Participating in this cruise has been a learning experience in so many ways, going back to before we even got on the ship. I was selected as a co-chief scientist back when we were all notified that we’d been accepted for this cruise, I think based solely on the criteria that I’d been to sea to take cores before (thanks, Yair). The other three co-chiefs and I were given a few weeks to put together a cruise plan for 21 different people with 21 different projects, with the only criteria being “you can go wherever you want within 200 nm of San Diego, except Mexico.” We worked well together via Skype and e-mail planning things out, and the cruise plan went through many iterations until we settled on something that we all felt really good about.

Like all good plans, it barely survived the first station (at which the MC failed to trigger and required a second deployment), and our on-the-fly revisions didn’t stop until we finished coring at the last station on Friday night. My favorite catalyst of change was the notification from the second mate that one of our initial coring sites was in the middle of an old Navy ordnance disposal dumping ground, which is not a good place to being lowering gear to the seafloor.

The nature of this cruise, with no unifying science goal and no real head chief scientist, is fairly unique, but the group problem-solving every time something had to change was fun and rewarding, and I think we all really enjoyed that aspect of the chief scientist experience. This is drifting a bit from the subject of What I Learned About Being a Chief Scientist, but I think we were very lucky in that everyone got along very well, worked well together, and were good about prioritizing each other’s research goals along with their own. This kind of large cruise could easily develop a too-many-cooks in the kitchen dynamic, but we all worked very well together, and it definitely contributed to the success of everyone’s science goals.

But back to Chief Scientist things: I think this extensive planning along with the ability to easily roll into back-up plans is the main lesson they were trying to teach us, and it seems to me that it’s probably the most important aspect of being a Chief Scientist. Our cruise plan changed daily, sometimes in fairly significant ways, but we were always ready to change things around to accomplish the same goals. This type of flexibility is something that I am familiar with (“Scramble; Be Flexible” was a mantra at summer job I had as a backcountry guide through college), even at sea (thanks Yair; I learned to never waste a minute of ship time if you can help it), but it’s a lot of fun to think on your feet and adapt like that. I think the main thing I took away from this cruise is that I really like doing this, and can’t wait to sail again as a real chief scientist on my own research cruise.

I also spent the whole week with that really awesome feeling of “I can’t believe I get paid to do this” that I’ve been chasing since that first summer job that I really liked. I really can’t believe I get paid to do things like this, and feel so lucky to get these opportunities.

Posted by Chris

Photo credit: Robyn Von Swank, instagram @vonswank

After a busy few days of packing up and getting all the gear and samples shipped out to their respective institutions, we are off the ship and on to new adventures!  Stay tuned for a few closing thoughts on the workshop and experiences!

Bubbles

Jellyfish

swimming crab

?????

Posted by Chris

Chief-Scientist-In-Training Dr. Molly Patterson studiously works on a sampling plan. (Photo: Dr. Alysia Cox)

Ever wondered how to plan your own research voyage? Concerned that you might forget something important or not quite sure where to start? The UNOLS Chief Scientist Training Cruise will cover all of the gritty details and more! We’ve been at sea almost a week and have learned many of the things we would need to know to execute our own research voyage ranging from how to submit a proposal to NSF with a ship time request, to communicating with the crew and science party, to how one properly analyzes CTD data post-cruise. Our mentors have been instrumental in sharing their positive (and negative) experiences with us as we walked through the process of successful cruise planning and execution. Rapport is excellent as we co-chief scientists are all learning the ropes together. Definitely highly recommended to participate in one of these cruises if you are at all interested in becoming a well-prepared chief scientist!

Posted by Alysia Cox

Darcy and the A.B.s helping with glider deployment. Photo credit: Robyn Von Swank, instagram @vonswank

This week at sea aboard the RV Thompson has given us a great opportunity to collaborate with other young researchers, learn the ropes of being a chief scientist, and conduct oceanographic research along the California coast. While we’ve all helped each other along the way, collecting hundreds of gallons of waters and many cubic feet of mud (all in the name of science!), the Thompson captain, crew, and marine technicians are really the ones that have made all our work possible.

The crew helping Bridget recover her glider.

