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.

Roy Moffitt: Headed Home, Cruise Summary, August 25-26, 2018

NOAA Teacher at Sea

Roy Moffitt

Aboard USCGC Healy

August 7 – 25, 2018

 

Mission: Healy 1801 – Arctic Distributed Biological Observatory

Geographic Area: Arctic Ocean (Bering Sea, Chukchi Sea, Beaufort Sea)

Date: August 25-26, 2018

Past – Current – Future locations/conditions:

72.5 North latitude: This past week we had 3-4 days of below freezing temperatures (27) with snow showers

Nome, Alaska: (8/25/18) Departing temperature 51 and cloudy

Contoocook/Hopkinton, NH: First day of school Tuesday (8/28/18)- Forecast 94 degrees Mostly Sunny (did I mention we don’t have air conditioning in New Hampshire?)

 

Ashore and I am headed back to NH

After completing our work in our most Northern point stop, we steamed back to Nome with just one more set of measurements on the way back, then had one final day of travel. It was sunny on the first day back but rougher seas than we had experienced thus far.

Rough Seas

Rough Seas

There were estimated 8-12 ft waves and some even larger that crashed over the Healy. To the right is a picture that I captured of the bow during this portion of our trip and the rocky seas.   Keep in mind that for most of the day we were lucky enough to be on the front deck of the boat! After the waves calmed we were in the fog for most of the way home so spotting more whales and seals was difficult.

 

 

Cruise Summary

In short, the trip was a success with the tremendous amount of data collected. This data will now be analyzed by scientists and students and I hope to see some scientific papers on this research in the future. Here is a list of what was done on this trip:

  • 31 mooring deployments and 24 mooring recoveries

(To review what the work involved in this see my blog: Moorings all day

  • 142 CTDs (that’s a lot of up and downs!)

(To review what a CTD see my blog: Measuring Ocean Properties with the CTD)

  • 51 Bongo samples

(To review what a bongo see my blog: Bring in the Bongos)

  • There were several Methot net tows.

To review what a Methot net tow is see my blog: Catching the Tiny Fish in the Big Sea

  • There was constant monitoring for birds and marine mammals with all sightings recorded. This experience was my personal favorite of the trip.

To review, see my blog: Walrus and Polar Bears on Ice

Van Veen cup of catch

Van Veen cup of catch

In addition to the above, there were many (I don’t have the exact count) Van Veen Grabs.  I did not get to explain these in a blog so here is a quick overview. Scientists that study the sea floor, including the top layer of soil called the benthic zone, use a VanVeen Grab Sampler pictured below. It is lowered to the sea floor and then the scissor-like arms close the catch capturing a hunk of the sea floor and everything that was living on it. Once on shore the catch is rinsed through a sieve until all the clay is rinsed away leaving just the organisms that were living there (such as mollusks, clams, starfish, worms and more) and a few stones.

van veen process

Van Veen Grab Sampler process

The scientists on the team also took HAPS core samples. I did not get to explain these in a blog so here is a quick overview. The HAPS corer, pictured below, is a gravity corer. This is a device that is lowered to the sea floor and then the weight of the device settles into the sea floor. When the HAPS corer is lifted, the bottom of the tube containing the cut into sediment closes, trapping the sample. These samples are then stored in clear tubes as shown in the picture. Scientists can examine sentiment layers to gain a better understanding of the sea floor at that location by studying the sedimentary layers.

 

All this above data has been copied and specimens are stored. The primary focus of this trip was to gather data and now the long process of analyzing and communicating the results will begin.

Cruise Reflections

This was such a great opportunity for me to meet so many different scientists and to both observe and assist the varied scientific studies occurring all at once. I needed all three weeks to get a handle on it all. I am looking forward to sharing what I have learned with my Maple Street School students back in New Hampshire and following the scientific studies as they move forward. Thanks to NOAA, Maple Street School, everyone else that allowed this learning opportunity to happen. It was a summer I will not forget experiencing a ship crash through ice in August! I leave you with some of the reflections of the birds I captured on those calmer days at sea.

The tufted puffin is not all that graceful at taking off. (below)

tufted puffin take off

The tufted puffin is not all that graceful at taking off.

