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.

Jillian Worssam, July 3, 2008

NOAA Teacher at Sea
Jillian Worssam
Onboard U.S. Coast Guard Vessel Healy
July 1 – 30, 2008

Mission: Bering Sea Ecosystem Survey
Geographic Region: Bering Sea, Alaska
Date: July 3, 2008

Science Log

We are underway, a tug helped our vessel move away from the dock and we are now heading towards station number one.

Local tug used to get the Healy from the dock.

Local tug used to get the Healy from the dock.

Before we get to our first sampling point, which will be a CTD deployment and Mocness, I would like to give you a little background on some of the science that will be accomplished over the next 30 days.  At first I was told there would be approximately seven concurrent scientific data sampling experiments being conducted, well that estimate is off by a bit,  The scientists on board are studying:

Physical Oceanography and water circulation Hydrography Carbon productivity Nitrogen uptake and cycling Particle flux Iron Analysis Euphausiid and microzooplankton Euphausiid rate measurements Organic tracers and trophic transfer Ichthyoplankton Microzooplankton grazing Benthic biogeochemical fluxes Bird distribution and abundance Marine mammal observation: right whale observer Bio-optical and phyto plankton variations Water column bio-optics and phytoplankton  characteristics.

Alexie and team working on deployment of the Mocness.

Alexie and team working on deployment of the Mocness.

Phew, I am out of breath, and to be honest hope to by the end of the cruise to know more about each and every one of these scientific studies, how to pronounce their names, and explain their importance to this amazing ecosystem called the Bering Sea!

Stop in tomorrow to learn more about quantitative zooplankton studies with Alexei Pinchuk.  We will use the Mocness collect samples and well, I can’t tell it all today, there needs to be some surprises for tomorrow.

Here is today's photo challenge, what is this item, and what do you think it is used for?

Here is today’s photo challenge, what is this item, and what do you think it is used for?

Quote of the Day: On the path that leads to nowhere I have sometimes found my soul.  Corrine Roosevelt Robins

FOR MY STUDENTS: How long do you think you can go without sleep and still function effectively?

Elsa Stuber, June 8, 2007

NOAA Teacher at Sea
Elsa Stuber
Onboard NOAA Ship McArthur II
June 4 – 9, 2007

Mission: Collecting Time Series of physical, chemical and biological data to document spatial and temporal pattern in the California Current System
Geographical Area: U.S. West Coast
Date: June 8, 2007

Weather from the Bridge 
Visibility: clear
Wind direction 282 NW
Wind speed: 18.9 knots
Sea wave height: 3-5 feet
Sea temperature: 10.5 C
Air temperature: 13.5 C
Sea level pressure: 1013.36
Cloud cover: 100 % status clouds

Science and Technology Log 

Wind woke me up at 06:00, boat rolling.  Early morning 03:00—05:00 winds were 30 knots. Casts 31, 32, and 33 processed by other teams.

Cast 34 @ 09:24 Station H3  Latitude 36.44117 N  Longitude 122.01108 W Cast depth 1000 meters CTD cylinders tripped at 1000, 200, 150, 100, 80, 60, 40, 30, 20, 10, 5, 0 meters Samples processed and stored.  Data for cast is Table 16 at the end of the report.  Worked on chlorophyll analysis with flurometer.

Cast 35 @ 11:47 Station C1  Latitude 36.478487N  Longitude 121.508392 W Cast depth 225 meters CTD cylinders tripped at 225, 200,. 150, 100, 80, 60, 40, 30, 20, 10, 5, 0 meters Samples processed and stored.  Data for cast is Table 17 at the end of the report. I worked on chlorophyll analysis off and on throughout the day.

The HyperPro instrument to measure light up to 40 meters depth in the water has been tested at mid-day each day.  One tube is pointed down and opposite tube is pointed up sensing light levels. A third tube is strapped to the railing registering light levels at all times.  Seechi was used during the daylight hours as well. MBARI staff gave us some Styrofoam cups, two sizes, to decorate as we wanted using different permanent colored markers.  We put all of them in a mesh laundry bag and attached it to a 1000-meter depth cast.  When they came back up they had shrunk to 1/6th of the original size. It demonstrates the amount of air in the Styrofoam, which should be a good illustration for my students.

