Wednesday, May 8, 2013

What is Deep DOM?

by Winn Johnson, Woods Hole Oceanographic Institution

Catherine extracts DOM by pumping seawater through a
cartridge to which DOM sticks. (Winn Johnson, WHOI)
As the DeepDOM cruise draws to a close, it is high time to talk about deep DOM itself. Marine dissolved organic matter (DOM) is a vast reservoir of carbon, containing 660 petagrams of carbon, which is as much as is held in the atmosphere.

A single petagram is approximately equivalent to the mass of the entire population of Brazil—if each person was an elephant. Despite the size of this carbon reservoir, relatively little is known about the structure of the organic molecules in it. That’s what we’re trying to find out.

Currently, geochemists classify organic matter in the ocean based on how quickly it is removed from the ocean. Organisms can remove DOM by converting it to carbon dioxide through respiration or DOM can stick to particles sinking into the sediments of the ocean floor. The oldest organic matter in the ocean is thousands of years old meaning that it has been circulating in the ocean for longer than a full ocean circulation cycle (~1000 years).
Winn and Liz filter water for an experiment  using
isotopically labeled carbon to study how marine microbes
change DOM. (Krista Longnecker, WHOI)

At the other extreme there are organic compounds that are easily used by the microbial populations of the ocean, making them difficult to even measure, as they exist only fleetingly before being consumed. In the middle of the spectrum are molecules that organisms can use, but that require a specialized enzyme or more energy to degrade, or that are broken down by a physical mechanism, such as light. We are particularly interested in understanding the role marine microbes play in transforming and degrading DOM, as well as how the microbial community is shaped by the DOM that is available.

As we approach Barbados we have sampled the ocean down to 5,500 meters, dangling the CTD rosette a mere 20 meters above the ocean floor. We have traveled 5,000 miles collecting about 200 samples along the way. These samples will allow us to see how DOM is transformed on the molecular level as it is transported within different water masses, such as Antarctic Bottom Water, North Atlantic Deep Water, and Antarctic Intermediate Water (see the CTD video to learn more about these water masses). Not only will this give us a picture of how DOM varies spatially in the ocean, but it will allow us to compare the molecular make-up of DOM as it changes with time and while traveling in these water masses.

With this information we can learn more about the processes that transform DOM and the factors that control what types of DOM persist in the ocean and what is removed. We will also combine our results with the biological analyses that have been described in the blog to identify connections between biological activity and the make-up of DOM.  
Catherine and Krista filter seawater to remove particles so that
we can analyze the dissolved matter. (Liz Kujawinski, WHOI)

How do we analyze DOM? 

Back in our lab back at WHOI we have an instrument called a Fourier transform ion cyclotron resonance mass spectrometer or FT-ICR-MS, to make it a little less of a mouthful. This instrument can detect molecules present in very low abundances and distinguish between molecules of different masses out to approximately four decimal places. These characteristics make it well suited to analyze the mixture of molecules that comprise marine DOM. Our analysis of a single sample typically yields only about 10,000 molecules, illustrating the truly incredible complexity of working with marine DOM.

Monday, May 6, 2013

Ocean Particles Big and Small

Colleen Durkin takes a look at the sediment and the things she catches in it (intentionally and unintentionally).

Sunday, May 5, 2013

A Note from a Heterotrophic Bacterium

by Monica Torres Beltran, University of British Columbia


I’m a heterotrophic bacterium from the deep ocean. Actually, to be more specific, from the deep South Atlantic Ocean. I’m also a proud member of the microbial community in charge of the degradation of dissolved organic matter.

A heterotrophic bacterium's first introduction to Monica Torres
Beltran (left) and Maya Bhatia. (Colleen Durkin, WHOI)
 I recently heard that there is a group of scientists on board the R/V Knorr passing through the Atlantic Ocean. Among these scientists there are two members of Steven Hallam's lab at the University of British Columbia, Maya and Monica.

I know about this research group because our Canadian cousins in the Northeast Subarctic Pacific Ocean have told us about them, so we would like to tell you about what they are doing aboard the R/V Knorr. On the Knorr, as part of the Deep DOM cruise, Maya and Monica are collecting seawater samples to determine the taxonomic composition of our bacteria friends that inhabit different deep-water masses in the South Atlantic.

I wonder who they are going to find. I was told once that my relatives inhabit the low-oxygen region in the Atlantic. I hope they can find them.