While at sea the ship becomes like a small town, with each person working to help one another. Steve, Mike, and Darcy, the Thompson’s marine techs have helped us work effectively by helping us organize our labs and deploy our instruments into the ocean all while cracking jokes and showing us how to tie a mean bowline in between deployments. “Awesome miracle worker” doesn’t quite cut it as a job title, but it comes close.

The crew helping the science team assemble a drifter on the back deck. Photo credit: Robyn Von Swank, instagram @vonswank

The marine techs also work alongside the captain (Eric) and the mates (Bree, Lucas, and Maggy) to organize our cruise and get us where we need to go quickly and safely. As you can imagine steering a 300 foot ship is no small feat, especially when the wind blows hard and the waves get bigger, but the team up on the bridge have made our sailing smooth as can be. The captain is also responsible for the crew, who are also important in making our science dreams come true. The engineers and oilers, working in the engine room, keep the ship’s engines in top shape, allowing us to swiftly move between stations. The abled bodied seamen (A.B.) work with us on the deck, helping us with deployments while also maintaining the ship (think painting, cleaning, organizing, etc). And finally, and perhaps most importantly, the steward, second cook, and mess attendant have kept our bellies filled and the ship’s morale up by serving delicious meals three times a day. That, and cookies.

Captain, A.B. and marine tech deploying the multicore. Photo credit Robyn Von Swank, instagram @vonswank

After a week at sea, working day and night, we have all gotten to know each other at our best and most tired, and had many funny moments along the way. Jelloed hard hats and glider wing sandwiches put a light-hearted note on long work days, as did beautiful views of the coastline, and an occasional song and dance in the lab. We’ve had a great week together in our little ship community, and we are all already looking forward to our next adventure on the Thompson.

Pam and Todd returning Bridget’s missing glider wings in a submarine sandwich after posting a ransom note.

Posted by:

Nicholas Beaird

Randie Bundy

Mattias Cape

Bridget Seegers

Although I’m pretty exhausted, there is something in the air on a ship that motivates me to keep going.  It’s similar for everyone, I’d imagine.  There is this feeling of “wow, this ship is out here for me to do my work, and I only have a few days to do it, so I should make the most out of it”.  You also hit a kind of adrenaline high when the CTD/multicore comes on board and there is a mad rush to start collecting samples.  Also, chances are very good that you are not the only one awake at any given time.  The galley is always open with snacks and things to keep you occupied.  It’s also great to stand out on deck and look at the stars, or try to spot wildlife (myself and the core team watched a pod of dolphins chase the chip ~3AM today).

So, inevitably, you end up awake at 5AM, having only taken a short nap since the night before.  Yet there are samples to be processed, time points to take, and a new CTD going into the water in an hour.

How do you survive and not end up fast asleep at your bench?

Here are a few things that get me through the night:

1. Spontaneous dance parties (admittedly not so spontaneous; they are most effective when they last the length of your sample processing time, and are better with friends; note that you need a good playlist or four)
2. Laughter (see above; you and/or your friends are most likely not very good at dancing)
3. ‘MidRats’ (mid-night rations; snacks and leftovers from previous meals in the galley that are ripe for the picking; tonight, mac & cheese hit the spot)
4. ‘Fat Kid’ Coffee (1 packet of hot cocoa, mixed into coffee with cream and sugar; whipped cream optional but recommended; the right mix of caffeine and sugar with a touch of childhood nostalgia)
5. Constant movement (walking across the ship to freeze samples or put them in an incubator makes this easy; otherwise, you don’t really need an extra excuse to go outside and look at the moon and stars)
6. Companions (it is much easier to stay awake when someone else is fighting off sleep at the same time – you can keep each other focused and encourage any of the above)
7. Data (yes, it will take months to process and write up results, but day-dreaming – night dreaming? But like, not when you’re actually asleep – of a future publication helps keep me going).
8. Cold (personally, I fall asleep when I’m too warm, so cold air helps keep me awake. It also helps that the Hydro Lab feels like Antarctica, though my companions may disagree that this is a positive aspect)

Hopefully that provides a little insight as to why we oceanographers don’t dread working into the night.  It isn’t always fun, but you never want to leave a cruise feeling like you didn’t sample enough.  As I mentioned before, chances are good that you won’t be the only one awake at 4AM, and the delirium of sleep deprivation lends itself to great conversations and lots of laughter as you commiserate your long hours together.  Plus, inevitably the cruise will end and you can sleep for real when you get back home.

