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 9, 2007
Science and Technology Log
Up at 06:00 and arrived in San Francisco @ 08:00 Unloaded equipment, mostly by winch onto truck; cleaned quarters and wet and dry labs.
In preparing my report I have included the data from the casts I worked on. As they were a dollar each to reproduce at Kinkos, I decided to only include those four-colored graphs for beam transmission, depth, salinity, and temperature that illustrate different types of locations, near shore or at sea of varying depths. These graphs certainly show the increase in salinity with depth and the falling of temperature with depth. They show the inverse relationship between the beam transmission and fluorescence. Compare Table 3, Table 6, Table 7, and Table 9 that are from very different depths. There is a lot of information here for my students to analyze.
This has been a stimulating learning experience. My students like most high school students are not near the ocean, maybe have never been to an ocean. I think sharing this first hand experience along with the pictures and doing demonstrations of our work and showing the data collected will open a perspective in their minds about the ocean. They will realize from the chlorophyll analysis and fluorescence the narrow level of the bottom of the food chain. This will bring home the concern for the protection of the health of the biotic life in our oceans. I intend to do a mock set up of our lab procedures and have them brainstorm how experimental error could be introduced. This should reinforce the importance of careful procedure in any scientific work.
The scientific staff on this cruise has been exceptional in willing to share their knowledge and, even when we were all tired, to answer my many, many questions about each individuals work in oceanography. I have found them to be conscientious scientists very interested, stimulated in their work. Some have given me pictures. Several have done extended work in Antarctica, which was particularly interesting to me. As well, the MBARI staff was very supportive as the other Teacher At Sea and I were learning procedures for our work. It felt good to see how cooperative, flexible they all were with one another no matter how long the days. I wish we could have been able to go to the MBARI lab this coming week to see how the work continues there. I intend to go on line and read more about their research and research findings. This will be something to investigate and follow with my students and extending their understanding of the oceans and the oceanographers’ work.
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
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.
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
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.
NOAA Teacher at Sea
Turtle Haste
Onboard NOAA Ship McArthur II June 4 -7, 2007
Mission: CalCOFI Survey: Ecosystem Survey and Seafloor Recovery Evaluation Geographical Area: Central CA National Marine Sanctuary Date: June 5, 2007
The Oblique Bongo nets.
Weather Data from Bridge
Visibility: 6 miles
Wind Direction: Northwest
Wind Speed: 10-20 knots
Sea Wave Height: 2-4 feet
Swell Height: 3-5 feet at 10 second intervals
Surface Water Temperature: 13.96 – degrees Celsius
Air Temperature: 16.1 – degrees Celsius
Sea Level Pressure: 1017.6 millibars
Science and Technology Log
Bongo Nets-Upon arriving at station 60-50, Kit Clark and I began the zooplankton tows with the oblique Bongo nets, also referred to as the “bongos.” The process involved is to tow the nets an oblique angle acquired by calculating the wire put out with the angle it is towed at. There is an angle measuring tool that looks like a level attached to the payout line that is monitored. Adjustments are made depending on the angle to achieve an angle of 45 degrees +/-3 degrees for the nets to reach an approximate depth of 200 meters. The bongo device itself has a 22 kg weight attached to the bottom of the yoke frame to cause it to sink. As the ship is traveling at 1-2 knots, a fixed amount of cable is paid out; the net is held at depth for 30 seconds and then is retrieved at a constant rate of 20 meters per minute. Upon retrieval of the bongo, samples are hosed into the cup at the end of the net to collect as much material as possible. A volume displacement measure is acquired by subtracting the amount of water the zooplankton displaces in a 1000 milliliter cylinder. The time to reach depth, time at depth, and retrieval time are recorded to monitor angle and depth.
Kit Clark identifies various zooplankton caught in a Bongo net to Charlotte Hill.
A tow was made at each station along the 60 survey line after the first station. The first station had too many crab pots and was too shallow to acquire a depth of 200 meters. At night, the anticipated nocturnal rising of krill occurred to present a sample dominated by krill as compared to the daytime samples of copepods. Daylight hours also presented samples of ctenaphore tendrils that “gunked” up the net. An obvious difference between daylight and night tows was the presence of krill in greater numbers. This is expected as especially near Monterey Bay over the canyon is known for Humpback and Blue whales who stop to feed on their migration. Kit noticed that the krill out past the continental shelf and along most of our tows with the exception of the ones conducted in Monterey Canyon were not as “fat and well fed” as the ones within the canyon area itself. Krill over the canyon are in overall better condition due to a localized upwelling feature in the canyon that brings nutrient rich deep water up to increase the productivity of phytoplankton.
Kit Clark strains zooplankton from the bongo nets to evaluate the displaced volume of organisms trapped while towing.
A general list of zoo plankton collected: Euphausiid (krill) and Copepods Pteropods (sea butterfly) Heteropods (Gelatinous Molluscs) Velella velella (By the Wind Sailors) a surface traveling creature Doliolids and Salps Ostracods Argyropelecus aculeatus (Hatchet fish) Atolla (deep water jelly) Cephalopods Tomopferiids Myctophild Ichthyoplankton Flashlight fish Siphonophore Radiolaria have used with students is identifying water masses in the Atlantic by physical characteristics. We use Temperature-Salinity (T-S) diagram at specific depths to identify water masses based on the density. I was hoping to collect water samples from various depths in the Pacific as well to use in the same activity. In discussions with Dr. Collins of the US Naval Post-Graduate school I learned that the Pacific is less uniquely identifiable than the Atlantic. The layered masses of the central Atlantic would not be as easily recognizable. We spent several days discussing the formation and circulation of deep waters in the Pacific in an attempt to understand the interaction between the atmosphere, chemistry, and surface current contribution to deep water mixing. From these discussions I learned that there are actually three sources of North Atlantic Deep Water (NADW). Furthermore, I learned that the mixing of NADW and Antarctic Bottom Water (AABW) in the Pacific created what is known as Common DeepWater (CDW) and that it is more difficult to actually identify Pacific water masses that I originally understood.
