoon on Wednesday. Smith Island – with peaks rising 2000 m directly from the sea encased in snow was mesmerizing. Due to the low angle of the sun at this time of the year, a yellowish alpenglow reflected from the snowy peaks. The calm waters continued into the night as we made our way into the Bransfield Strait. Here in some heavy fog we found conditions ripe for sea ice formation. We passed through miles and miles of newly forming pancake ice, then the following morning in the northern Gerlache Strait, the ship cut through newly forming fast ice which had recently set up (sounded like the ship was cutting through a giant slurpy).

Few links of interest:
To see where the RV Lawrence M. Gould is now… go to the following link. http://www.sailwx.info/shiptrack/shipposition.phtml?call=WCX7445

There are some great high resolution maps of Antarctica recently released at the Landsat Image Mosaic of Antarctica (LIMA) website. http://lima.usgs.gov/access.php

See our growing photo gallery

July 17-31. Palmer Station: Moving in and getting started...

Arriving in the evening on Thursday July 17… the 21 people at Palmer Station welcomed us with a cross-town Mexican dinner night. With those of us arriving to Palmer we brought the population to 34 with six people in our group (B-229 as they refer to us) and B-005 – Art DeVries’ group of five people (they are here to study antifreeze proteins in fish) along with Wally the plumber and Liz the painter. Following lots of orientation the next day, and boating training classes held both on land that day and in the field the next day - we were ready to go out and fetch some microbes.

The weather that greeted us was not what we expected for Antarctic winter! The temperatures were mild, just below freezing – and there was NO wind, and several partially to mostly clear days. We are on an island just off the Antarctic Peninsula – at the latitude of 64 degrees South. This is a maritime environment, with lots of wind and cloudy skies. August and September typically bring the highest amounts of precipitation in the form of snow – though it does rain here, rain is more common in the austral summer to fall seasons. If you’re interested in following the weather, see this site: http://www.wunderground.com/global/stations/89061.html and for those interested in the sea surface temperature... there’s a website which posts the temperature and salinity, and even has a webcam (just checked it and it’s dark outside -- http://4dgeo.whoi.edu/tsg/index.html). Pasted in below is a snapshot of the current weather conditions outside today (8/1/08) – we look at this data often as we’re trying to figure out what were going to do for the day. We can’t go boating when the wind is above 20 knots. Today’s a boating day!

Graphs

The high pressure system set in for a whole first week and blessed us with great conditions to get out and sample two times. Though it was cold and the surface of the ocean was freezing when we arrived, the ice really never developed, and a warm storm arrived about a week later. We had some incredible days though – I uploaded some pictures to show the great colors of the sky, as well as trying to show the moon – which didn’t ever set… the full moon just went around in a circle given the high latitude and time of year! Daylight, now that we’ve been here 2 weeks, has already increased an hour a day. At this time of year we gain 6 minutes of light a day. Still strange in the afternoon when the sun is setting around 2:30… not dark for a long time, but sort of gives the false feeling that the day should be over soon. Below are graphs showing the differences in day length at Palmer, McMurdo, and South Pole Stations – kind of interesting to see what the effect of latitude has on daylight!

graph
graph
graph

We spent some time unpacking and setting up the lab (and are still doing that to some degree…) and got the first seawater samples. Our two primary goals were (1) to start our large volume seawater collections in which we concentrate the cells for further studies back home to study the gene and protein expression of the wintertime microbial community and (2) to get the first experimental mesocosm study underway in which we were investigating the abilities of the microbes to respond to different carbon sources.

The DeVries group took the ship on two fishing trips since we’ve arrived, so it’s been kind of exciting seeing what they collect. I included a few pictures of these organisms that are currently in the aquarium tanks.

In addition to the sampling efforts we are running a number of assays to measure microbial activities, some through substrate uptake to show different kinds of microbial growth, and others that indicate what kinds of carbon utilization activities these organisms have. On the laboratory side of things, the carbon analyzer is up and running as are some nutrient analyses so that we can monitor certain properties of the ocean and our experiments in near real time. We also began extracting DNA and RNA from the environmental samples and the first mesocosm experiment to see whether there are differences in the microbial community between the three sites we’ve sampled, and to see what we can learn of the effects of our treatments.

On the recreational side of things, we’ve been mostly indoors the last week (though got out to sample between wind-storms) on Monday. We had rain and snow for about four days, including Sunday which is the day off around here. None of us expected RAIN in Antarctic winter. The low pressure system must have had a subtropical origin, as temperatures got up to 4C (~40 F)! I did sweep up at the poker tournament on Saturday which is my current claim to fame. Am sure that my title will be challenged soon.

