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Sea ice bacteria review published

Chasing Microbes in Antarctica - Tue, 10/13/2015 - 12:25

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.

Taken from Bowman, 2015. Sampling locations for sea ice studies that have collected community structure data (blue), ecological physiology data (red), and both (orange). Note the strong sampling bias, particularly in the Antarctic. The black arrows point to the locations of the two community structure studies (at the time of writing) that we sufficiently deep to actually describe community structure.

Taken from Bowman, 2015. Sampling locations for sea ice studies that have collected community structure data (blue), ecological physiology data (red), and both (green). Note the strong sampling bias, particularly in the Antarctic. The black arrows point to the locations of the two community structure studies (at the time of writing) that we sufficiently deep to actually describe community structure.

*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.

Bangladesh and India, Too

Geohazards in Bangladesh - Tue, 10/13/2015 - 07:44
Standing in front of the 240-foot tall Qutub Minar, which dates from the 1200s.

Standing in front of the 240-foot tall Qutub Minar, which dates from the 1200s.

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

The inscription on the Iron Pillar, still unrusted despite being 1600 years old. It mentions Chandragupta's conquest of Bengal.

The inscription on the Iron Pillar, still unrusted despite being 1600 years old. It mentions Chandragupta’s conquest of Bengal.

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.

The massive South Gate entrance to the Taj Mahal complex.

The massive South Gate entrance to the Taj Mahal complex.

 

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 Taj Mahal. You can see its enormous size from the line of people waiting to get inside standing on the pedestal. The line completely circled the tomb on this holiday weekend.

The Taj Mahal. You can see its enormous size from the line of people waiting to get inside standing on the pedestal. The line completely circled the tomb on this holiday weekend.

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

The entrance to the Red Fort at Agra, a seat of the Mughal Emperors, and still used as by the Indian military.

The entrance to the Red Fort at Agra, a seat of the Mughal Emperors, and still used as by the Indian military.

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

Standing next to a window in the Agra Fort with a view of the Taj Mahal farther down the Yamuna River.

Standing next to a window in the Agra Fort with a view of the Taj Mahal farther down the Yamuna River.

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.

DSCN4598

A highly decorated marble palace inside the Agra Fort. It has a beautiful fountain built into the floor.

 

Anatomy of an ‘Ice Station’

TRACES of Change in the Arctic - Sun, 10/11/2015 - 19:58
Moving equipment on and off the Healy for sampling requires organization. (photo T. Kenna)

Moving equipment on and off the Healy for sampling requires organization and creativity. (photo T. Kenna)

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!

Sampling on the ice also means being aware of your environment. A required component is the Polar Bear watch. Fortunately we have not seen a polar bear when out on the ice.

Sampling on the ice also means being aware of the environment,  requiring a polar bear watch. Fortunately the team has not seen a polar bear when out on the ice. (Photo T. Kenna)

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.

Tim Kenna collecting a snow sample. The sample area is generally 1 or 2 square meters and collected down to the ice. (Photo B. Schmoker)

Tim Kenna collecting a snow sample. The sample area is generally 1 or 2 square meters , with the snow collected down to the ice surface below and carefully bagged. (Photo B. Schmoker)

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.

Bagging up the snow from the snow station. Each sample is labeled by quadrant of ice collected. (Photo B. Schmoker)

Lamont’s Tim Kenna (r) and Wright State University graduate student Alison Agather (l) bag up snow. Each sample is carefully bagged and labeled by quadrant of ice collected. (Photo B. Schmoker)

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.

Section of sea ice core collected by drilling into the ice. (Photo Cory Mendenhall, USCG)

Section of sea ice core collected by drilling into the ice. As the cores are collected they are photographed, labeled by sections, and ice properties were measured in situ prior to being taken back to the labs. (Photo Cory Mendenhall, USCG)

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.

Surface Melt Pond Team collecting water sample. (Photo T. Kenna)

Surface Melt Pond Team collecting water sample. (Photo T. Kenna)

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.

Pumping water through the hole drilled by auger. (photo B. Schmoker)

The Beryllium team first uses a gas powered auger to create a hole for a pump and a CTD instrument (used to measure salinity, temperature and depth)  to fit through. They then pump water through the hole for collection. Because beryllium is in very small amounts they pump thousands of liters of water from 3 or 4 depths. Each is pumped through big cartridges that absorb the Be. (photo B. Schmoker)

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.

Tim sampling dirty ice. (photo C. Mendenhall).

Tim sampling dirty ice with a pick and bucket. (photo C. Mendenhall).

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.

Microbial ecology of the cryosphere

Chasing Microbes in Antarctica - Wed, 09/23/2015 - 13:38

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.

Taken from Boetius et al., 2015.

Taken from Boetius et al., 2015.  Top: a schematic of different elements of the cryosphere, b: warm, summertime sea ice, c: the supraglacial environment, featuring a meltriver, d: cold winter sea ice, e: the subglacial environment, featuring the Blood Falls outflow from Taylor Glacier.

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!

Arctic Magic – One research vessel multiplies to hundreds!

TRACES of Change in the Arctic - Mon, 09/21/2015 - 16:16
Ship crew is deployed to position the boxes of small 'seaworthy vessels' and the tracking buoy onto the ice. (Photo Bill Schmoker)

Ship crew is lowered in a basket down to the ice to deploy two boxes of small ‘seaworthy vessels’ and the tracking buoy onto the ice, part of the ‘Float Your Boat’ project. (Photo Bill Schmoker)

Geoscientist Tim Kenna works with his son's class to decorate boats for the Float Your Boat project. Jack Kenna works to get his boat 'Arctic ready'.

