Pam Schaffer: Oceanographers Toolbox: What is a CTD? July 7,2018

NOAA Teacher at Sea

Pam Schaffer

Aboard NOAA Ship Bell M. Shimada

[July 2-10, 2018]

Mission: ACCESS Cruise

Geographic Area of Cruise: North Pacific:  Greater Farallones National Marine Sanctuary, Cordell Bank National Marine Sanctuary

Weather Data from the Bridge

Date July 7 2018
Time 1200  (noon)
Latitude 37° 58.3’ N
Longitude 123° 06.4’ W
Present Weather/ Sky Cloudy
Visibility (nm) 10
Wind Direction (true) 341°
Wind Speed (kts) 18
Atmospheric Pressure (mb) 1018
Sea Wave Height (ft) 3-5
Swell Waves Direction (true) 330°
Swell Waves Height (ft) 3-5
Temperature  Sea Water (C) 13.2°
Temperature Dry Bulb (C)

Air Temperature

13.1°
Temp Wet Bulb (C ) 12.1°

 

Science and Technology Log

Marine life is not evenly distributed throughout the World’s oceans.  Some areas contain abundant and diverse life forms and support complex food webs whereas other areas are considered a desert.  This variation is due to environmental factors like temperature, salinity, nutrients, amount of light, underlying currents, oxygen levels and pH.  Some of these variables, such as temperature, oxygen levels, and pH, are experiencing more variability as a result of climate change.  In order to understand the health of marine environments, scientists explore the chemical and physical properties of seawater using a set of electronic instruments on a device called a CTD.   CTD stands for conductivity, temperature and depth and is the standard set of instruments used to measure variables in the water column.

Source: ACCESS www.ACCESSoceans .org

Source: ACCESS http://www.ACCESSoceans .org

The CTD is the bread and butter of oceanography research. It is primarily used to profile and assess salinity and temperature differences at varying depths in a water column.  But the device can also carry instruments used to calculate turbidity, fluorescence (a way to measure the amount of phytoplankton in the water), oxygen levels, and pH.  Conductivity is a way of determining the salinity of water. It measures how easily an electric current passes through a liquid.  Electric currents pass much more easily through seawater than fresh water.  A small electrical current is passed between two electrodes and the resulting measurement is interpreted to measure the amount of salt and other inorganic compounds in a water sample. Dissolved salt increases the density of water, and the density of water also increases as temperature decreases.  Deeper water is colder and denser.  Density is also affected by water pressure. Since water pressure increases with increasing depth, the density of seawater also increases as depth increases.

Optical sensors are used to measure the amount of turbidity, fluorescence, and dissolved oxygen at various depths in the water column.  Dissolved oxygen levels fluctuate with temperature, salinity and pressure changes and is a key indicator of water quality.  Dissolved oxygen is essential for the survival of fish and other marine organisms.  Oxygen gets into the water as gas exchange with the atmosphere and as a by-product of plant photosynthesis (algae, kelp etc.).

Photo Credit: Julie Chase/ACCESS/NOAA/Point Blue

Photo Credit: Julie Chase/ACCESS/NOAA/Point Blue

Typically, CTD instruments are attached to a large circular metal frame called a Rosette, which contains water-sampling bottles that are remotely opened and closed at different depths to collect water samples for later analysis. Using the information and samples collected, scientists can make inferences about the occurrence of certain chemical properties to better understand the distribution and abundance of life in particular areas of the ocean.

Scientist Carina Fish collects samples from CTD

Scientist Carina Fish collects samples from CTD

On our mission, scientists deploy the CTD to a depth of 500 meters at most stations. On the shelf break, the researchers deployed the CTD to 1200 meters (more than 3/4 of a mile below the surface) to collect samples.    The pressure is so great at this depth that a 1 foot by 1 foot square of Styrofoam is crushed to a quarter of its size(3″x 3″).

Retrieving the CTD Rosette

Retrieving the CTD Rosette

Personal Log

Around 01:30 last night we lost our Tucker Trawl net as it was being re-positioned.  The winds had picked up to around 20 knots and the sea height was around 5-8 feet according to the bridge log.   The sea state complicated the retrieval and as best we can conclude the wind and seas pushed the net bridle into a prop blade which swiftly and effortlessly cut the 1/3” thick metal wire cable and separated the net from its tether.  Mishaps at sea are part and parcel of working in a harsh and variable environments. Even the very best and most experienced captain and crew encounter unforeseen issues from time to time.   Dr. Jaime Jahncke quickly stepped into action and made contact with onshore colleagues to arrange for another net for the next research cruise.   In the meantime, we plan to use the hoop net to collect krill samples, weather permitting.

Did You Know?

According to NOAA scientists, only about 5% of the Earth’s oceans have been explored.