Monica prepares to collect me onto a filter. (Colleen Durkin, WHOI)
Maya and Monica are also interested in understanding how we are able to degrade dissolved organic matter. They do this by looking at our gene content and expression. To do this, they filter and filter seawater, sometimes up to 50 liters through a 0.2 micrometer filter! That has to take a while! However, I can assure you that they have not lost their enthusiasm to keep sampling and filtering with the goal of understanding how our community works.

It’s too bad they can’t just ask us, as that seems like it’d be a lot easier!

Their ultimate goal on the DeepDOM cruise is to determine the microbial community and metabolic pathways associated with the degradation of organic matter across different scales of time and space and across oxygen gradients in the ocean. They will do this by comparing their results with those from Liz Kujawinski's group who are studying the composition of the organic matter and also by comparing their results from the South Atlantic to those from the Northeast Subartic Pacific Ocean.

I admit that my fellow bacteria and I are very interested to hear about their results. It is not often that we have the chance to learn what is going on with our distant relatives across the world!

Thursday, May 2, 2013

Carbo-loaders of the South Atlantic : How does microbial consumption of complex organic matter vary with latitude and depth?

by Adrienne Hoarfrost, University of North Carolina at Chapel Hill

Adrienne puts some seawater into her
autoclave—a machine used to sterilize
materials under very high temperature
and pressure. (Winn Johnson, WHOI)
Ahoy from the high seas! We are currently at 6°N, having traveled all the way from Uruguay at 38°S aboard the R/V Knorr. On this cruise I’m investigating what microbes eat, how much of it, how fast, and how their appetites vary at different latitudes and depths. Specifically, I’m looking at high-molecular-weight polysaccharides (sugars), which make up a large component of dissolved organic matter (DOM) in the ocean. These carbo-loading microbes, and the differences in their activity at different locations, can give us clues as to how biological activity drives organic matter transformations in the ocean.

As Gwenn masterfully explained in her post on the biological pump, phytoplankton at the surface of the ocean convert carbon dioxide into the material that makes up their bodies (organic carbon) via a process called photosynthesis, producing oxygen in the process. When they die, they sink into the deeper ocean, which sequesters carbon dioxide away from the atmosphere, and provides a source of food for organisms living below the surface. As this organic matter sinks, microorganisms at different depths consume and transform it still further. These organisms are called heterotrophs, meaning they use organic matter as a food source. (You and I are also heterotrophs, with the spaghetti, meatballs, and broccoli I had for dinner last night all qualifying as organic matter.

I’m interested in the appetites of these heterotrophs. Different microbes have varying abilities to eat different components of organic matter—not every heterotrophcan consume every organic molecule. Instead, the microbial community as a whole works together, cumulatively breaking down complex organic matter into smaller pieces that are easier to digest by a greater fraction of the community. Despite this communal effort, not every community can break down every component of organic matter.

Adrienne samples her seawater-
polysaccharide incubations.
(Winn Johnson, WHOI)
What they can do, they do by using enzymes—molecules made by the microbes that break down a specific target organic substrate. Because the majority of marine organic matter that microbes eat is large and bulky, these microbes eject their enzymes outside of the cell (extracellularly, we say) to break down their food into manageable pieces before bringing it into the cell to finish eating it. Imagine trying to swallow an orange whole—it just can’t be done. You need to break it apart into smaller, more manageable segments first.

On this cruise, I’m tracking microbial consumption of several high-molecular-weight polysaccharides in seawater from different latitudes and depths. I’m looking for differences in what organic materials get eaten, how much of it gets eaten how fast, and which microbes are doing the eating.

Because different microbes have varying abilities to eat different things, and microbial communities are different depending on latitude and depth, I expect this to be reflected in which and how much of my substrates are eaten. Ultimately, I want to understand what specific features of these substrates make one more tantalizing than the other and why different microbial communities have differing appetites according to latitude and depth. This might help us understand how biological activity, along with latitude- or depth-dependent variations in that activity, contributes to the composition and transformation of organic matter as it moves through the ocean and down the food chain from source to sink.

Saturday, April 27, 2013

Neptune's Realm

Erin Eggleston from Cornell University contemplates their place on King Neptune's realm. (video by Colleen Durkin, WHOI)

Friday, April 26, 2013

Deep-sea Souvenirs

by Hilary Close, University of Hawaii 

Evan Howard carefully attaches a bag of cups
to the rosette frame. (Hillary Close, U.H.)
In keeping with a time-honored tradition among ocean-going scientists, the DeepDOM team has been spending some of our spare time with the humble Styrofoam cup. Some lucky first-graders from Belmont, Mass., and scores of friends and family members are eagerly awaiting the results of our efforts. Why?

