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)