DJ Kast, Interview with Megan Switzer and the Basics of the CTD/ Rosette, May 28, 2015

NOAA Teacher at Sea
Dieuwertje “DJ” Kast
Aboard NOAA Ship Henry B. Bigelow
May 19 – June 3, 2015

Mission: Ecosystem Monitoring Survey
Geographical area of cruise:
Gulf of Maine
Date: May 28, 2015, Day 11 of Voyage

Interview with Student Megan Switzer

Chief Scientists Jerry Prezioso and graduate oceanography student Megan Switzer

Chief Scientist Jerry Prezioso and graduate oceanography student Megan Switzer

Megan Switzer is a Masters student at the University of Maine in Orono. She works in Dave Townsend’s lab in the oceanography department. Her research focuses on interannual nutrient dynamics in the Gulf of Maine. On this research cruise, she is collecting water samples from Gulf of Maine, as well as from Georges Bank, Southern New England (SNE), and the Mid Atlantic Bight (MAB). She is examining the relationship between dissolved nutrients (like nitrate and silicate) and phytoplankton blooms. This is Megan’s first research cruise!

In the generic ocean food chain, phytoplankton are the primary producers because they photosynthesize. They equate to plants on land. Zooplankton are the primary consumers because they eat the phytoplankton. There are so many of both kinds in the ocean. Megan is focusing on a particular phytoplankton called a diatom; it is the most common type of phytoplankton found in our oceans and is estimated to contribute up to 45% of the total oceanic primary production (Yool & Tyrrel 2003). Diatoms are unicellular for the most part, and a unique feature of diatom cells is that they are enclosed within a cell wall made of silica called a frustule.

Diatom Frustules. Photo by: 3-diatom-assortment-sems-steve-gschmeissner

Diatom Frustules. Photo by: Steve Schmeissner

Diatoms! PHOTO BY:

Diatoms! Photo by: Micrographia

The frustules are almost bilaterally symmetrical which is why they are called di (2)-atoms. Diatoms are microscopic and they are approximately 2 microns to about 500 microns (0.5 mm) in length, or about the width of a human hair. The most common species of diatoms are: Pseudonitzchia, Chaetocerous, Rhizosolenia, Thalassiosira, Coschinodiscus and Navicula.

Pseudonitzchia. Photo by National Ocean Service

Pseudonitzchia. Photo by National Ocean Service

Thalassiosira. Photo by: Department of Energy Joint Genome Institute

Thalassiosira. Photo by: Department of Energy Joint Genome Institute

Photo of Coscinodiscus by:

Photo of Coscinodiscus

Diatoms also have ranges and tolerances for environmental variables, including nutrient concentration, suspended sediment, and flow regime.  As a result, diatoms are used extensively in environmental assessment and monitoring. Furthermore, because the silica cell walls are inorganic substances that take a long time to dissolve, diatoms in marine and lake sediments can be used to interpret conditions in the past.

In the Gulf of Maine, the seafloor sediment is constantly being re-suspended by tidal currents, bottom trawling, and storm events, and throughout most of the region there is a layer of re-suspended sediment at the bottom called the Bottom Nepheloid Layer. This layer is approximately 5-30 meters thick, and this can be identified with light attenuation and turbidity data. Megan uses a transmissometer, which is an instrument that tells her how clear the water is by measuring how much light can pass through it. Light attenuation, or the degree to which a beam of light is absorbed by stuff in the water, sharply increases within the bottom nepheloid layer since there are a lot more particles there to block the path of the light. She also takes a water sample from the Benthic Nepheloid Layer to take back to the lab.

Marine Silica Cycle by Sarmiento and Gruber 2006

Marine Silica Cycle by Sarmiento and Gruber 2006

Megan also uses a fluorometer to measure the turbidity at various depths. Turbidity is a measure of how cloudy the water is. The water gets cloudy when sediment gets stirred up into it. A fluorometer measures the degree to which light is reflected and scattered by suspended particles in the water. Taken together, the data from the fluorometer and the transmissometer will help Megan determine the amount of suspended particulate material at each station. She also takes a water sample from the Benthic Nepheloid layer to take back to the lab. There, she can analyze the suspended particles and determine how many of them are made out of the silica based frustules of sinking diatoms.

 This instrument is a Fluorometer and is used to measure the turbidity at various depths. Photo by: DJ Kast

This instrument is a Fluorometer and is used to measure the turbidity at various depths. Photo by: DJ Kast

She collects water at depth on each of the CTD/ Rosette casts.

Rosette with the 12 Niskin Bottles and the CTD. Photo by DJ Kast

Rosette with the 12 Niskin Bottles and the CTD. Photo by DJ Kast

Rosette with the 12 Niskin Bottles and the CTD. Photo by DJ Kast

Rosette with the 12 Niskin Bottles and the CTD. Photo by DJ Kast

Up close shot of the water sampling. Photo by DJ Kast

Up close shot of the water sampling. Photo by DJ Kast

CTD, Rosette, and Niskin Bottle basics.

The CTD or (conductivity, temperature, and depth) is an instrument that contains a cluster of sensors, which measure conductivity, temperature, and pressure/ depth.

Here is a video of a CTD being retrieved.