Signing off for now – we intend to upload a weekly update to this website, so stay tuned!

Best,

B-229 team

August 1-11. Palmer Station: Full speed ahead

Now after 3 full weeks of being here - we’re all fully engaged in a variety of activities. These include: environmental sampling, subsampling mesocosms, conducting four different microbial activity assays on environmental samples and mesocosm subsamples, spending time at the microscope observing and counting the cells from the mesocosm experiments and environmental samples, as well as photographing the hybridization experiment in which we target specific groups of organisms with probes that bind to their ribosomes. We’re also running chemistry assays to determine seawater properties, and have been conducting polymerase chain reactions to amplify the ribosomal RNA gene and ribosomal RNA itself for microbial community profiling experiments.

Ribosomal RNA brief: This gene is in all organisms and is a good one to target when we want to understand the species diversity of a sample. The gene encodes the ribosomal RNA which is the backbone of a ribosome. When we look at the RNA itself – it tells us something about the relative activity of the cells we’re sampling (species which are more active in these winter conditions will have more ribosomal RNA in comparison to ones that are not as active.

Though the weather has not continued to be as sunny, windless and warm as it was during our first week, temperatures have been in the mid 20’s F, between -5 and 0 degrees Celsius. This is a windy place though – which limits our boating abilities – the rules here state that we can’t go out when it’s over 20 knots. This makes for exciting days at times when we’re trying to get out as we’re watching the wind, communicating with the boating coordinator, Lily, and then once we get a window – we drop everything else and get out there. It can also go from 10-30 in an hour when we’re out which also makes for exciting times! Lots of communication between the folks on the station, and on the boat work to make the outings as safe as possible. That’s happened a few times. It seems that today (Aug 11th) is the coldest I think since we’ve been here. It’s -9 deg C (15.8 deg F).

We uploaded a set of photos this week and have put together a short movie that shows what’s involved with our large volume sample collections from the ocean here. We have sampled at three different sites in the local region six times, with an additional two samples collected from the seawater intake system. Sampling involves using a submersible pump (the stainless steel monsoon from Waterra Inc.) to pump up water from a depth of 10 meters (~ 30 ft). It takes about 1.5 – 2 hrs to sample depending on the volume we’re targeting. We also drop the CTD (see pictures) which records the temperature, salinity and depth through the water column. Some days we’ve enlisted the help of station personnel to help on the water. This both helps us and provides an opportunity for station personnel to get to learn about what we’re doing.

Returning to the station with 10-20 50 liter bottles (1200 L is the most we’ve reaped in one day so far), the operator of the skytrak (one of the RPSC staff trained to drive this very useful vehicle) helps pluck our bottles out of the zodiac. At 100 lbs each – heaving them over the side of the boat and up the slippery, rocky shore is really not feasible. Instead, the Skytrak grabs the bottles (it can lift 8 at a time) and transports them up the hill where the boardwalk is located that leads to the aquarium environmental rooms where we do the filtrations and high volume concentrations.

We experienced a good example of how fast conditions can change last Friday when we were out at Loudwater Cove. Over the two hour period in which we were sampling – a broad band of brash ice was blown towards us such that we had to cross this band (see photo with Kristen at the helm) in order to get back to station (the water was completely ice-free when we arrived at that station).

Other than keeping busy sampling we did have a long weekend here (2 days, rather than the typical Sunday day off), which provided opportunities for people to get out in the boat to go and tour the local region, as well as go and visit the site of the first Palmer Station, Old Palmer where there’s a large ice-cave that collapsed 2 years ago. Friday night after a barb’cue dinner, everyone gathered to watch the entries into the film festival – this was hilarious. Across the continent, different Antarctic research stations were given 48 hrs to come up with a movie that had to include a few essential things: a box, a new person (here called a finge), and mention of a day off on midwinter’s day. There was something like 12 entries from McMurdo Station, Rothera - the British Station, Scott Base – the New Zealand Station, Casey Base and Mawson Base – the Australians, Neumeyer Base – the Germans, and SANAE - the South African base… talent spanning the full spectrum was captured! Ok that’s all for now – until next time,