Wildlife observations: humpback whales, dolphins, sea gulls, cormorants, sooty shearwaters, and albatross. Kathryn said the sooty shearwater cannot take off from the ground very well. This bird will climb up the trunk of a tree a ways and take off from there. They will wear the bark down going up a path on the tree.  She hoped we would see a Yaeger bird, a bird that chases other birds that have been feeding, making them drop their food. That’s how the Yaeger feeds. It is very aggressive she said in pursuing other birds.

Moved to an area in Monterey Bay where whales had been sighted.  Saw five at a distance of half a mile, sometimes a fin, but mostly the whale’s spout from the blowhole.

Packing up equipment so ready to unload early tomorrow in San Francisco.

Each day the plan of the day is posted by the FOO.  I include an example at the end of the report.

We did extra stations as we are ahead of schedule.   Cast 36 @23:58 nutrients only. Final station done by Troy, nutrients only at 03:00 June 9, 2007

Bed at 01:00 June 9th

Elsa Stuber, June 7, 2007

NOAA Teacher at Sea
Elsa Stuber
Onboard NOAA Ship McArthur II
June 4 – 9, 2007

Mission: Collecting Time Series of physical, chemical and biological data to document spatial and temporal pattern in the California Current System
Geographical Area: U.S. West Coast
Date: June 7, 2007

Weather from the Bridge 
Visibility: clear
Wind direction: NW
Sea wave height: 5-8 ft.
Sea temperature: 12.79 C
Air temperature: 14.7 C
Swell wave: 5-8 ft.
Sea Level pressure: 1016.
Cloud cover: partly cloudy

Science and Technology Log 

Up at 06:30. Breakfast and watched with mammal observer on flying bridge.  Saw a few albatross. Very rough water, windy, cold.

Cast 21, 22 and 23 taken by other teams.

Cast 24 @ 08:55 Station 67-75 Latitude  35.5749N Longitude 123.504491 W Cast depth 1000 meters CTD cylinders tripped at 1000, 2000, 150, 100, 80, 60, 40, 30, 20, 10, 5, 0 meters Very windy. Data for cast is Table 12 at the end of the report

Cast 25 @ 11:35 Station NPS 5 Latitude  36.026137 N  Longitude 123.400087 W   Cast depth 1000 meters CTD cylinders tripped at 1000, 900, 800, 700, 600, 500, 400, 300, 200, 100, 50, 0 meters Nutrient samples only taken at this cast.  Data for cast is Table 13 at the end of the report.  Very windy (23 knots)

Spent time again on the flying bridge with mammal observer.  She said on the Beaufort Scale winds above 4 one doesn’t expect to see wildlife out in the ocean. Beaufort scale today is “5”.

Casts 26, 27, and 28 ( wind 26 knots) processed by other teams.

Cast 29 @ 21:27 Station NPS 3 Latitude 36.22583N Longitude 122.57275 W Cast depth 1000 meters CTD cylinders tripped at 1000,900, 800, 700, 600, 500, 400, 300, 200, 100, 50, 0 meters Nutrients samples only collected at this cast. Very windy (wind 22 knots) and water is rough. Data for cast is Table 14 at the end of the report. Worked on chlorophyll analysis.

Took photos of some of the net tow specimen jars to show the extreme of near shore and out at sea differences in material.  Specimens observed today–some shrimp, a few jellyfish, a squid, pteropods, heteropods.  There is not the large amount of krill as observed in the net tow collections closer to shore.

Cast 30 @ 23:37 Station 67-60  Latitude  36.275608 N  Longitude 122.466380 W Cast depth 1000 meters CTD cylinders tripped at 1000, 200, 150, 100, 80, 60, 40, 30, 20, 10, 5, 0 meters Very windy (23 knots) Samples processed and stored Data for cast is Table 15 at the end of the report.