The same properties that make Styrofoam a perfect material for insulating your hot cocoa also make it the perfect souvenir of deep-sea expeditions: It is composed mostly of air. As our deep-sea instruments descend into the ocean, the weight of the overlying water presses down (and all around) harder and harder. When Styrofoam cups go along for the ride, this intense pressure squeezes out the air bubbles and compresses the foam material to a fraction of its original size.

To collect water from near the seafloor, we send our CTD rosette down to 5,500 meters (18,045 feet, or 3.4 miles) below the sea surface (see video in Evan’s post). When we attach a mesh bag containing our Styrofoam souvenirs very carefully to the rosette frame, they accompany it on its long journey to the seafloor. The pressure at this depth is approximately 550 times the pressure we feel up at the surface: 550 bar or 8000 PSI (pounds per square inch). That would be equivalent to several large elephants standing on the palm of your hand!

Method for measuring the volume of "unshrunken" and shrunken
cups by water displacement. (Hillary Close, U.H.)
We tried a little experiment on board to measure just how much air was pushed out of the cups. We measured the volume of an "unshrunken" cup and a shrunken cup using the principle of displacement. (Remember Archimedes? Eureka!) It proved to be very difficult to measure water volumes on a rocking ship. However, our answers converged after several trials: our shrunken cups lost about 90 percent of their original volume (all air)! If we assume that the mass of the cup remained about the same, that means that the shrunken cup is ten times denser than the unshrunken cup (density = mass/volume).

The cups also have artistic merit: the scientists on board and some very lucky first-graders carefully decorated these cups before we sent them to the depths. See more of our handiwork in the More Photos page above.

Advanced calculation: Eureka! Try reading more about Archimedes’ principle: it is actually a bit more complex that simply calculating volume from displacement. Given that it is very difficult to use a scale to measure mass on board a rocking ship, how might we use Archimedes’ principle to confirm the mass of each cup? Hint: the shrunken and unshrunken cups have different volumes, but they also float differently, or have different buoyancy.

Finding the Unicorn

by Harriet Alexander, Woods Hole Oceanographic Institution

Harriet Alexander and Sarah Hurley pull a plankton net  up
through the water from the side of the ship. (Colleen Durkin, WHOI)
One week ago, R/V Knorr stumbled across the elusive unicorn of the open ocean. Before anyone gets too excited, no, we did not just prove the existence of a mythical creature, nor did we run across a pod of narwhals. I am referring to what my advisor, Sonya Dyhrman, and I have laughingly called the unicorn of my Ph.D. research: a large diatom bloom in the middle of the open ocean.

The open ocean might be generally described as a nutrient-poor region, where small picophytoplankton are better able to acquire the things they need to grow than large phytoplankton, such as diatoms. As such, picophytoplankton tend to be numerically dominant over larger diatoms. However, there is mounting evidence that a confluence of events occasionally sparks a large bloom of these bigger phytoplankton in regions where they usually have a hard time growing. Imagine poppies suddenly blooming in the middle of the Sahara Desert.

Everyone, including Harriet, was surprised by the color and smell
of the phytoplankton that we captured. (Carly Buchwald, WHOI)
Why do we care about whether picoplankton or diatoms are blooming? As Gwenn Hennon explained in her blog post on the biological pump, phytoplankton convert carbon dioxide to energy and oxygen in the surface waters. Some of these organisms sink, taking their carbon to the deep ocean away from the atmosphere, and some phytoplankton are better at sinking than others—this is due to both their size and their density relative to seawater. Bigger, denser things, as you might intuit, are better at sinking. Diatoms are not only bigger than the small picoplankton that tend to dominate the open ocean, but are also denser, due to their silica frustule (a glass-like shell). Thus, diatoms may be a particularly efficient vehicle for the movement of carbon to the deep ocean.

So, back to the unicorn.

Up until about a week ago, we had been traveling through the subtropical gyre, which is sparsely inhabited by large diatoms. The morning of April 17, I had been trying to snag a little bit more sleep, as I did not have any planned sampling that day. Suddenly, my roommate came and woke me, saying that we had found something interesting . I stumbled upstairs, slightly blurry-eyed to find everyone in a frenzy deploying a CTD at an unplanned station.

Harriet sampled a small amount of "goo" to
identify it. (Colleen Durkin, WHOI)
Evan Howard and Gwenn Hennon, who, respectively, monitor oxygen and picoplankton communities continuously through underway systems, had identified a huge peak in oxygen production and a major shift in the picoplankton community composition. Lowering the CTD reinforced what they had found: there was a ton of chlorophyll in the surface water.