Depth measurements are derived from measurement of hydrostatic pressure, and salinity is measured from electrical conductivity. Sensors are arranged inside a metal housing, the metal used for the housing determining the depth to which the CTD can be lowered. Other sensors may be added to the cluster, including some that measure chemical or biological parameters, such as dissolved oxygen and chlorophyll fluorescence. Chlorophyll fluorescence measures how many microscopic photosynthetic organisms (phytoplankton) are in the water. The most commonly used water sampler is known as a rosette. It is a framework with 12 to 36 sampling Niskin bottles (typically ranging from 1.7- to 30-liter capacity) clustered around a central cylinder, where a CTD or other sensor package can be attached. The Niskin bottle is actually a tube, which is usually plastic to minimize contamination of the sample, and open to the water at both ends. It has a vent knob that can be opened to drain the water sample from a spigot on the bottom of the tube to remove the water sample. The scientists all rinse their bottles three times and wear nitrile or nitrogen free gloves to prevent contamination to the samples.

On NOAA ship Henry B. Bigelow the rosette is deployed  from the starboard deck, from a section called the side sampling station of this research vessel.

The instrument is lowered into the water with a winch operated by either Adrian (Chief Boatswain- in charge of deck department) or John (Lead Fishermen- second in command of deck department). When the CTD/Rosette is lowered into the water it is called the downcast and it will travel to a determined depth or to a few meters above the ocean floor. There is a conducting wire cable is attached to the CTD frame connecting the CTD to an on board computer in the dry lab, and it allows instantaneous uploading and real time visualization of the collected data on the computer screen.

 

CTD data on the computer screen. Photo by: DJ Kast

CTD data on the computer screen. Photo by: DJ Kast

The water column profile of the downcast is used to determine the depths at which the rosette will be stopped on its way back to the surface (the upcast) to collect the water samples using the attached bottles.

Niskin Bottles:

Messenger- The manual way to trigger the bottle is with a weight called a messenger. This is sent down a wire to a bottle at depth and hits a trigger button. The trigger is connected to two lanyards attached to caps on both ends of the bottle.  When the messenger hits the trigger, elastic tubing inside the bottle closes it at the specified depth.

Todd with the manually operated Niskin Bottle. Photo by: DJ Kast

Todd holding a messenger to trigger the manually operated Niskin Bottle. Photo by: DJ Kast

IMG_7209

Todd with the manually operated Niskin Bottle. Photo by: DJ Kast

Todd with the manually operated Niskin Bottle. Photo by: DJ Kast

Manual CTD fully cocked and ready to deploy. Photo by DJ Kast

Manual CTD fully cocked and ready to deploy. Photo by DJ Kast

Here is a video of how the manual niskin bottle closes: https://www.youtube.com/watch?v=qrqXWtbUc74

The other way to trigger Niskin bottles is electronically. The same mechanism is in place but an electronic signal is sent down the wire through insulated and conductive sea cables (to prevent salt from interfering with conductivity) to trigger the mechanism.

Here is a video of how it closes electronically: https://www.youtube.com/watch?v=YJF1QVe6AK8

Conductive Wire to CTD. Photo by DJ Kast

Conductive Wire to CTD. Photo by DJ Kast

Photo of the top of the CTD. Photo by DJ Kast

Photo of the top of the CTD showing the trigger mechanism in the center. Photo by DJ Kast

Top of the Niskin Bottles to show how the white wires are connected to the top.

Top of the Niskin Bottles shows how the lanyards are connected to the top. Photo by DJ Kast

The pin on the bottom is activated when an electronic signal is sent through the conductive sea cables. Photo by DJ Kast

The pin on the bottom is activated when an electronic signal is sent through the conductive sea cables. Photo by DJ Kast

Using the Niskin bottles, Megan collects water samples at various depths. She then filters water samples for her small bottles with a syringe and a filter and the filter takes out the phytoplankton, zooplankton and any particulate matter. She does this so that there is nothing living in the water sample, because if there is there will be respiration and it will change the nutrient content of the water sample.

Filtering out only the water using a syringe filter. Photo by DJ Kast

Filtering out only the water using a syringe filter. Photo by DJ Kast

Photo by: DJ Kast

Syringe with a filter on it. Photo by: DJ Kast

This is part of the reason why we freeze the sample in the -80 C fridge right after they have been processed so that bacteria decomposing can’t change the nutrient content either.

Diatoms dominate the spring phytoplankton bloom in the Gulf of Maine. They take up nitrate and silicate in roughly equal proportions, but both nutrients vary in concentrations from year to year. Silicate is almost always the limiting nutrient for diatom production in this region (Townsend et. al., 2010). Diatoms cannot grow without silicate, so when this nutrient is used up, diatom production comes to a halt. The deep offshore waters that supply the greatest source of dissolved nutrients to the Gulf of Maine are richer in nitrate than silicate, which means that silicate will be used up first by the diatoms with some nitrate left over. The amount of nitrate left over each year will affect the species composition of the other kinds of phytoplankton in the area (Townsend et. al., 2010).

The silica in the frustules of the diatom are hard to breakdown and consequently these structures are likely to sink out of the euphotic zone and down to the seafloor before dissolving. If they get buried on the seafloor, then the silicate is taken out of the system. If they dissolve, then the dissolved silicate here might be a source of silicate to new production if it fluxes back to the top of the water column where the phytoplankton grow.

