Marine Technical Internship Blog

On Monday we took an official tour of all the spaces in the CMORE building associated with the HOT team. We had been introduced to the spaces we were using so far but it was cool to see the full picture!

Unfortunately due to an allergic reaction I was out for part of Monday and Tuesday, but by Wednesday I was feeling ready to jump back in!

On Wednesday I learned how the HOT team determines the total dissolved inorganic carbon (DIC) in seawater samples. They use a machine called a Single Operator Multi-parameter Metabolic
Analyzer, or SOMMA. Dan Sadler walked us through each step that the SOMMA uses, and I practiced running samples.

First, water samples are placed in a water bath to achieve a constant temperature. A second water bath surrounds the sample when it is connected to the SOMMA for processing. The SOMMA begins the analysis process by rinsing the interior plumbing twice with sample, then pumps a set volume of sample into a secondary flask, also surrounded by a water bath. The SOMMA uses an open circuit and the conductivity of seawater to determine when each chamber is sufficiently filled.

The set volume of sample then moves on to the ‘stripping chamber’, where it is reacted with phosphoric acid. This change in pH shifts the chemical equilibrium so that all DIC in the sample is in the form of CO2. In the same chamber in the SOMMA, carbon dioxide free air bubbles through a frit to carry CO2 derived from the sample on to the next processing step without any seawater or acid.

The CO2 derived from the sample moves through a condenser that removes water vapor by chilling the sample, then passing it through a column of magnesium perchlorate. Then, the gas moves on to the coulometer cell.

In the coulometer cell, the CO2 derived from the sample is returned to solution by reacting with an absorbent containing ethanolamine. As CO2 enters the coulometer cell, it acidifies the solution( producing H+), causing a blue indicator dye to fade to clear. A beam of light passes through the solution, and when the transmission of light begins to increase, the machine understands that CO2 is being added and starts to titrate.

The machine titrates by adding a measurable number of electrons to the coulometer cell. An electric current is applied to a silver anode submerged in an anode solution, attached as an ‘arm’ alongside the larger cathode chamber of the coulometer cell where the sample is deposited. The anode and cathode chambers are separated by a frit that allows electrons to pass through, so when more electrons are added to the anode chamber, the concentrations balance and more electrons are added to the cathode chamber as well. When the SOMMA detects CO2 in the coulometer cell and starts to titrate, it keeps a ‘count’ that directly corresponds to the number of electrons added, based on the time interval, current and voltage.

When electrons move into the cathode chamber, they react with water, producing hydrogen (H2) and hydroxide (OH-), a base that neutralizes the H+ created by introducing CO2 from the sample. This neutralization is reflected by the indicator dye, which becomes darker in color. When the transmission of light drops to 29%, the machine stops adding electrons and waits. The SOMMA records counts every minute, but since CO2 continuously moves into the coulometer during the analysis process, it doesn’t stop titrating until the count is below baseline for four consecutive minutes. When the count is at or below baseline, this means that no more CO2 is being introduced to the sample because all of the CO2 has already been ‘used up’, neutralized, and accounted for.

Finally, we can account for the number of counts included in the background rate (about 5 counts for minute with the HOT team’s current SOMMA) by multiplying the background rate by the time required for analysis, which can vary for each sample. Then, we can subtract this from the total counts and calculate the corresponding number of electrons needed to neutralize all of the CO2. Since the ratio of H+ to OH- is one to one, this also tells us the moles of CO2 present in each sample.

We already know that the SOMMA uses a fixed volume at a specific temperature, so with the moles of CO2 in the final step we can calculate the concentration of DIC per kilogram of seawater.

All of these reactions happen internally within the SOMMA, and proceed automatically after inserting the sample and starting the analysis process on the associated computer. It’s an incredible instrument and I was so excited to learn how it works!

The SOMMA only uses a small portion of each water sample for its analysis: so the remaining water is titrated to determine alkalinity. The HOT team collects enough water to redo either the SOMMA analysis or the alkalinity titration, in case any problems arise during analysis.

In the afternoon, I met with Dr. Fanny Girard, a professor studying deep sea corals. My undergraduate research focused on habitat mapping at a methane seep, and I’m also interested in deep sea ecology, so I was excited to talk in person! She was able to help me identify the family of some black corals that I had observed at my study site (Pythia’s Oasis) and show me some beautiful corals of her own from her latest cruise.

On Thursday, we went to work with Dan Fitzgerald and saw his lab at the Marine Sciences Building. He had recently returned from a WHOTS cruise where a mooring was recovered, so he had some ADCPs and mini-CATs with new data to download! ADCPs, or acoustic doppler profilers, measure current speed throughout the water column by interpreting the reflectance of acoustic pings off of particles moving with the water.

Mini-CATS measure conductivity (salinity) and temperature. We pressure washed the instruments to clean off biofouling before carrying them up to the office.

