After a tough couple of weeks things are starting to look up. I’ve got the flow cytometer up and running, and Colleen’s instrument received a complete makeover (thanks to the über instrument tech at Palmer) and is producing good data. The big question is whether I can gain enough proficiency over the next two days to keep it going after Colleen leaves on Sunday.
The operational instrument status comes just in time; yesterday we went back to the sea ice station that we established on Tuesday to do some science. In addition to collecting some pretty novel data it was a good chance to practice the measurements we’ll be making all season for the Palmer LTER. It felt good to get out but hopefully for most of the season it will be a little warmer, however. That it would be cold in early spring in Antarctica is kind of a no-brainer, but that didn’t keep it from surprising me yesterday. And the downside to doing fieldwork cold is that it takes longer, so you end up getting colder, and things take even longer…
In addition to making all the core LTER measurements (see the end for descriptions); chlorophyll a, nutrients (inorganic nitrogen and phosphorous), primary production, bacterial production, dissolved organic carbon, particulate organic carbon, bacterial abundance, photosynthetically active radiation, and UV, we took multiple RNA and DNA samples (my main focus for this trip), large amounts of water for lipidomics (Jamie’s project) and samples to measure hydrogen peroxide. This last measurement was a consolation prize since we couldn’t measure superoxide – the two species have some similarities – and it gives us some indication of what to expect now that Colleen’s instrument is up and running.
So what did we find? It’s early in the season, and there isn’t that much happening yet below the ice. Everything is driven by light, and it’s pretty dark under there. But things are starting to happen, and all the action is near the ice. We measured only two depths in the water column (and that still took us over three hours), just below the ice and 2 meters further down. Even over that short distance there was a big difference in what’s going on. The concentration of hydrogen peroxide – a byproduct of photosynthesis – was much higher near the ice, and there were about four times as many bacteria just beneath the ice than 2 meters below it.
Hopefully, if the weather’s good we’ll get a chance to go back out on Monday. If the ice holds together for just a couple more weeks we’ll be able to document the transition from an ice-covered to an ice-free state, and get the data to test some hypotheses about how bacteria and phytoplankton respond to this transition. In the meantime yesterday’s bitterly cold wind has given way to calm conditions and outside the snow is falling. The woodstove in the Palmer Station galley is putting out a nice glow and the stress of fieldwork is dissipating for a moment…
As promised here’s a quick description of the core LTER measurements:
Chlorophyll a: The principal (but certainly not only) photosynthetic pigment in phytoplankton. Oceanographers having been measuring the concentration of chlorophyll a in the water for a long time as a measure of phytoplankton biomass, and as an estimate of how much primary production is happening.
Primary production: The amount of carbon dioxide that is being taken up by phytoplankton and converted into organic carbon. The whole food web depends on primary production, and much of our work is focused on what aspects of the ecosystem control the amount that happens.
Bacterial production: Sort of the inverse of primary production, this is the amount of organic carbon taken up by bacteria. We can’t measure this directly so we estimate it from the uptake of certain carbon compounds that we can track.
Dissolved organic carbon: One of the most mysterious types of carbon out there (see this article for some indication why). This is organic carbon in pieces small enough for bacteria to take them up.
Particulate organic carbon: Phytoplankton die, they become particulate organic carbon. It’s sad.
Bacterial abundance: The number of bacteria in the water, measured on our now operational flow cytometer.
Nutrients: Nutrients in the ocean are operationally divided into macro and micro categories, depending on their biologically relevant concentrations. We measure nitrogen and phosphorous, the principal macronutrients.
Photosynthetically active radiation (PAR): In addition to nutrients phytoplankton need light to grow. PAR is the part of the electromagnetic spectrum that can actually be used in photosynthesis. Too little PAR (like under thick, snow covered ice) and you get very little photosynthesis. Too much PAR (like at the surface of the ocean during the Antarctic summer) also produces very little photosynthesis!
We’re off to a rough start this season! Two of our instruments are down, including our flow cytometer – annoying, but we can deal with it – and Colleen’s instrument for measuring superoxide. That’s a real problem. Colleen is only with us for five more days. When she leaves the instrument stays, but we will no longer have a skilled operator! Measuring superoxide is not trivial and I was supposed to spend a good chunk of this week learning how to do it. That’s going to be tricky with no instrument. Fortunately the instrument tech at Palmer this season is handy with a soldering iron and seems to have some ideas. We’ll see how that plays out tomorrow.
The one piece of good news this week is that the big storm last Sunday didn’t do much damage to the land-fast sea ice near Palmer Station. At least for now we can do a little science on the ice. This afternoon Jamie Collins, Nicole Couto, and I went out with the SAR team to establish a sea ice sample site near the station. Hopefully we can get a couple weeks of sampling at this site before the sea ice deteriorates.
Being able to do some science on the sea ice at Palmer Station is actually a pretty big deal and an unexpected bonus for this season. In some ways this is a very logical place to study ice. Palmer Station is the United States’ premier polar marine research station, and you can find dozens of papers describing the ecological importance of sea ice in this region. It’s been years however, since anyone was able to routinely access sea ice from the station. Considering the amount of ecological research that takes place here this actually seems a little silly; the single most important feature is virtually ignored for practical reasons. Working on ephemeral, dynamic sea ice requires a set of skills, equipment, and intrepidness that simply doesn’t exist in this day and age within the US Antarctic Program.
Our very small adventure today (on relatively thick, static ice) is reason to hope that that might eventually change. There isn’t a lot of institutional knowledge about sea ice at Palmer Station, but Station staff and management are open minded and seem eager to learn. As a further indication the Cold Regions Research and Engineering Lab recently provided new recommendations for sea ice operations at McMurdo Station, a major step toward a rational, data-based policy for traveling and working on ice (which I’ll link it I can find, too tired to search now… must fix flow cytometer…).
Hopefully we can get some good science done on the sea ice this season. In the Arctic large, under ice phytoplankton blooms are a major source of new carbon to the ecosystem. In the Antarctic blooms of algae at the ice-water interface are an essential food source for juvenile krill – adult krill being the major food source for virtually everything else down here. Getting some indication of when, where, and how often these events occur along the West Antarctic Peninsula will tell us a lot about how these ecosystems function, and what will happen to them as the ice season and range continues to decline.
