Southern Ocean GasEx Blog

Dispatches from the Southern Ocean Gas Exchange Experiment

Shake and Bake!

Posted by sogasex on April 4, 2008

By Ludovic Bariteau, CIRES/NOAA PSD

Among the numerous measurements made on the ship are the flux measurements. I have learned and simplified this flux recipe from Chris Fairall, my spiritual Guru.

Yield Unlimited servings

Time About 45 days

Ingredients required for determination of air-sea fluxes:

  • Wind speed and direction
  • Air temperature and humidity
  • Atmospheric pressure
  • Downward shortwave and longwave radiations
  • Rainfall
  • Sea surface temperature
  • CO2, DMS and Ozone

Utensils and Personnel used for the GasEx recipe

  • A ship, the RHB.
  • 4 cooks. Persons used on this project are: Ale, Dr Zap, Byron and I.
  • On the foremast: 3 sonic anemometers, 3 motion packs, 5 Licors 7500 (fast CO2/hygrometer), 3 mean RH/T (Relative Humidity/Temperatures) sensors and an optical rain gauge.
  • 4 Eppley radiometers setup on a wood pole
  • 3 Licors 6262
  • 1 fast ozone instrument and 1 fast DMS instrument with the sampling inlets located on the jackstaff
  • A bunch of data loggers, computers, cables, tie wraps…

The previous sensors used for fluxes have been adapted for observations over the ocean. They are designed for marine applications and thus are protected from the corrosive effect of sea salt and spray. These instruments are also used because of their accuracy and frequency response. Our sampling is typically done at 10 or 20 Hz in order to get the turbulent fluctuations of the atmospheric variables (wind, temperature, humidity, gas …).
We most certainly make sure that all sensors are freshly calibrated.


  1. Get the sonic anemometers and motion packs. These instruments are the center pieces of the flux system, so taking good care of them is very important.
  2. Put these sensors together forward on the ship. The jackstaff is a perfect location for that as it is ahead of the engine exhausts, and it’s as far away as possible from any obstacles. Nevertheless the ship’s central superstructure will always create some flow distortion. The wind is deflected upward, and the wind speed is modified. Some modest flow distortion corrections are done later in the recipe.
  3. Add the other sensors to the mast: Licors, RH/T, sampling inlets…
  4. Secure everything with tie wraps, clamps, bolts…
  5. Install the rest of the equipment on the ship (ozone, DMS, radiometers, Licors 6262); forward on the ship is an excellent spot.
  6. Put the RHB in the Southern Ocean for ~45 days and let everything shake gently… or vigorously.
  7. Meanwhile, log all sources of data to a central data acquisition system, commonly called “DAS”.
  8. Put the cooks at work (they were already working on previous steps). They will get the data out and bake them. The baking process is very straightforward. Take the three components of the wind vector and mix them with the motion data. Rotate them to fixed earth coordinates and you get the corrected wind velocities (it’s a bit more complicated than that!).
  9. Add your favorite variables to the corrected wind components: more sonic for momentum flux, some moisture for latent heat flux, some CO2, DMS or O3, for gas fluxes… it’s your choice!
    Finally, take everything out of the RHB and bring the data home for meticulous analysis.

  10. Bulk meteorological variables and eddy-correlation fluxes based on preliminary analysis during the cruise taste good fresh and hot. But quality controlled fluxes produced later during post-processing are even better. Scientists love them as it brings them tons of information!

Bon appétit!


What you need to make good fluxes! From back to front: Sonics and motion packs standing up high with the sampling inlets of various sensors, Licors, RH/T sensor. Other sensors are down below on the mast.


Flux kitchen and the 4 cooks. All recipes are prepared with tradition. Left to right: Ale, Ludovic, Byron and Chris.


A good baking process removes the motion peak in the power spectra of the wind components. Measured (black broken line) and corrected (blue solid line) vertical velocity power spectra. The green straight line represent the -2/3 inertial subrange slope.


Freshly baked fluxes! Covariance spectra for the longitudinal component of the momentum flux (blue) and for the sensible heat flux (red).