Bed 01:00 June 8th

Elsa Stuber, June 6, 2007

NOAA Teacher at Sea
Elsa Stuber
Onboard NOAA Ship McArthur II
June 4 – 9, 2007

Mission: Collecting Time Series of physical, chemical and biological data to document spatial and temporal pattern in the California Current System
Geographical Area: U.S. West Coast
Date: June 6, 2007

Weather from the Bridge 
Visibility: clear
Wind direction: 291
Wind speed: 16 knots
Sea wave height: 2-3 ft.
Swell wave: 5-7ft.
Sea temperature: 14.671 C
Air temperature: 16.1 C
Sea level pressure: 1021
Cloud cover: 25% scattered cumulus

Science and Technology Log 

Up at 07:00 Discussion continued on how to do deep casts with CTD and avoid kink in wire: lower it slower or put on more weight or etc.  Some staff short on sleep after working with CTD repair last night. I do fine on six hours a night but I feel it when it’s five.  I will try for a nap today.

Cast 13 and 14 were done with other staff and went without problems.  They will try a deep cast again today.

Cast 15 08:00 Station 65-90 Latitude 35.03387N  Longitude -127.45604 W at depth to 1000 m; CTD cylinders tripped at 1000, 200, 150, 100, 80, 60, 40, 30, 20, 10, 5, 0 meters In the wet lab work the funnel for sample #8 was not locked tightly and the apparatus leaked. I put on a new filter and took another seawater sample for #8.  Samples processes and stored. Data for cast is Table 7 at the end of the report.

The two 4′ by 6′ incubators on deck contain the C14 spiked samples placed in a continually flowing seawater bath for twenty-four hours.  Samples are placed in metal tubes with various numbers of holes in the tubes.  The various tubes are designed so that the samples are exposed to 50%, 30%, 15%, 5% and 1%.  One set of samples is not in tubes, but in full sunlight. Then they are evaluated for the rate the phytoplankton incorporate the Carbon 14 as described in Day 3.

Began chlorophyll analysis on the filtered specimens from the range of depths at each station that have been in the freezer more than twenty-four hours.

Marguerite went over the procedure using the flurometer to process the sample. It must be turned on at least one hour before running the tests and the chlorophyll samples #1-12 plus 1 and 5 micron samples must be at room temperature in the dark for at least one hour before beginning. She calibrated the flurometer with acetone.  We rinse the cuvette three times with a couple of milliliters of sample, and then add the remainder to the cuvette.  It will be about 2/3 full or more.  Wipe the cuvette well with a lab wipe to remove any oil on glass from your hand/fingers, place sample gently into flurometer.  The first reading should be taken after it has stabilized, usually 15-20 seconds.  Then two drops of 5% hydrochloric acid are added to degrade the chlorophyll pigment.  A second reading is taken to measure the remaining pigment. These are recorded on a “Bottle Sample Data Sheet”, an example of which is included as Table 8 at the end of the report.  After measurements are recorded, the sample is thrown out in a collection container and the vials disposed of in a waste container.

The cuvette is rinsed three times with acetone and then begin processing the next sample. Again it really helped to have seen this procedure demonstrated on the DVD that was sent to me ahead of the trip.  I was much better prepared.  It was important for the research done as well because if one made a mistake in the sample procedure, there was no sample in reserve to be able to run the test again. I did samples for a couple of hours in the afternoon and a couple more in the evening when I was scheduled for working but waiting for a cast to come up.

Cast 16 and 17 were processed by other team.

Cast 18 @ 15:35 Station 67-90 Latitude 35.4670N  Longitude -124.9409 W Cast depth 4380 went very well. Processed by Erich and Charlotte. Cylinders tripped at 4380 bottom, 4000, 3500, 3000, 2500, 2000, 1500, 1000, 750, 500, 250, 0 meters; Data for cast as Table 9 at the end of the report.

I observed a couple of bongo net tows today. Live net tows are collecting zooplankton and other seawater specimens from the first 200 meters of depth.  The bongo nets have two .8-meter diameter rings with a mesh net and a polycarbonate tube at the end.  The nets were deployed using the ship’s starboard winch equipped with at least 300 meters of wire. The ship maintains a vertical wire angle during the tow of approximately 45 degrees. Kit Clark, the oceanographer in charge of net tows said it was important that the winch be able to maintain a slow, constant retrieval speed.  When nets are retrieved, they are hosed down to wash specimen sticking to the mesh down into the polycarbonate tube. The specimens are transferred to jars and fixed with formalin. There were a lot of krill and one viper eel in the specimens I observed this morning.