We arrived at Palmer Station last Thursday morning after a particularly long trip down from Punta Arenas. Depending on the weather the trip across the Drake Passage and down the Peninsula to Anvers Island typically takes about four days. This time however, the Laurence M. Gould had science to do and a NOAA field camp to put in at Cape Shirreff on Livingston Island. This was a particularly welcome event as it gave us an opportunity to get off the boat and get a little exercise unloading 5 months of supplies for the NOAA science team.
Since arriving at Palmer Station the activity has been nonstop. In addition to lab orientations and water safety training there is the seemingly never-ending job of setting up our lab and getting instruments up and running. Yesterday evening following the weekly station meeting we did manage to go for a short ski on the glacier out behind the station. I’m glad we did because today the weather took a real turn for the worse; winds are gusting to 55 knots and strengthening. This is a real concern for us because wind strength and direction are the primary determinant of the presence and condition of sea ice in this area. As I wrote in my previous post we are hoping for sea ice to be either very solid, so we can sample from it or clear out completely, so we can get the zodiacs in the water. We’ll have to wait until the storm passes to see what conditions are like but very likely it will be neither!
We finished our work at the river transect. Now we had one more sample to collect. It was to the north where the abandoned valley is still flooded at the site of the tube well that started this idea. It is well BNGB013 along one of the transects that was done for the BanglaPIRE project. It was done along the side of a major “highway”, so will be accessible and it not far out of our way home. Alamgir had a contact in a nearby village and arranged, and rearranged a driller. We were glad to be heading back
to Dhaka. The hotel we stayed in was the best in Brahmanbaria, but it had bedbugs. In this moderate sized town, the choice of restaurants was limited.
The drillers arrived at our meeting place late. There was a fight between two villages the night before and some people were stabbed. They own a plot of land along the main road in the other village. Those villagers wanted them to swap it for land perpendicular to the road, but they refused. The land along the road is valuable for shops. The result was a fight until the police broke it up, but several people ended up injured. They came without their equipment so
they could sneak quickly through the other town. They got what they needed at the store where we met about 2 km west of the well site. I went ahead and located the exact place we wanted to sample.
Since the well had already been logged and sampled, we only needed to drill down to the sands, making sure the stratigraphy agreed. Relooking at the logs of the well, I realized that we barely had enough extension rods to make it to the sampling depth. Luckily we hit the sands with a couple of feet to spare. We
got our sample and headed for Dhaka. Of course, we hit terrible traffic and were late to dinner with other scientists from our project that just arrived from the U.S. Over dinner I learned that Kazi Matin Ahmed, one of the Dhaka University professors we work with was from a town right near our sampling. He said that growing up he would go to school by boat during the monsoon. The next day was packing up at the university and making copies of everything. We also had to pack up a number of GPS and seismic recorders that need to be returned to the U.S. for repairs. Unsalvageable was one from Madhupur that was destroyed in a fire. This trip was very successful; we achieved all our goals, although as usual, there were a lot of changes of plans on the fly. In Bangladesh, nothing goes as planned, but we always get everything
done. Bangladesh is a country of resilient people who know how to get things done.
We planned to drill four or five tube wells across the abandoned channel and pick one for OSL dating samples. With the success of yesterday’s tube well drilling, we were optimistic that we could actually do the sampling. We met the drillers in the morning and headed to the next site. Since only two or three people are needed for logging the well, we left Céline and Basu and the rest of us headed off to do a short resistivity line near the first drill site. We scouted it during the drilling of the first well. On the way to the resistivity
site, we selected locations for three more wells. Depending on time, we will either drill two and then the sampling well or just three stratigraphic wells. Since it will be only 2 meter spacing between the electrodes, it will be quicker to set up despite less people. We are only trying to image the channel, so we don’t need a larger spacing. The site was also drier than the first two resistivity lines. We laid it out and started collecting data. My only concern was that the route was used as a path for local farmers collecting hay. I didn’t want them to knock off the electrode connections or to have them
shocked by the pulses of electricity we sent through the electrodes.
Once the line was running, I headed back to the drill site. They once again found a think mud layer over sand. They continued drilling deeper and found the silt clay that marks the boundary between the Holocene and Pleistocene, when sea level rose following the end of the last ice age. This was a bonus and confirmed that we were on line with the Lalmai anticline farther south. We shifted to the next line, a more difficult location next to a pond, but they managed. I headed back to the resistivity line and found them starting to pack up the equipment. When I went to take a look at the instrument, I found it hadn’t finished. It had run out of memory for recording line and stopped. We quickly reinstalled the electrodes that had been
pulled that we still needed. I deleted some older files that had already been downloaded and restarted acquisition. We had only lost four of 584 command lines.
By the time the second well and the resistivity line were done, it was questionable as to whether we could do the sampling well, which will take longer. The drillers going off for a lunch break settled it. We would do a third tube well today. During the drilling, the skies that had been threatening all day opened up.
The drillers and loggers got completely soaked, but kept going and we completed our five-well transect of the river valley. In the evening we compiled all the logs and discussed a sampling plan. Rather than take four samples in one well, we decided to take two, one above and one below the sand-mud transition in two different wells.
The OSL sample is over 2” wide and the wells we drilled were 1.5” wide. The driller decided it was best to drill a 1.5” well to the depth of the first sample, a few feet above the transition, and then overcore it to 3.5”. Then 3” wide PVC pipe
was lowered to keep the well from collapsing. Finally, we put the sampler on the auger rods and lowered it to the bottom of the well. We, actually people younger and stronger than me, pounded the sampler 30 cm into the bottom. Then we all had to pull up on it to get it out. The next step was to extrude the sample in its liner into a thick PVC pipe casing. The sample must be kept in the dark, so this was done inside a black plastic bag. Then the entire sample is wrapped in the black plastic bag and taped securely. The ends and outside of the sample will be discarded and only the core of the sample will be used for dating. Later, sample preparation will all have to be done in a darkroom. I helped sample on my last trip, but the was the first time I was in charge of the procedure. It went well. After the first sample, the drillers drilled to 1 ft. past the contact, overcored to the same depth, added the PVC liner and we sampled again. We
repeated everything for the second well and we had four OSL samples. We celebrated with green coconuts.
El Niño is earth’s most powerful climate cycle, influencing weather and affecting crops, water supplies and public health globally. What may be the strongest El Niño ever measured is now getting underway, and is already affecting parts of the world.