Dan uses a variety of cables to establish direct communication with each instrument, run commands, and download data, depending on the generation of each instrument. He gave us an introduction to serial communications and gave us some tips on navigating and troubleshooting. I got to ask lots of questions about ADCPs and take them apart to access the data! We learned that mooring ADCPs have additional considerations compared to shipboard ADCPs, since you can’t use a ship’s heading, and moorings can spin and tilt in the current. Instead, WHOTS ADCPs have a magnetic compass and tilt sensors. The magnetic fields around the battery packs, which are created in-house, can interfere with the compass – so Dan taught us that it’s important to degauss our instruments.

That afternoon, I had the chance to meet with Dr. Julia M. Hummon and Dr. Eric Firing, who lead shipboard ADCP management in the UNOLS fleet and beyond. They reach out to ships if they notice problems with any of their ADCPs, guide troubleshooting, and oversee installation, as well as leading workshops and processing ADCP data for their clients. They had some great insights about the skills and qualities necessary to be successful in their field.

On Friday, I traveled back down to the beach lab to work with Hunter Adams, a SUBSEAS technician. The SUBSEAS program focuses on understanding the cycling of organic carbon between the surface ocean and the mesopelagic. This program works closely with the HOT team and will be joining us on our next cruise!

While working with Hunter we learned how to replace hardware on a trace metal CTD rosette, and got an introduction to some of SUBSEAS’ other instruments.

We saw the WireWalker, a profiler that uses wave energy to ‘climb’ down its own tether to record data across the water column, and Hunter demonstrated how to talk to the instrument using serial communications. He gave us some advice for troubleshooting and walked us through testing the connection for each pin on a cable when interfacing between multiple instruments. WireWalker uses a CTD logger in combination with other instruments, so proper communication and programming is especially important for this profiler.

Though SUBSEAS’ Seaglider was all boxed up, there were some other Seagliders in the lab! Hunter talked us through their basic mechanics and deployment process. SUBSEAS’ Seagliders have a CTD, fluorometer, dissolved oxygen, and a fragile shear sensor that makes deployment and recovery a delicate operation!

Finally, we bench tested a Vertical Microstructure Profiler, an instrument that measures small differences in shear. We blocked off the instrument in a faraday cage of tinfoil connected to ground, turned off the lights, and avoided moving around the room while the instrument ran. The sensors operated as expected once we had blocked out background electrical noise, so they should be ready to go for their next use case.

All in all, I had an amazing week continuing to learn and meet new people!

We embarked on HOT Cruise 367 early Sunday morning. After a little time to unpack, we completed our safety drills and left the harbor.

We practiced sampling a CTD for oxygen, chlorophyll, and nutrients on our first cast, and recorded the surface temperature with a thermometer over the side. We also shadowed a HOT technician while they prepared and analyzed pH samples from the CTD. Each sample was placed into a specialized container with a set amount of pH indicator dye, and run through a spectrophotometer. In order to ensure accuracy, the pH of the dye was tested and adjusted before use, and samples were kept at a constant temperature using a water bath.

Next, we got started preparing sediment traps for deployment. The first step was preparing the ‘HOT sauce’: a mixture of formalin, seawater, and salt to fix sediment samples and keep them in place. After filling each sediment trap, we deployed them over the side on a cross.

Finally, we learned how to record meteorological observations. Every four hours, we recorded latitude, longitude, atmospheric pressure, and humidity. We measured the humidity manually using a psychrometer on the ship’s bow.

After my shift, I had the chance to go star gazing, and saw beautiful views of the Milky Way!

On Monday, we focused on sampling our CTD for particulates, including carbon, nitrogen and phosphate (BPO4).

For particulate carbon and nitrogen, we collected large carboys of water from each CTD bottle, then filtered each carboy using positive pressure (nitrogen gas). Some carboys took longer to filter than others – another HOT technician noted that certain depth ranges (~175 m) had more material in the water and clogged up the filters more quickly. Once each carboy finished filtering, we collected the filters for further processing. Back on shore, each filter will be combusted – thermal conductivity sensors can be used to determine the composition of carbon and nitrogen present on each filter. The filters themselves are made of glass microfiber and will not burn – in fact, they are combusted before use as well, in order to remove any contamination.

The process of collecting particulate phosphate (BPO4) samples was similar to collecting particulate carbon and nitrogen – large carboys were filled with water and filtered. However, the preparation and analysis is conducted differently. BPO4 filters are acid cleaned as well as combusted before use. After BPO4 found on the filters is combusted and converted into orthophosphates, they are dissolved in various acids to create a colored solution that is then measured with a spectrophotometer.

On Tuesday, we learned how to sample for ATP – a useful method to estimate microbial biomass (excluding viruses). First, we filtered the seawater from our CTD using negative pressure (a vacuum pump). This step captured ATP associated with living biomass but not ATP dissolved in the water, which passed through the filter. Next, each filter was boiled in a test tube containing Tris-buffer, to extract the ATP, before being frozen to preserve each sample for further analysis.