Geoscientist Tim Kenna works with his son’s fifth grade class to decorate boats for the ‘Float Your Boat’ project. Jack Kenna works to get his boat ready for an Arctic deployment.

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.

A note on the computer station of Tim Kenna announces that it is time to deploy the  'Float Your Boat' project.

Sometimes the best way to deliver information on a ship is to tack up a sign on a high use item. A note on the computer station of Tim Kenna is used to notify him that it is time to deploy the ‘Float Your Boat’ project. (Of course smiley faces always help!)

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.

The location of the Arctic drift boats was close to the North Pole. In many earlier years his would have been an area that was inaccessible for a ship to penetrate to set up this drifter experiment.

The location of the Arctic drift boats was close to the North Pole. In many earlier years this area would have been inaccessible for a ship to penetrate to set up this drifter experiment.

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.

Boxes one and two are deployed on the ice with the tracker and the sip crew is pulled back up to the Healy. (Photo T. Kenna)

Boxes one and two are deployed on the ice with the tracker and the ship crew is pulled back up to the Healy. (Photo T. Kenna)

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)

Annotated historic map from the International Geophysical Year (1957-1958) of the Floating Arctic Stations. Red line shows Alpha Station, the US first floating ice research station, representing some of the original 'Arctic drift studies'. (Photo/annotation M. Turrin; map Ken Hunkins)

Annotated historic map of the Floating Arctic Stations, from the International Geophysical Year (1957-1958) . The red line shows Alpha Station, the US first floating ice research station, and one of the original ‘Arctic drift studies’. (Photo/annotation M. Turrin; map Ken Hunkins)

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.

Float Your Boat 'vessels' were loaded into boxes and shipped to the Healy in advance of the deployment.

Float Your Boat ‘vessels’ were loaded into boxes and shipped to the Healy in advance of the deployment.

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’.

Tim Kenna is shown here on the right with Marty Fleischer on the left at the North Pole. Tim  worked with several groups of local students including  Pearl River High School A.P. Environmental Science Students and his son's fourth grade class at Upper Nyack Elementary School. 

Tim Kenna is shown here on the right with Marty Fleisher on the left at the North Pole. Tim worked with several groups of local students including Pearl River High School Marine Science Club and his son’s fifth grade class at Upper Nyack Elementary School in the ‘Float Your Boat’ project for GEOTRACES.

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.

And now…

Chasing Microbes in Antarctica - Wed, 09/16/2015 - 00:24

…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[1] == sex: if len(start_letters) > 0: if line[0][0] in start_letters: n = float(line[2]) p.append(float(n)) names.append(line[0]) else: n = float(line[2]) p.append(float(n)) names.append(line[0])

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)

figure_1Ignore 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[0] 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

A Week of Firsts for This Arctic Nation

TRACES of Change in the Arctic - Fri, 09/11/2015 - 18:06
47 AM the ship reached the North Pole, becoming the 1st U.S. surface vessel to do so unaccompanied. (photo U.S. COAST GUARD)

Gathered at the North Pole are the crew of U.S. Coast Guard Cutter Healy and the GEOTRACES science team. On Sept. 5 at 7:47 a.m., the ship reached the North Pole, becoming the first U.S. surface vessel to do so unaccompanied. Photo: U.S. Coast Guard

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.

GLACIER Conference logo

GLACIER Conference logo

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.

Ship camera as the US Cutter Healy arrives at the North Pole. (Photo US Healy)

Ship camera as the U.S. Cutter Healy arrives at the North Pole. Photo: U.S. Healy)

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.

Members of the team who are not out on deck with the equipment 'manage' the cast from the aft control room. (photo T. Kenna)

Members of the team who are not out on deck with the equipment “manage” the cast from the aft control room. Photo: T. Kenna

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.

The 'man-basket' lowering Tim Kenna and crew member to the ice via crane to do sampling from a pressure ridge. (photo Bill Schmoker)

The “man-basket” lowering Tim Kenna and crew member to the ice via crane to do sampling from a pressure ridge. Photo: Bill Schmoker

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.

It’s as Clear as Mud

TRACES of Change in the Arctic - Sun, 09/06/2015 - 21:30
Core sample

Attempting to get a small sediment sample from the bottom of the Arctic. Photo: Bill Schmoker

Sediment coring the bottom of the world’s oceans is something that Lamont knows a lot about. Since 1947 Lamont has been actively collecting and archiving sediment from around the world. Currently our Core Repository contains sediment cores from every major ocean and sea in the world, some 18,700 cores. This is in large part due to Lamont’s first director, Maurice Ewing, who instilled a philosophy of “a core a day” for all ocean research vessels. Ewing firmly believing that if we had the sediment, we would be able to piece together patterns and stories about our planet, so every day at noon, or thereabouts, the ship would collect a core.

core repository

Historic Image of Lamont’s Core Repository. Photo: Lamont archive

Scientists from around the world have requested slivers of mud from the cores in the repository to unlock Earth’s mysteries and secrets. The cores in Lamont’s Core Repository are no stranger to revealing stories of Earth systems, including those of climate cycles. Almost 40 years have passed since the groundbreaking work of the CLIMAP group that used the cores to connect the start of Earth’s glacial cycles to changes in eccentricity, precession and tilt. (Hayes, Imbrie and Shackleton, 1976) . Collecting sediment on this Arctic GEOTRACES cruise will help us understand more of the stories locked in the oceans.

