Volunteers at Work

We have a fantastic group of researchers, engineers, technicians, students, and volunteers out here in the science party, all putting in long hours under often-challenging conditions. Yes, 3 volunteers are working 12-hour watches and participating in the full range of our activities, from assembling and fixing equipment to launching and recovering gear, to watching the mind-numbing screen of the automated SWIMS winch system for days at a time. Here's a tremendous "thank you" to all of them for their contributions to our science!

Volunteer Keaton Snyder and Co-PI Eric Kunze during the pre-cruise loading in Honolulu. (photo credit: James Girton)

Co-PI John Mickett and volunteer Ethan Brush prepare the over-the-side ADCP pole. (photo credit: JG)

Volunteer Keaton Snyder, biologist Kate Kouba, and grad student Hyang Yoon demonstrate their safety gear during a drill the first day of the cruise. (photo credit: JG)

Volunteer Olga Mironenko discovers a treasure-trove of sea life and drifting plastic in the ship's water intake strainer. (photo credit: JG)

Cast away

With the advent of technology that allows us to measure conductivity, and by association salinity, with great accuracy, the CTD has become a standard oceanographic instrument. They come in all shapes and sizes, depending on the platform to which they are applied (ship, float, towed instrument, etc). Most, if not all, oceanographic research vessels have a ship-board CTD, but other instruments that get deployed from a ship also typically carry some form of a CTD.

The ship-board CTD suspended over the water from its crane. The red spring-loaded disk at the top protects the CTD cage from damage by the crane. The numbered bottles of the rosette are visible in gray, with the sensors mounted below. (Photo credit: Rosalind Echols)

 The value in a CTD, which is short for “conductivity-temperature-depth” sensor, is that it allows oceanographers to measure the three variables that affect the density of the water, and density is a primary driver of circulation in the ocean. Warmer water is less dense than cold water, fresh water is less dense than saltier water, and (even though water is mostly incompressible) water at great depth with a huge column of water stacked on top of it is denser than water at the sea surface. As a result, knowing each of these three values is of great interest in determining the density of the water. On our particular project, we are using CTDs on SWIMS, the floats, the buoy, and the ship. Each of them is a different size and has a different sampling frequency according to the limitations of the platform. Ultimately, the measurements each CTD provides allow us to calculate density and then look at how this changes in time and space, which in turn governs how water can mix and move.

Marine techs Jen and Bern and Bosun John guide the CTD back into its home inside the ship. You know what's awesome? A door in the side of the ship opens when it's time to deploy the CTD. (Photo credit: RE)

 Ship-board CTDs are often accompanied by additional instruments, such as a fluorometer (which enables subsurface chlorophyll measurements) and a dissolved oxygen sensor. This expands the range of the CTD from purely physical properties to those of interest to biologists as well. Many CTDs are also equipped with a “rosette” (seen in the picture here), which is a set of large bottles that can be closed on demand to gather water from various depths. Once the water is on board the ship, the water can be tested for pH (acidity, effectively), nutrients, and various other chemical species (like CFCs, heavy metals, and so on), and samples can be collected for biological analysis. Each of these tests allows oceanographers to say something about the ocean: who lives there, what nutrients it uses, how long since a particular chunk of water last interacted with the atmosphere, how the water is changing over time, how organisms are effected by physical changes to a system, and so on.

 

Kate preserves samples by freezing them in liquid nitrogen. (Photo credit: RE)

On this trip, our biologist Kate is collecting water samples at depths ranging from 5 to 200 meters, using the density profile shown by the CTD on the way down to decide where to collect bottle samples on the way up. Once the CTD is back on board, she collects samples for two later analyses: flow cytometry (which will be used to look at chlorophyll levels) and DNA analysis. Some research cruises are equipped with more elaborate biological equipment on board, but in this case much of the space is taken up by the physics equipment, so she is preserving the samples for later use. The goal of the project she is working on with Dr. Anne Thompson of Portland State University is to look at the prevalence of different strains of the cyanobacteria Prochlorococcus, and to see how this relates to what is happening in the physical system (particularly how they adjust their chlorophyll levels after mixing events that move them to a new location in the water column). This is a great example of a project where physicists and biologists are collaborating to understand how two different aspects of a system relate, something that is incredibly important in a complex arena like the ocean.

