The Ross Ice Shelf is much like the Rosetta Stone. The historic stone was inscribed in three different scripts; each telling the same story but in a different tongue. When matched together the information was enough to allow scholars to decode an ancient language. The Rosetta Project in Antarctica also brings together three different ‘scripts’, but in this case they written by three Earth systems; the ice, the ocean and the underlying bed each have a story to tell. Mapped together these three systems can be used to unlock the mysteries of Antarctic ice history in this region and help us to develop models for predicting future changes in Antarctic ice.
The multi-institutional project is multi-disciplinary in nature and takes advantage of the recently commissioned IcePod integrated ice imaging system as the main science platform. IcePod is package of geophysical instruments packed into a 9 ft. container and loaded onto the large LC130 transport planes supporting science in the polar regions. Flown by the US Air National Guard these planes are the workhorses of the science program. A unique ‘arm’ that fits into the rear side-door of the plane is used to attach the IcePod outside the aircraft, allowing it to be used on both dedicated missions and flights of opportunity.
IcePod’s instruments include two radar to image through the ice, lidar to measure to the ice surface, cameras for surface images, and a magnetometer to better understand the tectonics and origin of the bed below the ice shelf. Together with the IcePod instruments the project will use two separate gravimeters in order to develop a bathymetric map of the seafloor under the ice shelf. Gravity is a critical data piece in this project as the radar is unable to image through the water under the ice shelf.
The Ross Ice Shelf is a thick slab of ice that serves to slow and collect ice as it flows off the Antarctic peninsula. Ross is the largest of the Antarctic ice shelves moving ice at rates of 1.5 to 3 meters/day. Somewhat triangular in shape, it is bounded by the West Antarctic ice sheet on the west, the East Antarctic ice sheet on the east, and the Ross sea along the front.
This three year project involves 36 separate flights in a two season field campaign. The first field season is underway now, and will focus on building the larger framework for the dense 10 km spaced grid of flights that is planned for the following season. As each day’s flights are logged they are being posted on our interactive website. You can follow our campaign by linking directly to this data portal to watch the grid develop. You can select the project proposed flight plan (v9) on the Data Map to get a complete look at the project plan. The end product will be a dense grid of flightlines evenly spaced and crossing with regular tie points.
First flights included two survey lines across the ice shelf. The most southern of the two lines was flown by IcePod in 2014 during commissioning flights, and by the NASA IceBridge project in 2013. These two flights provide a calibration line for the system. The northern line is the first new line for the project. The map also shows a small test flight for the equipment and a line up to South Pole that was a piggy back flight with another mission of the plane.
You will note that flights originate from McMurdo so there is a dense radiating line from the base. Minna Bluff is a prominent volcanic promontory that sticks out close to MCM. The bluff was first identified by Capt. Scott in 1902 and is mentioned often in Antarctic exploration history.
Check the flight tracker daily for updated flight lines.
For more about this NSF and Moore Foundation funded project please check our project website: ROSSETTA
Margie Turrin is blogging for the IcePod team while they are in the field.
Many experts at Columbia University’s Earth Institute are attending or closely watching the Paris climate summit. These include world authorities on climate science, politics, law, natural resources, national security, health and other fields, who can offer expert analysis to journalists. Also, this week we start our Paris Climate Summit blog, with news, views, and scientific perspective from our staff. Below, a guide to resources that journalists covering the summit can tap.
The Paris Climate Summit A frequently updated blog from Earth Institute experts with explainers, commentary and other features.
Recent Climate Research The top Earth Institute scientific papers from 2015 and previous recent years.
Milestones in Climate Science A 60-year timeline of studies from Lamont-Doherty Earth Observatory that have shaped modern climate science.
Copenhagen Climate Conference 2009 Our blog from the last major summit provides historical perspective.
(Not an exhaustive list. *Denotes person attending the summit.)