Below are five images called depth slices. These indicate the silicate concentration (rainbow gradient) over a geographical area (Gulf of Maine) with depth (in meters) latitude and longitude on the x and y axis.

Depth slices of nitrate and silicate. Photo by: This is the type of data Megan is hoping to process from this cruise.

Depth slices of nitrate and silicate. Photo by:  GOMTOX at the University of Maine
This is the type of data Megan is hoping to process from this cruise.

Lesley Urasky: Smile and say, “Squid!”, June 20, 2012

 NOAA Teacher at Sea
Lesley Urasky
Aboard the NOAA ship Pisces
June 16 – June 29, 2012

 Mission:  SEAMAP Caribbean Reef Fish Survey
Geographical area of cruise: St. Croix, U.S. Virgin Islands
Date: June 20, 2012

Location:
Latitude: 18.1937
Longitude: -64.7737

Weather Data from the Bridge:

Air Temperature: 28°C (83°F)
Wind Speed:  19 knots (22 mph), Beaufort scale: 5
Wind Direction: from N
Relative Humidity: 80%
Barometric Pressure: 1,014.90  mb
Surface Water Temperature: 28°C (83°F)

Science and Technology Log

The cameras are a very important aspect of the abundance survey the cruise is conducting.  Since catching fish is an iffy prospect (you may catch some, you may not) the cameras are extremely important in determining the abundance and variety of reef fish.  At every site sampled during daylight hours, we deploy the camera array.  The cameras can only be utilized during the daytime because there are no lights – video relies on the ambient light filtering down from the surface.

Camera array – the lens of one of the cameras is facing forward.

Deployment of the array at a site begins once the Bridge verifies we are over the sampling site. The camera array is turned on and is raised over the rail of the ship and lowered to the water’s surface on a line from a winch that has a ‘quick release’ attached to the array.  Once over the surface, a deck hand pulls on the line to the quick release allowing the array to free fall to the bottom of the ocean. Attached to the array is enough line with buoys attached. The buoys mark the array at the surface and give the deck hands something to aim for with the grappling hook when it is time for the array to be retrieved.  Once the buoys are on deck, a hydraulic pot hauler is used to raise the array from the sea floor to the side of the ship.  From there,  another winch is used to bring the array on board.

Vic, Jordan, Joey, and Joe deploying the camera array.

When the array is deployed, a scientist starts a computer program that collects the time, position and depth the array was dropped at. The array is allowed to “soak” on the bottom for about 38 minutes. The initial 3-5 minutes are for the cameras to power up and allow any sediment or debris on the bottom to settle after the array displaces it. The cameras are only actually recording for 25 of those minutes. The final 3-5 minutes are when the computers are powering down.  At one point in time, the cameras on the array were actual video cameras sealed in waterproof, seawater-rated cases. With this system, after each deployment, every individual case had to be physically removed from the array, opened up, and the DV tape switched out.  With the new system, there are a series of four digital cameras that communicate wirelessly with the computers inside the dry lab.

We did have a short-lived problem with one of the digital cameras — it quit working and the electronics technician that takes care of the cameras, Kenny Wilkinson, took a couple of nights to trouble shoot and repair it.  During this time period, we reverted back to the original standard video camera.  Throughout the cruise, Kenny uploads the videos taken during the day and repairs the cameras at night so they will be ready for the next day’s deployments.

Squid (before being cut into pieces) used for bait on the camera array

Besides the structure of the camera array which is designed to attract reef fish, the array is baited with squid.  A bag of frozen, cut squid hangs down near the middle.  The squid is replaced at every site.

Adding bait to the camera array.

In addition to the bait bag, a Temperature Depth  Recorder (TDR) is attached near the center, hanging downward near the bottom third of the array. The purpose of the TDR is to measure the temperature of the water at various depths.  It is also used to verify that the depth where the camera comes to rest on the ocean bottom and is roughly equivalent to what the acoustic sounding reports at the site.  This is important because the camera generally doesn’t settle directly beneath the ship.  Its location is ultimately determined by the drift as it falls through the water column and current.  The actual TDR instrument is very small and is attached to the array near the bait bag.  After retrieving the array at each site, the TDR is removed from the array and brought inside to download the information.  To download, there is a small magnet that is used to tap the instrument (once) and then a stylus attached to the computer is used to read a flash of light emitted by an LED.  The magnet is then tapped four times on the instrument to clear the previous run’s data.  The data actually records the pressure exerted by the overlying water column in pounds per square inch (psi) which is then converted to a depth.

TDR instrument

Computer screen showing the data downloaded from the TDR.

The video from each day is uploaded to the computer system during the night shift.  The following day, Kevin Rademacher (chief scientist), views the videos and quickly annotates the “highlights”.  The following things are noted:  visual clarity (turbidity [cloudiness due to suspended materials], what the lighting is like [backlit], and possible focusing issues), substrate (what the bottom is made of), commercially viable fish, fish with specific management plans, presence of lionfish (an invasive species), and fish behavior.  Of the four cameras, the one with the best available image is noted for later viewing.