While everyone was gearing up for some on-the-spot sampling, we decided that a net tow might prove interesting. By dragging a net up and down through the water column we can capture and concentrate all the organisms larger than a certain size into a smaller volume. In this region, we might expect a typical net tow to contain a few animals and maybe some algae. When we recovered the net, it was full of (to use the scientific terminology) goo—greenish-yellowish-brownish goo, smelling strongly of sulfur. Gwenn Hennon and Colleen Durkin grabbed a sample to look at under the microscope and reported that we had, in fact, stumbled upon my unicorn—a huge bloom of diatoms.

My Ph.D. research is focused on trying to better understand the nutritional physiology of diatom growth in a nutrient-limited environment. By sampling the RNA (the genetic material being expressed) of the diatom community in the environment and in on-deck incubations, I will be able to create a metabolic fingerprint for the diatoms that are growing in the system. Coming across this large bloom of diatoms provides me with the opportunity to gauge what these organisms are doing and experiencing during such an event.

Examination of the sample under a microscope revealed it to be
a bloom of diatoms--large cells encased in glass-like shells. The
left photo shows how abundant these cells were and the left shows
a cell about to divide. (Colleen Durkin, WHOI)
Because these blooms only occur episodically and are spatially patchy, we were very lucky to cross paths with it during our cruise (and even luckier to have a great underway team to notice it). The opportunity to do research at sea makes these fortunate encounters possible, giving us the flexibility to study the unexpected and potentially discover something new.

This type of discovery is nearly impossible to make intentionally. Kind of like finding a unicorn.

Tuesday, April 23, 2013

Viruses of the Deep Ocean

by Erin Eggleston, Cornell University

Viruses are notorious vectors of diseases in humans, crops, and animals. However, they also play important roles in cycling nutrients in the ocean. On this research expedition I am studying viral composition in the deep ocean and the roles they play in biogeochemical cycling.

Erin pre-filtering 200 liters of water for a viral addition
experiment. (Gwen Hennon, University of Washington)
In the ocean, viruses are so abundant that they outnumber bacteria by at least a factor of ten. They are obligate parasites, meaning they rely on a host to reproduce. The more hosts that are present, like bacteria and zooplankton, the more viruses can replicate. Some viruses hijack the cellular machinery of their host to replicate their genetic material, and then emerge from the host, resulting in the host's death. These events lead to die-offs in host populations, increased viral abundance, and also a release of nutrients and dissolved organic matter. My goal on this research expedition is to characterize the viral populations and capture their dynamics in the deep ocean.

Who’s there?
Due to limitations in culturing hosts and their viruses, we use nucleic acids to identify viral populations in water samples. To do this, we pre-filter water to capture the bacterial size fraction, which we can use to look at particle-associated viruses, and viruses themselves, which we capture on a filter with very small pore size.

Once back on land, we will extract these nucleic acids and, using a molecular amplification technique, quantitatively track different viral types in the samples. In addition, we will characterize the overall diversity of viruses using a viral metagenomic approach. For this I will use viral concentrate to assess all viruses present in water from six major water depths (Antarctic Bottom Waters, North Atlantic Deep Water, Antarctic Intermediate Water, mesopelagic, deep chlorophyll maximum and surface waters).

Viral nucleic acid filtration. (Erin Eggleston,
Cornell University)
How many viruses are produced?
 In addition to investigating what types of viruses are present, we want to get a sense of how viral abundance and community structure change over time. This involves diluting or concentrating viruses through tangential flow filtration and then adding either viral concentrate or virus-free water to ambient water. With these studies I can look at both natural viral production and induced viral production, which we trigger using the chemical Mitomycin C, as well as viral numbers and their effect on host organisms.

One unique aspect of this research expedition has been collaboration between many research groups. The Kujawinski research group has taken samples to analyze organic matter at timepoints for some of my incubations. Using these measurements I will be able to assess the impact viruses have on dissolved organic matter. In collaboration with Harriet Alexander I will assess viral abundance and community composition in a diatom bloom. Combining my data with data of other research groups on board, I will begin to piece together the story of viruses and the role they play in Atlantic Ocean waters.

Monday, April 22, 2013

Sampling the Depths: How oceanographers study the ocean

by Evan Howard, Woods Hole Oceanographic Institution

We are in the South Atlantic, but some of the water underneath us came from near Greenland, and some from Antarctica. That water has traveled a long way, and the central goal of this cruise is to see what happens to dissolved organic carbon carried by the water on its journey away from the surface. How do we know where the water came from, and how do we sample water from great depths?  