The length of a core is dictated by the goal of the collection. Early Lamont cores were more about collecting just to gather the material because the ship was there. These early cores were generally 6 to 9 meters long, although one incredibly long 28.2m core was collected from the Central Pacific. Locally cores have been collected on the Hudson River and local marshes that are closer to 1 or 2 meters in length.

Coring in the Hudson River

A file photo of Tim Kenna collecting a sediment core from the Hudson River. Note the length of core and the heavy weights on top to help with penetrating deep into the mud on the bottom of the Hudson. The very short cores to be collected for GEOTRACES will be much different. Photo: Margie Turrin

For the sampling GEOTRACES is doing in the Arctic, there is a specific goal of collecting just the top few dozen centimeters of sediment and the water just above it, yet at a depth of ~2,200 meters. This will require a much different technique than what was used for the Central Pacific core.

core

Mono-corer with the small section of core retrieved. Note the small weights to help penetrate the sediment, much less weight than is used on the Hudson River core pictured above. Photo: Bill Schmoker

The sediment in this region is soft, so the plan was to drop a small, general-purpose device called a mono-corer over the side of the ship with a few small weights on top to help drive the core tube in straight. The corer would hang below the bottom of the rosette of water samplers, far enough below that the rosette would remain mud-free but still able to collect near-bottom water samples. The mud in the mono-corer would be held in place by a spring-loaded door that snapped closed once the mud was inside and the tube began its return trip to the ship. All sounded good.

core

Core on its way up to the Healy. Note the “cone-of-silence” rigged by Tim Kenna and Marty Fleicher to stop any interference with the rosette altimeter used to lower the device. Photo: Bill Schmoker

Although the plan was good, things don’t always go perfectly. Making sure the corer actually penetrated the sediment without tipping over or over-penetrating and compressing the top sediments proved challenging, as did ensuring the sample made it back to the ship intact. After several attempts a special “cone-of-silence” (any Get Smart fans out there?) was rigged up by the two Lamonters, Tim and Marty Fleischer, to avoid interference with the communications that were connecting with the rosette altimeter, controlling the lowering of the device. The cone was installed and the speed of the core lowering was slowed. Success! ‘Houston we have mud!’

Now to unpack its secrets.

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.

Scouring Arctic for Traces of Fukushima and Cosmic Rays

TRACES of Change in the Arctic - Sat, 08/29/2015 - 21:50
ice breaker

The Healy is doing a lot more ice breaking now that we have moved into the Arctic ice cap. Photo: Tim Kenna

Sounds like the basis for a great scifi thriller… “scientists scour Arctic, hunting for traces of nuclear fallout and ejections from cosmic ray impacts.” In reality this thriller theme is the actual core of the GEOTRACES mission. Let’s break it apart a bit to better understand it.

Fukushima and Other Nuclear Fallout

The project Tim is focused on is the human introduced (anthropogenic) radionuclides that are released into the environment as a result of nuclear industrial activities, things like weapons production and testing, as well as nuclear power generation and fuel reprocessing. This includes isotopes of plutonium, neptunium, cesium, strontium, iodine and uranium that are not normally found in the environment. The major sources of these nuclides include fallout from atmospheric weapons testing and liquid releases from European nuclear fuel reprocessing.

Radionuclides lab

The workspace set aside for the radionuclides work. If you have ever done “Where’s Waldo?” see if you can find Tim’s spot. Photo: Tim Kenna

One goal of our project is to determine the budgets (overall input and export) of these contaminants. Samples collected along our cruise track combined with those collected on the European GEOTRACES cruise taking place on the Polarstern will allow us to do this.

We are also collecting samples to evaluate for the presence and distribution of contamination related to Fukushima. Two cesium isotopes were released into the environment as a result of Fukushima; Cesium 137, with a half-life of 30 years, and Cesium 134, with a much shorter half life of two years, so little is left from past nuclear testing. Fallout from Fukushima is an excellent tracer to help us learn more about ocean circulation and transport models.

Cosmic Ray Interactions

Paul Aguilar

Paul Aguilar, part of the Beryllium 7 sampling team, signals thumbs up to the winch operator on a hydrocast. Hand signals are a major method of communication between ship operators and scientists and crew on deck. Photo: Tim Kenna

Another part of the GEOTRACES team is measuring Beryllium-7 (Be-7), a cosmogenic nuclide that is created when a cosmic ray breaks apart heavier atoms into smaller atoms. Be-7 is a short-lived isotope with a half-life of 53 days. We can use this short half-life to tell us something about water circulation and exchange rates under the ice. Currently the team is measuring Be-7 in the marginal ice zone. Once the ship reaches a section of ice that is large and thick enough for the scientists to work on, we will drill through to measure under the ice as well.

