Betsy Petrick: Core Sampling in the Lab, June 30, 2019


NOAA Teacher at Sea

Betsy Petrick

Aboard R/V Point Sur

June 24 – July 3, 2019


Mission:
 Microbial Stowaways: Exploring Shipwreck Microbiomes in the deep Gulf of Mexico

Geographic Area: Gulf of Mexico

Date: June 30, 2019


Science Log

When the ROV returns to the ship, the scientists jump into action.  The sediment cores are brought into the lab for sampling.

Core samples
Core samples are loaded on the ROV in crates and with luck they all come back the same way.

Dr. Justyna Hampel, an aquatic biogeochemist and postdoctoral research assistant at the University of Southern Mississippi, is researching how microorganisms colonize on and around deep sea shipwrecks.  She is taking sediment samples for DNA testing, and identifying nutrients in sediment pore water, the water trapped inside the sediment. Her study will help us learn about the relationship between microbes and shipwreck biomes. It took many hands to process the core sediments for her research.

As assistant to graduate student Rachel Mugge, I felt a bit like a nurse in an operating room. Every sample was taken carefully to ensure it was not contaminated.

Here’s how it went: Carefully remove the plug from the bottom of the core sample tube.  Slide the core onto the extruder quickly so as not to lose any sediment.  (An extruder is a wheel on a threaded bolt. It is precisely calibrated to measure 2 cm increments as you turn the wheel 4 2/3 times.  )

Remove the lid and use a siphon hose to remove the sea water on the surface.  Rachel does this by placing one end of the hose in the core tube and the other end in her mouth and sucking gently to get the flow of water going.  Once it is moving she lets the water drain into a basin. Try this at home! You can get water to flow up and over an obstacle with this technique.  

siphon
It takes finesse to get the siphon working.

Next Rachel turns the extruder wheel until the mud is exposed at the top of the tube.  She describes the mud to lab manager Anirban Ray, who writes it down next to the sample number. (“S 54, brown, unconsolidated, black streaks, tube worm burrows.”)  I snap the paper wrapping off a wooden tongue depressor and hand it to her. She uses it to dig a sample out of the center of a sediment core. I hand her an open vial and she fills it.  I cap it. Next she puts some sediment into a petri dish and Anirban seals and labels it. Then I hand her an open sterile whirl-pak for a final blob of sediment. I whirl this little baggy and twist tie it closed.  Vials and whirl-paks go in the deep freezer. We do these three steps 40 times for 120 samples. The challenge I find in this kind of repetitive task is how quick and efficient can I be while still being careful and precise?  Let me tell you. Pretty fast and efficient. 

sediment sample
Putting a sediment sample into a vial. The core is on the extruder, which pushes the sediment upward when you turn the wheel.

At the same time this was going on, Justyna was extracting pore water (water that comes from inside the sediment) to analyze it for nutrients.

Extracting pore water
Justyna attaches syringes to the peepers to extract the pore water from the sediment.


Personal Log

While we worked, I had a porthole at my station to keep an eye on the ocean as we cruised out to our third and final shipwreck.  Dolphins raced with our ship this evening. Silvery flying fish skittered over the water reminding me of hummingbirds, the way their fins were a blur of movement.  The color of the ocean now can best be described in terms of watercolors. Ultramarine. That says it all.

Calm sea
Clouds are reflected in a calm sea.

One response to “Betsy Petrick: Core Sampling in the Lab, June 30, 2019

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