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Deep Breathing

Posted by sogasex on April 3, 2008

By Byron Blomquist, University of Hawaii

Oceans and forests are the lungs of our planet. Oxygen that makes life possible for animals (like us) was originally produced by the first microscopic plants in ancient oceans. We rely on green plants to sustain us. And as they exhale oxygen they inhale carbon dioxide, converting it to wood, leaves and the carbonate shells of marine plankton. Some of this carbon is returned to the atmosphere as CO2 through respiration when bacteria, fungi and animals feed on plants and organic matter. A small amount settles into long term storage as coal, oil and chalk deposits. This in brief is the system we call the carbon cycle, and the ocean surface is part of the planetary lung, like the lungs in our bodies, that carbon transits during its cycle.

It has been our goal over the past few weeks to examine a patch of our planet’s lung and observe the details of gas exchange between the ocean and atmosphere, to better understand how our planet “breathes”. Ultimately, we would like to accurately predict when, where, and how much CO2 (or dimethylsulfide, DMS) passes through the ocean surface, since this information is critical to understanding how the climate system functions and to predicting how it may change in the future. But gas exchange is controlled or influenced by numerous physical processes like wind stress, ocean currents, temperature and, in the case of CO2 and DMS, by biological activity in the surface ocean, which itself is modulated by nutrients, seasonal cycles, sunlight, ocean currents, population dynamics, etc. Unravelling the mystery is more than any one of us can hope to achieve alone or more than any one group of scientists can achieve in a single study, but it keeps us focused to have the big picture in mind as we labor in the trenches of our sub-disciplines.

Those of us involved in observing atmospheric flux – the rate at which gases are going into and out of the ocean – have managed to keep our feet dry and our hands warm so far. Our daily routine, between eating and sleeping, consists of monitoring our sometimes finicky instruments and coping with an avalanche of data streaming at 10-20 samples a second per channel, 24 hours a day. We sift through the accumulating gigabytes, identifying and removing the bad data (typically occurring when wind blows from behind, sending the ship’s exhaust and vapors from the galley’s deep frier to our instruments on the bow). Then, from small turbulent variations in gas concentration and wind velocity, aided by considerable mathematical manipulation, we can observe the rate of gas exchange.


The graph above, called a covariance spectrum, summarizes an hour of DMS and wind data. It shows us the flux of DMS is upward – that is, it comes out of the ocean – because the points on the curve are positive. And the sweep of the jagged curve reveals the flux is carried on turbulent eddies at frequencies from 0.002 to 2 Hz (or eddies from roughly 5 meters to more than a kilometer in size) and the dominant frequency is about 0.1 Hz (100 meters). The area under the curve is the flux – in this case about 370 micrograms of DMS per square meter per day. We have seen the ocean “breathe”, and in collaboration with our friends and colleagues on SO GasEx we may be able to discover some details of how this “breathing” actually works.

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Where’s the tracer, man?

Posted by sogasex on April 2, 2008

By Paul Schmieder, LDEO

I am a graduate student at Lamont-Doherty Earth Observatory (LDEO) working in the Environmental Tracer Group, and at sea I am assisting the LDEO and NOAA/AOML team with the collection and analysis of SF6. SF6 is my tracer of choice, both out in the open ocean and in coastal waterways.

Nearly two weeks ago, in the early morning hours of March 21st, we successfully injected a second patch of tracer containing both 3He and SF6 gases infused in seawater. Deliberately, this tracer patch was smaller in area than the first patch in order to obtain higher SF6 (and 3He) concentrations in the water. Higher concentrations would allow us to conduct a longer survey. Our plan to increase the SF6 concentrations was successful! Surveys through the patch conducted on the day following injection yielded concentrations as high as 1024 fmol/L (fmol = femtomol = 10^-15 mol). The peak concentrations have now fallen to ~20 fmol/L, a difference of 2 orders of magnitude since the start of the survey.

Since the time of injection, the patch has displayed a pulsed migration to the east, with periods of fast advection and moments where the patch remained stationary. Overall the center of the patch advected 80 km to the east. Approximately 8 days ago, the MAPCO2 buoy, which was deployed at the same time as the tracer, began to migrate along a different path than the portion of the patch we were following (picture below). We retrieved the buoy two days ago, and to my surprise there was tracer present 50 km to our south. Currently, the patch has decided to migrate in a new direction to the southwest. Using ADCP current measurements as a guide, we should be able to keep up.