Posted by Bradley Tolar

Photo credit Robyn Von Swank, instagram @vonswank

To separate metabolic rates of the photosynthetic (light-utilizing) versus non-photosynthetic communities, some bottles were incubated in the dark for comparison to those incubated under natural light. These measurements along with additional information on community structure (through DNA analysis and flow cytometry) will allow us to connect activity with plankton community structure and diversity. In other words, we want to find out: ‘who’ is doing ‘what’ metabolic activities, and ‘when’ (i.e. how fast) are they doing it?

Posted by Bryn and Bradley

We want to know what microbes are living in the water and what they’re doing. Although they are invisible to the human eye, these bacteria and phytoplankton are an integral part of the aquatic ecosystem. Did you know that about half of the Earth’s primary production (carbon made by photosynthesis) comes from the oceans? The other half comes from plants on land. Just like phytoplankton are converting inorganic carbon (carbon dioxide) into organic carbon (stuff that leaves are made of), there are other organisms in the water that are converting molecules with nitrogen, phosphorous, iron and other elements into some other form. These chemical conversions are integral to the ocean ecosystem.

Some of us will be targeting our laboratory analysis for different molecules to learn what microbes are in the water, and what they’re doing. The following chart summarizes what we can analyze and what that tells us:

As you may have learned in Biology class, all living organisms carry DNA. These are instructions for functions within an organism. Not all of these instructions are used at the same time. Instructions for active processes are converted into mRNA, which are then translated into proteins. The part of this biological process that you analyze depends on your scientific question of interest. Some of us are just interested who’s present (pigments/DNA) or the instructions (DNA). Others are interested in the processes that are active (mRNA, proteins). By analyzing these molecules, we are able to figure out which microbes are in the ocean and what they’re doing.

Filtration setups. Can you spot all the vacuum pumps?

Posted by Grace

Posted by Alicia

Adding chemicals to a tube with the filter to keep the phytoplankton cells preserved. Photo credit Robyn Von Swank, instagram @vonswank.

Using a vacuum pump to concentrate phytoplankton cells onto a filter.  Photo credit Robyn Von Swank, instagram @vonswank.

Posted by Alicia

generating sea spray from water collected offshore California

The R/V Thomas G. Thompson

Posted by Matthew

pH is measured by adding an indicator dye, which turns the water purple, and precisely measuring the color with a spectrophotometer. Although the measurements are simple to make, the instrument is not always available and preparing the samples requires special care, so as not to allow any CO₂ to escape and alter the pH.  It would be much easier for many to collect samples and ship them back to a lab, rather than measuring them immediately on board the ship, but since CO₂ loss and biological activity can contaminate the sample it is currently unknown if it is possible to preserve the samples for measurement in the lab.

On this cruise, I am collecting 2 samples of pH from several stations and water depths. I measure one sample immediately on board. The second one, I add mercuric chloride to halt all biological activity, and seal the bottles tightly to prevent any CO₂ loss. The second bottle will then be shipped back to the lab and measured. The two measurements will be compared to determine if the pH is stable and can be measured in the lab, rather than on board.

Posted by Ryan

Phytoplankton (the microscopic plants that form the base of the marine food chain that directly control carbon dioxide levels) are not the only consumers of nitrogen in the ocean. Certain groups of bacteria known as “denitrifiers” also consume this nutrient, but in contrast to phytoplankton, they do not also draw down atmospheric carbon dioxide. Furthermore, these denitrifiers convert nitrogen to a molecular form not accessible to most other life and therefore prevent phytoplankton from growing. One caveat: denitrifiers are not “bad” by limiting the fertility of the ocean. They are natural and serve essential roles in the climate system. My research attempts to understand what controls these organisms and how in turn they help shape the climate of the planet.