The CTD is visible below the surface in the super clear water. (Photo credit: RE)

(Deploying the CTD off the ship is called a "cast", hence the title of the post). 

Looking at Data, Episode 2

As mentioned in a previous post, one of the ways we make sure that our instruments are functioning properly is to plot the data in real time and make sure there are no bizarre glitches. This has already allowed us to catch at least one issue, which was fortunately a problem with the data transfer between computers rather than a problem with the sensors on SWIMS (and therefore more easily resolved). Another advantage of looking at the data as we collect it, even if the plotting is fairly rough and not something you would put in a paper, is that it allows us to see interesting features and keep an eye on how things are changing in time and space. One example of an interesting plot we saw during our first survey is shown below. As with many plots of oceanographic data, there’s quite a bit going on.

To orient you to the plot, we’ll start with the basic set up. Each section of the plot captures roughly two hours worth of profiles from SWIMS (the instrument we are towing behind the ship). Time is plotted horizontally (“Yday”), but since the ship is moving, this also represents change in position horizontally along the ship track. Rather than plotting the profiles themselves, as with the plot shown in the previous post about data, here we are gridding the data, which essentially means filling in the blanks between measurements to get a general idea of the three dimensional structure. These plots may not be publishable in a formal setting yet, but they are incredibly valuable for understanding approximately what we are measuring. The top plot shows the temperature from near the surface down to about 100 meters; the middle plot shows the same thing for salinity and the bottom plot shows the same thing for density (which is calculated from the temperature, salinity, and depth since there is no way to measure it directly with a sensor at the moment).

Plot of temperature, salinity, and density from SWIMS data. We look at plots in color scales like these to help make trends in the data be more visually apparent.

The colorbar to the right of each plot shows what each color represents in terms of a number. For temperature, this is degrees Celsius, with red being warmer temperatures and blue being cooler temperatures. Intuitively, looking at this plot makes sense because in some way we expect warmer things to be reddish. For salinity (in “practical salinity units”), saltier is red and fresher is blue, and with density (kilograms per cubic meter, minus 1000), heavier water is red and lighter water is blue. As we expect to see, the densest water is at the bottom, with progressively lighter water above it. We call this “stably stratified”, because there don’t appear to be any situations where heavy water is sitting on top of light water. When this does happen, we expect it to lead to an overturning circulation where the dense water sinks and the light water rises.

The most interesting feature of this plot is the bands of high and low salinity and high and low temperature that we see. In the very first profile, which would be on the left of each plot, we see a fairly typical temperature progression, where it starts out warm and gets progressively cooler. However, as we move farther to the right on the plot, we can see that the temperature goes warm-cool-warm-cool, and the salinity alternates fresh-salty-fresh in a similar way. Put together, this ends up leading to a warm and fresh bit of water at the surface, followed by a cool and fresh chunk of water, then a warm and salty chunk of water, and finally another cool and relatively fresh chunk of water. As we discussed in the last data post, there doesn’t seem to be much of a mixed layer: both temperature and salinity show substantial variations almost all the way up to the surface.

Observing the evolution of structures like this in time and space, and speaking to why they occur, is one of our goals. This could be an example of “interleaving” (or some other comparable restratification process), where two adjacent water masses with different properties and densities slide past each other horizontally, with the lighter water sliding on top and the denser water below. Cool fresh water could also be the result of a rain storm, that then got covered up with another water mass. One of the things that we will be doing once we have finished collecting data is going back to look at features like this to see if we can combine this data with that gathered from our other instruments to get a more complete picture of what’s going on. This will require some effort to separate spatial features associated with the ship moving from temporal features associated with the dynamics of the region, which is not a trivial problem.

