Ecosystem Responses to El Niño

Month: April 2016

When life hands you lemons, make SKrillEx 3.

A few days ago we were nearshore and a storm was rolling in. The weather was so bad that the captain said we had to stay nearshore for an extra day before beginning the two-day steam out to our next study location.  It felt like we were going to waste an entire day, except to Cat Nickels of the Ohman Lab.

For the last two summers, Cat has carefully planned two student cruises in these nearshore waters for her PhD thesis, in a place called Nine Mile Bank. Nine Mile Bank (nine nautical miles offshore, if you couldn’t guess) is a feeding ground for blue whales during the summer, but she has seen blues, fins, and the occasional humpback there.  Cat’s thesis focuses on whale-krill interactions, and she is interested if the topography of the bank affects krill aggregations and whale feeding patterns. SKrillEx 1 (Student Krill Expedition) took place in the summer of 2014 and took months to plan; it had students from multiple labs working on chemistry, benthic ecology, microbiology, microbial ecology, and microplastics. SKrillEx 2 (summer 2015) also took months to plan and revisited the same site to ask similar questions.

SKrillEx 3, as we came to call this day at sea, was planned by Cat in 20 minutes. When the captain said we had to stay nearshore, Mark Ohman asked if we could go to Nine Mile Bank. Soon Cat was plotting coordinates for an MVP transect and an all-night bongo tow transect like we had done the last two summers. This pre-blue whale season third replicate may end up being extremely useful for Cat’s thesis and it was all because of stormy seas and quick thinking by Mark and Cat.

The all-girl night shift on the bongo:


Cups! Cups! Cups!

It is that time of the cruise for the sacred maritime tradition of….shrinking styrofoam cups.

I have no idea who figured out this odd pastime at sea, but the reasoning goes like this: As you move deeper into the ocean, pressure increases due to the weight of the water above you.  All of our equipment has to be rigorously pressure-tested, and is all graded to only go to a certain depth.

Styrofoam is polystyrene plastic that is formed by blowing air into  the plastic during creation.  So, what happens when you attach Styrofoam to said equipment and send it to the bottom of the sea? The increasing pressure with depth pushes the air out of the plastic, and you are left with condensed Styrofoam, sans air. In simpler terms, the pressure causes everything foam to shrink, while the metal equipment, not comprised of air, comes back up in the same shape.

Anything you draw on the cups shrinks with them. We sent down one bag of decorated foam cups, wig heads, and cubes from the science party on board, and two bags from a local San Diego middle school.


First Cat, Maitreyi, Belli and Ali prepared all the cups by filling them with paper towels and tape to maintain their shape, and then zip tying the laundry bags closed so we didn’t lose any to the ocean.


Then the Science Techs kindly zip tied them to the CTD for the deepest cast of the cruise. The cups went to 3000 m!

The cups came back a little smaller (note the difference in bag size):


The most impressive part are the before and after shots:


My head shrunk a lot at 3000 m!



Pulling up the sediment trap!

The Landry/Stukel labs have sediment traps that drift in the ocean (measuring a water parcel in a Lagrangian way).  On the sediment trap array there are traps at various depths as well as buoys and a drogue that cause resistance with the water and allow the drifter to drift with a certain parcel of water. These sediment traps, as well as the Landry lab drifters, are the first thing put in for each of our measuring cycles and the last thing taken out, and each cycle’s area is partially defined as the water parcel that the drifter covers.

We normally put the sediment traps and drifters in and take them out in the middle of the night, but due to some complications with Cycle 1, we removed the sediment trap today in broad daylight, which allowed those of us who work during the day to finally see what happens!


First there was a lot of waiting over the side as we saw it approach. Then the crew caught it with a grappling hook and pulled it to the A-frame in the back of the ship.


Once we had it securely tied off, it was pulled through the winch in the A-frame and the 150 meters of line was pulled up on deck. Each piece of the array (the buoys, the drogue, the sediment traps) were removed from the line as they were pulled up.  Ali and Belli were manning the capstain pulling up the line –  good work girls!