*Peter deMenocal, professor, Lamont-Doherty Earth Observatory. Paleoclimatologist DeMenocal leads the observatory’s new Center for Climate and Life, which will examine globally how climate change affects ecosystems and human sustainability.
Jason Smerdon is a Lamont-Doherty climate researcher and educator who co-directs the Earth Institute’s undergraduate sustainable development program.
Gavin Schmidt directs the NASA Goddard Institute for Space Studies. He is a leading communicator on the fundamentals of climate science, and the implications.
*Scott Barrett, Earth Institute professor of natural resources; expert in dynamics of transnational negotiations, treaties and conflict resolution, especially climate. Barrett is coeditor of a new e-book prepared especially for the summit.
*Michael Gerrard, director, Sabin Center for Climate Change Law, leader in the study of climate’s legal implications on state, national and international levels.
Michael Burger, executive director, Sabin Center for Climate Change Law, consults internationally on efforts to reduce carbon emissions, and on climate adaptation.
Steven Cohen, Earth Institute executive director, comments frequently on political developments surrounding climate and sustainable development.
Solutions, adaptations, sustainable development
*Lisa Goddard, director, International Research Institute for Climate and Society (IRI), which works with governments around the world to predict and adapt to medium-term climate swings.
*Cynthia Rosenzweig, Earth Institute senior research scientist, is a pioneer in studying how cities can adapt to climate change.
*Guido Schmidt-Traub, executive director, Sustainable Development Solutions Network. SDSN is a UN effort hosted by the Earth Institute that mobilizes teams across the world to solve global challenges, including climate change.
*Laura Segafredo manages SDSN’s Deep Decarbonization Pathways Project, a global collaboration of energy researchers charting steps for nations to cut emissions.
Upmanu Lall directs the Columbia Water Center, which tackles water-supply challenges and their relation to climate across the world.
Pedro Sanchez, director, Agriculture and Food Security Center, helps direct multiple projects in developing countries to ensure a robust food supply in changing conditions.
Shahid Naeem, director, Earth Institute Center for Environmental Sustainability, is an ecologist who deals with issues of conservation and biodiversity.
Marc Levy, deputy director, Center for International Earth Science Information Network (CIESIN), is a political scientist who studies the human dimensions of environmental change, including climate’s potential for violent conflict.
Alexander deSherbinin, CIESIN senior researcher, maps out the human consequences of climate change, including potential large-scale population migrations.
*Madeleine Thomson, IRI senior researcher, works to understand the health effects of climate, and help provide adaptations.
*Patrick Kinney, Earth Institute professor based at Mailman School of Public Health, studies the health effects of climate change, especially in cities.
Anthony Annett, an economist, leads the Earth Institute’s initiative to engage religious communities with climate and sustainable-development issues.
*Ben Orlove, anthropologist and co-director of the Center for Research on Environmental Decisions, studies how the public apprehends climate change issues.
# # #
More information: Kevin Krajick, Senior editor, science news, The Earth Institute firstname.lastname@example.org 212-854-9729
The storms of the past week cleared most of the pack ice out of Arthur Harbor, although the land fast ice that we’ve been sampling from has survived. In anticipation of the start of the boating season there was a flurry of activity yesterday as station personnel cleared off the boat ramp and got the zodiacs ready. Unfortunately Jamie and I didn’t think to start the time lapse below until yesterday afternoon after most of the three-ring circus had died down, but you still get a sense of the activity.
There are two science groups waiting to start boating operations; our group and a group of penguin researchers (aka “the birders”). Both groups are part of the Palmer LTER. While we will spend the summer investigating water column processes however, the birders will spend their summer visiting the various penguin rookeries and maintaining a remarkable long term dataset of penguin population.