Matt Reid (LDEO) and myself have been holding down the fort, mapping out the tracer 24 hours a day for 13 consecutive days now, and it looks like we might have 2 days of survey remaining. The routine of the daily SF6 surveys is punctuated, though, with the excitement of both ‘Pump and Dump’ and the pending CTD casts. It is our duty to direct the ship to the CTD station, and it is always a bit of a struggle to predict where we might find the highest tracer concentrations, and there is the added pressure to arrive at station on-time. We don’t always get the highest concentration, nor do we always hit our waypoints on schedule, but in the end I think we have fulfilled our duties and successfully obtained the samples we need.


This is a composite map of the SF6 concentrations for the second tracer patch. The concentrations are plotted on a logarithmic scale with units of fmol/L. The black dots show the position of the MAPCO2 buoy in time, migrating from west to east.


When David asks “Where’s the tracer, man?” this is my response…

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Amphibious Rodents

Posted by sogasex on April 1, 2008

By David Ho (LDEO) and Pete Strutton (Oregon State University)

Despite the years of planning that have gone into SO GasEx, we should never discount the role of serendipity in pushing back the frontiers of science. Penicillin, Teflon®, Post-it® Notes, Formula 409®, Viagra®, and indeed the Americas themselves all owe their discovery to an element of luck. So it is that one of the major discoveries of SO GasEx actually hasn’t been about air-sea gas exchange at all, but has been the first reported sighting of the Southern Ocean amphibious squirrel (Sciurus australisaqua) in almost a century. It is a rarely seen, and therefore assumed to be extinct, creature described in the travel diaries of Charles Darwin, Ferdinand Magellan, James Cook, and Francis Drake. In fact, Ernest Shackelton and his crew are believed to have survived on seals caught using these amphibious rodents as bait.

For those who have not had the privilege of seeing one first hand, the Southern Ocean amphibious squirrel is substantially larger than an eastern gray squirrel that one often finds in New York City. In the aforementioned diaries, there are descriptions of these rodents that suggest that they could grow to the size of capybaras. The Southern Ocean amphibious squirrel is mostly white with some brown and black speckles, and characterized by its smooth hairless body, except for the white bushy tail.

We consulted Walter Rodin from Department of Zoology at Université Paris, who specializes in giant rodents. He believes that the Southern Ocean amphibious squirrel is descended from a species of rodent which underwent an evolutionary explosion during the Miocene and Pliocene (2 to 23 million years ago), creating many species of rodent in what is now Argentina, Brazil, and Uruguay.

Our news about the Southern Ocean amphibious squirrel, embargoed still because we are awaiting decision from Science Magazine, is in line with the recent announcement of the discovery of new species of giant sea creatures in the Southern Ocean. The emergence of these creatures, including the Southern Ocean amphibious squirrel, could be a result of climate change, although no effort has been made to study the connection.


This is not a Southern Ocean amphibious squirrel


Neither is this

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ASIS – The Return of Big Bird

Posted by sogasex on March 31, 2008

By Will Drennan, University of Miami

ASIS, the University of Miami’s “Air-Sea Interaction Spar” buoy, was recovered by the Ronald H Brown over a week ago, after a week at sea. The comment most people make when seeing ASIS for the first time is “Wow, that’s big”. At 6 x 2 x 2 m (36 x 6 x 6 ft), and weighing close to a ton, it is indeed one on the larger pieces of kit on the deck. As Mike Rebozo can tell you, it can also be difficult to deploy and recover. While he’s likely lost count of how many times ASIS has gone over the side of various ships over the past decade, the real question is how many of Mike’s grey hairs are a result of ASIS ?

The role of ASIS in SO GasEx is to make measurements at, and close to, the ocean surface. Above the surface, we measure basic meteorological parameters, as well as the air-sea fluxes of CO2, water vapour, heat and momentum. In collaboration with Ian Brooks and Sarah Norris of the University of Leeds, we are also measuring aerosol fluxes and concentrations. At the surface, we measure surface waves and wave slopes at various scales. This is particularly important for gas transfer work, as small scale waves are thought to be significant control on gas transfer rates. Below the water, we measure temperature, salinity and energy dissipation rates (a measure of surface mixing, which acts as a control on gas transfer). There is also one of Mike DeGrandpre’s SAMIs (see Mike’s blog) measuring carbon dioxide, dissolved oxygen, and light (PAR). Finally we also measure how ASIS moves in the water. Equipped with three ARGOS beacons giving position, we wanted to make sure to find it again.

