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.