The birders were supposed to get their final zodiac training today, but although the harbor is clear of ice the winds are back up (gusting around 30 kts at the moment) so everything is getting shifted back. In the meantime we will have a late night sampling another time point from the experiment that we started on Tuesday. As I described in the previous post, for this experiment we are making use of the highly unusual ice conditions to study what happens to the microbial community when the ice is suddenly removed (as has happened to much of Arthur Harbor and the surrounding area in the last week). Although we won’t know the results of most of our analyses for several months, we can make some interesting qualitative observations as the experiment progresses.
One of the interesting observations so far was the initial condition of the microbial community. During a down moment yesterday I took a look at water from just 24 hours into our experiment to see what was growing (so this isn’t exactly the initial condition, but a close approximation of it). What we found really surprised me. Here are a couple of images that illustrate the phytoplankton community in our experiment:
The traditional wisdom would suggest that the spring phytoplankton bloom should start with diatoms. Following the initial diatom bloom there are successive, mixed blooms of haptophytes, cryptophytes, dinoflagellates, and other groups of phytoplankton. Observations from this time of year are very sparse however, so it is difficult to know if we are seeing something that is unique or the normal phytoplankton assemblage for this time of year. The composition of the phytoplankton assemblage is not merely academic; it dictates how carbon will flow through the food web in a given season. Large diatoms for example, are easily feed upon by krill, resulting in high krill biomass and more and more healthy top predators (e.g. penguins, seals, and whales). Smaller phytoplankton (like cryptophytes) produce a more complex food web that might ultimately channel less carbon to the top trophic levels. We will have to wait and see how the situation plays out this year…
During the Copenhagen climate meetings in 2009, I posted a piece in the Huffington Post assessing the conference. At that time I observed that:
“There is a broad consensus about the need for reductions in the emissions that cause global warming. Copenhagen is providing the entire world a crash course in climate science and policy. Over the past decade, the politics of national and global climate policy has shifted from the fringes of the public policy agenda to the center. The real story of Copenhagen is the maturation of this key issue of global environmental policy. … Climate change is just the first global environmental problem we have come to understand. At Copenhagen we are barely discussing the other global environmental issues such as species extinction, the destruction of the oceans and degraded fresh water supplies. But we could.”
As we approach the Paris version of these endless talks, COP21, to be held next month, it’s fair to ask: What has changed over the past six years, and did Copenhagen stimulate any of these changes?
What has changed is the broad consensus on climate change has broadened, and recent polls show that even Republicans in the United States understand the nature of the problem. Globally, individual nations have volunteered greenhouse gas reduction targets in anticipation of the Paris meetings. Unlike Copenhagen, where calls for mandatory reductions and transfer payments to the developing world caused the collapse of any potential agreements, the world community seems more realistic as it approaches the Paris meetings. An agreement that codifies the reductions already pledged seems within reach, even if its value is more symbolic than real.
There remains a possibility that the call for transfer payments from wealthy nations to developing nations could disrupt the effort at building a global consensus. Previous aid promises were not fulfilled, and there is some political pressure to get the issue back on the global agenda. One of the major changes since 2009 is the clear perception that some nations once classified as developing, such as China, Brazil and India, can no longer be thought of in that way. While this was also the case in 2009, six years later, they are clearly in a category of their own.
My own view of the Paris talks and the ones that came before is that they have value, but it is important to understand their inherent limits. The climate issue is really an issue of the energy base of a nation’s economy. Modern economies require energy, and economic development depends on plentiful, reliable, reasonably priced energy. The issue is so central to economic growth and the stability of political regimes that no nation state will fundamentally limit its flexibility in delivering energy for any reason. It is central to sovereignty in the modern world. But communicating the dangers of fossil fuels and the need to transition to a renewable energy based economy is something these meetings have achieved, and the importance of that achievement should not be underestimated.
The climate issue seems to generate a high level of ideologically based politics, emotional rhetoric and political symbolism. It is time to move past symbols to pragmatism and political reality. We need to move toward an acceptance of nine fundamentals if we are to address the climate change crisis:
- Human induced climate change is real, already underway and will continue into the future.