Many leading El Niño authorities are at Columbia University’s Earth Institute. They include scientists who helped form the modern understanding of El Niño; who make the official U.S. monthly global and regional El Niño forecasts; who study the deep history and future of El Niño; and who are working across the world to help nations take practical measures to cope with El Niño-related weather.
Below, a guide to people and resources at our International Research Institute for Climate and Society (IRI), Lamont-Doherty Earth Observatory (LDEO) and other centers. NOTE: In conjunction with the World Meteorological Organization and others, IRI will host a Nov. 17-18 El Niño international conference in Palisades, N.Y. Press wishing to attend, please contact Francesco Fiondella. Parts of the event will be livestreamed.
Tony Barnston is IRI’s chief forecaster, responsible for monthly and seasonal El Niño forecasts in concert with the U.S. government and World Meteorological Organization.
Simon Mason is chief climate scientist, working globally with governments to apply IRI’s forecasts to practical issues including preparation for natural disasters.
Andrew Robertson is head of IRI’s Climate Group, and studies regional climate variability, predictability and change, at both short and long timescales.
Lisa Goddard is director-general of the IRI, working on a broad variety of El Niño-related issues.
Madeleine Thomson studies health effects of El Niño and other climate cycles, and advises governments how to deal with them.
Richard Seager is a climate modeler who studies how El Niño and other cycles affect rainfall, and how cycles may shift as the world warms, especially in the U.S. West.
Adam Sobel is an atmospheric scientist specializing in extreme weather, and can address how El Niño might affect the United States, especially in the East.
Suzana Camargo is a climate modeler who studies how El Niño influences cyclones and other violent weather worldwide.
Mark Cane is an oceanographer who co-designed the first model to successfully predict El Niño, in the 1990s; also, coauthor of research linking warfare with El Niño.
Xiaojun Yuan is a polar scientist who studies land-sea-ice interactions, particularly in relation to El Niño and related climate cycles that connect the poles with the mid-latitudes.
Marc Levy is a political scientist at the Center for International Earth Science Information Network, which studies interactions between people and natural systems.
- El Niño comes every 2-7 years. Winds over the tropical Pacific Ocean abate, and the sea surface warms. The current cycle started this spring, and will probably peak this winter before subsiding in spring 2016. It will likely rank among the top events ever recorded.
- El Niño dramatically reshapes precipitation and temperature over much of Asia, the Americas and Africa. Effects vary by region.
- Indonesia is already suffering giant wildfires and resulting deadly haze due to El Niño-related dry weather.
- El Niño may bring needed rain to the U.S. West, but also torrential rains and mudslides. Areas of the U.S. East may see an unusually warm winter. Parts of Asia, South America and Africa could become drier, compromising food production. Weather shifts in eastern Africa could bring disease outbreaks.
- A recent Earth Institute study suggests that civil wars are more likely to start or worsen during the disruptive weather of El Niño.
- Mainly due to human carbon emissions, 2015 will probably be the warmest year ever recorded; El Niño will add even more heat in 2015 and 2016.
I’m currently sitting in the Dallas airport waiting for a flight to Santiago, Chile, enroute to Palmer Station for the 2015 spring season. Since there is no airfield at Palmer we’ll go in and out by boat (the ARSV Laurence M. Gould). Hopefully we’ll be at the station by October 28 and able to start doing some science not too long after that. There are a couple of reasons why I’m excited about the upcoming season. First, as I discuss in this post, conditions are highly unusual this year, with the extent of sea ice reaching a level not seen at Palmer Station for many years. The reason for this seems to be the persistent warm El Niño conditions in the tropical Pacific Ocean, now complemented by a near zero to negative Southern Annual Mode (negative SAM values are correlated to high sea ice conditions). This increase in sea ice is a counter intuitive but very real effect of global climate change; increased heat in one area of the globe alters global wind patterns and decreases the flow of heat to other areas of the globe. It hasn’t actually been very cold at Palmer Station (the high today was a balmy 24 °F at the time of writing) and how long the sea ice lasts will be depend very much on what happens to winds in the region.
Coming in an era defined by decreasing sea ice along the West Antarctic Peninsula the presence of heavy ice cover could have some interesting ecological impacts. There is a strong likelihood that it will be good for the Adélie penguins, but my primary interest is a little lower down in the food web. I’ll be studying interactions between phytoplankton, the basal food source for the WAP ecosystem, and bacteria at the onset of the spring bloom, hoping to identify cooperative interactions through patterns in bacterial gene expression. Toxic compounds produced by phytoplankton, for example, may be cleaned up by bacterial partners, allowing photosynthesis to proceed more efficiently (ultimately meaning more food for the whole food web). Observing the expression of genes coding for the bacterial enzymes that carry out these processes would be strong evidence for this kind of synergy, which leads me to the second reason I’m excited about the upcoming season.
This year I’m joined by Colleen Hansel and Jamie Collins from the Woods Hole Oceanographic Institute. Colleen and Jamie are chemical oceanographers and experts in identifying specific compounds produced by phytoplankton. Colleen has pioneered a technique to measure superoxide, a damaging free radical, directly in the water column. This is not a trivial undertaking as the half-life of superoxide is only seconds, making traditional oceanographic sampling techniques (such as a Niskin bottle) impossible to employ. Instead we will focus on sampling water in the first few meters of the water column, just above the maximum zone of primary production. Superoxide is produced during photosynthesis, when energetic electrons glob onto free oxygen. The extra electron makes oxygen highly reactive (hence superoxide; it’s a superoxidant) and physiologically damaging. Bacteria have some interesting molecular tools to deal with superoxide however, so perhaps they’ve evolved the ability to perform this service for phytoplankton in exchange for fixed carbon. Coupling observations of gene expression with measures of superoxide and other reactive chemical species is much more powerful, and will tell a much more complete story, than either does alone.
It’s impossible to anticipate how the ice will impact our science plan until we’re at the station and get a feel for how logistics will work this season. Typically sampling at Palmer Station is done by zodiac, which requires reasonably ice-free conditions. The zodiacs can push around a small amount of brash ice but lack the mass (and shrouded propeller) to deal with large quantities. The ice is solid enough this year that we may be allowed to use this ice as a sampling platform – something I’ve got plenty of experience with from previous trips to the Arctic and Antarctic. This is a little out of the norm for Palmer Station however, so we’ll have to see how negotiations proceed.