The vertical ocean and the CTD 
At any given location, all ocean water is not the same with depth and time—parcels of water move around and under each other. As water from different sources meet, the heavier water slides beneath lighter water. Water parcels move most easily through similarly light or heavy water, and only mix with difficulty into other parcels—it is hard for light water to sink into heavy water. This movement can carry along with it chemicals and organisms, or prevent them from moving vertically to mix with other water parcels. For example, we are interested in the amount of nutrients available to phytoplankton. If there are only shallow and deep parcels of water, we may want to consider nutrient concentrations from each water mass separately—phytoplankton grow near the surface and cannot easily access deep nutrients, even if there is plenty below.

Monica Torres Beltran and Erin Eggleston recover the
CTD rosette. (Winn Johnson, WHOI)
The Conductivity, Temperature, Depth instrument (CTD) is one of the most widely used oceanographic tools. We use the CTD to determine at what depths different water parcels are found. Salinity tells us how fresh or salty the water is. Your tongue is very good at detecting even tiny amounts of salt, but the CTD can’t taste salt. However, when salt is dissolved in water it conducts electricity more easily—this is the conductivity in the name of the CTD, and what the instrument can actually measure in place of salinity. Temperature also varies between water parcels. At the surface of the ocean, the sun heats up the water, so there is often a layer of warmer water at the surface. But warm water can travel deeper too if it is in a heavy water parcel. Heavier water parcels tend to not change salinity or temperature much from where they first began to sink away from the surface. For this reason, temperature and salinity measured on the CTD can tell us where deep water originally came from.

Often an oxygen sensor is also attached to the CTD. Oxygen is mixed into the water from the air, particularly in the cold regions where deep water forms, because cold water holds more gas than warm water—have you ever noticed how your soda goes "flat" as it warms up and the bubbles escape? It can’t hold as much gas when it is warmer, just like the ocean. So the amount of oxygen in the water can help identify water parcels that have traveled from far away, just like temperature and salinity—this is how we know that some of the water beneath us came from the far ends of the North and South Atlantic (see the video below for more).

Bringing water back to the surface with Niskin bottles 
 When we look at CTD and oxygen measurements they pinpoint at what depths important or exciting features are found in the water parcels. If we want to measure other physical, chemical, or biological properties in that water, we need to bring some back to the surface. The most common way to do this is using a Niskin bottle, a special sampling container that closes around a sample at a target depth. Such bottles were originally designed by Norwegian oceanographer and Nobel Peace Prize winner Fridtjof Nansen for exploring the Arctic and North Atlantic Oceans. The bottles were later improved by an inventor named Niskin (hence their name).

The Niskin bottles are on  a circular rack called a rosette that is secured to a metal cable. The CTD and other sensors are also attached to the rosette. A crane lifts the rosette using the cable and lowers it into the ocean. The Niskin bottles are held open at both ends until they reach the depth we want. Aboard ship, we send an electronic command down the cable—this triggers a latch that releases the end caps to snap shut on one or more bottles. When all the Niskin bottles on the rosette are full, we return it to the surface so that we can collect the water from each depth. This water is analyzed to develop a more detailed picture of the vertical ocean beneath us.

The CTD Rosette

The CTD (conductivity, temperature, depth) rosette is one of the most common tools in oceanography. See how it is used and what ocean scientists are able to learn with it. (video by Colleen Durkin, WHOI)

Monday, April 15, 2013

How to Tie a Bowline

The bowline is an incredibly useful knot to know how to tie at sea. WHOI technician Justin Ossolinski held an informal workshop for the science team on how to tie one. (Colleen Durkin, WHOI)

Friday, April 12, 2013

Team SeaFlow

Gwenn Hennon from the University of Washington explains how she is creating a continuous picture of life in the ocean between stations using a SeaFlow cytometer--something that would take her  many years using just a microscope. (Colleen Durkin, WHOI)

Monday, April 8, 2013

Persistent Organic Pollutants in the Water and Atmosphere of the Western South Atlantic

by Erin Markham, University of Rhode Island Graduate School of Oceanography

Persistent organic pollutants (POPs) are compounds that have been created by humans and have the tendency to persist in the environment and to bioaccumulate in organisms through the food web. They can be transported long distances and have been known to cause adverse effects in both humans and the environment.

The majority of these contaminants became common somewhere between the 1940s and 1970s as industrial chemicals, pesticides, and byproducts; many have since been banned. "Legacy POPs" are those chemicals that have been banned for decades, but that still persist in the environment. This includes a group sometimes known as "the dirty dozen," things like PCBs and DDT that have largely been banned since the 1970s.