As for who these denitrifiers are: that’s a tough question, and the reason I have a job. My goal on this cruise is to understand which microbes are responsible for consuming nitrogen, and how these organisms structures themselves to form an efficient (or not) community. By sampling for DNA at a variety of conditions (namely dissolved oxygen concentrations) found along the southern California coast, we can begin to evaluate how nitrogen is transformed in the environment, who is doing it, and how fast it is happening.

The ultimate beauty in doing what I do is that it necessarily requires me to go to sea to sample the natural environment because none of the great complexity of life observed in the ocean can be reproduced synthetically in the laboratory. While at sea, I am exposed to the sensational nature of the world around me: gorgeous sunsets, gallivanting whales, and awesome new friendships with the other scientists and crew on board.

Photo credit: Chris Lowery

Posted by Andrew

Recovering sediment with the Multi-corer. This device allows us to bring up 8 tubes of sediment (mostly mud) from the seabed. Sediments accumulate on the sea floor in each year in layers, so the longer the core we recover, the further back in time we can study. Photo credit to Robyn Von Swank, instagram: @vonswank.

Napoleon once said he made all his generals out of mud. Here on the RV Thomas G. Thompson future chief scientists are elbows deep in mud. Today we head back towards shore with an intense coring plan for San Pedro Basin, the region between Catalina Island and the Long Beach area. Although this large (approximately 15 x 25 miles) depression in the seafloor is not the deepest of the region, it has the potential to contain water with very low oxygen content near the bottom. Due to a shallower sill depth of around 800m, the oxygen minimum zone (OMZ) we have been observing in our CTD casts (seen from 650-800m deep) may be trapped at the bottom. This zone occurs because microorganisms living in the water “breathe” oxygen similar to us, in the process of respiration, depleting the finite supply within the water. Previous research from this area has shown that the bottom waters of this basin do sometimes seasonally exhibit this characteristic.

For the coring group aboard, this would provide the opportunity to examine some interesting features of the seabed. Dr. Josh Williams (Virginia Institute of Marine Science) will use a combination of radioisotopes to date the intact sediments we recover. Some of these radioisotopes are naturally occurring (²³⁴Th, ⁷Be, ²¹⁰Pb, ²²⁶Ra), and decay within the sediments over a range of time scales from a few months to a century. Others were introduced with nuclear bomb testing in the 1950-60’s (¹³⁷Cs, ^239+240Pu). Based on the depth and amount present of these radioisotopes in the cores, we can determine the rate at which sediments are accumulating on the seafloor, and therefore assign an approximate age to each specific depth. With lower oxygen waters, there are fewer organisms that are adapted to live on the seafloor in those conditions, so the amount of sediment mixed (bioturbated) will be less, and the thin layers of sediment accumulating will be better preserved. In San Pedro Basin, the sediment accumulating is sourced from a combination of those produced by phytoplankton in the water column (marine) and river run off (terrigenous). The relative input on any given year of these two sources is determined by a multitude of factors, including the amount of coastal rainfall (increases the sediment delivered by rivers) and upwelling conditions (increases the amount of phytoplankton). Evaluating changes in these inputs over the last century, we may be able to see the impacts of humans (e.g., building dams on rivers) and changing climatic conditions recorded in the sediments.

Preparing to process the sediment cores in the ship’s staging bay. Before we extrude (push out of the tube) the sediment, we evaluate the amount of sediment recovered (i.e., the depth the tube penetrated the seafloor) and the condition it is in to distribute among the coring group of scientists based on our individual scientific goals. Photo credit to Robyn Von Swank, instagram: @vonswank.

Dr. Molly Patterson (UMass Amherst) will examine the remnants of organic material deposited on the surface of the sea floor. This organic material is used by paleo(ancient)ceanographers to reconstruct past changes in sea surface temperature (SST) from sediment archives spanning millions of years. These SST reconstructions combined with modeling experiments is widely used to assess forcings, feedbacks and the surface temperature response of past climates. While several analytical techniques exist and have been successfully applied to various environmental settings each has it’s own set of uncertainties. SST reconstructions derived from the degree of unsaturation of C₃₇ alkenones (U^K’₃₇) provide the basis for some of the most reliable estimates of past changes in mean annual SST. Whereas the relatively new proxy based on archaeal tetraether lipids, the TEX₈₆ (tetraether index of tetraethers consisting of 86 carbon atoms) proxy is considered and argued to be less reliable in areas of oceanic upwelling and from sediment records underlying OMZs. Molly will be using the sediments recovered from San Pedro Basin to assess the relationship between these two proxies.