In our worst-case scenario the ice conditions deteriorate to the point that we can’t sample from it, but not so much that we can push a zodiac through it. The normal sampling procedure in this case is to use a plumbed seawater intake to sample from below the ice (with the added benefit that you can sample from the comfort of the lab), however, this won’t work given the short half-life of superoxide. In this eventuality I think we can salvage the project by focusing on ice algae in place of phytoplankton. Ice algae are essentially phytoplankton which have given up their free-living lifestyle and formed colonies on the underside of the sea ice. These dense mats are a very important food source for juvenile krill, but are understudied in the region given the inconsistent nature of sea ice along the WAP. If we can access some decent ice floes from shore I think we can make a good study of the superoxide gradient, and bacterial response, toward the ice algal colonies. Previous work has shown that ice algae can be under significant oxidative stress so they may have good reason to solicit a little help from bacteria.
The next day we went out again for resistivity and augering. Céline picked out two alternative sites that might be drier. We drove through the abandoned valley to the site. We took the direct route and found the local road to be in a terrible state of disrepair. The vans could barely make it through. Then we hit a spot where slumping off each side of the road narrowed it too much. The villagers helped make a temporary road with bricks and wood, but it was still too narrow. Then they filled a sandbag and together with the bricks, wood and other
handy items we got across. It turned out that since the Upazila (county) voted for the opposition party, they have not had their roads repaired for over a decade. This level of politicization of everything in Bangladesh really hurts the country. When we reached the location of the line, we found that ponds between the road and the fields limited our access. We walked around and found a site next to a brick factory. The line was along an irrigation ditch. Fine to walk on either side, but submerged to mid-shin if you
stepped in the middle. The data looked very good after processing. We may have found the top of the Pleistocene as relatively shallow depths consistent with the site being the top of a buried anticline (folded hill).
The delays from the bad road, site searching, and a longer distance to lug the equipment meant that we couldn’t do augering. We came to the conclusion that we have to alternate days of resistivity and drilling. Not enough time in a day to do both properly. That meant
the next day was for augering. We went back to the soccer field site, officially BNGTi1, and started augering with all six of us. We hurried past the section we had already described. To minimize hole collapse, we switched between two augers and tried to work quickly on the descriptions. It took all of us all morning to make it to 4.8 meters. The mud was too hard. We needed to go to plan B. We would drill tube wells and sample inside the wells. Alamgir and Basu went off to the village to find a driller. The rest of us
cleaned off the equipment and ourselves at a nearby pond and well and had lunch. After several attempts, they found a driller, but he couldn’t come until 3 p.m. I like to use all the available time I have here, but we now had a few hours break.
The three-person drill team arrived right at 3, unusual in this part of the world. I have seen the drilling technique before, but never the initial set up. In 20 minutes they set two vertical bamboo poles in the ground, tied on the cross piece to make a large H, attached a lever arm and the drill pipe, dug a mud pit for water and a
channel to the actual well location. Then they started drilling. It was so much faster and easier than augering! In 10-20 minutes they were past the depth we reached. We don’t get continuous samples described every 10 cm (4 in.), but the lithology averaged every 5 ft. Muds come up as solid cylinders that we collect, sands as a slurry that we decant. We subdivide the 5 ft. sections if there is a lithology change. The driller caught on quickly to what we wanted and kept us informed of all changes in sediment type, which he could easily feel. Céline and Basu, an experienced logger of tube wells, did most of the sediment work,
with some help from the rest of us. As expected, the section was primarily mud with some silt. We reached the sands from the abandoned channel at 42 ft., a little deeper than I expected but reasonable. It was still early enough for us to do another. Alamgir and I scouted a second location as they finished and packed up the equipment. We completed that one, with the sands at only 20 ft. North of our transect looks like there was an island splitting the channel in two. Here would have been downstream of the island, so we
expected it to be shallow. Finally, things were going well. Using tubewells, we should have plenty of time to drill several stratigraphic wells and then pick one for sampling. We celebrated with dinner at the local Chinese restaurant.
A couple of months ago I published paprica v0.11, a set of scripts for conducting a metabolic inference from a collection of 16S rRNA gene reads. This approach allows you to estimate the functional capabilities of a microbial community if you don’t have access to a metagenome or metatranscriptome. Paprica started as a method for a paper I was writing but eventually became complex enough to warrant it’s own publication. Paprica v0.11 reflected this origin – it produced nice results but was cludgy and cumbersome.
Over the last couple of weeks I’ve given paprica a complete overhaul and am happy to introduce v0.20. There are a number of major differences between v0.11 and v0.20, but the most significant difference is a more clear division between construction of the database for those who want full control (and access to the PGDBs) and sample analysis, which can proceed with only the provided, light-weight database (however you will not have access to the PGDBs). Executing paprica v0.20 is as easy as (from your home directory, for the provided file test.fasta):git clone https://github.com/bowmanjeffs/genome_finder.git cd genome_finder chmod a+x paprica_run.sh ./paprica_run.sh test
One really important distinction between this version and v0.11 is that metabolic pathways are NOT predicted directly on internal nodes. This was done for reasons of organization and efficiency, but I’m not sure that it made much sense to do this anyway. Instead the pathways likely to be found for an internal node are inferred from their appearance in terminal daughter nodes (that is, the completed genomes that belong to the clade defined by the internal node). If a given pathway is present in some specified fraction (0.90 by default) of the terminal daughters it is included in the internal node. You can change this value by modifying the appropriate variable in pathway_profile.txt. Some (including myself) might like to have a PGDB for an internal node for purposes of visualization or modeling. In the near future I’ll release a utility to create a PGDB for an internal node on demand.
Some other major improvements…
- Fewer dependencies. For the scripts called in paprica_run.sh you need pplacer, seqmagick, infernal, and some Python modules that you should probably have anyway.
- Improved reference tree. I’m still working on this, but the current method uses RAxML for phylogenetic inference and Infernal for aligment, which seems to work much better than the previous (albeit much faster) combo of Fasttree and Mothur. Thanks to Eric Matsen for helpful suggestions in this regard.
- More genome parameters. I have a particular interest in how genome parameters (e.g. length, coding density, etc.) are distributed in the environment. Paprica gives you a whole list of interesting metrics for the terminal and internal nodes.
Paprica is still in heavy development and I have a lot of improvements planned for future versions. If you try v0.20 I’d love to know what you think – good, bad, or otherwise! You can create an issue on Github or email me.