Yes We Have a Bubble Room!

bubble room

Jess and Sarah work in the heavily protected bubble room to keep their samples from being contaminated by elements on the ship. Photo: Tim Kenna

When we said “trace” elements we weren’t kidding! Jess and Sara are part of the team working on contamination-prone trace elements. Their work is done in an inflatable bubble to keep it ultra clean. The bubble is inflated using high-efficiency particulate arresting (HEPA) filtered blowers. Trying to measure very small trace elements without contamination is extremely difficult, and it is a testament to their skills that they can measure elements such as zinc and iron, which are extremely low in seawater but very common on the ship (rust never sleeps!). Getting an accurate measure means not picking up any of that ship input.

caught wires

Sampling in and among the ice floes can mean equipment wires get caught on the ice, as happened here. It can be tricky to untangle caught wires to free equipment. Photo: Tim Kenna

In order to run all these great experiments, we need samples, so we are collecting and filtering water at as many stations as we can. Sampling in the ice pack is very different than sampling in an open ocean. Station locations must be very carefully selected to reduce the risks of the equipment getting entangled in the ice and ending up either crushed or ripped away. Even in less dense ice, we caught the hydrowire on an ice floe (above).

Supersized

Everything is supersized on a ship like the Healy, from the large metal A-frame support that is used to lower collection equipment (yellow/buff colored) to the circular metal rosette which is filled with niskin collection bottles for gathering water samples. The deployment of a rosette for sampling is called a “hydrocast.” This allow scientists to collect water at a variety of depths. The images below are from a few days ago, before we hit denser pack ice.

hydrocast

You can see if you look carefully at the photos that these bottles have snapped closed, sealing the water sample inside. When deployed the bottles are opened at both ends so water freely flows through as the rosette descends to the sample depth. Photo: Tim Kenna

The rosettes can hold up to 36 bottles. Each bottle can be programmed to snap closed at a specific depth, so in one deployment, water can be collected at up to 36 different depths. This is extremely valuable for teasing apart circulation through tracking small particles entrained in the water column at different depths. The water collected in these sampling bottles will be used for a range of studies.

hydrocast

The rosette takes several people to stabilize and guide it over the side of the ship, and the A frame is several stories high. Photo: Tim Kenna

This sequence of the retrieval of this hydrocast involves four people to collect and stabilize the rosette, as well as the personnel up above operating the winch to lower the equipment, and several people in a console monitor verifying both the depth of the rosette and that the cable on the equipment is sending up the necessary data. Operating the equipment on a ship is labor intensive, but each deployment retrieves enough sample material for not only the team on board the Healy, but for colleagues and partners waiting back at their home institutions for samples.

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.

 

Moving into the Realm of the Polar Bear

TRACES of Change in the Arctic - Mon, 08/24/2015 - 18:15
Looking out over the Arctic sea ice as the ship moves out over the deeper ocean. (Photo credit Tim Kenna)

Looking out over the Arctic sea ice as the ship moves out over the deeper ocean. Photo: Tim Kenna

The Healy has now moved off of the shallow continental shelf that extends around the Arctic land border (shown in white in the map below) into the deeper center of the Arctic Ocean. In our last blog we noted that some of the questions Arctic GEOTRACES is addressing include quantifying the fluxes of trace elements and isotopes into and out of the Arctic Basin from the two oceans through choke points like the Bering Strait, as well as characterizing how much comes from rivers. Arctic GEOTRACES is also studying what regulates the Arctic shelf to deep basin exchange, and the role of sea ice in the transport of trace elements and isotopes. (Follow the expedition here.)

The position of the research vessel Coast Guard cutter Healy on August 24, 2015.

The position of the research vessel Coast Guard cutter Healy on Aug. 24, 2015.

The oval shaped blue area in the map above is the basin of the Arctic Ocean, ranging from ~3,500 meters to ~5,000 meters at its deepest. The Healy is currently over a ridgeline named the Mendeleev Ridge, after a Russian chemist and inventor, Dmitri Mendeleev, long dead when the ridge was first discovered by fellow Soviets in 1948. Mendeleev Ridge is about 1,000 meters shallower than the deep Arctic, bottoming out at ~2,500 meters in depth. The Russians maintain that the ridge, with its long reach into the Arctic basin, gives them claim to large sections of the ocean stretching out to the North Pole. The claim remains unresolved, in part because there are so many questions that still remain about the Arctic. As we move into the basin, we will be sampling to try and better constrain what happens at the shelf/basin interface.

polar bear text

All hands on deck alert – huge polar bear 100 yards ahead! Photo: Tim Kenna

When we venture into the Arctic for research, for most of us there is the lingering hope that a polar bear will appear on our watch; at least as long as we are safely outside of its reach. Several polar bear have been spotted by the watchful eyes of the crew as we have moved into the more tightly packed heavy ice away from the marginal ice zone. However, today a very large bear (yes the alert text says “huge”!) was spotted, and it seemed to have us under thoughtful consideration. The following is a string of images that relay the majesty of this incredible creature in its natural environment, moving with great agility over the sea ice.

 Tim Kenna

Polar bear taking a drink and assessing the ship full of researchers. Photo: Tim Kenna

Polar Bear (photo credit Tim Kenna)

Polar bear carefully testing the thinning stretch of sea ice.  Photo: Tim Kenna

Polar Bear (photo credit Tim Kenna)

The polar bear coloring matches easily to the Arctic ice surroundings. Photo: Tim Kenna

Polar bear live only in the Arctic and rely almost entirely on the marine sea ice environment for their survival. They use the ice in every part of their daily life, for travel, for hunting ringed seal, their favorite food, for breeding and in some cases for locating a birthing den. Their wide paws, which you might be able to see in these photos, distribute their weight when they walk on the sea ice, which late in the season can be quite thin in the annual ice region, melting down to only a thin crust over the water. Their large size, clearly visible in these photos, belies the fact that they are excellent swimmers, helped by their hollow fur, which traps air to keep them buoyant, as well as the stiff hair and webbing on their feet. For all their cuddly appearance, they are strong hunters. Currently polar bear range in conservation status from Vulnerable internationally, to Threatened in the U.S., primarily the result of a warming climate that is melting their habitat…sea ice.