The air sampler is located up on the flying  bridge of
the Knorr, as high as possible and forward of
the exhaust to eliminate any ship-borne
contamination. (Winn Johnson, WHOI)
Even though these compounds have been out of production for decades, they are still detected at trace levels in the environment. Hydrophobic ("water-hating") compounds such as these attach to organic material or accumulate in fatty tissues. As a result, they tend to bioaccumulate and biomagnify up the food chain as one organism consumes several other contaminated organisms. POPs also sorb to settling particles in coastal ecosystems and collect in bottom sediments.

There are also emerging classes POPs that have either recently been banned or are not yet restricted. Per- and poly-fluorinated compounds (PFCs) fall under this category. PFCs have been in production since the 1950s, with high-volume production beginning in the 1970s, but most research on them has only been conducted within the past 15 years. The two compounds that are most prevalent in the environment are perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA).

Unlike the legacy POPs, these compounds are hydrophilic ("water-loving"), and so the ocean is believed to be their ultimate destination. PFOS was added to Annex B of the Stockholm Convention in 2009, meaning they are only permitted to be used only for limited purposes, but PFOA is still in common use and is a key component of such things as Teflon and Gore-Tex. Most PFCs, including PFOS and PFOA are found in both humans and the environment worldwide and more research needs to be conducted on their potentially adverse health effects.

This water sampler connects to the seawater
flow-through system on the ship, running first
through a filter and then through threepieces
of polyurethane foam. (Winn Johnson, WHOI)
My research on this cruise is focusing on both the traditional hydrophobic compounds as well as perfluorinated compounds. For the more traditional POP contaminants, I will take high-volume air and water samples (600-800 liters), and pass these through a glass-fiber filter and polyurethane foams (PUFs). The idea is that the compounds are likely to sorb to the PUFs and that by taking both water and air samples, we may be able to determine any air-water exchange gradients occurring in this region.

For the perfluorinated compounds, I will take one liter of water from various depths and analyze these for PFOS and PFOA. Much of the globe has been surveyed for surface water concentrations of PFCs, but very little is known about these contaminants at depth. We are particularly interested in the spread of these PFCs away from land via major rivers, such as the Rio de la Plata and the Amazon. Most likely, the transport of these persistent hydrophilic compounds to depth is their main removal pathway from the surface ocean. Sadly, this does not really remove them from the oceans, but is a step towards their ultimate dispersion and dilution worldwide.

Friday, April 5, 2013

Spontaneous Collaborations and the Big Picture

by Colleen Durkin, Woods Hole Oceanographic Institution

Yesterday we deviated from our science plan just a little bit. Usually we stay at one longitude and latitude, called a “station”, while we take samples and make all of our measurements. In the future we or another group could presumably return to these fixed locations to repeat our work here, but the water that we sample is always flowing and changing with the currents.

At the station yesterday, we instead decided to follow our sediment traps for 24 hours as they drifted with the currents (see our video from April 2 for a description of the drifting sediment traps). By following the path of the sediment traps we were able to stay with the same parcel of water and measure how its biological and chemical properties changed over time. This new opportunity prompted something special to happen: spontaneous collaboration.

Most of the scientists did not know each other before we boarded Knorr. In the past week of living together on the ship, chatting at meal times, and watching each other work, we have started to learn about each others’ science. Each scientist is making observations and conducting experiments that will, by themselves, be very interesting and important pieces of research. But yesterday’s opportunity to drift with the sediment traps inspired us to be particularly mindful of taking complementary samples that could together enable a more complete picture of the processes occurring there.

Growth of phytoplankton and fixation of atmospheric carbon dioxide into organic matter (also known as primary production) occurs in the surface waters. The amount of production that occurs, and the fate of that production, is tangled up with many other processes. Here is a brief description of a few of the things we did to try to disentangle them:

· Gwenn Hennon continuously measured changes in phytoplankton composition in the surface water, the ultimate source of the organic carbon (see her post from March 29). She also conducted an experiment to find out how fast the microscopic predators in the surface waters were eating the phytoplankton.

· Evan Howard continuously measured how much inorganic carbon was incorporated into the phytoplankton as organic matter.

· Harriet Alexander collected these surface phytoplankton onto a filter, which she will later use to discover which genes they were using while growing in the surface waters.

· Monica Torres Beltran, Maya Bhatia, and I collected particles from the sediment trap onto a filter so that we can later discover which genes were being used by the phytoplankton and bacterial cells while they are sinking.

· Liz Kujawinski will measure what types of dissolved organic matter these particles produce.

· Ben van Mooy will identify the molecules used by organisms in these particles to influence decomposition. He also measured how much carbon was being respired (and returned to the atmosphere), while I quantified the amount of carbon exported from the surface to the deep ocean in the form of sinking particles captured in the sediment traps.