Along with colleagues from New Zealand, Argentina, and Malaysia I’m convening a session on microbial ecology and evolution at the upcoming biennial SCAR meeting in Kuala Lumpur (because there’s no better place to talk about ice than the tropics). If this sounds like your sort of thing check it out!S23. Microbes, diversity, and ecological roles Walter MacCormack, Argentina; Charles Lee, New Zealand; Chun Wie Chong, Malaysia; Jeff Bowman, USA
The ecology of Antarctica is largely shaped by microbes, with microbial life, including prokaryotes and unicellular eukaryotes, serving as the main drivers of ecosystem function. Given this, it is perhaps surprisingly that our current understanding of Antarctic biota has been derived primarily from studies of metazoans. Despite major advances in the field of Antarctic microbiology in recent years there remains a knowledge gap in our understanding of the distribution, functions, and adaptations of Antarctic microbes. There is a general consensus that Antarctic microorganisms are highly diverse, and in many cases encompass endemic gene pools with unique physiological and genetic adaptations to the extreme conditions of their environment. Relatively recently, the advent of ‘omics platforms has allowed researchers to observe these processes in great detail. This session welcomes submissions on all aspects of microbial ecology and evolution in Antarctica and the Southern Ocean. This includes ‘omics-based approaches to understanding prokaryotic and unicellular eukaryotic diversity, function, adaptation, as well as laboratory and field-based studies of microbial and ecological physiology. Special consideration will be given for abstracts addressing the following issues: (1) Microbial biogeography, functional redundancy, and ecosystem services; (2) Trophic connectivity between prokaryotes and eukaryotes; (3) Cold adaptation strategy and evolution; and (4) Multiple ‘omics integration addressing systems biology of Antarctic ecosystems.
Six of us headed out on Oct. 8 for Brahmanbaria, northeast of Dhaka. Our target is a large winding abandoned river valley that we believe used to be the course of the Meghna River. Currently, the much smaller Titas River flows northward in the channel. Why would a river in the world’s largest delta flow the wrong way? We think that an earthquake uplifted the Comilla District area to the south. That caused the Meghna River to shift westward to its present channel and the Titas to flow up the old channel. A well drilled in the channel in 2012 shows a layer of muds overlying coarser sands.
We think the sands represent sediments from the old Meghna and the muds are sediments filling up the channel. We will be using resistivity to image the channel and an auger to first sample and describe the sediments and then to collect samples for dating.
Finding organic matter to date by carbon 14 is rare, so we plan to use a technique called OSL dating. OSL stands for Optically Stimulated Luminescence. Electrons from the radioactivity of all rocks get trapped in defects in quartz grains. However, they
are so weakly trapped that sunlight can release them. When traveling down the river, the electrons are released and then start accumulating when they are buried. By measuring the light released by the sample when optically stimulated, we can calculate the time since the sample last was exposed to light. By sampling the top of the sands and the bottom of the muds, we can date the time the river switches, or avulsed. The details of the procedure to get an OSL age are pretty complicated, but if this works, we
will date the earthquake that caused the river avulsion.
This technique is new to me. I helped with some sampling the last time I was here, but I have not been in charge of doing it. I am also more comfortable with the quantitative data from the resistivity than the qualitative geologic descriptions we will make of the sediments. Luckily I have a good team with me, Céline, my postdoc, Matt, my former teaching assistant, and Alamgir, Atik and Basu from Dhaka University. I have spent time in the field with Alamgir and
Atik before. Alamgir has conducted his own resistivity surveys. Basu was recommended to me as someone with a lot of experience in describing sediments.
We set out early in the morning for the four-hour drive. However, when we reached the river valley, we found it was almost completely flooded. We walked out on an elevated road and there was pani—the Bangla word for water—everywhere. The abandoned valley is still slightly lower in elevation than the surrounding land. Even that land has the rice fields flooded with shallow water, although the
boundaries between the fields are above water. But our main target is submerged! In the winter this will be dry land, but we are a month and a half too early. A number of scheduling issues required me to come now, although I knew it was too soon after the monsoon, but I didn’t expect so much of the land to still be flooded. Time to come up with an alternative plan.
For the resistivity, we need long straight stretches of dry land. We decided to
do it west of the valley to try to image the thickness of the entire Holocene (last 10,000 years) section. It should vary because of the folding of the strata from the tectonics. Mapping the thickness will help us to map the position of the buried fold. For augering, we only need a small patch of land to stand on. To find it we headed south towards where the valley was uplifted more and might be drier. Not as ideal as the original location, but possible. The next morning we headed farther south and crossed the river valley. It was drier and we noted some potential augering sites. We continued to a location for resistivity. The six of us set up the >350 m long resistivity line, then Céline, Basu and I headed back to try augering while the resistivity data was collected. The augering proved very difficult. We were very slow describing the core that the auger brought up, and while we were doing it the hole would start to collapse. The muddy sediment was very stiff, and we had to hammer the auger in. We only got to 2.7 m when we stopped, nowhere near the depth we needed. Things were pretty discouraging.
I’m really excited (and relieved) to report that my review on the taxonomy and function of sea ice microbial communities was recently published in the journal Elementa. The review is part of a series on biological exchange processes at the sea ice interface, by the SCOR working group of the same name (BEPSII). I’m deeply appreciative of Nadja Steiner, Lisa Miller*, Jaqueline Stefels, and the other senior members of BEPSII for letting (very) junior scientists take such an active role in the working group. I conceived the review in a foggy haze last year while writing my dissertation, when I assumed that there would be “plenty of time” for that kind of project before starting my postdoc. Considering that I didn’t even start aggregating the necessary data until I got to Lamont I’m also deeply appreciative of my postdoctoral advisor for supporting this effort…
The review is really half review, half meta-analysis of existing sea ice data. The first bit, which draws heavily on the introduction to my dissertation, describes some of the history of sea ice microbial ecology (which goes back to at least 1918 for prokaryotes). From there the review moves into an analysis of the taxonomic composition of the sea ice microbial community, based on existing 16S rRNA gene sequence data, takes a look at patterns of bacterial and primary production in sea ice, and then uses PAPRICA to infer metabolic function for the observed microbial taxa (after 97 years we still don’t have any metagenomes for sea ice – let alone metatranscriptomes – and precious few isolates).