- We cannot precisely predict the future impact of climate change on human settlements and economic well-being.
- Fossil fuels are the largest single generator of greenhouse gases.
- Our economic way of life and therefore the political stability of our world are highly dependent on energy that mainly comes from fossil fuels.
- The transition from fossil fuels to renewable energy is necessary but will take decades to accomplish.
- Reducing the use of fossil fuels by raising the price of these fuels is unlikely to achieve political support or be supported by the world’s governments.
- Reducing the use of fossil fuels by developing lower priced, reliable and renewable sources of energy requires additional technological development.
- Reduced energy costs will have great political appeal and positive economic impact.
- The increased use of current renewable energy technologies will be facilitated by government policy to attract capital and reduce the price of energy.
In my view, the battles over oil pipelines, fracking and divesting capital from fossil fuel companies are symbolic battles that serve to distract us from the operational issues that will facilitate the transition to a renewable energy economy. One issue to engage in is the coming battle to renew the favorable tax treatment of renewable energy in the U.S., now slated to end in December 2016. Ending that tax expenditure would slow down the growth of the solar and wind industry and have an immediate and dramatic impact on the production of greenhouse gases.
The Department of Energy and the National Science Foundation’s research budget for renewable energy technologies needs to be increased dramatically. The federal government should take the lead in purchasing electric vehicles and installing renewable energy. A federal fund to restore and build infrastructure will probably appear on the federal agenda during the next decade. Some part of that funding should be devoted to upgrading the electric grid to make it smarter and more efficient, funding public charging stations for electric vehicles, funding mass transit, and providing resources to make coastal infrastructure more resilient and better able to adapt to the impact of climate change.
The action required to transition off of fossil fuels and other single-use resources requires a sophisticated partnership between the public and private sectors.
The greatest danger to America’s transition to a renewable resource based economy is not industry, which will make plenty of money off of this transition, or the public, which appears ready to move, but the anti-government ideology that continues to paralyze our federal government.
The action required to transition off of fossil fuels and other single-use resources requires a sophisticated partnership between the public and private sectors. There will be some instances when the work that needs to be done—for example, basic research or infrastructure finance—will require federal funds. There will be other instances when the tax code or other incentives will be needed to attract private capital and companies into the market. And there will be even more instances when government action is not needed, and the best thing government can do is get out of the way and let the private sector act. By sophisticated partnership, I mean one that is guided by results-oriented pragmatism rather than symbols and ideology.
The climate talks in Paris will focus attention on the climate issue and increase understanding of the nature of the problem. Then the spotlight shifts to nations and cities, and hopefully from talk and chit-chat to funding and action. There are many signs that the transition from fossil fuels has begun. The speed of that transition is at issue and will require creativity, consensus and cash to be completed.
This post is one in a series reflecting on what has changed since the climate talks of 2009 in Copenhagen.
Editors’ note: This is the first in a series of posts on the 2015 Paris climate summit. You can follow all of our coverage on a special State of the Planet feature page.
What is it?
COP21, the 2015 United Nations Climate Change Conference, will be held outside of Paris in Le Bourget, France, from Nov. 30 to Dec. 11. It is called COP21 because it is the 21st annual meeting of the Conference of Parties to the 1992 United Nations Framework Convention on Climate Change. The parties meet each year to assess their progress in dealing with climate change; its objective is to achieve “stabilization of greenhouse gas concentrations in the atmosphere at a level that would prevent dangerous anthropogenic interference with the climate system.”
The 195 countries who make up the UN Framework Convention on Climate Change will send over 40,000 delegates to the talks in Paris. At least 80 world leaders will attend, including the leaders of Germany, South Africa, Brazil and England, and those of the three biggest carbon emitting countries: President Barack Obama from the United States, Chinese President Xi Jinping and Indian Prime Minister Narendra Modi.
What is the goal?