In future blog posts we will explain in more detail these and all the other measurements being made.

Pulling all these measurements together once the cruise is over will be a big task for us all and, like all things in science, the outcome is unknown. But when you are on a ship it is easy to get excited about the science, come up with new ideas, and be inspired to take those ideas in new directions. It helps to be working as part of such a great group of scientists. Nice job putting us all together, Liz (Liz is our chief scientist and invited the people who are on board).

As the cruise continues, I look forward to more of these spontaneous collaborations. This is just one way that going to sea facilitates the collaborative and interdisciplinary culture in oceanography.

Thursday, April 4, 2013

A Source of Deep DOM

by Carly Buchwald, Woods Hole Oceanographic Institution

Morning rainbow off the port side of Knorr.
(Sarah Hurley, Harvard Univ.)
There is a unique and abundant, but often less-well-known group of microbes in the ocean known as chemoautotrophs. Like phytoplankton, as described in Gwenn’s previous blog, they are autotrophs, meaning they get their carbon from inorganic sources such as carbon dioxide (CO2) and bicarbonate (HCO3-). Unlike phytoplankton, however, which get their energy from sunlight, chemoautotrophs get their energy by oxidizing inorganic materials, such as ammonia, nitrite, and sulfide, which means they can survive in the deep ocean.

The main purpose of this cruise is to focus on the sources and sinks of dissolved organic matter (DOM). Other researchers on the cruise are targeting the surface sources of DOM, while others are looking at the meso (mid-water) and bathy-pelagic (deep) heterotrophic sinks of this DOM. I’m here on the R/V Knorr working for Dr. Alyson Santoro, a research scientist at Horn Point Laboratory in Cambridge, Maryland, studying a specific type of chemoautotroph known as microbial nitrifying organisms. Nitrifying organisms include bacteria and archaea that get their energy by oxidizing ammonia and urea, a dissolved organic nitrogen compound, to produce nitrite. We want to determine the importance of this deep autotrophic source of DOM, in particular how it affects the composition of deep DOM.

Who are they and where are they?

Carly Buchwald filtering seawater with peristaltic pumps.
(Winn Johnson, WHOI)
As micro-bio-geo-chemists [it sometimes helps to add all the hyphens, ed.], our research lies at the boundary of biological and chemical oceanography. We are using a variety of microbiological and geochemical techniques to assess the importance of nitrification in the deep ocean. One way of determining which and how many nitrifying organisms are in the ocean is to use gene quantitative PCR (qPCR).

This technique targets a specific gene, in our case the gene used by organisms to oxidize ammonia (ammonia monooxygenase), amplifying and measuring the quantity of this gene at different depths in the water column. This will give us an idea of where nitrifying organisms are most abundant. On the cruise this means filtering many liters of water using a peristaltic pump, collecting the filters (now full of microbes), and freezing them for analysis back on land.  

What are they doing and how fast are they doing it? 

--> 0.2 um filter after filtering 4 liters of water
from the deep chlorophyll maximum at
105 meters. (Carly Buchwal, WHOI) Although knowing the organisms are present is important, this does not tell us what they are actually doing. So, our second goal is to measure the rates of nitrification and carbon fixation using incubations with special isotopically labeled substrates. To one set of incubations we add isotopically labeled ammonia or urea that we can track as it is incorporated into nitrite and nitrate over time. To measure carbon fixation, we add labeled bicarbonate and track the label as it is incorporated into particulate organic carbon.

In addition to these incubations we will also be conducting novel experiments using a new and powerful mass spectrometry tool called nanoSIMS. This tool allows us to track the incorporation of isotopic labels into individual cells, which means that, along with our bulk oxidation and fixation rates, we will be able to track rates in individual cells, as well as learn where the nitrogen and carbon is going inside the cell. Nitrification, particularly by archaea, still presents many unknowns. For example, the use of urea in nitrification was only recently discovered. Our experiments on this cruise will not only teach us about the mechanisms used by these organisms, but also how important they are globally as a primary producer, as a carbon dioxide sink, and as a source of dissolved organic matter in the deep ocean.

Tuesday, April 2, 2013

Whale Talk

Retrieving a drifting sediment trap in the open ocean requires the use of an acoustic device that closes the trap before it's recovered. What happens when there's a pod of whales nearby listening in on the acoustic communications? Click above to find out.
(Video by Coleen Durkin, narration by Benjamin Van Mooy)

Friday, March 29, 2013

The Biological Pump

Greetings from Knorr! Right now we are at the edge of the Sub-Antarctic Gyre and the Subtropical Gyre in the Atlantic Ocean (learn more about gyres). My name is Gwenn Hennon and I’m a graduate student from the University of Washington. I am running an instrument called SeaFlow, a flow cytometer that continuously measures the tiny cells in the ocean that make up the base of the food web: phytoplankton.