Polar Bear moving easily across the ice. (photo credit Tim Kenna)

Polar bear move easily across the ice, even though males can weigh up to 1,500 lbs. Photo: Tim Kenna

Polar bear

Polar bear use their natural agility to avoid the thinner sections of sea ice. Photo: Tim Kenna

Polar Bear takes measure of the Healy. (Photo credit Tim Kenna)

Polar bear takes measure of the Healy. Photo: Tim Kenna

Polar bear taking a moment to drink. (Photo credit Tim Kenna)

Polar bear taking a moment to drink from an open lead in the Arctic. Photo: Tim Kenna

Arctic Sea Ice Extent

Daily Arctic sea ice extent Aug. 23, 2015. Source: National Sea Ice Data Center

The Arctic is approaching the annual low for sea ice extent, which occurs each year in September. An image of sea ice extent for today (shown in white) against an average of the last thirty years (outlines in yellow) shows how our annual sea ice cover has dropped. Today’s cover is 2.24 million square miles (5.79 million square kms), which is  521,200 sq. miles (1.35 million square kms) below the last 30 year average period. Aside from being of concern to the polar bear, this is part of why Arctic GEOTRACES is so important. We need to understand the role of sea ice in current circulation patterns and delivery of trace elements and isotopes in the Arctic, and then bring this more complete understanding forward to our careful examination of the changing Arctic.

Tim Kenna captures himself in the field surrounded by Arctic sea ice. (photo credit Tim Kenna)

Tim Kenna captures himself in the field surrounded by Arctic sea ice.

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.

Tracing the Arctic

TRACES of Change in the Arctic - Wed, 08/19/2015 - 00:07
Leaving Dutch Harbor

The U.S. Coast Guard cutter Healy leaving Dutch Harbor, Alaska, and heading to the high Arctic for the GEOTRACES research cruise. It doesn’t take long to move from a landscape of steep carved cliffs to one of endless waves on an Arctic passage. Photo: T. Kenna

Dutch Harbor Alaska is located on that long spit of land that forms the Aleutian Islands of Western Alaska. Research vessels launch from this location and head northeast into the Bering Sea on their way to the Bering Strait, the gateway to the Arctic.

map of Dutch Harbor

Dutch Harbor, Alaska (from http://www.vacationstogo.com)

Our research cruise is part of the international Arctic GEOTRACES program, which this summer has three separate ships in the Arctic Ocean. The Canadian vessel headed north in early July, and the German vessel will follow a week behind the Healy. Each will be following a different transect in the Arctic Ocean to collect samples. The U.S. vessel has 51 scientists on board, each with a specific sampling program. We will focus our time in the western Arctic, entering at the Chukchi Sea. (Follow the expedition here.)

What is GEOTRACES studying? The program goal is to improve our understanding of ocean chemistry through sampling different trace elements in the ocean waters. Trace elements can be an asset or a liability in the marine system, providing either essential nutrients for biologic productivity, or toxic inputs to a rapidly warming system. This part of the larger program is focused on the Arctic Ocean, the smallest and shallowest of the world’s oceans and the most under siege from climate change. Results from this cruise will contribute to our understanding of the processes at work in the Arctic Ocean, providing both a baseline of contaminants for future comparisons as well as insights into what might be in store for our future.

The land surrounding the Arctic Ocean is like a set of cradling arms, holding the ocean and the sea ice in a circular grasp. Within that cradle is a unique mix of waters, including freshwater from melting glacial ice and large rivers, and a salty mix of relatively warm Atlantic water and cooler Pacific water. Our first sample station lasts over 24 hours and focuses on characterizing the chemistry of the water flowing into the Arctic from the Pacific Ocean. This is critical for locking down  the fluxes and totals of numerous elements in the Arctic.

Map of sea ice

Daily map from the ship showing sea ice cover. Yellow is the marginal ice, and the red is heavy ice. The location of the Healy is visible at the lower edge of the photo at the edge of the red dot.

In the past the “embrace” of the Arctic land has served as a barrier, holding in the sea ice, which is an important feature in the Arctic ecosystem. In 2007, however,  winds drove large blocks of sea ice down the Fram Stait and out of Arctic. In recent years the Arctic sea ice has suffered additional decline, focusing new attention on the resource potential of this ocean.

Unexpectedly this year, the sea ice is projected to be thick along the proposed cruise track, thick enough that it might cause the ship to adjust her sampling plan.

Walrus

Walrus resting on Arctic sea ice. Photo: T. Kenna

The walrus in the above image are taking advantage of the Arctic sea ice. Walrus use the ice to haul out of the water, rest and float to new locations for foraging. Walrus food of preference is mollusks, and they need a lot of them to keep themselves satisfied, eating up to 5,000 a day, using the sea ice as a diving platform. As the ship moves further from shore, we will lose their company.

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.