Ph.D. candidate Emily Osborne (South Carolina University) studies the geochemistry of microscopic plankton (planktonic foraminifera) that are deposited and preserved on the seafloor to understand how the chemistry of the ocean has changed since the onset of the Industrial Revolution. As atmospheric CO₂ concentrations have increased exponentially, mainly due to fossil fuel consumption, one-third of that total concentration is incorporated in to the surface ocean. The incorporation of CO₂ in the ocean triggers a series of reactions that cause the pH of the ocean to decrease; this phenomenon is known as Ocean Acidification.

Dr. Chris Lowery (University of Texas, Austin) is a foraminiferal micropaleontologist whose research focuses on the response of marine organisms to climatic and oceanographic perturbations, particularly changes in dissolved oxygen. As the modern ocean warms, its ability to hold dissolved gases like oxygen will decrease. (Kind of like how a cold beer is nice and fizzy, while a warm beer is more flat.) Therefore, it is vitally important to study changes in dissolved oxygen both in the modern ocean and in past environments where oxygen concentrations were more extreme than can be observed today. Chris’s research on this cruise is focused on the former, which will hopefully improve the study of the latter. To put it another way, we have to study the modern ocean to improve our knowledge of oceans of the past, so that we can better predict the future. Makes sense? No? OK.

Chris’s research on the Thompson is focused on two avenues: 1) Studying the assemblage of benthic foraminifera that are currently living in a variety of oxygen conditions and 2) with collaborators, using those living foraminifera from known oxygen concentrations to test a new geochemical proxy for ancient changes in dissolved oxygen. To do this, Chris takes mud from the upper few centimeters of the seafloor, adds a biological stain that marks living foraminiferal protoplasm, and then sticks his sample in the refrigerator for at least 12 hours to incubate. Then he adds ethanol to kill everything in the mud, puts it back in the fridge, and forgets about it until he can return to his lab in Texas to begin the long task of sieving his samples and picking out the foraminifera that were stained.

Multi-core tubes with a recovery of approximately 6 inches of sediment. Although this does not seem like a lot, with a sediment accumulation rate of around 1/16 -1/8 inch per year, these sediments have likely recorded at least the last 50 years. Once back to land, I will use a combination of different radioisotopes to determine these rates more precisely. Photo credit to Robyn Von Swank, instagram: @vonswank.

Posted by Molly, Emily, Josh, and Chris

February 18, 2016
The R/V Thomas B. Thompson constantly measures current speeds during the cruise using an acoustic doppler current profiler (ADCP) mounted to the hull. The ADCP data also reveal the movements of fish and zooplankton as they move vertically in the ocean during diel vertical migrations. During the night, fish and zooplankton are near the surface ocean foraging for food. During the day, fish and zooplankton migrate to deeper depths to avoid visual predators.

The plot shows the ADCP data collected from the cruise so far… One of the daily migrations of fish and zooplankton is marked. Can you find additional signals of migrations in the data? (We were sampling in an area called Cherry Bank, which is really shallow. Cherry Bank is apparent in the plot as an absence of data.)

Posted by Allison

I think the water sampling people are pretty happy, though. They look happy in this picture below, don’t they? A nearby seal has been happy all night, too, eating the school of fish that’s gathered in the lights of the ship.

Prior to the departure of this oceanographic expedition, two (overly-personified) scientific instruments met in the back of a snugly packed minivan as it made the long rush hour trek from L.A. to San Diego to catch the ship. Packed snugly between toolboxes, backpacks, and a (soaking wet) stinky wetsuit, these two beloved pieces of oceanographic research machinery truly hit it off: One a Slocum glider named Rusalka and the other being a Membrane Inlet (quadrapole) Mass Spectrometer appropriately named MIMSy.

Both Rusalka (left) and MIMsy (in the metal box right) packed for their journey to San Diego.

