• Nicole Pittoors

Let's get this PhD Started

Updated: Jun 1

During this cruise, I have been posing as a fraud geochemist/secret biologist by helping out the geology team collect fluid and rock samples. It is common that lead scientists on cruises will have room for additional scientists and students to join the cruise in exchange for some help and funds to support your travel to the port and shipping costs for equipment and samples. Fortunately, Dr. Jill McDermott needed extra hands to help with fluid sampling, and the Deep Sea Biology Society had offered me funds through their Cruise Bursary Award to support my participation in this cruise. This made it possible to use extra dive time to conduct research of my own and foster collaborations with leading scientists in my field.

As the cruise was reaching its final dives, it was time to be a biologist and begin my own experiments at the East Pacific Rise, which are also the first experiments of my PhD research!

For my experiment, I am testing to see if Autonomous Reef Monitoring Structures (ARMS) can be used in deep-sea hydrothermal vents to assess the biodiversity of benthic invertebrates. ARMS are a globally standardized method that is used to assess and monitor the biodiversity of shallow-water reefs. They are 9" x 9" x 9" tired units of alternating open and semi-closed layers of PVC plates that create a 3D habitat for benthic invertebrates to colonize:

Thousands of ARMS have been deployed worldwide over the last decade and are beginning to be deployed in deeper ecosystems such as mesophotic reefs, continental shelves, and cold seeps. ARMS are typically deployed from months to years. Once they are recovered, they are taken apart, photos are taken of each plate, and then the entire surface is scraped off and blended together. We can then use the blended mixture to identify all the species that were living on the plates by sequencing their DNA and looking at their "barcode". The barcode is a region of their mitochondrial DNA that is unique to their species. This process is called metabarcoding:

above image from

Past recruitment studies at hydrothermal vents have used colonization surfaces designed by Dr. Lauren Mullineaux at WHOI, called sandwiches. Sandwiches are made from Lexan plates and are about 1/8 the size of ARMS. They have been a successful method to sample local recruits at hydrothermal vents and are analyzed by looking at the animals under the microscope and identifying them by their visual characteristics.

The goal is to compare the ARMS to the Mullineaux sandwiches to see if the ARMS methods are consistent with and/or complementary to the sandwiches.

First, I had to assemble the sandwiches, ARMS, and larval traps. I decided to start off with making the sandwiches. The first step was to stamp IDs onto each sandwich plate using a hammer and metal stamps.

Next, I assembled the sandwiches by placing nylon spacers in between each plate, threading zip-ties through the plates and spacers to fasten them all together in a stack, adding a rope handle for the ROV manipulator to grab, and attaching small shackles to the bottom to weigh the sandwiches down.

Once the sandwiches were ready to go, it was time for the deluxe sandwiches- ARMS. This was a similar assembly process where I used nylon bolts and nuts to fasten all the PVC plates together. Assembling the ARMS was a little slower of a process since they weigh about 25 pounds and it can be tricky to get the nuts to screw onto the bolts correctly.

Next, I added some low-temperature loggers (loaned to me from Dr. Tim Shank from WHOI) to the side of the base that will record the water temperature every 10 minutes until I recover them in a year. I then added some color-coded tape that is associated with an ID number to the handles on the base. Now that the ARMS were ready to go, they needed to be put on ROV Jason and the elevator for decent!

The last things that needed to be prepped were the larval traps. These larval traps were designed by Dr. Craig Young at the Oregon Institute of Marine Biology. They are PVC pipes that have been assembled to hold falcon tubes upright in order to catch down-dwelling larvae that are falling to the seafloor. The falcon tubes are filled with RNA later that is denser than seawater, keeping the RNA later and the larvae from escaping the tube. The traps for this cruise were deployed for Dr. Shawn Arellano from Western Washington University and assembled by her student, Dexter Davis (Thanks, Dexter!). All I needed to do was fill all the tubes with RNA later and secure the rubber lids that will release 24 hours after hitting seawater. Craig's PhD student, Caitlin Plowman, kindly taught me how to assemble the traps.

It was then was time to put the larval traps and sandwiches on ROV Jason! I put the larval traps and sandwiches in one of Jason's swing arm bio boxes.

Time to shower while Jason descends to the bottom, get to my watch in the Jason Van, and work with the pilots to deploy all my equipment!

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