Gwen and the SeaFlow (Winifred Johnson, WHOI)
Like plants on land, phytoplankton use sunlight to convert carbon dioxide into oxygen and energy. As a result, they are responsible for about half of the oxygen in Earth's atmosphere. When they die and sink into the deep ocean they carry the carbon in their bodies, which they got from carbon dioxide, down into the ocean far from the atmosphere. The carbon carried by sinking phytoplankton into the deep sea is called the "biological pump" because it pumps carbon from the atmosphere into the interior of the ocean.

I am interested in how different types of phytoplankton change the strength and efficiency of the biological pump. During this cruise we will be crossing into areas of the Atlantic Ocean with different water types and, hence, different types of phytoplankton. Right now we are in the Sub-Antarctic Gyre, which generally contains larger phytoplankton that we think probably sink faster and therefore create a stronger biological pump. In the Subtropical Gyre the phytoplankton are smaller and sink more slowly, taking less carbon into the deep ocean.

With the SeaFlow instrument I can measure the size of the phytoplankton as well as the number of cells in the ocean where we are and the amount of chlorophyll in each cell. Since my measurements happen all day and night I can see how the cell size changes over the course of a day. From this I can calculate how fast the cells are growing and dividing. Evan Howard, another scientist on this cruise, is measuring how much oxygen the cells produce and how much carbon they take up. When we put our data together we will be able to see whether different types of phytoplankton affect how much oxygen is produced and how much carbon is carried to the deep ocean by the biological pump.

This is important because we know that tropical areas of the ocean are likely to warm as the climate changes. As a result, the types of phytoplankton that can live there will probably be smaller cells. We want to understand what types of phytoplankton live in ocean regions like the Subantarctic and Subtropical Atlantic and how those phytoplankton types affect the biological pump. With that information we can start to think about how climate change will affect where phytoplankton groups are found and how much carbon is carried to the deep ocean by the biological pump.

Tuesday, March 26, 2013


The tugboat Montevideo gently pulled us out of our berth at the port of Montevideo, Uruguay, today. It is a busy port with massive cranes loading cargo ships and the smell of manure filling the air as live cattle are loaded onto ships.

Tugboat pushing R/V Knorr out of its berth and toward the
South Atlantic (Winnifred Johnson, WHOI)
This port is the entry and exit for goods going to and from Uruguay, Paraguay, parts of Brazil, and Argentina. As we wait for our turn to leave the port ,a tugboat pulls a cargo ship, many times the size of the Knorr out of its berthing place. The port is located in the mouth of the Rio de la Plata and the water is full of mud and silt. On the horizon there is a barely visible streak of blue that shows where the river and the ocean meet.

We will be working on the R/V Knorr  for the next 45 days. Our most southerly samples will come from a latitude of 38S. We will then travel north along the western Atlantic, crossing the equator and disembarking in Bridgetown, Barbados (13.2N). This journey will take us from temperate latitudes through the tropics, sampling more nutrient-rich water in the south and entering low-nutrient water as we move north, while also crossing the Amazon River plume. There will be a variety of sampling to look at microbial life and chemistry of this part of the Atlantic Ocean. We will also be sampling for everything from viruses to phytoplankton and chemical analyses ranging from broad snapshots of the small organic molecules present to identify of individual lipids.
A cattleship loading as Knorr leaves the Port of Montevideo
(Winnifred Johnson, WHOI)

The cruise track is being dictated by the presence of north Atlantic deep water. This is water that is cold and salty, which makes it dense and causes it to sink down to around 3000-4000 meters in the North Atlantic near Greenland. This body of water then travels down the western Atlantic, transporting any matter that is associated with it. This is part of a deep ocean transport system that results in carbon and nutrients eventually being moved all the way into the North Pacific.

Radiocarbon dating shows us that some of this material is thousands of years old. Part of the goal of this cruise is to understand how the organic matter that is being transported along this route changes and the processes that are transforming it.

Over the coming weeks we’ll be uploading videos and blog posts highlighting all of the diverse work occurring on this cruise.

Friday, March 22, 2013

DeepDOM: Coming soon!

Tune in soon for updates from the DeepDOM cruise. In the meantime, you can read more about our home for the next five weeks, R/V Knorr (above).