There is a lot of info in this paper but I hope a few big points make it across. First, we have a massive geographical bias in our sea ice samples. This is to be expected, but I don’t think we should just accept it as what has to be. More disconcerting, there has been very little effort to integrate physiological measures in sea ice (such as bacterial production) with analyses of microbial community structure. A major exception is the work of the Kaartokallio group at the Finnish Environmental Group, but their work has primarily taken place in the Baltic Sea (an excellent system, but very different from the high Arctic and coastal Antarctic). This all translates into work that needs to be done however, which is a good thing… we are just barely at the point where we can make reasonable hypothesis regarding the functions of these communities.
*This image of Lisa pops up a lot. If you can identify what, exactly, is going on in this picture I’ll buy you a beer.
I am heading back to Bangladesh, but this time I am stopping in New Delhi before heading to Bengal (West Bengal and Bangladesh). It is the first time that I will be in a part of India that is not adjacent to Bangladesh. Several of us are meeting there to plan for a new project that will span Bangladesh to India to Myanmar. I arrived a few hours before Nano Seeber and Paul Betka and used the time to get a new Indian SIM for my phone. After meeting up, we headed to the guesthouse of the Ministry of Earth Sciences, where we will be staying. If only the U.S. had a cabinet level department for earth sciences. It was difficult to find at night without a Hindi speaker, but we managed.
Over the next few days we had meetings about the project, but also some time for sightseeing, while
discussing the project in the car. Most of our meals were vegetarian, and Gandhi’s birthday, which occurred while we were there, is celebrated by eating vegetarian. When two more scientists arrived from Singapore, we started the day by visiting the Qutub Minar, dating back to the 1200s and the arrival of the Muslim Delhi Sultanate, followed by the Mughal Empire in the 1500s. In the Quwwat-ul-Islam mosque, there is the famous Iron Pillar originally erected by Chandragupta in the 4th century, probably at Patna, and brought here much later. Near the beginning of the inscription it says: “in battle with the Vanga countries, he kneaded (and turned) back with (his) breast the enemies who, uniting together came against (him).” Vanga is Bengal, now split into West Bengal in India and Bangladesh.
After mostly finishing discussions, the others decided to take a day trip to Agra to see the Taj Mahal. I was able to change my flight to Kolkata to the following morning and joined them, continuing to talk science on the 4-hour drive. We had to buy the expensive tickets at 750 rupees rather than the 10 rupees the Indians were paying. However, the premium ticket lets us bypass the long lines. The Taj Mahal is the tomb of Mumtaz Mahal,
the beloved wife of Shah Jahan, the Mughal Emperor. It was built over 17 years from 1631-1648. She died in childbirth of her 14th child. He was buried there as well when he died in 1668, after being overthrown by his son. I have seen many pictures but was not expecting how enormous the structure is. The entire place is beautiful and enormous with flanking buildings, gardens and gateways. I kept wondering about the cost of building it and how many man-years of India’s peasants financed it. Perhaps this excess was why this was the peak of the Mughal Empire. Within a 100 years, the British were
taking over. Afterwards we went to Agra Fort, which is similarly gigantic, and another seat of the Mughals. There are palaces and a throne inside the red fort with views of the Taj. There are 30 buildings left, the rest having been leveled by the British to erect barracks for their troops. We didn’t get back to our hotel until 11.
I left early the next morning for Kolkata, the British Indian capital until 1911, when they moved it to Delhi. It was done to punish the Bengalis for opposing the
splitting of the Bengal Presidency into more manageable size, which would have cut Bengal in two. I spent the day at Calcutta University then headed back to the airport to fly to Dhaka. At my usual hotel, I met up with Jenn Pickering, a student at Vanderbilt University, and Céline Grall, my postdoc. They were teaching a short course at Dhaka University. I spent the next few days in multiple meetings and making arrangements for a week of fieldwork. It will be good to get out into the countryside.
Completing an ‘Ice Station’ means collecting samples over a wide range of Arctic water and ice conditions. Each station means a major orchestration of people and resources. The teams gather, equipment is assembled, and the trek off the ship begins. After the first off ship exodus the sample teams are well practiced in moving equipment and setting up work areas so as not to interfere with the other stations. There is no shortage of space so spreading out is not a challenge!
Collecting a wide range of samples at multiple Arctic locations allows GEOTRACES to get an integrated look at the trace elements moving through the Arctic ocean ecosystem, and to better understand how these elements connect to the larger global ocean. Each is carefully collected. Whether the elements are ‘contaminants’ or essential nutrients there is a specific protocol in order to quantify the inputs without ‘dirtying’ the sample. It may seem odd to think of ‘dirtying’ something we label a contaminant, but in order to fully understand the concentrations and methods of transport for each element, every sample is handled with the same amount of care.
The following photo essay showcases the various ice/water sampling stations and reviews what is being collected at each.
Snow Samples: The snow collected at this station is being used in part to determine the presence/absence of contamination related to the March 11, 2011 Fukushima event.
Both the snow samples and the ice core sections will be analyzed and examined along with the information collected from seawater, suspended particulates, and bottom sediments, in order to better understand the influence of processes specific to the Arctic on the transport and distribution of several anthropogenic radionuclides.
Ice core samples: The ice cores are sections of sea ice, and again are being collected to determine the presence/absence of contamination related to Fukushima. In general the samplers were able to obtain 1.5 – 2 meters of ice in the cores.
Melt Ponds: Surface melt ponds form on the sea ice in the long says of the Arctic summer. The warmth of the sun creates ponds that sit on top of the ice. The water collected in these ponds carries different properties than the either the sea ice from which it melted, or the ocean water from which the sea ice formed. Most often these ponds have a frozen surface layer that needs to be drilled through before water is pumped out for collection.
Beryllium-7 (7Be) Samples: Produced in the atmosphere when cosmic rays collide with nitrogen atoms, 7Be is constantly being added to the surface of the water, and therefore is a great surface water tracer. With its very short half-life, ~ 53 days, 7Be can be used to track water parcel circulation as it moves between surface and deep water (which has no significant source of the 7Be isotope). The surface water pulls the 7Be with it as it moves down deeper into the ocean, allowing us to track and time the mixing process.
Dirty Ice Samples: The dirty ice work is more opportunistic, and therefore is not be part of each ice station. If dirty ice is spotted it will be sampled, and while it may not be part of each ice station, it is part of the overall GEOTRACES protocol. While most of the stations sample for quantification, i.e. grams of sediment/ml ice, the dirty ice samples are used more for characterization, i.e. composition or mineralogy. For Tim’s work the collection of dirty ice is used to look at sediments originating from continental shelves bordering the Arctic, with the goal of evaluating or characterizing dirty ice as a transport vector for anthropogenic radionuclides.