While many of these atmospheric measurements are also made on board the Brown, a ship disturbs the near surface too much to measure many air-sea processes, such as small scale waves. ASIS was designed precisely to fill the need for a platform for such high resolution near-surface measurements. On its previous cruise on the Brown, during Gasex-2001, ASIS was christened “Big Bird”, after its less than graceful flight over the deck during deployments. The bird is still big, but hopefully the flights are becoming more graceful.


ASIS being deployed


ASIS in the water

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Primary Productivity

Posted by sogasex on March 30, 2008

By Veronica Lance, LDEO

If you have been following the science of the Southern Ocean GasEx project, you know that our major goal is to measure and better understand what controls the rates of exhange of carbon dioxide (and other gases) between the atmosphere and the surface ocean. Where do phytoplankton fit into this picture?

Phytoplankon, the microscopic single-celled “plants” of the sea function similarly to terrestrial plants – that is they take up inorganic carbon, then, using the energy of sunlight and an important enzyme (“RuBisCO”) form chemical bonds among carbon atoms leading to the production of simple organic carbon molecules such as carbohydrates. This “fixed” carbon plant material forms the base of the food chain – small metazoans and zooplankton feed on phytoplankton, which in turn feed fishes and marine mammals. In the Southern Ocean, this “food chain” has been found to be quite short and direct as compared with many other ocean environments…. As few as 3 links to the “top”: Diatoms … krill … whales!

Our understanding is, that over geological time scales, the ocean has been acting like a big sponge soaking up some of the high concentrations of atmospheric carbon dioxide during warm periods and perhaps ventilating carbon dioxide out of the oceans back into the atmosphere during cold, glacial periods. In modern times (the “Anthropocene Age”) the ocean has been soaking up some proportion of the huge amounts of carbon released into the atmosphere by the burning of fossil fuels and by other respiration processes accelerated by industrialized methods (for example, large scale agricultural practices). In an imaginary bathtub-in-a-closed-room model ocean, the gases in the atmosphere (room air) will equilibrate with those in the water (bathtub) – that is, the water will absorb the gases until it can absorb no more and the conditions will be steady or stable. If we make now make our bathtub very, very deep and add some phytoplankton, the conditions are no longer stable. The phytoplankton will use up some of that dissolved inorganic carbon. Eventually some of that carbon material (now in organic forms such as dead phytoplankton cells or fecal pellets from animals farther up the food chain or bacterial clusters of decaying matter) will sink very deep and become isolated from the surface waters where it was formed. As the organic carbon disappears from the surface ocean, more carbon dioxide from the atmosphere has a chance to be soaked into the surface ocean. The fate of the sunken carbon is that it could be respired again on a relatively short time scale (geologically speaking, years to hundreds of years) and be circulated back into the surface ocean (for example by upwelling) OR it could be buried into the sediments for relatively long time scales (thousands to hundreds of thousands of years). This process has been given the descriptive phrase “biological pump” (see picture below). 

In 1952, Steeman-Nielsen described the method he developed for estimating organic carbon productivity in the sea using radioactive carbon (14C) as a tracer. In light of the many high-tech methods being used on this cruise, this one feels old-fashioned now – but the beauty and satisfaction of this method is that it pretty much always works! There are some finer details about what this method actually does or does not measure which I am not getting into here, but in a general sense, we can get a good estimate of the rate of net carbon uptake by phytoplankton throughout the depths of the ocean where sunlight penetrates (the “euphotic zone”) on a daily basis in a given water mass (“primary productivity”). These rates will go into the bigger carbon flux equations that the SO GasEx project is all about.

I’m sure my colleagues think I am nuts, but I enjoy doing these incubations. While we are at sea, I see almost every sunrise and many sunsets in all kinds of weather. Some of the scientists aboard collect water samples and bring them back to the lab for analysis. My 14C samples get analyzed “live” and so it is satisfying to be able to walk off the ship at the end of the cruise already knowing something about my observations and being able to start thinking about how they fit into the bigger pictures of the SO GASEX project and the regulation of primary productivity in the Southern Ocean (see Fig. 2 for example of data).