The Common Murre (below)

The common murre

The common murre

Three male Eider Ducks

Three male eider ducks

Three male eider ducks

Mark McKay, June 24, 2009

NOAA Teacher at Sea
Mark McKay
Onboard Research Vessel Knorr
June 10 – July 1, 2005

Mission: Ecosystem Survey
Geographical Area: Bering Sea, Alaska
Date: June 24, 2009

St. Paul Island only a few miles away

St. Paul Island only a few miles away

Science Log

It has been a very busy couple of days here on the Knorr. I haven’t received very much sleep. But then again, none of the science team has either. We have been a little ahead of schedule so it was decided that we could stay on station at a pretty interesting site for a longer period of time and due some diurnal studies, meaning, how are the organisms and ecosystems we are studying changing as we cycle through daytime to night. I am working on a project on phytoplankton so this was especially interesting for my work. So I was up several time thorough out the night collecting water samples and analyzing them. We headed to a particularly productive area right between the Pribilof Islands. As you can see from the photographs you can just barely make out St. Paul Island. As usual everyone scrambles to get his or her experiments in the water.  A familiar face on the deck is Ebett Siddon who is a graduate student working on zooplankton and juvenile fish on this trip.

Ebett: Master of the MOCNESS

Ebett: Master of the MOCNESS

She frequently uses the MOCNESS Sampler, which allows the researchers in her team to open and close bottle at specific depths. It’s a pretty good-sized device so it takes a fair amount of skill to operate it. The sediment core people have been just as busy. They pulled up a core with a very cool deep water shrimp. Notice the large reflective eyes on this creature. There is a lot of life around here. When I got up this very early this morning to collect samples there were some porpoises hanging around one of or floating sediment traps. There wasn’t enough light to get any pictures. My bird survey friend have promised me some great pictures of Albatross so stay tuned.

 

Deep water shrimp with large reflective eyes

Deep water shrimp with large reflective eyes

Mark McKay, June 19, 2009

NOAA Teacher at Sea
Mark McKay
Onboard Research Vessel Knorr
June 10 – July 1, 2005

Mission: Ecosystem Survey
Geographical Area: Bering Sea, Alaska
Date: June 19, 2009

Sediment Trap Buoy along side the Knorr

Sediment Trap Buoy along side the Knorr

Science Log

Some very interesting activities have been going happening on board the Knorr the last couple of days. While everyday there is a routine of cruising to a station, stopping and dropping plankton nets and/or other probes, other, more exotic experiments get deployed. For example, yesterday researcher Pat Kelley from the University of Rhode Island and his team retrieved sediment traps that they had set out 24 hours before. Their interest is seeing what is settling to the bottom of the ocean and at what rate this material is settling. To do this, they use a rather ingenious device. They take tubes and fill them with salt water that is many times more concentrated then regular seawater. Because it is so dense, the concentrated saltwater stays in the open toped tube as it is lowered into the ocean.  Anything that falls into this liquid stays in the trap and can be recovered for analysis. That’s where it gets interesting. Deploying and then recapturing a drifting probe can be a little tricky. After letting the sediment trap loose for 24 hours, you first have to go back and find it.

Lefting Buoy onto Knorr deck

Lefting Buoy onto Knorr deck

Fortunately the trap uses a satellite beacon that broadcasts its position to the ARGOS satellite system. The Argos program is administered under a joint agreement between the National Oceanic and Atmospheric Administration (NOAA) and the French space agency, Centre National d’Etudes Spatiales (CNES). The system consists of in-situ data collection platforms equipped with sensors and transmitters and the Argos instrument aboard the NOAA Polar-orbiting Operational Environmental Satellites (POES). The Argos system will lead you right to your instrument, then you have t get it on board. After they locate the instrument, they bring the ship along side and “lasso” so the deck crew can attach a cable and lift it out of the water using the A-frame crane located on the aft portion of the ship. The sediment traps are attached to a long line comprised of a heavy weight at one end with floats and a buoy at the other. The device is separated and brought up in sections so that they can be brought aboard using one of the ships cranes.

Removing float section of Sediment Trap

Removing float section of Sediment Trap

This takes a lot of skill to do, especially when on a deck that is slippery and rocking with the waves. Remember that this is done in between the other experiments and device tows. The deck crew is probably the busiest and hardest working group on this cruise. Another group on the cruise is the U.S. Fish and Wildlife Service “bird people” as they seem to be know as on the ship. They are made up of Elizabeth Labunski and Sophie Webb, both of which position themselves on the ships bridge so that they can survey what birds and marine mammals are present in-between stations. The Eastern Bering Sea is a very productive area and is rich in bird life.  I went up to visit them on the bridge.While there they identified a rather unhappy Red-legged Kittiwake (Rissa brevirostris) sitting rather pitifully near the bow of the ship.