The most important part of the array – the sediment traps themselves – were positioned at 100 m and 150 m.  Each tube was carefully removed from its array as they came up – ready for Mike Stukel and Tom Kelly to analyze before the start of Cycle 2 tomorrow.

Tie It Down!

When you’re out at sea, you have to think about where your gear is so it is easy to get to at a moment’s notice, and so it is in a logical place for everyone to find, on the day and night shift.  But you also have to tie it down so that your expensive gear doesn’t go flying if the boat hits rough weather. You have to think about your gear moving in multiple directions as the boat moves.  You don’t want things to shatter or spill because you tied things down worrying about things moving front-to-back and the boat starts lurching side-to-side.

We have been steaming along and hit some rough weather the last few days, so our skills at tying down our science equipment have been tested. Steven our Science Tech said on the first day that we won the award for the best tied-down labs he had seen, and two nights ago that definitely proved true. The boat hit one huge turn, and everyone felt it. The crew lounge lost a painting off the wall, and I was in a chair that may or may not have gone flying into a wall. (The bruises aren’t that bad Mom, I swear).  But the science gear stayed intact! The only things that were really moving around were the chairs.  We had a few things we needed to tighten down, but we had no disasters.

Here is a list of the most common tie-down techniques at sea:

  1. Ratchet straps. You can tighten down everything from big boxes of gear to CTDs and Bongo frames.  And they can get as tight as you need with easy release when the supplies are needed.
  2. Bungee cords. Perfect for shelves in lab and drawers you need to open often. They’ll hold things in rough weather, but are easy to move and you can get into the boxes they’re securing.
  3. Rope. If you’re good at knots, this is good for tying things that aren’t moving for the whole cruise, like microscopes and vacuum pumps.
  4. Wood. We screw little pieces of wood (called fering strips) in to wedge things in to tight spaces. We also screw eye bolts into the wood and then tie rope over things.
  5. Unistrut and Eyebolts. This really goes along with the other things, but the ships have unique strips on the wall (Unistrut) that allow us to put eyebolts at whatever height we need.  There are also bolt holes at set intervals in the floor of the deck and lab spaces, as well as the lab counters that can be filled with eyebolts.  The boat is designed with securing in mind!
  6. Latches. Every door and cabinet is built with extra latching in place so it doesn’t fly open.  There are also lips and metal bars on all the shelves to keep things secure.

We make life at sea as secure as possible, so things flying across the room doesn’t ruin the science!

Spotlight on: Mike Stukel’s Research

Mike Stukel, a former CCE grad student, is now a professor at Florida State University.  He and his grad student Tom Kelly are on the cruise deploying sediment traps and filtering countless liters of water. I could explain what they are doing, but here it is in Stukel’s own words:


What you are researching:

I study the role of microscopic organisms (plankton) in the global carbon cycle. Phytoplankton (the tiny plants of the ocean) float in the surface layers and constantly take up carbon dioxide while doing photosynthesis. In fact, they are responsible for half of the world’s photosynthesis and as these tiny organisms remove carbon dioxide from the surface ocean, carbon dioxide is drawn out of the atmosphere. However, most of these phytoplankton will die in the surface layers of the ocean and the carbon that they have fixed will be respired by zooplankton (tiny animals like krill), bacteria, and fish and hence go back into the atmosphere. However, if the carbon taken up by these organisms sinks into the deep ocean, it will be removed from the atmosphere for periods of decades to millennia.


What instruments you are using:

I use two primary types of instruments. One is called a sediment trap, and it is an instrument that I deploy in the ocean. It will drift along with the water for a period of 3-4 days, while communicating its position back to me by satellite. While it drifts it will also collect particles that are sinking in the ocean, so that I can measure carbon flux. I also use a beta counter that allows me to measure low-level radioactivity in the ocean. The background radiation levels in the ocean are incredibly low (they are not at all harmful to you or me), but the information they provide allows us to learn about ocean processes.