The B-229 team

August 10-17. Palmer Station: Winter arrives

The synopsis of week 4... started with some clear but windy weather – that significantly decreased air temperature from the 0 - -5C range the weeks before to the -8 and -12C range. This caused a few issues with sampling (like the seawater samples we collected on August 12th began to freeze in the 50 L bottles (this makes it difficult to filter!). See pictures with the frozen zodiacs, and sea ice. By the middle of the week we finished the second mesocosm experiment, testing the effects of both temperature – a difference of +4C – and light on bacterioplankton growth. Then as the week continued, strong winds did not block sea ice formation- this in turn blocked getting zodiacs in the water. This sent us to the seawater intake pumphouse to collect samples later in the week (see picture). We did a large collection (1300 liters) from this convenient location which made it a little easier in some ways to collect a ton and half of seawater!! - that many bottles would require 3 zodiac boats. With the large collection we started a new mesocosm experiment – testing the effects of light and a phytoplankton bloom on the bacterioplankton – and a second type of large batch experiment (120L ea) to see if we can stimulate and measure growth of chemolithoautotrophic microorganisms in these wintertime waters

Yes. a big word for the day - what is chemolithoautotrophy (also referred to as chemoautotrophy)? The word is derived from three parts (chemo – chemical; litho – from the earth (or stone); and autotrophy – supplying one’s own food). Chemolithoautotrophs use chemicals to convert inorganic carbon to carbohydrate. Another type of autotrophy is photoautotrophy (using the sun’s energy to reduce inorganic carbon to carbohydrate). The flowchart below shows how you would determine if a species is an autotroph, heterotroph, or a subtype – if they obtain their carbon from “elsewhere” that implies they do not fix their own carbon. (This is a file from the Wikimedia Commons).

Flowchart

One of the ideas we’re testing is whether wintertime marine bacterioplankton have fundamentally different metabolic strategies that they employ to get through the grueling winter in high latitude waters. Through sequencing DNA from winter and summer and comparing these data sets, we have recently been able to piece together some interesting hypotheses that can be tested this time of year. Typically, we think that most of the bacteria living in the upper ocean utilize organic carbon that is initially derived through phytoplankton photosynthesis. In these winter waters however, photosynthesis rates are meager (not much light to stimulate it) – and this directly influences the levels of utilizable organic carbon in the waters. So – we think that the marine bacterioplankton are basically starving… but if some of them can make their own carbon – they would be free of this limitation – and have a good way to get around the limitations of winter-time, low carbon conditions.

All right – enough science for this blog! It was a week filled to the brim with activities though – we were doing chemistry and molecular biology when not sampling, setting up and/or breaking down the mesocosm and batch culture experiments. (see the photographs for evidence of this!).

The week ended Saturday with a successful happy hour hosted by our group (B-229) which was followed by a great dinner and various activities including poker and dancing… not simultaneously! Sunday was downright wintery and cold for everyone’s day off.

Will sign off here – stay tuned for the next upload – as week 5 stands to be exciting with the arrival of our missing team member and Co-PI, Joe Grzymski.

- The B-229 team

August 20-30. We laughed, we cried… we worked, we came together again.

Our full group of 7 now was assembled for…. Exactly one week.

The last blog entry by Joe ended on August 19th, when he finally arrived. That’s when I’ll pick things up – this has been a challenging report to assemble – as it has been quite a wild few weeks of ups and downs. The ship left in haste that evening due to the high winds, sea ice, and fishing line that was stuck in the ice for a six day fishing trip. The first three pictures show the storm that was in place the day we did the offload onto the sea ice, and the zodiac next to the ship that was used with a pulley system to ferry Joe and others, and some cargo to the station (for the freshies – a long line of people pass the eggs, fruit, avocados etc., hand to hand from the ice up the hill).

As Joe got oriented and settled, we briefed him on the operations and results we’d assembled so far. At this point we had sampled the environment on eleven occasions and finished two studies utilizing experimental mesocosms. On August 15th we had started two new mesocosm experiments – one in which we’re studying how phytoplankton and light (summer conditions) influence the wintertime microbial community structure and growth rates. The other experiment is studying how different inorganic substances are used by the wintertime bacterioplankton to grow chemoautotrophically (see the blog in week 4 for description of this type of bacterial metabolism). One of the experiments that I have been conducting down here is to stain the microbial cells with fluorescent probes that reveal the identity of the cells. This technique is called fluorescent in situ hybridization- and has been quite informative for revealing differences in communities that are developing in the different mesocosm experiments we’re running.