Wildlife observer saw three albatross today.  Cast 19 @ 21:14 Station-NPS-8 Latitude 35.325665 N  Longitude 124.438304 W  Cast depth 1000 meters; Cylinders tripped at 1000, 900, 800, 700, 600, 500, 400, 300, 200, 100, 50, 0 meters; Nutrient samples only taken for this cast; Data for cast is Table 10 at the end of the report.

Cast 20 @ 11:29 Station 67-85 Latitude 35.6249 N Longitude -124.5544W  Cast depth 1000 meters; CTD cylinders tripped at 1000, 200, 150, 100, 80, 60, 40, 30, 20, 10, 5, 0 meters; Bottle # 2 leaked, was empty, so no sample collected. Always check that funnels are locked tight before I begin. Samples processed and stored; Data for cast is Table 11 at the end of the report.

Long discussion of the structure and movement of ocean currents.  Dr. Collins is a brilliant scientist, such depth in oceanography.  He uses vocabulary during his explanations that need explanation in themselves. The Great Lakes and fresh water bodies are a lot simpler.

Discussed with Dr. Collins the military value of the studies we are doing.  He said the military does sea floor mapping, looks for mines and things on the sea floor. He explained that there are levels of optimum transmission of sound, channels for submarines.  Determining these best channels relates to the salinity and temperature

Bed @ 01:00 June 7th

Elsa Stuber, June 5, 2007

NOAA Teacher at Sea
Elsa Stuber
Onboard NOAA Ship McArthur II
June 4 – 9, 2007

Mission: Collecting Time Series of physical, chemical and biological data to document spatial and temporal pattern in the California Current System
Geographical Area: U.S. West Coast
Date: June 5, 2007

Weather from the Bridge 
Visibility: Clear
Wind direction 275.64
Wind speed: 13 knots
Air temperature: 16.1 C
Sea wave Height: 1-2 feet
Seawater temperature: 13.98 C
Swell wave: 4-6 feet
Sea level pressure: 1017.4
Cloud cover: 50%, stratus

Science and Technology Log 

Up at 06:00 and went to flying bridge to observe with Kathryn.  Not much wildlife to see other than a few sea gulls. Color of water so blue.  Temperature is cool early in the morning. Breakfast good fruit, lots of starches, sausages.  A time to talk to crewmembers about the different trips of MCARTHUR II from Alaska to Peru.  Jim spoke in detail @ working as a fisherman in Alaska, ice in his moustache, not needing very heavy clothes because you worked so hard you got hot.  He said it was 06:00 until 22:00 in summer time.  He spoke about fishing limit rules, coordinating with Japanese fishing boats, and also how the catch numbers have fallen since ten or fifteen years ago.

Cast 6 and 7 were early in the morning with other cruise staff. All proceeded as expected.

Cast 8 @ 08:18 Station 60-75 Latitude 37.067N Longitude 124.4145 W Cast depth to 1000m; CTD cylinders tripped at 1000, 200, 150, 100, 80, 60, 40, 30, 20, 10, 5, 0 meters Data for cast is Table 5 at end of report. Cast information time is always written in Greenwich time; I subtract seven hours to show our time on ship for the station work.  The Cast information listing for latitude and longitude is close but not exact to Table 1 for the CalCOFI stations. In the 1000 meter depth casts it takes about forty minutes for the CTD to go down to depth and come up again, stopping at the different levels for the specific rosette to open.

I learned more information on the testing of samples from Marguerite Blum, MBARI oceanographer: The nutrient samples contain nitrates and nitrites as well as silicates, phosphates.  The nitrates and nitrites area examined at Moss Landing lab with an auto flow analyzer, which translates sample into voltage and indicates the amount of the nutrient in the sample.

QP (quantitative phytoplankton) will show up to fifteen general types of phytoplankton in a sample.  This is an expensive test to run.  The flow cytometry test divides the sample into four groups: bacteria, prokaryotes, eukarotyes, and zooplankton.  It will determine a general number of how many of each are present in the sample.