What types of data you are collecting:

I collect samples related to the transport of carbon from the surface ocean into the deep ocean. This includes direct collection of sinking particles and also biogeochemical proxies that allow us to estimate carbon flux. One example of a biogeochemical proxy is the ratio of Uranium-238 to Thorium-234. Uranium-238 is found naturally in the ocean at very low concentrations and it has a very long half-life (meaning it decays very slowly). When it does decay, its first long-lived daughter particle is Thorium-234 with a half-life of approximately a month. If you were to take a sample of seawater and put it in a bucket for a few months, the uranium and thorium would reach what is known as secular equilibrium – the thorium would decay away at the same rate that it is produced from uranium. However, thorium and uranium behave differently in the ocean. Uranium acts like a salt and stays dissolved in the seawater. Thorium sticks to particles so when those particles sink they take thorium with them and we find less thorium in the surface ocean than we would expect. Thus if we measure the concentrations of thorium and uranium in the ocean, we can calculate the rate of export of sinking particles from the surface ocean (and the amount of carbon and thorium that they have taken with them).


Why normal people would care why you are doing what you’re doing out there:

Humans are releasing ~7-8 petagrams of carbon dioxide into the atmosphere every year by burning fossil fuels. The biological pump, meanwhile transports ~5-10 petagrams of carbon dioxide from the surface ocean into the deep ocean, thus removing carbon dioxide from the atmosphere. It is important to keep in mind that this is a natural process and it is balanced (in part) but carbon dioxide that gets released from the ocean after upwelling. However, we do not know how the biological pump will change in the future as the ocean adjusts to warmer temperatures, greater stratification, and ocean acidification. If the biological pump becomes stronger, we would expect climate change to happen more slowly. If the biological pump becomes weaker, we expect that climate change will speed up. My goal is to help predict which of these scenarios is more likely.


Tom Kelly stands in front of one of their filtering racks.

The Things We Carried To Sea (an annotated packing list)

I packed my pink hard hat. Most people use the ship’s hard hats, but the color makes me easier to spot in pictures, and having my name on it helps the crew remember what to call me.

Ali is bringing a playlist to help keep her spirits up after hours of filtering. There is a 95% chance ABBA is included.

Jenni packed her Minnie Mouse sheets so that her bunk bed feels a little bit cozier. They also match my pink sheets but we didn’t plan that in advance. We did request to be roommates though, so the color coordination works out.

Angel brings his own Coca-Cola. As a non-coffee drinker, there is only one thing that keeps him awake and going on cruises, especially when he starts work at 2 am, and that is coke. When you work in a trace metal van, the last thing you want to do is to leave the van to get a drink to keep you working.  The van needs to be as clean and trace metal free as possible.

Ali packed salted caramel chocolates. Laura is bringing three jars of almond butter (one jar for each week of the cruise).

Laura is bringing extra running shoes. A big challenge of shipboard life is developing the physical balance to do squats after a 2 a.m. shift. Finding someplace to run is a challenge too, but there is a treadmill stashed in a hallway.

Ali, Jenni, Maitreyi, and I all packed knitting projects to work on during our downtime, along with watching movies and reading books.  Ali has her Kindle (and real, paper books) to read in the wee hours of the night when no one else is up and she is filtering liters and liters of water.

Laura is bringing at least seven binders of class notes to study for her upcoming end-of-first-year exam. However she will probably (metaphorically) toss all notebooks over the side when she realizes that sorting plankton, titrating water samples, and watching waves roll across the ship’s bow are the most effective ways to study oceanography!

Contributors: Ali Freibott, Angel Raucho, Jenni Brandon, Laura Lilly

Compiled and Edited by: Cat Nickels

Day 1: And We’re Off! Well, Kind Of.