The goal of COP21 is to negotiate a new international climate change agreement that can keep the average global temperature rise below 2° C by 2100 compared to pre-industrial levels. The agreement will be universal and include pledges from the parties to limit and reduce greenhouse gases, implement strategies to adapt to the impacts of climate change, and commit financial support to help developing countries deal with climate change. The agreement will also likely establish five-year reviews to make sure countries are keeping their commitments and to ratchet up emissions reduction targets in order to meet the 2˚C goal.
Why does it matter?
Human activities have generated greenhouse gases—carbon dioxide, methane, nitrous oxide and fluorinated gases—that have collected in the atmosphere and warmed the planet. Between 1990 and 2014, global greenhouse gases increased 36 percent. In 2011, Asia, Europe and the United States were responsible for 82 percent of total greenhouse gas emissions. Some of the carbon dioxide that we have already pumped into the atmosphere will remain there for hundreds of years.
The increase in greenhouse gases over the last 100 years has so far caused average global temperatures to rise .85˚C. Data for 2015 from the Met Office, the United Kingdom’s national weather service, shows that Earth’s global mean temperature will reach 1˚C above pre-industrial levels for the first time this year. While this does not sound like much, we are already feeling the effects of this warming with more extreme heat, heavy downpours, increased wildfires, insect outbreaks, loss of glaciers and sea ice, sea level rise and flooding.
Scientists and over 100 nations have agreed that limiting the global temperature rise to 2˚C is critical to avoiding more catastrophic climate change effects. According to the World Resources Institute, if we continue on a “business as usual” trajectory of generating greenhouse gases, we will reach 2˚C by 2045. This will increase the risk of sea level rise, intensify wildfires and make them more frequent, exacerbate heavy precipitation events and the severity of droughts, acidify the oceans, cause extinction of animal species and jeopardize our food supplies. With each degree above the 2˚C limit, the impacts of climate change will be more severe and the risks greater that tipping points could be passed, resulting in abrupt and irreversible changes in the global climate system.
In May, a UN Framework Convention on Climate Change report concluded that 1.5˚C would be a preferable limit, but would require a faster reduction of energy demand and an immediate scaling up of low-carbon technologies to curb greenhouse gases.
When does COP21 go into effect?
In 1997, at COP3, 192 parties adopted the Kyoto Protocol (the United States did not ratify the protocol), which legally bound developed countries to reduce their emissions. Kyoto’s first commitment period went from 2008 to 2012. A second commitment period, known as the Doha Amendment, began in 2013 and ends in 2020. The COP21 agreement will take effect in 2020 when the Kyoto Protocol ends.
How will it work?
At COP15 in Copenhagen in 2009, the 195 countries involved in the UN Framework Convention on Climate Change pledged to reduce their greenhouse gas emissions by 2025-2030.
Ahead of COP21, all the states were invited to submit their “Intended Nationally Determined Contributions” that indicate what actions the countries will take to reduce their emissions. Each plan takes into account a country’s particular circumstances and capabilities, and may address adaptation to climate change impacts, and what support they will need from, or be willing to give to other countries.
One hundred-thirty-one of these “intended contributions” have been submitted. Here are a few examples.
The United States has pledged to reduce greenhouse gas emissions 26 to 28 percent below its 2005 levels by 2025, with best efforts to reduce emissions by 28 percent. Strategies to achieve the goal include the U.S. Environmental Protection Agency’s regulations to cut carbon pollution from new and existing power plants, tighter fuel economy standards for light and heavy-duty vehicles, and the development of standards to address methane emissions from landfills and oil and gas production.
China pledges that its carbon emissions will peak by 2030 or sooner if possible, and that the country will reduce carbon dioxide emissions for each unit of Gross Domestic Product (its “emissions intensity”) by 60 to 65 percent from 2005 levels, derive 20 percent of energy from non-fossil fuels, plant more forests and improve the country’s adaptation to climate change impacts.