Introducing PAPRICA

Chasing Microbes in Antarctica - Tue, 08/18/2015 - 14:00

I’m very excited to report that our latest paper – Microbial communities can be described by metabolic structure: A general framework and application to a seasonally variable, depth-stratified microbial community from the coastal West Antarctic Peninsula was just published in the journal PLoS one.  The paper builds on two very distinct bodies of work; a growing literature on microbial community structure and function along the climatically sensitive West Antarctic Peninsula, and a family of new techniques to predict community metabolic function from 16S rRNA gene libraries, which we are calling metabolic inference.

The motivation for metabolic inference is in the large amount of time that it takes to manually curate a likely set of functions for even a small collection of 16S rRNA genes.  In today’s world, where most analyses of microbial community structure consist of many thousand of reads representing hundreds of taxa, it is simply impossible to dig through the literature on each strain to see what metabolic role each is likely to be playing.  Ideally a researcher would use metagenomics or metatranscriptomics to get at this information directly, but it is not advisable or desirable in most cases to sequence hundreds of metagenomes or metatranscriptomes (necessary for the kind of temporal or spatial resolution many of us want these days).  Metabolic inference provides a convenient alternative.

A quick Google Scholar survey of the number of studies since 2005 that have used high throughput 16S rRNA gene sequencing.

A quick Google Scholar survey of the number of studies since 2005 that have used high throughput 16S rRNA gene sequencing.  Over the last ten years we’ve collected an astonishing amount of sequence data from a diverse array of environments, however, much of this data has been from taxonomic marker genes like the 16S rRNA gene, leaving microbial community function largely unknown.  PAPRICA and other methods that try to infer microbial functional potential from 16S rRNA gene data can help bridge this gap.

The basic concept behind all metabolic inference techniques (e.g. PICRUSt, tax4fun, PAPRICA) is hidden state prediction (HSP) (you can find a nice paper on HSP here).  In 16S rRNA gene analysis metabolic potential is a hidden state.  The metabolic inference techniques propose different ways to predict this hidden state based on the information available.

Our small contribution to this effort was to develop a method (PAPRICA – PAthway PRediction by phylogenetIC plAcement) that uses phylogenetic placement to conduct the metabolic inference instead of an OTU (operational taxonomic unit) based approach.  Our approach provides a more intuitive connection between the 16S rRNA analysis and the HSP (or at least it does in my mind) and can increase the accuracy of the inference for taxa that have a lot of sequenced genomes.

Most analysis of large 16S rRNA datasets rely on an OTU based approach.  In a typical OTU analysis an investigator aligns 16S rRNA reads, constructs a distance matrix of the alignments, and clusters the reads at some predetermined distance.  By tradition the default distance has become a dissimilarity of 0.03.  This approach has some advantages.  By clustering reads into discrete units it is easy to quantify the presence or absence of different OTUs, and it allows microbial ecologists to avoid problems with defining prokaryotic species (which defy most of the criteria used to define species in more complex organisms).  To conduct a metabolic inference on an OTU based analyses it is possible to simply reconstruct the likely metabolism for a predefined set of OTUs based on the OTU assignments of published genomes.  This works great, but it limits the resolution of the inference to the selected OTU definition (i.e. 0.03).  For some taxa, such as Escherichia coli (and plenty of more interesting environmental bugs), there are many sequenced genomes that have very similar 16S rRNA gene sequences.  PAPRICA provides a way to improve the resolution of the metabolic inference for these taxa.

Our approach was to build a phylogenetic tree of the 16S rRNA genes from each completed genome.  For each internal node on the reference tree we determine a “consensus genome”, defined as all genomes shared by all members of the clade originating from the node, and predict the metabolic pathways present in the consensus and complete genomes using Pathway-Tools.  To conduct the actual analysis we use pplacer to place our query reads on the reference tree and assign the metabolic pathways for each point of placement to the query reads.  One advantage to this approach is that the resolution changes depending on genomes sequence coverage of the reference tree.  For families, genera, and even species for which lots of genomes have been sequenced resolution is high.  For regions of the tree where there are not many sequenced genomes resolution is poor, however, the method will give you the best of what’s available.

Fig_2

Figure from Bowman and Ducklow, 2015.  PAPRICA includes a confidence scoring metric that takes into account the relative plasticity of different genomes.  In this figure each vertical line is a genome (representing a numbered terminal node on our reference tree), with the height and color of the vertical line giving its relative plasticity (which we refer to as the parameter phi).  The genomes identified with Roman numerals are all known to be exceptionally modified, which is a nice validation of the phi parameter.  Many of these are obligate symbionts.  I) Nanoarcheum equitans II) the Mycobacteria III) a butyrate producing bacterium within the Clostridium IV) Candidatus Hodgkinia circadicola V) the Mycoplasma VI) Sulcia muelleri VII) Portiera aleyrodidanum VIII) Buchnera aphidicola, IX) the Oxalobacteraceae.

