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Month: August, 2017

in drift

Screen Shot 2017-08-24 at 12.46.44 PM copy.jpgAllie, Kyle, Jesse, Ron, Melissa, Alysia and me. Sampling water from the Niskin bottles after a CTD cast into upwelled waters along the Oregon coast. Above, Patrick drives the line that lowers the bottles down to a 100 meters and reminds us to wear safety vests. Photo credit: Frank Gonzalez

Yesterday ended our drifter journey following upwelled water, and it is refreshing now to have finally experienced 6 hours of sleep without interruption. The three day blur included a 2-day shift of waking up every 4 fours to take a surface water sample. Many thanks to Steve from the crew for cookies and snacks during this time.

Outside the wake-up-every-4-hours period, the whole science party also participated in CTD (conductivity, temperature, depth) deployments every 6 hours. My continuous, second-by-second optical measurements and those samples I took every 4 hours for Nina will resolve the surface ocean layer very, very well. The data fill in a rich, 2-dimensional picture of the water our ship has meandered through, and how it may have evolved in the last three days. CTD deployments, by contrast, illuminate a third dimension.  With each one, we cast water collection bottles and instruments that measure temperature and seawater optical properties down to a few hundred meters below surface.

Some immediate data that these CTD casts offer is the structure of the water “column” below our continuous surface measurements. Because the ocean has three dimensions, these vertical data help us understand our surface measurements as part of a greater volume of seawater rather than just a slice. Light profiles, for instance, tell us how deep sunlight penetrates this “column”, giving us an idea of how deep photosynthesizing algae can persist. Fluorescence profiles allude to concentrations of the algal pigment chlorophyll at each depth, sometimes revealing the famous “deep chlorophyll maximum”, which results from algae adapting to deeper, darker waters by packing more chlorophyll into their cells. The extra chlorophyll boost in their cells helps them harvest more light to continue photosynthesis at such depths.

From drifter round #1, we have grown wiser to the challenges of observing upwelling. Our drifter was no more than four orange Styrofoam balls, a GPS locator, and a submerged net that fanned out into the upwelled water mass. So, one purely logistical challenge was steering behind the windy path that this water pulled the drifter; R/V Oceanus could never stray too far if we wanted to be sure that were analyzing the right seawater. Moreover, while we shifted directions, we were certainly not alone. The ship’s steering crew were very busy alerting nearby fishing vessels not to run over our drifter device.

Today, we dropped drifter #2  into a new water mass, and this time the water we track is not upwelling water. But, it is another unique packet of water that differs from its surrounding waters. It has many fewer algae living in it that the water we tracked with drifter #1. It will be our natural, “controlled” laboratory for the rest of our cruise at sea, and hopefully it will allow us one more rare glimpse of how ocean life and conditions change day to day.


We found upwelling

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Kyle spotting Frank’s genomics experiment. Fire extinguisher never far from flame.

This time of year, prevailing summer winds push surface seawater away from the North American west coast, leaving room for deeper waters to rise to the surface. This upwelled water from the deep Northeast Pacific Ocean is chemically unique: cold, salty, and old. If you ever swam at the beach in California, Oregon, Washington or Vancouver Island, consider that some of this seawater has not seen the surface for a thousand years.

Most likely, when this seawater left the surface ocean, it brought with it some of the organic matter produced by phytoplankton living there. And, since residing in the deeper sea, bacteria decomposed this organic matter, releasing its building blocks, a lot of dissolved nitrogen and phosphorus, back into the water. These building blocks are the nutrients that fuel photosynthesis. Deep in the ocean, there are no algae to use those nutrients, but when this water finally resurfaces on the west coast of North America, it delivers the nutrients to the algae waiting there, stimulating spurts of population growth, sometimes massive blooms. Because algae are the foundation of the ocean food chain, we can also thank upwelling for the rich fisheries of the west coast.