Computer data entry form for camera array image logs

Once back at the lab, the videos are more completely analyzed.  A typical 20-minute video will take anywhere from 30 minutes to three days to complete. This is highly dependent upon density and diversity of fish species seen; the greater the density and diversity, the longer or more viewing events it will take.  The experience of the reader is also an important factor. Depending upon the level of expertise, a review system is in place to “back read” or verify species identification. The resulting data is entered into a database which is then used to assign yearly data points for trend analysis. The final database is submitted to the various management councils.  From there, management or fisheries rebuilding plans are developed and hopefully, implemented.

Spotted moray eel viewed from the camera array.  He’s well camouflaged; can you find him?

Coney with a parasitic isopod attached below its eye.

Two Lionfish – an invasive species

Personal Log

Today, we are off the coast of St. Thomas and St. John in the U.S. Virgin Islands.  We traveled from the southern coast of  St. Croix, went around the western tip of the island and across the straight.  When I woke up I could see not only St. Thomas and St. John, but a host of smaller islands located off their coastline.

Map of the Virgin Islands. St. Croix and St. Thomas are separated by 35 miles of ocean. It took us about 3 hours to cross to our next set of sampling sites.

Around dinner time last night we had an interesting event happen on board.  They announced over the radio system that there was a leak in the water line and asked  us not to use the heads (toilets).  A while later, they announced no unnecessary use of water (showers, etc.); following that they shut off all water.  It didn’t take long for the repairs to occur, and soon the water was returned.  However, when I went to dinner, I discovered that the stateroom I’m sharing with Kelly Schill, the Ops Officer, had flooded.  Fortunately, the effects of the flooding were not nearly as bad as I had feared.  Only a small portion of the room had been affected.  The crew did a great job of rapidly assessing the problem and fixing it in a timely manner.  After this, I have absolutely no fear about any problems on board because I know the crew will react swiftly, maintain safety, and be professional all the while.

Last night was the first sunset I’ve seen since I’ve been on board.  Up until this point, it has been too hazy and cloudy.  The current haze is caused by dust/sand storms in the Sahara Desert blowing minute particles across the Atlantic Ocean.

St. Thomas sunset

Today has been a slow day with almost nary a fish caught.  We did catch one fish, but by default.  It was near the surface and hooked onto our bait.  We immediately reeled in the line and extracted it.  It was necessary to remove it because it would have skewed our data since it was caught at the surface and not near the reef.  This fish was a really exciting one for me to see, because it was a Shark Sucker (Echeneis naucrates).  These are the fish you may have seen that hang on to sharks waiting for tasty tidbits to float by.  They are always on the lookout for a free meal.

Shark sucker on measuring board

One of the most interesting aspects of the shark sucker is that they have a suction device called laminae on top of their heads that looks a little like a grooved Venetian blind system.  In order to attach to the shark (or other organism), they “open the blinds” and then close them creating a suction-like connection.

The “sucker” structure on the Shark Sucker. Don’t they look like Venetian blinds?

I got to not only see and feel this structure on the fish, but also let it attach itself to my arm!  It was the neatest feeling ever! The laminae are actually a modified dorsal spines; these spines are needed because of the roughness of shark’s skin. When the shark sucker detached itself from me, it left a red, slightly irritated mark on my arm that disappeared after a couple of hours.

Look, Ma, No Hands! Shark sucker attached to my arm.

Tomorrow we’ll be helping place a buoy in between St. Croix and St. Thomas.  It will be interesting to see the process and how the anchor is attached.

With all the weird and wonderful animals we’re retrieving, I can’t wait to see what another day of fishing brings.

Kathleen Harrison: Shumagin Islands, July 9, 2011

NOAA Teacher at Sea
Kathleen Harrison
Aboard NOAA Ship  Oscar Dyson
July 4 — 22, 2011

Location:  Gulf of Alaska
Mission:  Walleye Pollock Survey
Date: July 9, 2011

Weather Data from the Bridge
True wind direction:  59.9°, True wind speed:  11.44 knots
Sea Temperature:  9°C
Air Temperature:  8.9°C
Air pressure:  1009.74 mb
Foggy with 1 mile visibility
Ship heading:  88°, ship speed:  11 knots

Science and Technology Log

The Shumagin Islands are a group of about 20 islands in the Gulf of Alaska, southwest of Kodiak Island.  They were named for Nikita Shumagin, a sailor on Vitus Bering’s Arctic voyage in 1741.  They are volcanic in origin, composed mostly of basalt.

Shumagin Islands

Bold and mountainous, the Shumagin Islands rise from the sea in the Gulf of Alaska.

Several islands even exhibit hexagonal basaltic columns.  There are about 1000 people who reside in the islands, mostly in the town of Sand Point, on Popof Island.  According to the United States Coast Pilot (a book published by NOAA with extensive descriptions about coastlines for ship navigation), the islands extend out 60 miles from the Alaskan Peninsula.  They are bold and mountainous.

hexagonal basalt

When this island formed, volcanic lava cooled into basalt hexagonal columns.

The shores are broken in many places by inlets that afford good anchorages.  The shores are rockbound close to.  Fishing stations and camps are scattered throughout the group, and good fishing banks are off the islands.  Fox and cattle raising are carried on to some extent.

long range view of SI, Alaskan Peninsula

Shumigan Islands to the left, snow covered peaks of Alaskan Peninsula in background. An amazing sight on a rare sunny day in the Gulf of Alaska.