India intends to reduce the emissions intensity of its GDP by 33 to 35 percent by 2030 from 2005 levels, increase forest and tree cover to provide additional carbon sinks and generate 40 percent of its electricity from non-fossil fuel sources by 2030 with help from the Green Climate Fund. (The Green Climate Fund was established by 194 nations in 2010 with the goal of raising $100 billion a year by 2020 to assist developing countries deal with climate change.)
Brazil will reduce its greenhouse gas emissions 37 percent below 2005 levels by 2025, then by 43 percent below 2005 levels by 2030. Strategies to achieve this include using renewable resources for 45 percent of its energy by 2030, stopping illegal deforestation by 2030, restoring forests and developing sustainable agriculture. It will also implement adaptation policies to make its population, ecosystems, infrastructure and production systems more resilient.
The European Union has committed to reduce greenhouse gas emissions 40 percent from 1990 levels by 2030, in part by getting 27 percent of its energy from renewable energy resources and improving energy efficiency 27 percent by 2030.
Are the climate pledges ambitious enough to meet the goal?
The Climate Action Tracker, an independent scientific analysis, estimates that the climate pledges submitted so far will result in an increase of 2.7˚C of warming by 2100. This is an improvement over the worst-case scenario of a 4.5 to 6° C increase, which is what scientists estimate will result if we continue with business as usual; but it does not get us where we need to go.
However, the goal of remaining under the 2° C mark is targeted for 2100; these first climate pledges extend to 2025 or 2030. Much greater emissions reduction efforts will be needed after 2025 and 2030 to achieve the 2˚C limit. So a five-year periodic review mechanism will be critical to spur countries to set increasingly ambitious goals to reduce emissions.
What would a successful COP21 look like?
COP21 may or may not produce a treaty that legally binds countries to meet their emissions targets. If it does not, this should not be considered a failing, since legally binding treaties can cause countries to make overly modest commitments for fear of falling short, or opt out altogether.
COP21 will be considered a success if it:
- Results in countries agreeing on shared long-term goals to reduce carbon emissions and work towards climate resilience.
- Recognizes that all countries must take action.
- Creates a climate financing arrangement that is acceptable to both developed and developing countries.
- Establishes five-year reviews to encourage countries to continually set more ambitious emissions reduction goals.
- Ensures that countries are transparent about their progress and actions through an effective reporting and verification process.
Why should you care?
COP21 is the best opportunity for the world to finally slow the rate of climate change. Its outcome will affect our lives and those of our children and grandchildren. If successful, COP21 will hopefully help us avert the most disastrous and potentially irreversible effects of climate change. As President Obama said, “We are the first generation to feel the impact of climate change, and the last generation that can do something about it.”
The Laurence M. Gould departed for Punta Arenas last night, taking Colleen with it and leaving Jamie and I on our own until reinforcements arrive in two weeks (you can check out Jamie’s blog here for more on what we’re up to this season). That should work out fine although we’ll be very busy on sampling days – when and if we get sampling days. We were supposed to get out today but the weather isn’t cooperating.
Shortly after the Gould departed the wind started to increase. Right now the Gould is getting 50 kt winds at the southern edge of the Drake Passage (sorry Colleen!), we’re getting a steady 35 kt wind the blew all night and should last through today. I’m nervous about what that will do to our sampling plan. So far the land fast ice where our ice station is has held together; it’s a nearly a meter thick and pretty well anchored to the land. Sometime this season it’s going to give out though, and I’m hoping that we can sample from it a couple more times before that happens.
The flip side is that when the ice goes away we’ll be able to start using the zodiacs to sample at our regular stations, at least until the ice blows back in. The worst case scenario is being in the awkward position of too much ice for the zodiacs, but no solid land fast ice from which to sample. To get an idea of how fast things can change compare the ice conditions in the following pictures to the conditions when the Gould departed:
The fast departure of the ice underscores an important ecological concept that is central to this region. The timing of the switch from ice covered to open water conditions has a major impact on the strength and timing of the spring phytoplankton bloom; the annual ecological event from which everything else derives (think of it like a burst of new green grass in the Serengeti).