Rusalka was raised in Cape Cod, and moved to California as a young glider. She has spent most of her time close to the Southern California coast, using her fluorometer to chase phytoplankton and dreaming of a world free of harmful algal blooms. Rusulka is capable of making 30-day journeys on her own and diving to 100m. She is intensely curious about the ocean’s oxygen, salinity, and temperature, and what these parameters can tell us about ocean life. On this Valentine’s Day, Rusalka was deployed for a 4 day mission. Upon hearing the news that they would not spend the day together, MIMSy was devastated, resulting in periodic noise observed in her spectra throughout the day.

Rusalka being lowered into the water from the Thompson for her deployment.

MIMSy was a child born of Russian and American parents in Southern California and has worked tirelessly for many years on research vessels from the tropics of the Eastern Pacific to the frigid, unforgiving waters of the Bering Sea. MIMSy’s specialty is to measure the abundances of dissolve oxygen (O₂) and argon (Ar) in seawater at the ocean surface as the ship is moving, throughout the entirety of the cruise track. Due to the nature of this business, she rarely sleeps, never rests, and wears the scars and decorations from each of these journeys:

MIMSy measuring gas abundances in the ship’s underway system.

O₂/Ar is one way to estimate the ‘net’ metabolic state of the ocean, i.e. how much oxygen is produced by photosynthetic plants, but not consumed by respiring animals. The researchers who rely on MIMSy and Rusalka to make measurements for them are very interested in the metabolism of life forms in the ocean, as well as where these microscopic plants and animals live. Early on in their relationship MIMSy and Rusalka realized the potential mutual benefit of their partnership. MIMSy is capable of making measurements of biologically-produced oxygen at the ocean’s surface, while Rusalka is able to dive to 100m making a suite of measurements that can estimate the vertical and horizontal distribution of organisms and chemical species. Together, they provide a rare view of biological production and the effect that it has on the chemical composition of the surface ocean over a large region of the Southern California Bight.

At the time of this post, Rusalka is closely following the R/V Thompson, and her beloved MIMSy, across the entirety of the Southern California Bight hoping that they will soon be reunited. Through the entirety of Rusalka’s deployment, MIMSy has stayed awake every night reciting her insignia, which she acquired along one of her many journeys:

O mistress mine, where are you roaming?

O, stay and hear! Your true love’s coming,

That can sing both high and low:

Trip no further, pretty sweeting;

Journeys end in lovers meeting,

Every wise man’s son doth know.

– William Shakespeare

Happy Valentine’s Day from Rusalka and MIMSy.

Posted by Bridget and Willie

Wait, what day is it?

Is today tomorrow yet,

or still yesterday?

Posted by Chris

Have you ever held your breath and tried to dive to the bottom of a swimming pool? If you have, you might have noticed that you have to ‘pop’ your ears at some point because pressure builds up the further down you go. You might notice that the same thing happens when you are flying in a plane and start descending into the landing. These effects are caused by the same thing: changes in pressure. But you’ll notice that it takes a lot bigger difference in altitude to cause this effect in the air than under the water. This is because water is much denser than air, so that for an equivalent area, say 1 square foot, 33 feet of water have the same weight as the entire column of atmosphere, nearly 60 miles up to space.

This fact is important for ocean life because the average depth of the ocean is over 12,000 feet, which equals nearly 400 atmosphere-equivalents of pressure! Marine life forms, from bacteria to whales, have evolved adaptations to deal with these changes in pressure. Fortunately for us, styrofoam cups have not.

Table 1. Adaptations to life in the deep sea

Styrofoam cups, like marine organisms, are composed of cells. In the case of biology, cells are water-filled sacs with enzymes, sugars, fats, and other organic chemicals that make up life. The cells of styrofoam cups are filled with air. This is a useful property because air is a very effective insulator, which means that it transfers heat poorly, which is convenient if you want to hold boiling water (or coffee) in your hand.

Water, which is the main component of biological cells, is nearly incompressible — if you squeeze it under high pressure, it doesn’t really get smaller. Air, on the other hand, is easily compressible, so that when you squeeze it, it gets a lot smaller. Probably you have several air compressors in your immediate vicinity — cars and refrigerators both have them, for example.