Algae blooms are so transient, rising and falling within weeks, that few chemical oceanographers get the chance to find them in the field and stay there long enough to observe all the biological and chemical changes in seawater that result from these blooms. In our last phase on Oceanus, we will use all of our remaining time to follow a parcel of recently upwelled water, easily noticeable by its cold, salty nature, as it slowly spreads out through the ocean surface. When we found that water today, we quickly dropped a drifter, a 30 foot net that caught onto the water mass for us and now relays its GPS location so that we know to stay close by. By entraining our ship and all our instruments on top of this water mass, we hope to witness the onset of an algae bloom and monitor it through the course of its life.

With this opportunity, there are many hypotheses to test: the algae species that grow, the amount of biomass that dies and sinks into the deeper ocean (again), the concentration of cells that remain at the surface, the amount of DMS production. All these hypotheses demand several types of measurements, and we have to collect them all frequently through the next six days—sometimes once every four hours. Now, the main lab on Oceanus overflows with color-coded spreadsheets, Nina’s creations, organizing people’s water sampling burdens and implicitly, all of our sleep schedules.

The only time we stop is tomorrow morning, which Ron reminded me is when we get to see the first total eclipse in all of North America! But, even then, we aren’t really stopping, as several scientists on board are using the eclipse to learn about marine life’s sensitivity to changes in light.

DMS tags


Melissa and Alysia getting ready to measure uniquely tagged DMS compounds in their algae cultures on the Oceanus back deck. Let’s be happy for them — today they weren’t drenched by any waves while working by  the starboard!

The vein of surface seawater continuously pumped into the ship’s wet lab splits across several pathways before analysis. One branch goes to my optical meters, another goes to a system that tells us how salty and warm the water is, and some other branches enter gas chromatographs and mass spectrometers to measure specific chemical constituents of seawater. The wet lab is noisy; every sound exists in that room, and Alysia’s music library will never overcome the mechanical symphony in the background (but it gets close).

Inside this symphony, our team can compare how several properties of the ocean are changing alongside each other in real time. And, last night, we saw something: my back-scatter meter registered higher numbers, while seawater DMS levels increased. When you look at thousands of data points per day, and try not to get seasick doing so, these shifts are exciting—even before you know what they mean!

When we woke up today with Vancouver Island in the distance, it was clear that the changes last night signaled our entry into more productive waters. From deck, we could see greener hues around us, indicating more algae, and thus more cells in the water to scatter light, produce DMS, and feed the higher ocean food chain. I like to think this is why today was full of dolphin and whale sightings, too.

Returning to the data and a lot more DMS chemistry: there are at least two processes in an algal cell that produce DMS. Each involves breaking up an even bigger molecule that is DMS plus either an oxygen or phosphorus atom (let’s call them DMSO and DMSP) to release DMS. And, I just witnessed Alysia’s clever strategy to compare how much and how quickly each process contributes to an algae cell’s DMS production. The approach: (1) Alysia and crew (aka Melissa) collect algae in seawater every morning, (2) grow them throughout the day in a tank on deck, and (3) monitor production of DMS from either DMSO or DMSP over time using Ross’s giant mass spectrometer on board. What is clever about it: how they derive separate DMSO-to-DMS and DMSP-to-DMS production rates by only measuring DMS, not DMSO/DMSP.

A lot of oceanographers that are not me, who have arguably cooler jobs, add tags to marine mammals to monitor their individual movements in a population. Hopefully, chemical oceanographers are about to get cooler because, actually, we do something very similar on the molecular level! Alysia differentiates DMS production pathways in an algae cell by making her own DMSO and DMSP molecules with different DMS’s in them and adding these tagged DMSO/DMSP molecules to the growing algae. In this case, the different DMS’s are the unique tags, DMSO/DMSP are the dolphins. Through time, the algae that Alysia and Melissa cultivate in all weather conditions break down the tagged DMSP/DMSO molecules, releasing the tags as free DMS. The DMS tags inside the DMSO molecules have eight extra neutrons, while the DMS tags inside the DMSP molecules have six. And so, the DMS tags released from DMSP are slightly “lighter” in mass than the DMS tags released from DMSO.