Microscopy images

Figure 1. The bright red dye has stained only cells which are in a group called Alphaproteobacteria, while the green stains “all” bacterial cells that have enough ribosomes to be detected. The stain is anchored to a short piece of DNA which binds to the complimentary sequence on the ribosomal RNA in the species or group of organisms of interest.

We haven’t been out to sample on the zodiacs since August 12th. See the photo of our boat (Wonderbread) buried in snow. We now however have sea ice everywhere which has prevented us from getting in the boats (the weather's been on average below -10C (12F) and it’s still forming [see the photo of the sea ice with noticeable brown colored algae between the pancakes]. The sea ice didn’t only cause problems for Joe’s arrival and our sampling program – it complicated retrieval of the fishing line that was tied to the pier (during open waters) – as the line was now frozen in ice. Station personnel put together a plan for extracting the line by working on the sea ice to basically saw through the ice and pull it up which in the end was successful – it was finally retrieved the 28th following a great demonstration of team work by a number of different people (see photo of two people working in immersion suits on the sea ice).

For us this was a busy week filled with various sampling activities from the seawater intake system and the two mesocosms (see photo of bottles, and Hugh Ducklow in the environmental room), molecular assays, Joe working on developing a new enzyme activity detection assay, … nice to have the whole group together finally.

The RPSC line-retrieval crew were making some progress on the line on Monday so they kept the ship off shore (as it was supposed to dock again and unload the fishing group who had been out since Joe arrived) and they set up an over night schedule of people working on the ice through the night.... and then since they were making some progress they asked to work through the day (and keep the ship sitting off shore not to disturb the ice which had gotten stronger and safer to work on).

Unfortunately, at the same time…. One member of our team (Kristen Myers) fell sick, enough such that upon consultation with doctors in the USA, it was determined that she needed to be med-evac'd. Thus, at about 1:30 pm Tuesday Aug. 26th they made this decision… and at 2:00 pm they had an all hands meeting to announce the change in plans (the fishing group was supposed to change personnel and go out again with one person from our group to do some sampling off-shore). Note that words and pictures here can not capture the mood and emotions as we received this news [I uploaded a few pictures from the all-hands meeting – which perhaps provides some glimpse into what was going on]. The med-evac meant that everyone who was supposed to leave the station in 10 days had 3 hrs to pack everything and get on the ship as the ship was heading out. This impacted both science groups and several RPSC folks - which were from our group.

We had about 1.5 hrs to get briefed on various parts of the project and 3 experiments in progress that Hugh, Kristen, Matthew and Jean-Franςois Ghiglione were working on – then they had to pack up all their belongings and head out to the ship. We used the video features of my digital camera to photograph both Matthew and Jean-Franςois giving instructions for various tasks [see the movie clip – which to some degree might reflect the intensity of the briefings]. Needless to say, this came to all of us as quite a surprise – and the gravity of the situation was felt for days. They used the zodiac/pulley system to transport cargo while people were able to walk across the sea ice for the med-evac operations (see photos; we prepared a help wanted sign… as losing more than ½ of the group at this point in time was leaving a serious hole!). The next day, following negotiations with the Chileans, Kristen was airlifted from the Chilean Station (Frei Base) on King George Island and flown in a Twin Otter to Punta Arenas. We’re happy to say that now she is resting at home, and is expected to have a full recovery.

The following morning we assembled a sampling matrix (see picture) and began digging in for a busy final month of the project – this situation caught us mid-stream with all of us involved in several different experiments. Following the successful airlift, it was decided that the ship could then return to Palmer – we were overjoyed, as were Chris and Art DeVries (who also lost the three students working with them). The ship made it back to the area on Friday the 29th (following successful extraction of the fishing line), though they had to contend with significant sea ice and what we call ice “growlers” that were lodged in the ice in front of the pier. This meant about 6 hrs of ship maneuvering operations to push the ice around (see pictures of the ice and ship as it was performing the ops). Finally on Saturday the 30th, the ship was back and we were together again! (see the morning photo of the ship taken Saturday where it stayed overnight). In addition to the good mood on station to have everyone back (except Kristen), a high pressure system had settled in and gave us a number of beautiful days starting Friday (see last few pictures of week 5-6 upload).

One of the things that I tell members of my field team when they are new to the Antarctic Program is that they need to pack their patience, and their flexibility. Jean-Franςois reminded me that I’d told him that after I had to break the news to him that he had to get ready to leave in 3 hrs. No doubt….

Expeditions to the Antarctic often bring surprises, interesting twists and turns – this trip is no exception!

The B-229 team