Sea water quality is very important to the scientists on the Oscar Dyson.  So important, that it is monitored 24 hours a day.  This is called the Underway System.  The sea water comes through an intake valve on the keel of the bow, and is pumped up and aft to the chem lab.  There, it goes through 4 instruments:  the fluorometer, the dissolved Oxygen unit, the Thermosalinograph (TSG), and the ISUS (nitrate concentration).

The fluorometer measures the amount of chlorophyll and turbidity in the sea water once every second.  A light is passed through the water, and a sensor measures how much fluorescence (reflected light) the water has. The amount of chlorophyll is then calculated.  The measurement was 6.97 µg/L when I observed the instrument.  The amount of  phytoplankton in the water can be interpreted from the amount of chlorophyll.  Another sensor measures how much light passes through the water, which gives an indication of turbidity.  Twice a day, a sample of water is filtered, and the chlorophyll is removed.  The filter with the chlorophyll is preserved and sent to one of the NOAA labs on land for examination.

chem lab

Here are all of the water quality instruments, they are mounted to the wall in the chem lab. Each one has a separate line of sea water.

The next instrument that the water passes through will measure the amount of dissolved oxygen every 20 seconds.  Oxygen is important, because aquatic organisms take in oxygen for cellular respiration.  From plankton to white sharks, the method of underwater “breathing” varies, but the result is the same – oxygen into the body.  The oxygen in the water is produced by aquatic plants and phytoplankton as they do photosynthesis, and the amount directly affects how much aquatic life can be supported.

The TSG will measure temperature, and conductivity (how much electricity passes through) every second, and from these 2 measurements, salinity (how much salt is in the water) can be calculated.  The day that I observed the TSG temperature was 8.0°  C, and the salinity was 31.85 psu (practical salinity units).  Average sea water salinity is 35.  The intense study of melting sea ice and glaciers involves sea water temperature measurements all over the world.  A global data set can be accumulated and examined in order to understand changing temperature patterns.

instrument to measure

This instrument measures the amount of nitrate in the sea water. It is called the ISUS.

The last instrument measures nitrate concentration in the sea water every couple of minutes.  It is called ISUS, which stands for In Situ Ultraviolet Spectrophotometer.  Nitrate comes from organic waste material, and tends to be low at the surface, since the wastes normally sink to the bottom.  The normal value is .05 mg/L, at the surface, at 8°C.  Values within the range of 0.00 to 25 mg/L are acceptable, although anything above 5 is reason for concern.

All of the data from these instruments is fed into a ship’s computer, and displayed as a graph on a monitor.  The Survey Technician monitors the data, and the instruments, to make sure everything is working properly.

New Species Seen today:

Whale (unknown, but probably grey or humpback)

Horned Puffin

Dall’s Porpoise

Krill

Chum Salmon

Eulachon

monitor shows current data

The current water quality data is shown on this computer screen beside the instruments.

Personal Log

Living on a ship is quite different from living at home.  For one thing, every item on the ship is bolted, strapped, taped, or hooked to the bulkhead (wall), or deck (floor).  Most hatches (doors) have a hook behind them to keep them open(this reminds me of when I put hooks behind my doors at home to keep little children from slamming them and crushing fingers).  Some hatches (around ladderways (stairwells)) are magnetically controlled, and stay open most of the time.  They close automatically when there is a fire or abandon ship situation or drill.  Every drawer and cabinet door clicks shut and requires moving a latch or lever to open it.  For some cabinet doors that you want to stay open while you are working in the cabinet, there is a hook from the bulkhead to keep it open.

bracket holds copier

The copier machine is held in place by a 4 post bracket that is bolted to the floor.

On every desk is a cup holder, wider on the bottom than the top, designed to hold a regular glass or a cup of coffee.  If one of those is not handy, a roll of duct tape works well for a regular glass.  All shelves and counters have a lip on the front, and book shelves have an extra bar to hold the books in.  Trash cans and boxes are lashed to the bulkhead with an adjustable strap, and even the new copier machine has a special brace that is bolted to the deck to hold it in one place (I heard that the old copier fell over one time when there was a particularly huge wave).  There are lots of great pictures on the bulkheads of the Oscar Dyson, and each one is fastened to the bulkhead with at least 4 screws, or velcro.  There are hand rails everywhere – on the bulkhead in the passageway (hallway) (reminds me of Mom’s nursing home), and on the consoles of the bridge.

hallway hand rails

This view down the hall shows the hand rail. It comes in handy during rough weather.

Desk chairs can be secured by a bungee cord, and the chairs in the mess (dining room)  can be hooked to the deck.