For the SO GasEx project, I do several different kinds of measurements, but I am doing the primary productivity work as a collaboration between my Lamont group (with Bob Vallaincourt and John Marra) and Pete Strutton (aka “bottle cop”) of Oregon State University. Basically, I collect water from the CTD rosette from several representative depths in the ocean into clear, polycarbonate, well-washed bottles. Next, I inoculate the water sample with a small amount of the radiotracer 14C and put the “spiked” jars into the on-deck incubator. The incubator (see pic below) is simply a plexiglass box which contains several tubes which are shaded to imitate light levels at the respective depths of the ocean from where we collected the samples. Seawater is pumped through the box to keep the samples at ambient temperatures. The spiked sample jars go into their respective light tube and there they will stay from dawn to dusk or from dawn to the following dawn (depending on the precise observation desired – I am doing both types on SO GasEx). The community of organisms trapped in the bottle are both “fixing” and respiring carbon – and some of the tracer 14C along with it. At the end of the incubation, the jars are gathered from the incubator and the seawater samples are filtered. The filters collect all the organisms in the jar – some of which have now incorporated some of the radiotracer. The filter goes through a few more procedures and then is placed into a liquid scintillation counter which is a way of determining the disintegration rates and ultimately the amount of the 14C tracer in the sample organisms. With a few more calculations, we end up knowing something about the rate of carbon uptake in the water column. A plot of an early station in SO GasEx is shown below. At the same time, Pete sets up similar dawn-to-dawn incubations using the stable isotope 15N as a tracer to determine the rate of nitrate fixation (perhaps the subject of another blog someday). The ratio of carbon uptake to nitrogen uptake gives us some clues as to how fast the fixed carbon might be sinking into that very deep bathtub ocean. Every morning at 0430, Pete knocks on the door of my rad van where I have been prepping my samples. Together in the pre-dawn greyness, we go out to the incubator to harvest our previous days’ samples and put out the next set (see pics below).

p.s. All this talk about radioactivity might provoke some health and safety concerns. We are concerned, but more for scientific reasons than health or human safety. This is why: First, the amount of radioactivity we work with is very small with respect to human health concerns. Second, humans are not plants, so any 14C tracer to which we might be accidentally exposed is not taken up into our bodies. Third, it is easily washed off of surfaces with a bit of soap and water – which is later properly disposed. Our biggest concern is not to leave any traces of 14C on surfaces of the ship. Why worry about the ship? Because other scientists who use the Ronald H. Brown measure ambient concentrations of carbon isotopes including 14C. Natural 14C concentrations are very low so that even miniscule contaminations, hardly noticed by our scintillation counting methods, could skew the measurements of the natural concentrations. So, out of respect for future science, we go through several steps to insure no radioactive carbon escapes out of our control. Our work is done inside a special container van (“rad van”) placed outside on the deck of the ship (see pic below). We wear special lab coats and booties which remain inside the rad van – it’s kind of like going through an air-lock. The samples which go out to the incubators have a short trip of only a few meters from the van to the incubator and are well-sealed.


The “biological pump” cartoon drawn by Zackary Johnson.


Data! Yippee!


Light tubes in incubator with flowing seawater.


Harvesting an incubation just before sunset.


Pete and I setting out our daily 24-h 14C and 15N sets at dawn.


Rad van being set into place on the deck of the NOAA ship Ronald H. Brown.


At work inside rad van. The red lights are to keep the phytoplankton “asleep” before they go into the incubator for the day.

Thanks to Bruce Hargreaves, Bob Vallaincourt and Paul Schmeider for photos.

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L’aventure, c’est l’aventure…

Posted by sogasex on March 29, 2008

By Bertrand Lubac, Naval Research Laboratory

[Après donc Tocqueville et BHL, me voici à mon tour parti à la rencontre des Etats-Unis. Pour ma part, les USA se limitent pour le moment au bâtiment océanographique le Ronald H. Brown, à son équipage et à la trentaine de scientifiques participant à la campagne de mesures SO GasEx. Plus précisément, le noyau dur autour duquel je gravite est l’équipe d’optique marine, appelée aussi dans le cercle des initiés l’équipe « Espuma ». Cette équipe vous a déjà était présentée par Richard Miller, et un de ces membres éminents, Christopher Buonassissi, vous a tout dernièrement fait partager son grand enthousiasme à être de la partie. Aujourd’hui c’est à mon tour de m’allonger sur le divan du blog pour vous raconter dans les grandes lignes les événements qui m’ont conduit jusqu’ici].