Collecting Sediment Trap Tubes

Collecting Sediment Trap Tubes

These birds are interesting because as opposed to their Black-legged cousins, they have a very narrow distribution. According to the Audubon Society, Red-legged Kittiwake’s breeding distribution is limited to just four localities in the Bering Sea: Alaska’s Pribilof Islands, Bogoslof Islands, and Buldir Island, and Russia’s Commander Islands. More than 75% of the species’ known population breeds on St. George Island in the Pribilofs, which were about 40 miles from where we were cruising. The weakened bird was captured so that it could be warmed up and released when it regained its strength.

 

Elizabeth Labunsk and Third Mate Alison Paz surveying Bering Sea birdlife

Elizabeth Labunsk and Third Mate Alison Paz surveying Bering Sea birdlife

Red-legged Kitiwake

Red-legged Kitiwake

Sophia Webb holding Red-legged Kittiwake

Sophia Webb holding Red-legged Kittiwake

Mark McKay, June 17, 2009

NOAA Teacher at Sea
Mark McKay
Onboard Research Vessel Knorr
June 10 – July 1, 2005

Mission: Ecosystem Survey
Geographical Area: Bering Sea, Alaska
Date: June 17, 2009

Great Weather on the Bering Sea

Great Weather on the Bering Sea

Science Log

During the night the Knorr turned south westward to start it’s collecting along the CN (Cape Newenhan) line. We had skirted the edge of Bristol Bay before heading back out to into the Bering Sea. The expedition is following a plan that lets it stop at locations they have stopped at in previous years. This allows the scientists to compare data from multiple years so they can get a more accurate picture of what’s happening in the Bering Sea.

When I got up this morning I had to double check to make sure we were still on the Bering Sea and not something more temperate. The sky has been clear and the air temperature has been a “balmy” 45º F. May be I’m getting used to the weather but I had to take my jacket off to stay comfortable. The weather change quickly up here and may be totally different, and more severe later today. Best to be prepared for anything! So far the trip has been surprisingly pleasant. The one thing I’m not used to is the fact that the sun is always up. At 10 o’clock at night I step outside and it’s just like noon back at home.

Looking for critters in the core sample

Looking for critters in the core sample

Today is going pretty much like previous days. Everybody knows their job and goes about it in a efficient manner, meaning don’t get in the way, you are likely to get bowled over. They sent down the Multicore Apparatus again this morning. Hit a pretty sandy bottom but this time they had an unexpected hitchhiker. One of the cores came up with a Echiuran worm. Interesting creature. It has the consistency of a full water balloon, and is similar to the “innkeeper worms” which are common back home in California. Makes is living eating detritus in sediments that it pushes to its mouth with its proboscis (snout). Some types of Echiurans feed by making a “net” of mucus that captures detritus in the water. They then pull in the mucus and eat the captured detritus.

The zooplankton people are having fun with their collecting with one exception. Apparently the waters we have been sailing are fairly heavily populated with Jellyfish. The “Jelly’s” apparently gum up the collection bottles making collection little more difficult. I was watching as they tried to clean them out of their nets and it is a sticky mess. More on that later. For now, dinner! The food on the Knorr is great by the way.

Echiuran Worm

Echiuran Worm

Mark McKay, June 15, 2009

NOAA Teacher at Sea
Mark McKay
Onboard Research Vessel Knorr
June 10 – July 1, 2005

Mission: Ecosystem Survey
Geographical Area: Bering Sea, Alaska
Date: June 15, 2009

Hanging Valley outside of Dutch Harbor

Hanging Valley outside of Dutch Harbor

Science Log

We are underway!!! Got up this morning to a flurry of activity as the Knorr was preparing to get underway. I hooked up with my researcher Dr. Ray Sambrotto from Columbia University. His interests are in phytoplankton and the different chlorophylls they produce. There is a lot of plankton work happening on this cruise, as well as some benthic (seafloor) studies and surveying of seabirds. It’s amazing how much science they squeeze into a cruise. One of the things I saw as we were heading out was a very cool example of a Hanging Valley. This geological feature is formed by glaciers. I saw it when we flew into Dutch Harbor but I didnt get a chance to get a picture of it. As we set out on the Knorr we passed right by it so I got my chance.

 Multicore Apparatus

Multicore Apparatus

The day before we departed was spent storing equipment, testing instruments, and getting settled in our quarters. Problems with equipment not arriving on time wont prevent the start of the mission. We got underway right about 11 am Alaska time and headed for our first station over the Bering Canyon.  Safety is everything onboard the Knorr so before anything really gets started we are required to undergo safety training. The ships crew is very concerned with making sure everyone is safe so they go through procedures in detail.

