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.