ATP samples are analyzed using the firefly bioluminescence assay, where the enzyme luciferase (found in fireflies) catalyzes the oxidation of ATP dependent D-luciferin to oxyluciferin, and emits light. The amount of light emitted is proportional to the number of enzymes activated, which is in turn proportional to the available quantity of ATP in each sample. By measuring the amount of light generated with a luminometer, we can measure how much ATP is present. I was super excited to learn about this method, which was new to me!

Next, I learned how to fix and flash freeze samples for microbial analysis. First, we added a low concentration of formaldehyde, and then we dipped each sample tube into a dewar of liquid nitrogen.

We continued taking samples from our CTD water. We sampled for chlorophyll, by filtering seawater and placing filters in test tubes with acetone to extract pigment. We were careful to wrap each chlorophyll sample with tinfoil to prevent the pigments from degrading with exposure to light. We collected water to test for salinity in order to ground-proof the conductivity sensors on the CTD.

I also shadowed a marine engineer while he collected zooplankton samples, and observed the plankton under the microscope.

Finally, we deployed our CTD on a deep cast to 4725 meters, and sent along a bag of Styrofoam cups! When we recovered the CTD, the Styrofoam cups had all shrunk in size due to the pressure at depth.

On Wednesday, I was trained on conducting Winkler titrations to determine the quantity of dissolved oxygen in a water sample. After my training, I worked on running titrations for the rest of my shift. I was excited to practice some chemistry!

On Thursday, I took a tour of the engine rooms belowdecks and finished up the rest of the oxygen titrations. I also spent some time familiarizing myself with the various instruments and data streams coming through the computer monitors in the CTD lab, including the ADCP. Near the end of my shift, a storm petrel flew into the loading bay and had to be relocated!

On Friday, we returned back to port in Honolulu. After packing up and cleaning our rooms, we unloaded all of our cruise gear and samples, and put them away back in the lab.

I loved spending time at sea, and I can’t believe my first cruise with the HOT team is already over! I learned so much about different instruments and sampling techniques, and I can’t wait to continue my work over the next couple of weeks.

The weather was beautiful as we unloaded and we had a little bit of a rain shower. Apparently, the real treasure at the end of the rainbow is a CTD!

I arrived in Honolulu this Tuesday and had the chance to meet the team and assist with mobilization for our upcoming cruise. It was amazing getting to see and participate in the work that goes into maintaining such a high-quality time series dataset!

On Wednesday, I completed a safety training quiz and assisted the HOT team at their onshore labs in the C-MORE Hale building on campus. I helped prepare water for nitrogen fixation incubation experiments, which was a lot of fun – after the team removed other gasses from the seawater, we chilled the water and enriched it with nitrogen. In order to dissolve the nitrogen bubbles into the water, we used a highly technical tool – a flyswatter!

Next, I helped out with acid cleaning to remove any trace metal contamination from some of the HOT team’s lab equipment. In between tasks, I could look out the window and see White Fairy Terns, or Manu o Kū, perching in the nearby trees. The team was very welcoming and showed me a good cafe to eat at for lunch, with amazing banh mi!

After that, I learned how to run chloropyll samples with the HOT team’s fluorometer. The team had conducted an extra transect between their normal station and shore, and still had samples left over, so I was able to practice. At first the fluorometer was acting up, but the readings returned to normal after we turned it off and back on again!

After work, I was able to explore the campus Japanese gardens near my lodging.

On Thursday, I toured the ‘beach lab’ at the marine operations center and got started preparing a CTD for the cruise. We got to see different winches, sediment traps, wave buoys, and the ROV Lu’ukai, as well as getting our first glimpse of the R/V Kilo Moana!

We learned how to string the niskin bottles on a CTD rosette – which, like a lot of things, is easier with a little teamwork! I had cocked CTD bottles before, but I had never previously worked with the internal springs that hold the caps in place. This experience gave me a much better understanding of how these instruments work – the top and bottom caps of each niskin bottle have to be connected with the right length of cable and spring, without damaging the O-rings that help the bottles seal shut after sampling. The HOT science team re-strings their CTD bottles before each cruise to avoid leaving them under tension and reduce unnecessary wear and tear on their equipment.

Next, we were introduced to the sensor array on the CTD itself. The CTD had hit the seafloor during a cast on a previous cruise, so they wanted to replace the more susceptible sensors in case of any damage. One of our mentors demonstrated how to replace a conductivity sensor, and then gave us a chance to practice. Then, we learned how to update the calibration files needed for the new sensors. The HOT team uses two duplicate temperature, conductivity, and oxygen sensors on each CTD to ensure consistent measurements, and updates calibrations after each cast by ground-proofing each measurement with lab analyses on water samples.

On Friday, we mobilized for our first cruise! The team worked seamlessly to get three vans full of equipment onto the ship and set up in the lab, including positive and negative pressure pumps for filtration. Next, we shadowed our mentor while he completed a CTD cable termination – a process we’ll be able to practice later in the internship. Then, the team tested the termination under tension using a crane on deck. For lunch, we stopped by a local fish market with amazing poke bowls!

All in all, I’m amazed by how much I’ve learned in just three days and I can’t wait for our upcoming cruise!