The point of departure has been the “Laboratoire d’Océanologie et des Géosciences” in Wimereux, a small seaside resort in the North of the France, where I met Professor Hubert Loisel. This led me to a PhD on the remote sensing of ocean color from 2004 to 2007. The principle of ocean color is to extract information on the biogeochemical and optical parameters of the ocean surface water from a radiometric signal measured by a sensor onboard a satellite. To accomplish this, two general steps are necessary to develop algorithms that relate satellite measurements to in-water information: atmospheric corrections and bio-optical inverse models. My research is mainly focused on the second step (bio-optical inverse models) and has led to a particular study that examines the influence of the marine particles on the variability of remote sensing reflectance, which defines ocean color.

This research topic has now led me to Dr Zhongping Lee. In November 2007, just after my PhD defence, Dr Lee invited me to tour his laboratory, as part of the Naval Research Laboratory (NRL) located at the Stennis Space Center. My first feeling was a mix between astonishment and wonder being faced with such human and material richness combined at NRL. This visit provided us with the opportunity to define a common research project that will be conducted during a postdoctoral fellowship at the University of Southern Mississippi (USM), also located at the Stennis Space Center.

Following this initial journey, there has been a long battle to obtain all the documents necessary to come and work in the USA. Today these administrative steps are almost finished and my postdoc at USM should start at the beginning of May. In the meantime, Zhongping Lee has given me the great chance to take part in the GasEx expedition in order to familiarize me with my new toys such the multispectral volume scattering meter (MVSM) to measure the volume scattering function of the marine particles (see picture below), and get to know the USA research and culture, and to overcome my seasickness.

As some researchers have previously confided in you, there is no marked break between work and rest on the boat. So, when the weather is not too bad and doesn’t force us to remain prostrate in our lab, days go by quickly due to a very busy daily schedule. During the GasEX III cruise, my job is to collect remote sensing reflectance spectra using a handheld spectral radiometer (see picture below), the volume scattering function of surface seawater using the MVSM, and the aerosol optical density using a sunphotometer. With these measurements we hope to improve remote sensing algorithms for primary production and optical properties of the Southern Ocean. In addition to the science, I must in my case add English courses as part of my job. One course in particular with Dr. Richard Miller is teaching me the basics to survive in Mississippi: “how’s it going “ – “Peachy”… But all this work doesn’t enable us to forget what the ship’s rules don’t allow us to have – a cool beer and a tenderness time with our girlfriends that remain at home.

After this cruise, the adventure will go on in Slidell, Louisiana and in Mississippi and I hope the adventure will always be as exciting…

[Et là-bas, on murmure « Tiens bon la rampe ! »].


The Multispectral Volume Scattering Meter (MVSM) was developed at the Marine Hydrophysical Institute in Sevastopol, Ukraine (M. E. Lee and M. R. Lewis, 2003). The MVSM performs light scattering measurements at angles going from 0.5° to 179°, with a resolution of 0.3° at eight wavelengths (443, 490, 510, 532, 555, 565, 590, and 620 nm)


Remote sensing reflectance measurements made using a handheld spectralradiometer on the ship’s bow


Thanks to Scott Freeman for this English version of the French book “Voyage au bout de la nuit”

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Posted by sogasex on March 28, 2008

By David Ho, LDEO

Being out at sea requires that we adapt to different situations and adjust our plans accordingly. Some of these adjustments are expected, while others are genuine surprises.

For instance, when we inject the tracer patch, we select an area that is relatively stable so we don’t end up chasing the tracer patch around the Southern Ocean. However, because there’s no guarantee that winds and currents won’t change, we really don’t know where the patch is going to go. As a result, we don’t have fixed survey lines and have to adjust them minute by minute. That’s expected.

During this cruise, we’ve had some surprises. For instance, what happened to the SuperSoar was a surprise (see Burke’s blog), but given the fact that they are pushing the cutting edge of water sampling technology, it’s not difficult to accept that it could happen.

What happened to us today topped that.

It was about 9:00 am, and time for our morning CTD. Paul and I were discussing something in the Hydro Lab and getting ready for sampling when we heard a loud thud. I said to him facetiously, “I hope that wasn’t the CTD going into the screws [the propellers].” I went to the Staging Bay to check things out, and ran into Carlos on the way who said to me with a panicked voice, “we just lost the CTD.”

I once heard an episode of WNYC’s Radio Lab about Stress, where they talked about what happens to us when we’re under stress. One of the common experiences that people under extreme stress has is that time slows down and thoughts become clear and lucid.