The Carbon 14 test shows the amount of carbon uptake by the phytoplankton.  C14 of specimen fluoresces and radioactive emission level counted on a scintillation counter. The chlorophyll analysis of the green chlorophyll is run on the flurometer.  Samples that have been in the freezer 24 hours we will process in the dry lab while on this cruise.  On this cast I also handled the A* filter, the HPLC filter and the POC filter, placing them in their red, blue, and green cryovials respectively, and then put in the liquid nitrogen container. The analysis of HPLC, POC, FCM and N15 samples are not done at Moss Landing but are sent out to other labs for processing.

Cast 9 @ 11:45 Station 60-80 Latitude 36.5677N  Longitude 125.0327 W Cast depth to 1000m; CTD cylinders tripped at 1000, 200, 150, 100, 80, 60, 40, 30, 20, 10, 5, 0 meters; Data for cast is Table 6 at end of report.

There have been bongo net tows at our stations, but often when I am working or sleeping. I have seen some of the specimens caught which are in jars with formalin.  I hope to see a net tow start to finish soon.

I have watched with Kathryn, the Mammal observer, during different periods today and have not seen any wildlife. She saw seven dolphins earlier in the day.  I asked her about the tagging of sea life and she talked about the guidelines. She said the organization had to apply for a permit to the National Marine Fisheries.  This may take up to a year to obtain. A boat doing tagging must display a special flag with a research number on it. The permit will specify the number of “takes” (getting close to or affecting the animal such as a whale or turtle).  She said a lot of information was available on line at TOPP (Tagging of Pacific Pelagics). When it’s on the surface, the signal from the tagged animal will beam up to satellite and transmit its location. How long it will function depends on the battery life, and of course a small animal can only carry a small battery.  The scientist will set the frequency of the beam according to the frequency of the animal at the surface. A sea lion surfaces every fifteen minutes so its battery will last three weeks.  A turtle will surface every second day so its battery will last six months to a year or more. Scientists want to recapture radio equipment so watch closely at the animal’s location.  The equipment will give off a signal for at least a week after it falls off.  Researchers put gummy worms under the suction cups on whales and know it will take about a week for that sugar to be dissolved, and then the apparatus will fall off.  Tic Tacs with suction cups also work.. The equipment is numbered for location and will be returned if found by any ships, any countries at sea. She said a problem that can occur is that is that the sensor on the collar could get algae grown over it so it stays off.

Cast 10 and 11 were with other cruise staff.

Cast 12 was started @ 22:45 and was to be a deep cast, 4500m.  When it reached @1100m transmission of data stopped.  The CTD was brought back to the surface and worked on by staff about three hours. A kink had developed in the wire.  That section was cut out and all connections redone.

Data retrieved gives information for the 1100 m at this location for beam transmission, salinity, temperature, and fluorescence all taken by the computer monitoring system in the dry lab. Bottle samples were not taken.

To bed @ 02:00 June 6th I am greatly stewing about the CTD problems with all it means to the research, to the cruise,  and the expense of it all.

Elsa Stuber, June 4, 2007

NOAA Teacher at Sea
Elsa Stuber
Onboard NOAA Ship McArthur II
June 4 – 9, 2007

Mission: Collecting Time Series of physical, chemical and biological data to document spatial and temporal pattern in the California Current System
Geographical Area: U.S. West Coast
Date: June 4, 2007

Weather DAY 2: San Francisco to sea 
Visibility: Some fog before 12:00, which later cleared
Wind direction: 282.14
Wind Speed: 9 knots
Sea wave height: 1 foot
Seawater temperature: 14.159 C.
Sea level pressure: 1017.15
Air temperature: 14.1 C
Cloud cover: 100% stratus

Science and Technology Log 

Awoke 06:00 and did journal work until 07:15 breakfast.  Studied cruise information.   As suggested by CS Tim, I took a Dramamine II last evening and one this morning.  I don’t want to have seasick problems.  I don’t feel any side effects from the medication.