Day 1, April 19th, 2016.

We left the dock. And made it all the way to… San Diego Harbor.

The first order of business was calibrating the acoustic equipment (the EK60).  The acoustics are used to find distributions of hard-bodied plankton and fish in the water column.  The difference between acoustics and nets is that the acoustics are running continuously throughout the cruise, and then the nets can help clarify what the acoustics are detecting by sampling those acoustic layers at discrete moments.

To calibrate the acoustics, we first anchored the boat.


Then we triangulated a metal sphere under the boat that the acoustic beam can see easily. To triangulate the sphere in different spots, we used down riggers that basically looked like fishing poles. It took all day, but the scientists helping were troopers!

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Loading Days, Day 2

Day 2 of Loading Days is about the details.

It’s about finding where things will actually go, seeing if they all fit there, and tying them down once they’re there.

Sometimes, you realize you need things just a little taller then you thought you did. That’s when it’s helpful to have someone like Ben Whitmore around who loves to build things with power tools.


Day 2 is about figuring out if you really have everything you need, and maybe running back to Scripps and Home Depot multiple times for those last precious things before you leave port the next day.

It’s about setting up your equipment and making sure everything is really working. Tristan Byard was literally inside the CTD rosette much of the day setting up his UVP plankton imaging system! (Look hard, he’s in the picture!)


Loading Days can also be a lot of hurry up and wait. The Barbeau lab was waiting for their winch for four days before it finally arrived late on Day 2. They need a special winch with rubber-coated wire because they are measuring trace amounts of metal in the water of their CTD bottles, and the normal iron wire on a normal winch would contaminate all their samples. There were also three separate trips from the liquid nitrogen supplier before we had everything we needed to fill our dewars.



The most important part of Day 2 is tying everything down. Especially with the Sikuliaq’s reputation for rocking and rolling!  You have to tie down every little thing, turning Ali Friebott’s fume hood into half chemistry experiment/half woodshop.


Loading Days, Day 1

Loading Days’ Day 1 was really yesterday, but I was too tired after it to post!

Steps to a successful loading day:

STEP 1) The week before, stack all the things you need in a few places. Because you’re guaranteed to forget things otherwise (and maybe anyways).


STEP 2) On loading day, rent a big truck and load all the goods with your lab mates.


(this photo was totally not staged I promise).

STEP 3) Get to the boat for the first time, be a little overwhelmed by how large it is, how many decks there are, and how much you have to load on to it.


STEP 4) Admire all the empty lab space.


STEP 5) Immediately fill it with every box imaginable, in no logical order, as they get craned off the trucks.


STEP 6) Spend the rest of the day slowly building some order out of the chaos, and figuring out how you’re going to work in the space for the next 24 days.




Cruise Prep Underway!

The cruise is less than two weeks away, and all the labs are hard at work preparing. In the Ohman lab, this requires preparing lots of filters for analyzing the biomass and gut fluorescence of zooplankton that we will pull up in the bongo nets. First, this requires cutting lots and lots of 47 mm filters. The quickest way to do this? Heating up a 47 mm “cookie cutter” and using it to cut through 202 μm Nitex.


Those filters are then used for three things: biomass, gut fluorescence, and gut contents.  To measure biomass, the filters were desiccated for 24 hours and then weighed, as Jeff Ellen is seen doing below.  After the cruise, the filters and their newly obtained zooplankton biomass will be again desiccated and weighed.


To measure gut contents, the filters are glued in cups that have holes drilled in the bottom and top (not pictured-Ben Whitmore drilling all those holes!).   Here Laura Lilly glues the filters in the fume hood (the glue is fragrant!) while Cat Nickels burns more filters.

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The cups are then pre-numbered and boxed up for the cruise. The gut fluorescence filters are put in plastic petri dishes and pre-numbered, as are the desiccated, weighed biomass filters. There’s a lot to keep track of, but Jenni Brandon seems to have a handle on it!