In the few steps that it took to get to the Staging Bay, all the different scenarios under which we could have “lost the CTD” crossed my mind. I was expecting to see the end of a frayed cable dangling in front of me; what I saw was more surprising.

The CTD was hanging off the side of the ship, and the block that used to hang from the CTD boom was laying on the deck. See pictures below for what I fail to convey with words. Apparently, the rosette was accidentally pulled into the block, breaking the block and sending the CTD crashing approximately 20 feet into the side of the ship. Disaster!

The good news out of all this is that nobody was hurt and the rosette/CTD package was eventually recovered. However, the rosette frame was severely damaged and eight sample bottles were crushed.

For the 9:00 am station, we adapted and went to our storm contingency plan, when we expected not to be able to deploy the CTD: Submersible pump. Even though the pump only had enough hose and cable to sample down to about 40 m, it was better than nothing. It was a nice sunny day and a communal atmosphere on deck as we took turns sampling water pumped up to the surface.

We’re working hard to put another rosette/CTD package together, but it will not be ready in time for the upcoming 9:00 pm station. This will be another pumped sampling station. We hope to have the CTD ready for the morning station tomorrow.


Damaged rosette/CTD hanging off the side of the ship


The broken block on deck


Recovering the damaged rosette/CTD


Close-up of the damage


Preparing the submersible pump


Sampling from the submersible pump


A new rosette/CTD being assembled in the Staging Bay

UPDATE: Sara, Geoff, Jonathan, Clay, and Bob worked hard all day and assembled a new rosette/CTD in time for the 9 am morning cast the next day. We’re back in business. Nice going!


The newly assembled rosette/CTD package, ready for the next cast

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Pump and Dump

Posted by sogasex on March 28, 2008

By Dale Hubbard, Oregon State University

There are approximately 60 people, including the crew and the science party, aboard the Ronald H. Brown. The good folks in the galley serve three meals each day, there are snacks available after hours, and there’s a seemingly unlimited supply of things to drink. This is a very good thing (it certainly beats going hungry and being dehydrated), yet it poses a quandary: once we’ve metabolized all of that food & drink, what to do with all of our waste?

There are basically two types of sewage generated aboard the vessel: grey water, which originates from sinks, showers, laundry, and the dishwasher; and black water, which originates from the toilets. (The engines also generate wastewater of a more industrial nature, e.g. oily waste, but this is contained separately and later pumped ashore when the ship is in port, as oily waste is illegal to discharge at sea.) Aboard the Ronald H. Brown gray water and black water are commingled and contained within a holding tank of approximately 5000 gallons capacity. Sewage aboard the Ronald H. Brown is not treated—it is mechanically ground up en route to the tank, then the contents are pumped overboard. Once the sewage tank has accumulated 4400 gallons, it’s time to break off from our study site and make a run for it.

Since our project involves continuously observing a relatively small patch of water in order to collect time-series measurements, we must move at least 3 nautical miles off-site before the ship evacuates the contents of its sewage tank. Sewage contains an assortment of compounds that serve as phytoplankton nutrients, so dumping the holding tank inside of our study area would drastically alter the biological and chemical processes within. Therefore, at least twice each day we must leave the patch to undertake what many aboard refer to as a “Pump and Dump.”

Unfortunately, several times during the course of a Pump & Dump, the ship’s underway seawater line entrained some of the sewage. This caused caused a great deal of excitement in the lab, as steaming through this particular hydrographic feature generates some of the most dramatic measurements observed during the cruise. This secondary “patch” is exemplified by elevated pCO2 and nitrate (both byproducts of the degradation of metabolic waste) and elevated temperature (see pictures below).

On at least one occasion we’ve been able to resolve a sewage signal in the data from our underway transmissometer, an instrument which essentially measures water clarity (or lack thereof) by passing a beam of light through a sample stream of water. Eeeewwww…

In order to pick these Pump and Dump events out when we’re processing the data long after the cruise is over, it’s important that we remember to log them carefully.


Effect of “Pump & Dump” on pCO2 and temperature. Pump and dump signal, from approximately 12:00-12:30, manifested in approximately 20 ppm increase in pCO2 (white trace) and approximately 0.5o C increase in surface seawater temperature (red). “H2O” parameter is water vapor measured inside of shipboard pCO2 equilibrator and also reflects higher surface seawater temperature. The surface salinity values are highly variable (and rather irrelevant) because it had been raining.