Safety meeting 09:00 with FOO Middlemiss. It is important to close the heavy doors when going and coming on the ship. We reviewed procedures for Man Overboard, Fire, and Abandon Ship.

Fire: signal = 10-second continuous bringing of the General Alarm bell and a 10-second continuous sounding of the ship’s whistle. Proceed to fantail of ship.

Abandon ship: signal =seven or more short blasts on the ship’s whistle followed by one long blast. Bring survival clothing and PFD to life raft location on the bridge.  We practiced putting on survival clothing:  feet and legs in then hood on your head before putting arms in sleeves and zipping up.  Difficult to do getting arms in by yourself; this is not a quick maneuver.  Mine was the smallest size; feet and arm-hand portion pretty big on me, but I would survive. I brought my mustang survival jacket along on the cruise as well.

Man Overboard: If witnessed throw life ring buoy into the water and call for assistance immediately. After one minute throw a second life ring buoy in the water.  Try to keep visual surveillance of the person in the water. Signal = three short blasts on the ship’s whistle.

For safety drills, dismissal from drill signal = three shorts blasts on the ship’s whistle. Mess hall information, store information, medicine location given.

Ship departed San Francisco approximately 10:15 with very foggy weather, foghorn blowing. It is very loud. If wearing plugs, the hearing of anyone working close to foghorn such as the wildlife observer on the flying bridge would be affected over time.  Special ear protection is needed for persons at that observational post.  Kathryn Whitaker is the wildlife observer on this cruise. She is stationed on the bridge with a lap top computer to record type and quantity of all birds and sea life she observes.  Kathryn is observing from daylight to sundown except going down for meals.  She uses powerful binoculars and camera to photograph whatever she sees.  On some cruises she has two or more staff working with her, one of whom is typing in the computer all that the observers are calling out that they are seeing which is often a great deal if the ship is nearer shore than we will be for most of this cruise.  As we leave SF Bay we see a dead gray whale floating, Kathryn points out the grease trail from the decaying whale blubber floating out on the water. There are cormorants and seagulls in large numbers flying in the area of the ship for the first three and a half hours of our trip. Then we only observe some seagulls.

The overall survey plan is to proceed offshore along CalCOFI (California Cooperative Oceanic Fisheries Investigation) Line 60, occupying stations each 10-20 nMi (nautical miles) to ~175 nMi offshore.  Then proceed to stations each 20nMi northeast to station 67-90 at the offshore terminus of Line 67, and work back into shore along Line 67 with stations 10-20 nMi apart. After the station work is completed, the ship will return to San Francisco and offload gear and personnel.  I will include the CalCOGI station information in Table 1 and Figure 1 of this report.

Operations at the stations are to collect physical, chemical, and biological data by CTD (conductivity, temperature, depth) and its rosette bottles, net tows, and underway surface measurements.  All CTD casts at the stations are to the bottom or 1000 dbars whichever is shallowest. At stations #12 and #16 two deep casts (4500m) are planned conditions and time permitting. Secchi disk cast will be made at daytime stations.  HyperPro optical sensor casts are to be made at midday stations.  Oblique bongo net tows will be to 200m depths.

CalCOFI survey continuous operations while underway will include logging meteorological and sea surface property, a pCO2 measuring system in the wet lab, the incubators for chlorophyll seawater samples on the fantail, and the marine mammal observer.

Cast 1 @ 13:51 Station 60-50, Latitude 37.948N & Longitude -122.888W, Cast depth 40m, Bottom depth 48m, CTD cylinders tripped at 40, 30, 20, 10, 5, 1.5, 0 meters   Data for cast is Table 2 and accompanying data graph including percent beam transmission, depth, temperature, and fluorescence at end of my report. Participants: Tim and Erich from MBARI, USN Charlotte, TAS Elsa  This was good hands on practice for the sampling work.  Charlotte and I received a lot of help, tips for technique.  Tim is very patient with our learning curve.