The challenges of marine technology

If you open up a magazine about marine technology, you will most likely be inundated with advertisements and articles for equipment that can resist corrosion, extreme pressures, and “biofouling”. These are all major threats to the successful deployment of equipment, particularly if it is intended for long-term use. This applies to oceanographic equipment as well: any metal pieces on our equipment must be corrosion resistant, and the sensors will universally work better if organisms don’t take up residence on or near them.

 

Another view of the recovered rope shown in Olga's post. (Photo credit: Rosalind Echols)

A couple days ago we recovered a length of rope floating in the ocean that we had passed several times while doing a circuit around a region. While rope may seem innocuous, if a ship drives over one and it becomes tangled in the propeller, it can go from a piece of trash to a huge issue, so it made sense to pick it up. When we get it on deck, we discovered that it was covered in gooseneck barnacles. Unfortunately for the barnacles, taking the rope out of the ocean means they won’t be able to survive, but the threat to navigation in this case seemed important.

Close up view of the top of a float. Notice the tiny grain-like creatures clustered around the bottom of the ports. (Photo credit: Rosalind Echols)

When we picked up our floats a few days later, we noticed that there were tiny organisms growing on them, mostly clustered where there are sharp right angles that create some sort of crevice. Upon further inspection at 50x magnification (using a microscope that looks like its heyday was in the 1950s), we pursued some amateur biological classification and decided that they were probably barnacle larvae. In the larval stage, like many other marine organisms (including benthic ones, or those that ultimately live on the bottom of the ocean as adults), they drift freely in the ocean until something comes along that they can attach to. The odds of them finding one of the floats, given the immensity of the ocean, seems staggeringly small, and yet in only 5 days there were hundreds clinging on.

The tiny critter (barnacle larva?) at 50x magnification. Picture taken with a phone through the microscope lens, so please excuse the quality. (Photo credit: Rosalind Echols)

This is just one example of the phenomenon of biofouling, which could also be described in a more positive light as the impressive determination of marine organisms to survive. Any instrument that is going to be in the ocean for a long period of time will likely have to contend with this at some point.

Encounters with marine life

A couple of days ago we came across a thick rope that had been adrift in the ocean for a while and pulled it up on board. A nice bonus: while we were at it a whale started breaching right off the ship and slapping its pectoral fins as if in a thanks. 

When we pulled the rope on board we found that it had become home for a whole community of gooseneck barnacles and crabs of all ages, from tiny transparent babies to well-grown sturdy reddish adults. Our team fished out all the crabs, much as they tried to run for it and escape from the big two-legged creatures in colored hard hats, which they did, and released them back into the water. 

The barnacles, being attached to the rope, were less lucky and, to be honest, we all feel really sorry for them. 

Prepping for Round Two

We just concluded a 24-hour transit to our new location with a cast from the ship's CTD and a midnight deployment of SWIMS to start surveying the area. During the transit, even though we weren’t actively gathering new data with most of our instruments, we still had plenty to do. As thoroughly as we tested everything before we left, the ocean is a harsh and unpredictable place, and there are always improvements to be made to insure that we make the most of our time out here, whether it’s cleaning an instrument, opening it up to check the circuits, or fixing glitches in our processing programs.  

One of the projects we undertook was stabilizing the ADCP attached to the bottom of the buoy chain. The design of the cage around the ADCP was such that the battery and instrument weren’t being held in place as tightly as they needed to be, threatening the power cable and reliability of the measurements. The new-and-improved design increases the friction between the clamps and the frame, and secures the power cable more tightly to the instrument.

The ADCP (black) and its battery (blue) in the holding cage. It hangs vertically from the buoy chain, which means preparing for strong vertical motions is important for keeping the instrument working. (Photo credit: Rosalind Echols)

Every time we use the big ship-board CTD with the rosette (a set of 24 bottles used to gather water samples from different depths for biological and chemical tests), we have to empty it, reset all the firing pins that close the bottles, and rinse it thoroughly with fresh water. In fact, every time we take an instrument out of the water we perform this fresh water rinse to minimize the corrosive effects of the salt water. One of the primary challenges oceanographers face when trying to make measurements in the ocean is that many of the interesting characteristics of the ocean (it is deep, turbulent, and salty, for example) are really bad for electronics, metals, and so on. Many of the engineering challenges are comparable to launching something into space.