Fortunately, Ross’s mass spec can see these differences. And thus, knowing the release of each DMS tag through time from Alysia and Melissa’s algae incubations reveals distinct rates of DMS production from each precursor molecule.


2017-08-12 21.28.40 copy.jpgWaves crash over the starboard side as we steam southeast through the Gulf of Alaska. The CTD rosette, pictured here, is a staple for chemical oceanographers because it allows us to collect water in up to twelve Niskin bottles as deep as the sea floor.

Five days at sea and the Oceanus is beginning to feel spacious. It will never feel large, but it feels spacious in a sense that my daily interests and necessities have adapted to the size of this vessel. When on land, you can’t imagine this happening. Yet, somehow, with less than a week in a bobbing steel capsule behind you: no more need for sea sickness pills; your limbs recalibrate the distances to dinner, the bathroom, the bedroom, the workplace (just one flight up and twenty feet forward); and you kind of feel okay about jogging on a treadmill at the bottom of the ship with just pictures of forest trails taped to the front of it.

Why do we adjust so fast? One reason is the nature of fusing lab and home. Sometimes, especially at night, because of the way I’ve scheduled instrument maintenance, I think about nothing else but how my optical meters are doing, what their numerical displays mean, and how to overcome the unending battle against faulty plumbing. I twist lids tight, climb up tables to screw hose clamps into awkward corners, clean up surfaces that get splashed again a minute later, and stare at clear tubes, searching for tiny bubbles in the seawater flow that could render my numbers erroneous.

Another reason is the high swells, typical for the subarctic Pacific Ocean, that confine us most of the day, unless we go outside for water collection/experiments. Thus, we see the ocean out of small portholes and do not get to appreciate the infinity of the sea in a way that you would on a vacation ferry in the warm summertime.

(If I’m allowed to take a stab at a grand simile) We are like the algae growing in several ongoing incubation studies on Oceanus! For example, Erin from University of Southern California is sampling algae from different stops along our cruise track, then growing them in capsules on board at conditions that are similar enough to the ocean but different enough to elicit measurable responses in their healthiness index (that’s what Nina does), and production of DMS/related compounds (that’s what Tara does). This week, she added vitamin B12 to these ocean algae.

Later in the month, Erin will switch things up: she will add seawater from the ocean to just one algae type, diatoms, that she grew in purity back home, and see how introducing bacteria from the seawater outside shift the DMS production of those pure diatoms. Thus, she’ll compare how both “wild” mixed algae and cultured diatoms interact with the DMS cycle.

In these confined and controlled spaces, my fellow scientists can hope to nail down the specific processes (e.g., what algae do) that add or subtract from the pool of DMS in the ocean.

Seeing light underwater

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My lab and port hole to the horizon outside! A maze of secured, non-leaking tubing and wires that go from seawater to ship to instruments to computer files.

See? I must have over three million data points now, and less than 3 days at sea have passed. In part, I owe this quantity to the relative “easiness” of characterizing light’s behavior in seawater- i.e., the fact that the measuring process can be automated by two key instruments that monitor light through the ship’s steady seawater intake. Hopefully, by the end of this cruise, you’ll agree with me that measurements like these are essential to understanding life in the ocean, and relatedly, the planet’s carbon cycle.

Visible light, like the ultraviolet radiation you block with sunscreen or heat emanating from a warm sidewalk in the city, is made of energy packets, or photons, that travel as waves. Waves with different energies have different crest-to-crest distances and humans see those differences as colors. So lower energy red light, for instance, would have the longest wavelengths, while violet light has shortest. Natural sunlight is a mix of light waves with many wavelengths between red and blue, each of which behaves differently in the ocean.