So, the question is: what happens to a styrofoam cup when it is taken out of its natural habitat and placed into the deep sea? To find out, we exposed dozens of cups to a pressure of 380 atmospheres by lowering them to the bottom of the Pacific Ocean. Take a look at what we found!

Figure 1. Before.

Figure 2. After.

Figure 3. Comparison.

Posted by Eric

“if you want the kids back alive (and mostly) unharmed… leave $2.50 by the coffee machine by 5pm. come alone. unmarked bills preferred.”

We took up a collection, and managed to raise $2.44 in ransom money, which was left at the desired location at the appointed time. Soon after, (since we then sat down to eat dinner), a large, um, submarine sandwich (sorry, it was the kidnappers’ pun, not mine) was brought out to Bridget’s table wings inside (also pictured below).

At this time the perpatrators are still at large.

Also, that bread was really delicious. The food on this ship is so good.

Posted by Chris

Today I filtered seawater from a variety of depths in the upper ocean (from the surface down to 120 meters) to collect marine plankton cells that live throughout the sunlit portion of the ocean. I am interested in microbial activities in the surface ocean because this is where sunlight and atmospheric carbon dioxide are captured and fixed by photosynthetic microbes, or phytoplankton, to create a vast pool of organic matter that fuels the ocean food web. The chemical makeup of marine organic matter is inherently complex, a product of the diversity of the hundreds of thousands of different planktonic organisms that make up seawater communities. To determine which of these compounds are most prevalent and potentially important components of the microbial food web, I have collected ocean plankton cells via filtration to return to the laboratory for chemical analysis. There, I will extract cellular (or particulate) organic matter and detect the hundreds of different organic molecules that were produced by the plankton cells. By looking at plankton from several depths throughout the sunlit ocean, I will be able to see which types of organic molecules are produced by the different plankton living throughout the upper water column.

Posted by Bryn

When we use the term “microorganism”, we can be referring to Bacteria (the most common), Archaea, or small Eukaryotic (like plants or animals) cells.  I study Archaea, which are similar to Bacteria in that they are organisms with only a single cell (whereas the human body is made up of 10¹³ cells).  However similar they appear on the outside, they are quite different on the inside, and some of their cellular functions match what is found in Eukaryotes like us.  This makes them an interesting group for study, especially in the ocean where it is estimated that 20-30% of all single cells come from one group of Archaea, called the Thaumarchaeota.

Thaumarchaeota (or “Wonder Archaea”) get energy from converting ammonia to nitrite, much like we eat food to do things like run.  I started working with this group during graduate school, and have been amazed at how little we know about them despite how many exist on Earth.  In particular, I am curious as to how changes in environmental conditions can impact their metabolism to help predict what may happen to these communities as the Earth changes over time.

For this cruise, I have been filtering seawater through small filters that trap the cells so I can extract their DNA and RNA.  Although this method does not select specifically for Thaumarchaeota, I will be able to view them in the context of all microorganisms in community.  I have been using the CTD sampling rosette to capture seawater from multiple depths in the ocean.  From each water sample, I will sequence the 16S rDNA to determine which microorganisms are present in the sample and use 16S rRNA as a proxy for which are active.  In addition, I am using stable isotope tracers of ammonia (¹⁵NH₄Cl) and bicarbonate (H¹³CO₃) to directly measure how quickly the community is oxidizing ammonia for energy or fixing carbon to build biomass.  I also have an experiment planned with Bryn that we will talk about later, involving differences in microbial growth under light or dark conditions.

Posted by Bradley

Sediment traps catch sinking matter in the ocean. Yesterday I deployed a drifting NetTrap close by Cherry Bank. NetTraps are very large, which allows them to collect a lot of material in a short time period.  We left the sediment trap floating in the ocean for 24 hours while we mapped Cherry Bank. Then today we had to find it again.  There was a satellite transmitter on the buoy, but the satellite only passes over once a day. We used the satellite reading to get a general idea of its location. Then when we were close, the ship used radar to identify some potential objects. Wendi finally found the sediment trap with binoculars from the bridge. When we found the trap, we had to grab it with a hook, attach it to a line and pull it onto the ship (see photo).  It all went smoothly, and I got a great sample!