Effect of “Pump & Dump” on NO3 concentration. “Amplitude” values represent voltage generated by photodiode detector (note scale is reversed). The ~0.1 V decrease between approximately 12:00 -12:30 represents an approximately 3mM increase in NO3. The variation in amplitude at approximately 13:30 is a standard sequence—a blank, 20 mM, and 9.5 mM KNO3 solutions.

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The Importance of Quenching

Posted by sogasex on March 27, 2008

By Bob Vaillancourt, LDEO

The most common measurement to make for a biological oceanographer is for chlorophyll a (abbreviated “Chl a”). This is the pigment that is common to all phytoplankton, so is a convenient proxy for the size of the plant crop in the ocean at a given time. We have two ways of measuring Chl a: by direct measurement of its concentration on discrete water samples captured in a bottle, or indirectly, by measuring the amount of fluorescent light the plants emit.

Fluorescence is a phenomenon by which a material (in this case, Chl a) absorbs light energy, then re-emits a portion of this energy as light at a lower energy. In the case of phytoplankton, their Chl a (and other pigments) absorb energy in the more energetic blue-green portion of the spectrum, and re-emit (or “fluoresce”) in the less energetic red portion. This light is too weak to observe with the human eye, so we use special instrument called fluorometers to measure it.

Typically, we lower a submersible fluorometer over the side of the ship to measure the “vertical profile” of Chl a fluorescence. If we don’t have time to stop the ship, then we can make “underway” measurements by piping surface seawater into the ship’s lab and running it through benchtop fluorometers. We then look at this profile (or time-series) as a “proxy” or suitable substitute, for phytoplankton concentration. As chlorophyll concentration increases, generally so does the level of fluorescence- but not always. So it is important to realize the situations when chlorophyll fluorescence is not a good proxy for concentration. We most often see this in surface waters where light levels are highest.

Figure 1 shows a time series of surface sunlight (upper graph, blue line) measured on the deck of the ship, and Chl a (lower graph, green and black symbols) measured at a depth of 3 meters, near the surface. As sunlight increased throughout the day, we observe a suppression, or “quenching” of Chl a fluorescence by about a factor of nearly two between early morning and mid-afternoon (approx 15:00 GMT). We see this happening on rather short time scales too, as dips in sunlight, perhaps caused by the passing of clouds overhead, cause momentary relaxation of quenching in the fluorescence traces at approximately 1200 and 1700 hrs (red arrows). The Chl a concentration, meanwhile, showed a nearly constant level throughout the day. Quenching of Chl a fluorescence causes a huge departure from the normal co-variation between concentration and fluorescence. But does this happen at all depths?

The next figure shows similar data, but taken on two vertical profiles: one during mid-day (Station 7, left graph), and the other near mid-night (Station 4, right graph). You see that during the daytime, quenching of fluorescence occurs down to about 20 meters depth, and decreases fluorescence by a factor of about ten, when compared to Chl a concentration measurements made on captured samples. During night-time, however (right graph), the Chl a concentration data (green symbols) and Chl a fluorescence track each other nicely.

Another way of viewing these data is by property-property plots (see figure 3). Here we see that when plotted this way, the night-time data show a nice linear relationship (although over a limited range), but the day-time data, corrupted by fluorescence quenching show no such correlation. So, if one were to use the Chl a concentration data to calibrate their chlorophyll fluorometers, it makes sense to use nighttime data only.


Solar Irradiance (upper) and corresponding Chl a (lower) level changes through the day on March 16. Green symbols are concentration values (units of micrograms per liter) and black dots are fluorescence values (units of voltage). As sunlight increases through day, the fluorescence from chlorophyll is quenched, without a corresponding decrease in concentration.


Two vertical profiles of Chla fluorescence (black symbols) and corresponding concentration values (green symbols) for mid-day station 7 (left graph) and mid-night station 4 (right graph). During daytime, Chl a fluorescence in the upper 20 meters is quenched and does not track Chl a concentration. The quenching phenomenon disapears during the night-time.


Property-property plots of Chl a concentration (x-axis) versus Chl a fluorescence (y-axis) for mid-day (black symbols) and mid-night (red symbols) from Figure 2. Night-time fluorescence, devoid of quenching, shows linear relationship to Chl a concentration.

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