PAPRICA provides some additional helpful pieces of information.  We built in a confidence scoring metric that takes into account both predicted genomic plasticity and the size of the consensus genome relative to the mean size for the clade (deeper branching clades will have a bigger difference), and predicts the size of the genome and number of 16S rRNA gene copies associated with each 16S rRNA gene, both of which have a strong connection to the ecological role of a bacterium

For our initial application of PAPRICA we selected a previously published 16S rRNA gene sequence dataset from the West Antarctic Peninsula (our primary region of interest).  One thing that we were very interested in looking at was whether we could describe differences between microbial communities organized along ecological gradients (e.g. inshore vs. offshore, or surface vs. deep water) in terms of metabolic structure in place of the more traditional 16S rRNA gene (i.e. taxonomic) structure.  Using PAPRICA to convert the 16S rRNA gene sequences into collections of metabolic pathways we found that we could reconstruct the same inter-sample relationships identified by an analysis of taxonomic structure.  This means that a microbial ecologist can, if they choose, disregard the messy and sometimes uninformative taxonomic structure data and go directly to metabolic structure without losing information.  Applying common multivariate statistical approaches (PCA, MDS, etc.) to metabolic structure data yields information like which pathways are driving the variance between sites, and which are correlated with what environmental parameters.  This information is much more relevant to most research questions than the distribution of different microbial taxa.  It is worth noting that while inter-sample relationships are well preserved in metabolic structure, the absolute distance between samples is much less than for taxonomic structure.  This might have some implications for the functional resilience of microbial communities, which we get into a little bit in the paper.

PAPRICA was an outgrowth of a couple of other papers that I’m working on.  At some point the bioinformatic methods reached a point where separate publication was justified.  As a result, and reflecting the fact that I’m much more an ecologist than a computational biologist, PAPRICA is not nearly as streamlined as PICRUSt (which is even available through an online interface).  I’ve spent quite a bit of time, however, trying to make the scripts user friendly and transportable.  Anyone should be able to get them to work without too much difficulty.  If you decide to give PAPRICA a try and run into an hitches please let me know, either by posting an issue in Github or emailing me directly!  Suggestions for improvement are also welcome.

Smooth Sailing Back to Tasmania

Melting Glaciers-Tracking Their Path - Fri, 05/01/2015 - 10:12
Antarctica, NBP1503 science team

The NBP1503 science team.

After a surprisingly smooth crossing of the Southern Ocean, with favorable winds we arrived back in Hobart, Tasmania. The weather maps show that we just got ahead of another big storm system.

Once the equipment is stored away and the samples are loaded off, we will all head back to our offices and labs to further process and analyze our data and eventually put all the results together.

Taking a 4,000-Meter-Deep Profile of Antarctic Waters

Melting Glaciers-Tracking Their Path - Mon, 04/27/2015 - 10:47
NB Palmer, West Antarctica, CTD system

The CTD system is lowered over the side from the NB Palmer. It measures temperature, salinity, and oxygen with depth.

In addition to understanding potential pathways for “warmer” circumpolar deep water to reach the ice shelf, we are also measuring what the structure and properties of the water column are and determining if there is already warmer water on or near the continental shelf that could already interact with the glaciers of East Antarctica today.

To measure water properties, we are using an instrument that can be lowered through the water column that measures conductivity, from which we calculate the salinity of the water, temperature, pressure (i.e. water depth), oxygen, and fluorescence, which is an indicator for phytoplankton or algae in the water. This system is called a CTD for short.

This system can also take water samples from different depths that can be used for further analysis or for calibration and verification of the sensors. When we lower this system in deep water, e.g. 4000 meters, (about 2.5 miles), the measurements take over three hours.

We have measured the water properties at 42 different locations during our expedition and will analyze the results carefully when we are back.

Follow @FrankatSea for additional updates and images from the Southern Ocean.

Mapping the Seafloor

Melting Glaciers-Tracking Their Path - Mon, 04/20/2015 - 11:53
In addition to depth, we can identify many features in the high-resolution multibeam data that we produce. Most of the seafloor near the shelf break (where the water is between 300 and 500 meters deep) is covered with these irregular furrows that are created when large icebergs are grounded here.

In addition to depth, we can identify many features in the high-resolution multibeam data that we produce. Most of the seafloor near the shelf break (where the water is between 300 and 500 meters deep) is covered with these irregular furrows that are created when large icebergs are grounded here.

One of the goals of this expedition is to investigate if water from the Southern Ocean with temperatures above the melting point of glaciers could reach the glaciers in East Antarctica, and if there are any obstacles on the seafloor of the shelf that impact the ability of such water to reach the glaciers and ice streams.

The continental shelf in our study areas along the East Antarctic margin has been mapped in the past, but the existing data are very sparse and have many gaps. However, it is important to know the actual water depth of the continental shelf if we want to understand if water from the Southern Ocean with temperatures above the melting point could reach any glaciers and ice streams in this part of Antarctica.

We use a multibeam echosounder system installed on the Nathaniel Palmer to map the depth of a wide swath of the seafloor along our ship track. Access to the continental shelf is often limited by dense ice cover, but using the multibeam, we have managed to determine detailed depths in several areas. We will later analyze the depth data together with measurements of water column properties that will tell us exactly how deep the “warmer” Southern Ocean water is.

Follow @FrankatSea for additional updates and images from the Southern Ocean.

In the Ice

Melting Glaciers-Tracking Their Path - Fri, 04/10/2015 - 09:12
 The Nathaniel B. Palmer steaming through dense sea ice cover.

Some examples of the sea ice that we have encountered so far. Top left: bands of grease ice. Top right: small pancake ice merged together. Bottom left: larger pancake ice; bottom right: our ship, the Nathaniel B. Palmer, steaming through dense sea ice cover.

Several days ago we reached our main work areas along the margin of East Antarctica. Our expedition is relatively late in the season and the seas around Antarctica are starting to freeze. While the abundance of sea ice makes it more difficult to get to all of our research areas, the different shapes and forms of newly forming sea ice are a great visual experience. We also have a group of Australian scientists aboard the Palmer who are studying sea ice and sea ice formation using an unmanned aerial system or drone, so they are especially pleased by our icy experience.