Another thing that is different from home is the fact that the Oscar Dyson operates 24-7 (well, in my home, there could easily be someone awake any hour of the night, but the only thing they might operate is the TV). The lights in the passageways and mess are always on.  The acoustics and water quality equipment are always collecting data.  Different people work different shifts, so during any one hour, there is usually someone asleep.  Most staterooms have 2 people, and they will probably be on opposite shifts.  One might work 4 am to 4 pm, and the other would work 4 pm to 4 am.  That way, only one person is in the room at a time (there is not really room for more than one).  There is always someone on the bridge – at least the Officer of the Deck (OOD) – to monitor and steer the ship.  During the day, there is usually a look out as well.

binoculars on the bridge

These binoculars are used by the look out to scan the surrounding area for anything in the water - whales, boats, islands, kelp, or anything else in proximity to the ship.

His job is to, well, look out – look for floating items in the water, whales, rocks, and other ships (called contacts or targets).  This helps the OOD, because he or she can’t always keep their eyes on the horizon.

I have thoroughly enjoyed living on the Oscar Dyson (we have had calm seas so far), and talking with the NOAA staff and crew.  They are ordinary people, who have chosen an extraordinary life – aboard a ship.  It has challenges, but also great rewards – seeing the land from a different perspective, being up close to sea life, and forging close relationships with shipmates, as well as participating in the science that helps us understand the world’s oceans.

Steven Wilkie: June 26, 2011

NOAA TEACHER AT SEA
STEVEN WILKIE
ONBOARD NOAA SHIP OREGON II
JUNE 23 — JULY 4, 2011

Mission: Summer Groundfish Survey
Geographic Location: Northern Gulf of Mexico
Date: June 26, 2011

Ship Data:

Latitude 26.56
Longitude -96.41
Speed 10.00 kts
Course 6.00
Wind Speed 4.55 kts
Wind Dir. 150.72 º
Surf. Water Temp. 28.30 ºC
Surf. Water Sal. 24.88 PSU
Air Temperature 29.20 ºC
Relative Humidity 78.00 %
Barometric Pres. 1012.27 mb
Water Depth 115.20 m

Before getting down to work, it is important to learn all precautionary measures. Here I am suited up in a survival suit during an abandon ship drill.

Science and Technology Log

After two days of travel we are on site and beginning to work and I believe the entire crew is eager to get their hands busy, myself included.   As I mentioned in my previous post, it is difficult if not impossible to separate the abiotic factors from the biotic factors, and as a result it is important to monitor the abiotic factors prior to every trawl event.  The main piece of equipment involved in monitoring the water quality (an abiotic factor) is the C-T-D (Conductivity, Temperature and Depth) device.  This device uses sophisticated sensors to determine the conductivity of the water, which in turn, can be used to measure salinity (differing salinities will conduct electricity at different rates).   Salinity influences the density of the water: the saltier the water the more dense the water is.  Density measures the amount of mass in a specific volume, so if you dissolve salt in a glass of water you are adding more mass without much volume.  And since Density=Mass/Volume, the more salt you add, the denser the water will get.   Less dense objects tend to float higher in the water column than more dense objects, so as a result the ocean often has layers of differing salinities (less salty water on top of more salty water).  Often you encounter a boundary between the two layers known as a halocline (see the graph below for evidence of a halocline).

Temperature varies with depth in the ocean, however, because warm water is less dense than cold water. When liquids are cold, more molecules can fit into a space than when they are war; therefore there is more mass in that volume.   The warm water tends to remain towards the surface, while the cooler water remains at depth.  You may have experienced this if you swim in a local lake or river.  You dive down and all of a sudden the water goes from nice and warm to cool. This is known as a thermocline and is the result of the warm, less dense water sitting on top of the cool more dense water.

Here is the fancy piece of technology that makes measuring water quality so easy: the CTD.

Temperature also influences the amount of oxygen that water can hold. The cooler the temperature of the water the more oxygen can dissolve in it.  This is yet another reason why the hypoxic zones discussed in my last blog are more common in summer months than winter months: the warm water simply does not hold as much oxygen as it does in the winter.

The CTD is also capable of measuring chlorophyll.  Chlorophyll is a molecule that photosynthetic organisms use to capture light energy and then use to build complex organic molecules that they can in turn be used as energy to grow, reproduce etc.  The more chlorophyll in the water, the more photosynthetic phytoplankton there is in the water column.  This can be a good thing, since photosynthetic organisms are the foundation of the food chain, but as I mentioned in my earlier blog, too much phytoplankton can also lead to hypoxic zones.

Finally the CTD sensor is capable of measuring the water’s turbidity.  This measures how clear the water is.  Think of water around a coral reef — that water has a very low turbidity, so you can see quite a ways into the water (which is good for coral since they need access to sunlight to survive).  Water in estuaries or near shore is often quite turbid because of all of the run off coming from land.

This is a CTD data sample taken on June 26th at a depth of 94 meters. The pink line represents chlorophyll concentration, the green represents oxygen concentration, the blue is temperature and the red is salinity.

So, that is how we measure the abiotic factors, now let’s concentrate on how we measure the biotic!  After using the CTD (and it takes less time to use it than it does to describe it here) we are ready to pull our trawls.  There are three different trawls that the scientists rely on and they each focus on different “groups” of organisms.

The neuston net captures organisms living just at the water's surface.