Minimal Processing of the samples collected at the stations will occur on the Healy. The snow and Ice gets melted and the seawater acidified. The focus of the trip is to collect as much material as possible. There will be plenty of time for processing when the researchers are back at their home institutions.
Margie Turrin is blogging for Tim Kenna, who is reporting from the field as part of the Arctic GEOTRACES, a National Science Foundation-funded project.
For more on the GEOTRACES program, visit the website here.
A quick post on an excellent review published last week by Antje Boetius and co-authors (including Jody Deming, my PhD advisor) in Nature Reviews Microbiology, titled Microbial ecology of the cryosphere: sea ice and glacial habitats. The review, focused on viral, bacterial, and archael microbes, provides an excellent overview of the major habitats within the cryosphere (broadly glacial ice, sea ice, and snow), the challenges and opportunities for microbial life, and the observed distribution of taxa and genes (to the extent that we know it). Like most Nature Reviews it is written for a broad audience and assumes no deep knowledge of microbial ecology or the cryosphere.
Plenty of reviews have been written on microbial life at low temperature, what makes this one stand out to me is the ecological focus. Although discussions of biogeography (i.e. what taxa are where) and metabolism are woven throughout the review, the emphasis is on habitats, including newly recognized habitats like frost flowers and saline snow. Check it out!
In preparation for their Arctic work GEOTRACES linked with “Float Your Boat”, an education program with a unique concept. ‘Float Your Boat’ blends the themes of historic Arctic drift studies, modern GPS technology and hands on science, to engage local communities with work in remote science locations. Scientists currently onboard the Research Vessel Healy spent time last spring recruiting and meeting with school groups to share information about the Arctic, their upcoming science cruise and collecting small student decorated wooden boats that would become part of the project.
For over a month the science team has been anticipating the deployment of these small wooden vessels since this builds a direct connection to their families and communities back home.
The student boats are deployed in a 100% biodegradable box lowered carefully onto an iceberg along with an iridium satellite tracking buoy. The tracker is activated ‘calling home’ so that it can be used to track the circulation of the ice. Over time the ice is expected to melt and the box will biodegrade sending these small floating wooden boats into the high seas of the Arctic Ocean.
Once the box degrades the boats will be separated from the tracker, but each boat has been identified by the students with their school and their own name and stamped with the project contact information. If any of the boats wash up onshore there is enough information for the locator to contact ‘Float Your Boat’ with a date and location. Through online tracking of the iridium satellite this project provides opportunities for students to learn about Arctic change, marine circulation, marine debris transit and maritime careers.
The ‘Float Your Boat’ project concept comes from early Arctic science, when drifting ice floes were used to track Arctic circulation. In the International Geophysical Year (1957-58) Lamont scientist Ken Hunkins resided for two 6 month stints on Ice Station Alpha, a station built on top of the Arctic sea ice. Science teams were flown in by plane and dropped, along with their equipment, about 500 miles north of Alaska. There they studied a range of ocean parameters, including tracking their own progress as they moved along with the ice drift. The 18 months of operations tracked the ice floe movement as it shifted ~2000 miles around the Arctic in a clockwise manner until it was just north of Ellesmere Island, Canada. (map below)
Somehow the rigid presence of the Healy seems infinitely more secure than a few tents and rigs set directly on the mile long by half-mile wide section of sea ice under station Alpha.
But even earlier than the science drift experiments were the expeditions of early Arctic explorers, like Fritdjof Nansen, who froze his ship the “Fram” into the northern icepack during his voyage of 1893-1896 in hopes of drifting to the North Pole. He did not succeed, however he did learn about Arctic drift and spurred additional research on this topic, perhaps leading to these young Arctic researchers and their ‘vessels’.
Margie Turrin is blogging for Tim Kenna, who is reporting from the field as part of the Arctic GEOTRACES, a National Science Foundation-funded project.
For more on the GEOTRACES program, visit the website here.
…for something completely different. My wife and I are expecting our first child in a few months, which is wonderful and all, but means that we are faced with the daunting task of coming up with a name. Being data analysis types (she much more than me), and subscribing to the philosophy that there is no problem that Python can’t solve, we decided to write competing scripts to select a good subset of names. This is my first crack at a script (which I’ve titled BAMBI for BAby naMe BIas), I’ve also posted the code to Github. That will stay up to date as I refine my method (in case you too would like Python to name your child).