  1.  We check stopper at bottom of rosette cylinder to determine that it didn’t leak.  Pull out stopper and should only be a couple of milliliters squirting out.  Then open valve at top of rosette to take the sample.
  2.  Open stopper by lining up black circle drawn on stopper with peg on stopper and pull out. Rinse 280ml sample bottle three times with @ 15ml of sea water from rosette and then fill sample bottle to overflowing, close stopper.  Rinse small nutrient sample bottle 3 times and then fill it half to two-thirds full. Tim and Erich were filling other bottles for C14, N15, POC, QP, HPLC, FCM, and A* tests which are described below.
  3.  In wet lab, nutrients numbered sequentially are put in cartons and then promptly put into the freezer.  These will be processed later at the MBARI lab.
  4.  Funnels with filters for the twelve samples were set up prior to reaching the station.  Turn on aspirator pump.  Filter solutions through flasks.  Suction for all samples is improved if you turn off valve on those that have already filtered through.  You can’t get paper filter off the filter piece if suction is still operating.  Be careful at all times to check that sample number matches its numbered filter apparatus, and glass vial the filter is stored in when filtration complete.
  5.  Put particular filter for the fractionated 5 micron and 1 micron filtering.  Sample is labeled “F” collected by MBARI scientist. Pour 100ml of sample into each funnel for these samples.
  6.  Add the 10ml. measured amount of 90% acetone to each glass vial with its filter to “fix” the phytoplankton on the filter.  Place these in the carton in sequential order to be placed in the freezer. These remain there in the dark for at least 24 hours before we can test for chlorophyll levels with the flurometer.
  7. Label samples for casts read for example S307c#2, #5.  Meaning June 3-9 Cruise S307 cast #2 sample #5
  8. Three other filtrations were done which are color labeled: green POC organic carbon, how much carbon is in the water other than the plankton detritus; red A* filter will be evaluated in spectrophotometer to get all wave lengths of life, not just chlorophyll; and blue, HPLC -high performance liquid chromatography which will show 23 pigment types commonly associated with different algae so they may be qualified and quantified for the level the sample was taken.
  9.  The MBARI scientists take the C14 and N15 radioactive samples.
  10.  Set empty bottles in rack and carrying case and put out on back deck to be ready for the next cast. Put new filters in the 12 funnels in the wet lab to be ready for the next cast.

Chief Scientist Tim Pennington sent a DVD with demonstrations on how different sampling and testing of the samples are handled.  It was very helpful to see this walk through ahead, with emphasis on the problems that can arise with the techniques and suggestions on what to do about them.

Cast 2 @ 15:35 Station 60-52.5 , Latitude 37.864N  Longitude -123.065W, Cast depth to 80m, bottom depth 90m; CTD cylinders tripped at 80, 60, 40, 30, 20, 10, 5, 0  meters Data for cast is Table 3 and accompanying data graph at end of report.

CTD goes down and is monitored by observer in dry lab, CTD technician Doug or Dr. Collins. The observer communicates with the bridge and crew to raise the CTD, stop at each specified depth, and to trip open the particular rosette flask at this depth.

I worked on Cast 2 and became a little more efficient.  I’m continuing to try to observe all very carefully so as not to make any mistakes.  Procedures are very precise for accuracy.

Casts 3, 4 were not on my watch.  During that time I went to the flying bridge to do wildlife observation with Kathryn. There were numbers of cormorants and seagulls.  She had seen four dolphins @ half a mile away earlier in the day.

Cast 5 at station 60-57.5 at 21:42 Latitude 36.86N Longitude -123.3612W  Cast depth to 1000m; CTD cylinders tripped at 1000, 200, 150, 100, 80 ,60, 40, 30, 20, 10, 5, 0 meters Data for cast is Table 4 and accompanying graph at end of report. The water from 1000 meters is very cold, 3.843 C compared to 12.144 C at the surface.

The seas are pretty calm so collecting water samples, working with the equipment,  walking around is not a problem.  I have no hint of seasickness so I won’t continue to take Dramamine unless I begin to feel queasy.

Spigot on rosette #12 black circle marker has faded and needs to be remarked.

Go to bed @ 00.30 6/5/07. I’m sharing quarters with three others and my bed is a top bunk. Bunks are not very big, but I’m only 5′ tall so size of bunk is not a problem.  I can just barely sit up though and it is tricky to make it up in the morning.  Plenty of blankets and linens supplied.