After the safety briefings and getting some of Dr. Sambrotto’s equipment running, I had a chance to play in the mud. Dr. Shull’s group from Western Washington University is looking at cores of sediment taken from the ocean bottom. Their interest is in how nutrients are cycled through deep-water sediments. They drop the sampling device, called a Multicore, which has specialized sampling bottles to the ocean bottom. The device pulls cores from the seafloor and when the sampling device is retrieved, the scientists have a sample of the sea floor.  My job came after the bottles were retrieved. The process was to slice through the cores at specific depths and save the samples for further analysis. Good way to get really dirty.

Mary Cook, January 3, 2005

NOAA Teacher at Sea
Mary Cook
Onboard NOAA Ship Ronald H. Brown
December 5, 2004 – January 7, 2005

Mission: Climate Prediction for the Americas
Geographical Area: Chilean Coast
Date: January 3, 2005

Location: Latitude 45°49.53’S, Longitude 75°03.22’W
Time: 0930

Weather Data from the Bridge
Air Temperature (Celsius) 11.90
Water Temperature (Celsius) 13.55
Wind Direction (degrees) 343.52
Wind Speed (knots) 5.85
Relative Humidity (percent) 66.50
Air Pressure (millibars) 1016.06
Cloud Cover 6/8 Altocumulus
Sunrise 0615
Sunset 2152

Question of the Day

What is phytoplankton?

Quote of the Day

“Dream no small dreams for they have no power to move men.” Johann Wolfgang von Goethe

Science Log

This afternoon I interviewed Co-chief Scientist, Julio Sepúlveda, an oceanography graduate student from the University of Concepción. Julio did his Master’s thesis work for eight months at Woods Hole Oceanographic Institution in Massachusetts. In April, he’s leaving for Germany to spend three years continuing his education toward a PhD. in marine organic geochemistry. Julio has been kind enough to further explain the work they’ve been doing onboard the RONALD H. BROWN. The Chilean group of scientists include Pamela Rossel, Sergio Contreras, Rodrigo Castro, Alejandro Avila, and Luis Bravo. He says that their work has two parts: the water column process and the sedimentary record. The water samples and the sediment traps give a “picture of the moment”. They conducted the transect of samples starting at the shallow coastal waters and moving into the deeper offshore waters. These samples will provide a gradient of the nutrient concentrations at the Bay of Concepción which is part of an active upwelling location. To put it simply, they are looking at how the phytoplankton (plant-like microscopic organisms) uses the nutrients in the water. In particular they are looking at the nitrogen stable isotopes (nitrogen atoms with different masses) and their concentrations. They are trying to see how this is related to El Niño which greatly affects Chile and many places around the world. Julio explained that normally the upwelling brings cooler water containing nutrient-rich materials up to the surface. During El Niño events, the upwelling brings warmer, less nutrient-rich waters to the surface. This changes many things including the weather. The causes of El Niño are multi-varied air-sea fluxes that are not fully understood. In the last ten years the scientific community has been especially interested in knowing the possible influence of global warming in the El Niño variability. It seems that its frequency is changing and several articles indicate that El Niño is occurring more often. So their research provides a few “pixels” for capturing the entire “picture” of El Niño.

The second part of their research involves the core samples. The purpose of the core sampling is to collect the layers of sediments on the ocean floor. Julio described the layers to be like pages in a history book. Each layer tells the “story” of what was going on in the water at that location during that time. They are also looking at the degradation of the organic matter in the core samples. So, Julio says the water samples tell us about the present and the core samples tell us about the past. Using these methods of research, it is their intention to better understand the history of El Niño and better predict future El Niño events.

Personal Log

This morning we entered the fjords! Several of us were up and outside on the deck at 0630, “ooohing” and “aaahing”, taking pictures even though it’s very cold and windy out there. It is an irresistible attraction. We’re passing by the peninsula Tres Montes and we’re headed for the Bay of Tarn. All morning we’ve been sailing by emerald forest-covered mountains and black craggy rocks that have been eroded into peculiar shapes by the waves relentlessly smashing against them. The clouds are ominous and hanging low. The albatross are soaring with wings spread wide. An occasional whale sends a plume of spray into the air. I want these scenes to be indelibly saturated into my mind’s eye. I never want to forget this. No dwellings. No other ships. It’s just us. Just us and the birds and the whales. It’s good. It’s all good.

Until tomorrow,

Mary