My general approach was to take the list of baby names used in 2014 and published by the Social Security Agency here, bias against the very rare and very common names (personal preference), then somehow use a combination of our birth dates and a random number generator to create a list of names for further consideration. Okay, let’s give it a go…
First, define some variables. Their use will be apparent later. Obviously replace 999999 with the real values.get = 100 # how many names do you want returned? wife_bday = 999999 my_bday = 999999 due_date = 999999 aatc = 999999 # address at time of conception size = (wife_bday + my_bday) / (due_date / aatc) start_letters = ['V','M'] # restrict names to those that start with these letters, can leave as empty list if no restriction desired sex = 'F' # F or M
Then import the necessary modules.import matplotlib import numpy as np import matplotlib.pyplot as py import math import scipy.stats as sps
Define a couple of variables to hold the names and abundance data, then read the file from the SSA.p =  # this will hold abundance names =  # this will hold the names with open('yob2014.txt', 'r') as names_in: for line in names_in: line = line.rstrip() line = line.split(',') if line == sex: if len(start_letters) > 0: if line in start_letters: n = float(line) p.append(float(n)) names.append(line) else: n = float(line) p.append(float(n)) names.append(line)
Excellent. Now the key feature of my method is that it biases against both very rare and very common names. To take a look at the abundance distribution run:py.hist(p, bins = 100)
Ignore the ugly X-axis. Baby name abundance follows a logarithmic distribution; a few names are given to a large number of babies, with a long “tail” of rare baby names. In 2014 Emma led the pack with 20,799 new Emmas welcomed into the world. My approach – I have no idea if it’s at all valid, so use on your own baby with caution – was to fit a normal distribution to the sorted list of names. I got the parameters for the distribution from the geometric mean and standard deviation (as the arithmetic mean and SD have no meaning for a log distribution). The geometric mean can be calculated with the gmean function, I could not find a ready-made function for the geometric standard deviation:geo_mean = sps.mstats.gmean(p) print 'mean name abundance is', geo_mean def calc_geo_sd(geo_mean, p): p2 =  for i in p: p2.append(math.log(i / geo_mean) ** 2) sum_p2 = sum(p2) geo_sd = math.exp(math.sqrt(sum_p2 / len(p))) return(geo_sd) geo_sd = calc_geo_sd(geo_mean, p) print 'the standard deviation of name abundance is', geo_sd ## get a gaussian distribution of mean = geo_mean and sd = geo_sd ## of length len(p) dist_param = sps.norm(loc = geo_mean, scale = geo_sd) dist = dist_param.rvs(size = sum(p)) ## now get the probability of these values print 'wait for it, generating name probabilities...' temp_hist = py.hist(dist, bins = len(p)) probs = temp_hist probs = probs / sum(probs) # potentially max(probs)
At this point we have a list of probabilities the same length as our list of names and preferencing names of middle abundance. The next and final step is to generate two pools of possible names. The first pool is derived from a biased-random selection that takes into account the probabilities, birth dates, due date, and address at time of conception. The second, truly random pool is a subset of the first with the desired size (here 100 names).possible_names = np.random.choice(names, size = size, p = probs, replace = True) final_names = np.random.choice(possible_names, size = get, replace = False)
And finally, print your list of names! I recommend roulette or darts to narrow this list further.with open('pick_your_kids_name.txt', 'w') as output: for name in final_names: print name print >> output, name
We are closing in on a week of intense focus and excitement for GEOTRACES and for the United States around the Arctic. It was barely a week ago (Aug. 31) that President Obama became the first sitting president to visit Alaska, refocusing the other 49 states on the fact that we are indeed an Arctic Nation. This historic first was followed closely by another, the Sept. 5 arrival of the U.S. Coast Guard Cutter Healy with the U.S. GEOTRACES scientists on board at the North Pole, completing the first U.S. surface vessel transit to the pole unaccompanied by another icebreaker. Combined with this, U.S. GEOTRACES became the first group ever to collect trace metals at the North Pole. You might assume these three items are unrelated, but they are in fact tightly linked.
In convening the GLACIER Conference (Global Leadership in the Arctic: Cooperation, Innovation, Engagement & Resilience) in Alaska, President Obama focused on a region that is fast changing due to its fragility and vulnerability to climate change. The meeting timing aligned nicely with the U.S. assuming chairmanship of the Arctic Council, and was a perfect platform for the president to address climate change, an issue that he has tackled aggressively. Conference sessions on the global impacts of Arctic change, how to prepare and adapt to a changing climate, and on improved coordination on Arctic issues all align with the work of Arctic GEOTRACES, although tackled from a different angle.
It was while he was in Alaska that President Obama announced a commitment to push ahead the schedule for adding to the U.S. icebreaker fleet. The “fleet” has dwindled to just 3 U.S. vessels at present, and limits our ability to work in the Arctic. The goal of adding another icebreaker by 2020 will help to address this. “Working” in the Arctic for this Coast Guard cutter includes supporting the research that is critical to our being able to develop a baseline understanding of conditions and more accurately predict the future changes.
Evidence for change in the Arctic is found in the ability of the U.S. Coast Guard Cutter Healy to cross the Arctic ocean along its longest axis (the Bering Strait route) and penetrate deep into the sea ice to make it to the North Pole unaccompanied. The ice has been thinner than expected and experiencing a much higher degree of melt. Ice stations, where the science team gets out onto the ice to sample, have been postponed because of safety concerns from the thin ice conditions. Everyone, including the captain, has been surprised by the conditions. The thin ice has increased the speed of travel. Although some thick (up to 10 feet) and solid ice has been encountered, much of the cruise has been spent traveling at up to 6 knots, and much less fuel has been used than expected because of this.
The last week has been action packed for all 145 people on the Healy. First. a “superstation” was run, a 57-hour sampling stop with a large number of samples collected in the ~4,000-meter-deep water. A super station includes additional hydrocasts and pump sampling for the groups like Tim Kenna’s, that require large volumes of sample water. This was also a crossover station with the German GEOTRACES cruise on the Polarstern. Crossover means some of the extra samples collected can be used to do intercalibration (check to see that the results compare) between the science teams on the two ships. The German ship will collect at the exact same location. With large sampling projects using multiple labs and sampling teams, intercalibration becomes extremely important for interpreting the results.
After our long superstation, the team went almost immediately into a dirty-ice station (ice that entrains sediment as it freezes). This ice can form in several ways: during the spring thaw when ice dams in Arctic streams force sedimented water out onto the ice, where it refreezes; during cold storms that churn up sediments in the shallow shelf regions to refreeze on the surface ice; and when shallow areas freeze solid, collecting sediment at the base, and later break away. Once the ice is formed, it moves into the Arctic circulation pattern, so identifying the source of the sediment can help us better understand the temporal and spatial nature of Arctic circulation. This type of ice has high value for Tim’s research, since short-lived radioactive isotopes are frozen into the ice with the sediments, providing a timer for the formation of the ice.
The dirty ice station was followed by an ice-algae station. Both of these entail stopping the ship and craning over two people in a “man-basket” where they can get out and sample (see image). This was followed closely by two full ice stations, where many groups went out on the ice to do their sampling; some for over 12 hours (brr). The second ice station had wind chills of -14 C.
Field time, especially in the polar regions, is expensive and limited, so while in the field it is critical to complete as much science as possible. Sleep happens later when the team is back home.
Lamont Note: As part of the Healy’s instrument package, they standardly carry a CO2 instrument from Lamont’s Taro Takahashi. This was onboard when the Healy reached the North Pole (89.997 °N). The partial pressure of CO2 (pCO2) in seawater was found to be 343.3 micro-atmospheres at the water temperature of -1.438 °C. This is about 50 micro-atmospheres below the atmospheric pCO2 of 392.7 micro-atmospheres, and indicates that the Arctic Ocean water is rapidly absorbing CO2 from the air. The measurements confirm that the Arctic Ocean is helping to slow down the accumulation of the green house gas in air and hence the climate warming.
Margie Turrin is blogging for Tim Kenna, who is reporting from the field as part of the Arctic GEOTRACES, a National Science Foundation-funded project.
For more on the GEOTRACES program, visit the website here.