Our team seeks three parameters for light behavior in the ocean: absorption, scatter and attenuation. I am interested in all of these parameters, but in these last four months on the new job, absorption has been the most intuitive to learn. For our ac-s meter to measure the light absorption in the ocean, it has to shine its own beam of light into a tube full of incoming seawater from one end, and then monitor the amount of light that exits the other side. With absorption, less light exits the tube than had entered, as is always the case with seawater.

I am most fascinated not by absorption itself, but by what in seawater causes light to get absorbed. The options we have are: terrestrial minerals kicked up from the ocean floor or delivered by rivers, mineral shells produced by algae like coccolithophores, and organic carbon in the cells of living and dead algae (yes finally the connection to carbon!). At 5 meters in the Gulf of Alaska, we can rule out the first two things, which means that our absorption numbers primarily tell us about algae in the water.

Moreover, the ac-s meter measures absorption at >150 wavelengths per seawater sample (per second)! With so many wavelengths, we can start to tease apart absorption by different pigment groups in algae cells, which in turn mark distinct species that are made of different pigments. You have heard of pigments: the most famous is probably beta-carotene, but among oceanographers, chlorophyll makes the top for its role in photosynthesis.

It is challenging to take a cup of seawater and say how many of what types of algae are living there. It is also challenging to look at enough cups seawater and make global interpretations, how the algae fuel the food chain or turn the carbon cycle. These rich measurements that optical instruments make at sea take us one step closer to overcoming both challenges.

We will swim in numbers

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Sideways image of Oceanus harbored in Resurrection Bay, Seward, Alaska.

The R/V Oceanus is my new home for nearly the rest of August. It is ~170 feet in length, roughly 2/3 that of a Woods Hole commuter ferry or (because I now live in Vancouver) half the length of a Vancouver Island ferry. And, as we steam out of the fjord that is Seward Alaska, where every direction is a Chugach mountain, it is easy to feel dwarfed by the world on Oceanus’s main deck.

Nonetheless, from now until August 27th, a remarkable quantity of science per square foot will happen on this ship. Most of thirteen scientists on board are interested in a chemical compound in seawater called dimethylsulfide (DMS is the acronym). So, for the first time, I travel among company that cares primarily about the movement of DMS in the ocean – not the carbon cycle (though the two cycles are related)! Like carbon, DMS transforms into other chemical forms in seawater. Sometimes, life in the ocean – mainly small things like algae and bacteria – drive these changes. Other times, abiotic factors, like UV radiation from the sun, can add an oxygen atom to the DMS molecule. These transformations are complex, and it makes sense that you’d need at least ten people per ship to study them; more details will come later as I get to know my all of my scientist roommates.

What I mostly know so far is this: the DMS molecule is responsible for the ocean’s smell. Which some of us love! As a gas, it easily escapes the sea into the atmosphere. Scientists have long posited that if DMS travels high enough in the atmosphere, it can trigger clouds to form, playing an important role in our planet’s climate. Thus, if something shifts the production of DMS in the ocean, it can ultimately affect the climate we experience on land, as well.

Coming from Philippe Tortell’s diverse team at University of British Columbia, I can still measure those constituents of seawater that tell us about the marine carbon cycle. Between here and Newport Oregon, I will continuously monitor how light at just 5 meters (~16 feet) below the ocean surface gets absorbed or scattered in seawater. These optical properties can tell us about the solid particles of organic carbon in the water, and more specifically, the different types of algae that produce these carbon particles. More later on that too.

And for a relatively small research vessel, the volume of numbers that we will get in just sixteen days is massive. My team alone, a group of five, specializes in the development and deployment of equipment that analyzes seawater incessantly by taking seawater that the ship pumps from 5 meters below surface to the main deck. One instrument I will use can provide me several seawater absorption numbers per second. Recall that this is quite different from graduate school, where I would spend weeks acquiring the equivalent of thirty data points on a graph. After two weeks, that is tens of thousands of numbers and 4-5 orders of magnitude more coverage of what is going on in the ocean’s surface.