Follow @FrankatSea for additional updates and images from the Southern Ocean.

Closing in on Antarctica

Melting Glaciers-Tracking Their Path - Mon, 04/06/2015 - 11:29
During our transit south to Antarctica we deployed seven ARGO floats (yellow device in picture) for the University of Washington. They drift with the currents in the oceans, measure profiles of salinity and temperature and send those via satellite to researchers on land. They are part of an international effort to better monitor the conditions of the oceans.

During our transit south to Antarctica we deployed seven ARGO floats (yellow device in picture) for the University of Washington. They drift with the currents in the oceans, measure profiles of salinity and temperature and send those via satellite to researchers on land. They are part of an international effort to better monitor the conditions of the oceans.

We are less than a day away from our first study area on the continental shelf in front of the Dibble Glacier. As we approach Antarctica we are starting our science program with a 4500 meter deep CTD and multibeam acquisition. The CTD is used to determine the conductivity, temperature and depth of the ocean, while the multibeam maps large swaths of the seafloor from the ship.

The main goal of our project is to investigate the continental shelf in front of different glaciers along East Antarctica. We want to find out what the water depths and the water properties are in front of these glaciers and ice streams. Deep troughs and connections between the glaciers and the open ocean could allow “warmer” ocean waters to reach the ice front and result potentially in melting of the ice. We are especially interested to compare the situation in front of different glaciers along East Antarctica to better understand the differences between them. Many of these areas are poorly charted, if at all. So we are all excited to discover what is there!

Follow @FrankatSea for additional updates and images from the Southern Ocean.

Sunrise...Sunset...Sunrise...Sunset...

The ENAM Seismic Experiment - Sun, 04/05/2015 - 03:46
A compilation of sunrise and sunset photos aboard the R/V Endeavor. 

Day 3 sunset

Day 4 sunset

There is a bizarre foggy mist across the entire surface of the ocean.

This was a huge cargo vessel off in the distance. I know it isn't a sunrise or sunset but its a sweet pic.

Day 6 sunrise with a storm front in the distance.

Panorama of Day 6 sunrise.

Porthole sunset with my refection.

First bit of sunset color directly off the bow of the Endeavor.

about 20mins later....





Terry Cheiffetz




Go Endeavor Go! Nighttime Adventures...

The ENAM Seismic Experiment - Sun, 04/05/2015 - 02:25
A unique low light vantage point of the Endeavor

A look at all the instrumentation on the bridge of the R/V Endeavor. 

The full moon as it shines over the ocean water! Creepy!

The OBS retrieval at night! One of the crew members installed a light at the end of the hook to aid in the equipment capturing process. 


This picture was take from the bridge of the Endeavor. It is the Quantum of the Seas cruise ship at ~0300 during an OBS retrieval. 
This picture is ~2 miles away from the Quantum of the Sea cruise ship and is as close as the Endeavor can legally pass another large ocean vessel under maritime law. The bright celestial object overhead is Jupiter.

This photo shows the Endeavor docked at port just before we embarked on this high seas adventure. The first evening we went to a chinese restaurant called 7 moons. By the time we arrived back at the shipyard the gate had been pulled shut and appeared to be locked and was topped with plenty of barbed wire. After some deep thought our highly intelligent group realized that it was pulled closed and all we had to do was roll it open haha. There is a geophysicists joke embedded in that experience. 

This is the WHOI crew carefully bringing the OBS back onto the ship. Hard hats and life preservers are required when on deck during retrieval operations. The OBS in this photo is hanging down beneath the orange apparatus.  

As the Endeavor aligns itself with the OBS in the ocean currents at night the WHOI crew get in position to capture the Ocean Bottom Seismometer. 


After a successful OBS capture the WHOI crew quickly disassembles the OBS and prepares it to be stacked with the other equipment that is strongly secured to the surface of the deck. 

This shows the spotlight at night. It is used to help orient the ship alongside the OBS in the pitch black darkness of the night at sea. We have also thankfully had the full moon over the last few days to assist us in finding the OBS once it pops up to the surface.

This lovely burry image is the spot light as it tracks the OBS. The spotlight is extremely useful once the OBS is within several ship lengths of distance. 


The OBS is starting to get closer now....

Full moon over a perfect OBS recovery.

Hammock in the middle of the night!

You can really get a good feel for spotting the OBS at night in this picture. It is obviously a ship length or two off the starboard bow. 





Terry Cheiffetz







  

Survival Suits to the Rescue!

The ENAM Seismic Experiment - Sat, 04/04/2015 - 16:20
Before the R/V Endeavor embarks on its research voyage the new crew/scientists get to enjoy the challenge of a mock sinking scenario where they have ~2mins to jump out of their shoes and wiggle into these fashionable lobster costumes.  

Dr. Maureen Long and one of the crew members race each other to safety!

Graduate Student intern Colton Lynner is almost unrecognizable once the survival suit is fully on. Only the last troublesome step up zipping up to go before full emersion can take place. 

Graduate Student intern Terry Cheiffetz struggles with the final zipper step as well. 

Dr. Maggie Benoit looks like she wants to really know how to put on the survival gear in case of emergency or... she can't believe she has to participate in these fun shenanigans.


The final product appears to be both fashionable and comfortable. We would interview the model in this photo but he declined to comment....hopefully next years model will have a mouth hole haha!



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