In the springtime Antarctic phytoplankton are limited in growth only by the absence of light. Nutrients have been replenishing all winter, there are no grazers around (yet), and the phytoplankton are relatively indifferent to temperature. Right now at Palmer Station we have nearly 18 hours of daylight, what keeps the phytoplankton bloom from exploding right now is the ice. Only 6 % of the light that hits the surface of the fast ice in Arthur Harbor is making its way down into the water. That’s enough to support the growth of specialized ice algae and low-light adapted phytoplankton just below the ice, but not a major bloom deeper in the water column. At just 10 m depth only about 0.01 % of the light that hits the surface remains; it is essentially totally dark.
So as soon as the ice departs the phytoplankton are primed to start growing. In Arthur Harbor the wind is driving the ice away, does this mean a bloom is about to start? Not necessarily. For phytoplankton, what the wind gives it also takes away. A strong wind induces strong vertical mixing in the water column. This impact of vertical mixing on phytoplankton has been studied in places like the North Atlantic for a very long time. Some phytoplankton can swim, but none can swim fast enough to outpace vertical mixing. Under a stiff, sustained wind phytoplankton in the surface are mixed deep into the water column. If they don’t go too deep that’s fine. Below a certain point they can’t photosynthesize enough to meet their metabolic demands (we usually take this to be the 1 % light level), but like all organisms they have energy stores and can wait to get mixed back above this depth. Pushed deep enough however, at what we call the critical depth a phytoplankton cell has insufficient energy stores to make it back to the surface. Under these conditions, although phytoplankton may be growing at the surface, the formation of the bloom will be suppressed.
So what does this have to do with timing? It’s no surprise that the strongest storms happen in the winter. In low sea ice years, with less land fast ice and an earlier retreat of both land fast and pack ice, the surface of the Antarctic ocean is exposed to late winter storms and strong mixing. Phytoplankton that have been overwintering safely in the stable water column below the ice start to grow, but are constantly mixed down below the critical depth. Eventually this stock of phytoplankton is depleted (or much reduced), leaving insufficient numbers to initiate the bloom when conditions finally calm down. This idea has been explored in a number of studies, including this great 1998 paper led by Kevin Arrigo at Stanford and this 2006 study led by Hugh Ducklow at the Lamont-Doherty Earth Observatory. This latter study is particularly interesting because it implicates the Southern Annual Mode (SAM) in determining the strength of the spring bloom. As the plot at right shows it’s clear that SAM isn’t the only thing that determines ice duration, extent, and the strength of the bloom, but it has a clear and logical role.
More recent studies have extended the link between sea ice and SAM to higher trophic levels, including krill. One of my favorite Palmer LTER papers is this 2013 paper by Grace Saba et al., which does a great job of illustrating the link and exploring the idea in the context of climate change. A negative phase in the SAM during the winter and springs leads to low wind and high ice conditions (a double bonus for phytoplanton). These conditions set the stage for a strong bloom and good krill recruitment (a large number of juvenille krill being “recruited” to the sexually mature, adult size class). A positive SAM during the winter and spring leads to low ice, high wind, and a taxonomically different and overall smaller phytoplankon bloom. This leads to fewer krill with a direct negative impact on penguins, seals, seabirds, and whales.
This post is getting long (this is what happens when a sampling day gets weathered out) so I want to end by wrapping it back around to the current season. As I described in a previous post things are a little different this year. The SAM index has generally been positive with some dips into the negative. Only for the month of October was the mean SAM negative, and not very. Despite this there is a definite positive sea ice anomaly. This seems to be driven by the strong, persistent El Niño in the equatorial Pacific that shows no sign of abating any time soon. Regardless of SAM, ice conditions are good this year, in a few weeks we’ll see what that means for the spring bloom when the ice clears out for good!
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.