Our biologist, Kate Kouba (from Portland State University) resets firing pins at the top of the CTD rosette after gathering water samples. (Photo credit: Rosalind Echols)

Before we put everything back in the water, we are also looking at the data we’ve already gathered, both to keep an eye out for interesting physics but also to see if there were any bizarre data standouts that might suggest a malfunctioning instrument. Sometimes, weird, unexpected features of the data are interesting phenomena, but they can also mean that a probe isn’t working correctly, so closely monitoring the data as it comes in is an important step in making sure that the data we come home is meaningful.

Looking at Data, Episode 1

After approximately five days of surveying our present area, following the floats and buoy, we’ve been able to gather some really interesting preliminary data. Today we’re going to talk about one particular characteristic of the float data that has caught our attention. As mentioned previously, each of the floats is freely drifting with the currents, profiling from approximately 200 meters depth up to the surface. On the way up, the floats gather temperature, conductivity, pressure, and velocity measurements. The conductivity is then converted into a value for salinity, or how “salty” the water is.  

In much of the world’s ocean, some portion of the top of the ocean gets thoroughly mixed by atmospheric forcing, and so up to some depth, the temperature and salinity remain relatively constant. This portion of the ocean is referred to as the mixed layer and this description is most true for regions or times with regular strong mixing events (such as a storm) without a lot of heat or freshwater input. For example, in the North Atlantic Ocean in winter, where there are incredibly strong storms with relatively weak shortwave radiation from the sun, the mixed layer can be several hundred meters deep. However, in regions where there is a daily cycle of intense solar radiation or extreme rain events under low wind conditions, there is very little mixing and so the ocean can be substantially stratified all the way up to the surface because substantial changes to the temperature or salinity are occurring at the surface that can’t be mixed down.

Depth profile of temperature (red), salinity (blue), and density (green). Notice the twists and turns in each profile between 0m and 50m, suggesting substantial changes in each quantity. 

 Climatological (average) data for the region we are currently in suggests that there should be a winter mixed layer on the order of 100 meters deep. However, the float data we have gathered thus far shows substantial changes in both temperature and salinity beginning from the near-surface. The profile shown here illustrates that (temperature is in red, salinity in blue, and density of the water in green). If there was a well-defined mixed layer, we would see the top section of each of these profiles almost completely vertical and uniform. What we actually see here is that the top 50 meters has variations in all three variables. If you look carefully, you can see that between roughly 50 and 125 meters there is a somewhat uniform section (or at least less variation), which could be the remnants of a previous mixed layer on top of which other effects have been superimposed.

Determining the exact cause of this pattern of surface stratification is difficult, and will certainly require more in depth analysis of our data from multiple sources. Increased temperature at the surface (which appears regularly in different profiles) could be due to strong solar radiation effects (which penetrate some distance into the water column) that are not being fully mixed in, for example. It seems unlikely that this is happening in this case because the near-surface temperature doesn’t show the exponential decay associated with radiation (because the floats typically stop measuring around 10 meters depth, we can’t rule it out yet). Another possibility is that the float is moving between different water masses as it profiles due to differences in horizontal velocity at different depths. A third option is that these variations could also be due to interleaving of pre-existing parcels of water from the type of restratification event we are looking for. At this early stage, it is hard to know for sure.

One step in the float retrieval process. Making sure the instruments at the top don't hit the side of the ship is of paramount importance. (Photo credit: Rosalind Echols)

Today we’re picking up the buoy and floats and heading north. 70 and sunny has been a lovely respite from winter weather, but in order to find the kinds of mixing events that will allow us to observe restratification processes in real time, we need to go in search of a front near some more interesting weather.

Bringing the buoy alongside the ship, while protecting the sensors at the top. (Photo credit: Rosalind Echols)