The neuston net (named for the neuston zone, which is where the surface of the water interacts with the atmosphere) is pulled along the side of the ship and skims the surface of the water.  At the end of the net is a small “catch bottle” that will capture anything bigger than .947 microns.  The bongo nets are nets that are targeting organisms of a similar size, but instead of remaining at the surface these nets are lowered from the surface to the seafloor and back again, capturing a representative sample of organisms throughout the water column.   The neuston net is towed for approximately ten minutes, while the bongo nets tow times are dependent on depth.   Once the nets are brought in, the scientists, myself included, take the catch and preserve it for the scientists back in the lab to study.

The bongo nets will capture organisms from the surface all the way down to bottom.

The biggest and baddest nets on the boat are the actual trawl nets launched from the stern (back) of the boat.  These are the nets the scientists are relying on to target the bottom fish.  This trawl net is often referred to as an otter trawl because of the giant heavy doors used to pull the mouth of the net open once it reaches the bottom.  As the boat moves forward, a “tickler” chain spooks any of the organisms that might be lounging around on the bottom and the net follows behind to scoop them up.  This net is towed for thirty minutes, and then retrieved and we spend the next hour or so sorting, counting and measuring the catch.

Here you can see the otter trawl net extending off the starboard side of the Oregon II. When lowered into the water the doors will spread the mouth of the net.

Personal Log
I thought that adjusting to a 12 hour work schedule would be tough, but with a 5-month old son at home I feel I am more prepared than most might be for an extended day.  I might go as far as to say that I have more down time now than I did at home!  Although the ship’s crew actually manages the deployment of the majority of the nets and C-T-D, the science team is always involved and keeping busy allows the hours to tick away without much thought.  Before you know it you are on the stern deck of the ship staring at a gorgeous Gulf of Mexico sunset.

As we steam back East, the sun sets in our stern every day, and we have been treated to peaceful ones thus far on this trip.

The sun has long since set.  As I write this it is well after midnight and my bunk is calling.

Tanya Scott, June 17, 2010

NOAA Teacher at Sea
Tanya Scott
Onboard NOAA Ship Miller Freeman
June 16 – 21, 2010

Mission:  Ecosystem Surveys
Date: Thursday, June 17, 2010
Current Location: Oregon/Washington Coast  44 55 N  124 37 W off Siletz Bay

Traveling from Newport, North Carolina to Newport, Oregon has been quite an adventure.  The most obvious difference has been the weather. When I left NC, the weather was typical for early June:  hot and muggy!!  Here in Oregon, it is a different story.  When I arrived, the skies were clear and the temperature was a comfortable 81 F.  It soon turned to overcast skies and cooler temperatures.  While I have enjoyed the cooler temperatures, I must admit that I do miss the NC sunshine!

One of the most striking differences between Newport, NC and Newport, OR is the coastline.  The coastline of Oregon is marked by cobblestone beaches made of breccia (a common igneous rock of the western coast), steep cliffs, and very unlike our sandy, quartz beaches of NC.  The Oregon beaches are breathtaking.  I have watched sea lions swim and rest on rocks jutting from the Pacific Ocean, seen thousands of nesting birds such as the Murre and Puffin, and collected many interesting pieces of driftwood to share with you when I return.

We made the drive north from Newport, OR to Astoria, OR yesterday morning after the captain determined that it was not safe to enter the harbor in Newport.  The Miller Freeman was underway at 1200 yesterday and we have steamed ahead since.  Currently, we are 26 miles off the coast of Oregon and are heading out to 50 miles offshore.  Along the way, scientists from Oregon State University have been preparing their gear and running tests to ensure that all equipment is running properly. Just as we do in science class, they conduct trials so that the data collected is reliable.  Remember, few things work correctly the first time around.  That rule is true even at sea!

Today marks the beginning of my first duty rotation. This means that I am responsible for helping the scientists with any jobs they have such as deploying equipment overboard and collecting data from 12:00 pm until 12:00 am.  I will be helping with one instrument called a “CTD”.  This device is lowered to 100 meters below the surface of the water and measures salinity, temperature, density, turbidity, dissolved oxygen, and fluorescence.  Those of you who went with me to Hoop Pole Creek in Atlantic Beach measured some of these same parameters. Using the Secchi disk determines the turbidity or the cloudiness of the water.  The CTD does the same thing except for the fact that everything is measured using a computer and sent directly to a monitor on the ship for all to see!  The CTD is much more advanced than any equipment we have used in class, but offers the same data that you have already collected.

Tonight, I look forward to helping deploy a number of different nets or trawls that will be used to collect juvenille fish species.  I am keeping my fingers crossed and hope to see some interesting organisms to share with everyone tomorrow.  In the meantime, I am anxiously scanning the horizon in search of a whale.  I did see a pod of Pacific Whiteside Dolphin this morning. They were bowriding, which is when they ride along the bow of the ship and jump from the wake. It seems that many species of dolphin do this purely for the fun of it. These dolphin are notably smaller than the Common Bottlenose Dolphin seen in NC. They are dark grey on the top half of their body and white on the bottom.  I was close enough to them to see scars on their dorsal fins.
I look forward to sharing my adventures with you tomorrow.  Wish me luck as I will be up until midnight tonight helping with large trawl nets and hopefully collecting many exciting marine organisms.