Posted by Clara

A Webb Slocum glider named Rusalka is an autonomous underwater vehicle aka a robot that is joining the cruise research efforts. Rusalka was deployed on Sunday afternoon and will be gliding through the water in the research area until Wednesday afternoon.  It was an exciting deployment day, because the first attempted was unsuccessful as Rusalka detected a leak during her first dive at a depth of 65 meters.  After detecting the leak Rusalka returned to the surface and sent us a message telling us to come for her. In a small boat launched from the R/V Thompson we had a smooth recovery of Rusalka in some rather large swell (10 feet).  After opening the glider, cleaning up the drips and troubleshooting back in the lab Rusalka was successfully deployed and swam off to begin her sampling. The glider will be checking in with the ship about every four hours to update us on her progress. The glider dives to a depth of 100m and then return to the surface in a seesaw pattern moving about 1 km/hr (about .6 miles/hour).

Gliders are neat research robots because they move independent of the ship and are one approach to study complex subsurface ocean dynamics. Gliders can estimate phytoplankton population and can observe physical subsurface features including fronts, eddies, internal waves, and integrated subsurface current velocities and direction.  Rusalka on this cruise will be running a 14 km transect over a seamount. It is theorized that the seamount might be having on influence on regional ocean physics, chemistry, and biology and Rusalka will be helping gather data to test the theory.

The glider was equipped with variety of sensors including a Sea-Bird conductivity-temperature-depth sensor, a GPS, Iridium communications enabling daily data transmission, and WET labs ECO pucks optical instruments. The optical sensors included three fluorometers with excitation/emission channels that measured chlorophyll a, colored dissolved organic matter (CDOM) and phycoerythrin/ rhodamine (540nm/570nm), and an optical backscatter sensor at 3 wavelengths.

Posted by Bridget

^Multicorer

This particular multicorer, which is owned and run by a coring group out of Oregon State (who provide coring support for all UNOLS cruises that need it) has been modified by the MISO imaging group from Woods Hole, who have installed a CTD oxygen sensor so that we can measure oxygen on the seafloor, and, more awesomely, a camera which takes still images every 10 seconds. This allows us to get images of the portion of the seafloor that we sample, and even choose to move our sample location if we don’t like it. Usually this process involves “hovering” over the seafloor, where we hold the multicorer about 5 m above the bottom and let it take pictures for a few minutes, before pulling it back up a few meters and the letting it land at around 15 m/minute. Obviously, it is pitch black on the seafloor, so the camera comes with two strobes to illuminate the scene.

Now, it’s important for you to understand how cool this is. Usually, when you’re coring, you have no idea what the seafloor looks like. You take a 4-inch diameter core, and that’s your only picture of what’s down there. Now, you can have a literal picture of what’s down there, and in this case many pictures. And it’s so cool. I mean, just look at this:

Note the differences between the two. The top is a submarine channel, where sediments flow down from the shelf into a basin. Because this is a higher energy environment it has larger grains (mostly sand) and the ripples that you can see in the image. The second is from the middle of San Nicolas Basin, at 1500 m water depth, in nice soft mud full of burrows and brittle stars and shrimp. You can see the whole benthic community, and have a real understanding of where your sample is coming from.

Also, for just a moment, put yourself in that crab’s shoes. You live on the bottom of the ocean, in pitch blackness. For your entire life, nothing has happened. Then one day, a strobe light comes down from above, and then this giant flashing contraption crashes down next to you, grabs some mud, and then disappears back up into the sky, still flashing as it goes.

Posted by Chris

I have always wanted to see dolphins swimming along the bow of a ship that I’m on, and when I heard we were going to sea off southern California (were that often happens) I really hoped to get some pictures of it. And oh man, did I get some pictures of it:

Soon after this, the bridge radioed down to say that there were a bunch of baby Mola Mola (aka, sunfish) swimming underneath a clump of kelp on the port side while we were stopped to deploy a CTD. More people ran on deck to see the Mola Mola than to see the dolphins. I was not able to get a picture of those, sadly, but they were cool.

My other main non-science goal is to use every condiment that’s laid out on the tables in the galley (there’s about a dozen various sauces at each table). I feel good about my progress toward this goal, too, and will keep you updated as I move forward with it.

Posted by Chris