The bottles on the CTD rosette. In the foreground is the bottle containing 4380 meter water at 1.518 degree water, the background contains the water from near the surface at 14.169 degrees.
The two casts were made at the farthest points from shore with the collection of water in the bottles to be used specifically for evaluation of dissolved oxygen and nutrients. Dr. Collins asked for my input to for the overall bottle collection depths to ensure that I would have a set of samples from similar depths to match the Atlantic set I use. The Pacific deep water cast bottles are from the following meter depths for the first cast: 4462, 4000, 3500, 3000, 2500, 2000, 1500, 1000, 7500, 500, 250. The Pacific deep water cast bottles are from the following meter depths for the second cast: 4380, 4000, 3500, 3000, 2500, 2000, 1500, 1000, 7500, 500, 250, and 14. The Atlantic deep water samples that I already have are from the following meter depths and associated water masses: 4000 (Antarctic Bottom Water), 2000 (Antarctic Intermediate Water), 1000 (North Atlantic Deep Water), 500 (Mediterranean Intermediate Water), and 100 (North Atlantic Central Surface Water). Once the CTD was brought on deck, I noticed that the bottles containing the deepest water, although insulated showed condensation. Even though I understand that the temperature of the deep water is considerable colder than sea water at the surface, the ability to observe this drove the point home. Erich Rienecker of MBARI suggested that I feel the water around the rosette of bottles to really understand the temperature difference. This was the first time I had the opportunity to work with the CTD as I was working specifically with the Bongo nets. The bottle from 4380 meters had a temperature of 1.518 degrees Celsius and the surface bottle (14 meters) Another activity that the MBARI folks made sure that all of the science team and MCARTHUR II crew members had the opportunity to participate in was to send a decorated Styrofoam cup down in a mesh bag to “squish” it, or remove the air as a result of the pressure differential. Science team members spent quite a bit of time decorating cups. We even sent down a cup decorated with Flat Stanley.
Charlotte Hill of the US Naval Academy prepares a cup to be sent down to -4500 meters with the CTD.
Zooplankton – Wikipedia has a good general description of most of the organisms listed. I found specific information as I used Google for the unique species, although some of the more specific critters were really hard to find. For further information visit: Scripps Institution of Oceanography. A census of plankton is being conducted through the Census of Marine Life.
AABW = Antarctic Bottom Water; NADW = North Atlantic Deep Water; AAIW = Antarctic Intermediate Water; SACW = South Atlantic Central Water; NACW= North Atlantic Central Water.
Water Mass – a body of water with a common formation history. “This is based on the observation that water renewal in the deep ocean is the result of water mass formation in contact with the atmosphere, spreading from the formation region without atmospheric contact, and decay through mixing with other water masses.”
Flat Stanley – A character from a story by Jeff Brown who has adventures as a result of being flattened by a bulletin board. Classes read the story, send out their versions of Stanley to friends and associated with a scrapbook to record his adventures here.
NOAA Teacher at Sea Elsa Stuber prepares a cup to be sent down to -4500 meters with the CTD.The CTD on the fantail of the MCARTHUR II with Styrofoam cups in the green mesh bag for the second deep cast of -4500 meters.This is a “regular” Styrofoam 10 oz cup and the two cups that returned from 4500 meters. The far right cup has a Flat Stanley drawn on it.
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.
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.
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.
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.
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.
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.
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.
Label samples for casts read for example S307c#2, #5. Meaning June 3-9 Cruise S307 cast #2 sample #5
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.
The MBARI scientists take the C14 and N15 radioactive samples.
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.
NOAA Teacher at Sea
Turtle Haste
Onboard NOAA Ship McArthur II June 4 -7, 2007
Mission: CalCOFI Survey: Ecosystem Survey and Seafloor Recovery Evaluation Geographical Area: Central CA National Marine Sanctuary Date: June 4, 2007
Charlotte Hill and Erich Rienecker collect water samples from a CTD cast.
Weather Data from Bridge
Visibility: 0 – fog
Cloud Cover: 100 %
Wind Direction: 280 – degrees
Wind Speed: 9 knots
Sea Wave Height: 1 foot in AM, 2 foot in PM
Swell Height: AM swells of 2-3 feet, PM mixed swells of 4-6 feet
Surface Water Temperature: 14.15 – degrees Celsius
Air Temperature: 14.16 – degrees Celsius
Sea Level Pressure: 1017.15 millibars
Science and Technology Log
Established survey lines on this cruise have been monitored by the Monterey Bay Aquarium Research Institute or MBARI, since the early 1990 by collecting the same biological and chemical data. I was referred to http://www-mlrg.ucsd.edu/data/data.html for more details and the overview of the survey. Our particular survey lines begins outside of the Golden Gate Bridge, traveling westward for a while, then we will perform a cast of 4500 meters then travel south to for another 4500 meter cast and turn East to finish the survey line near Monterey Bay. The survey lines are numbered in a particular pattern that will be used to identify all samples from each station. At some points we will be beyond the Territorial Seas of the United States, but within the Exclusive Economic Zone.
Kit Clark and Troy Benbow demonstrate the bowline to NOAA Teacher at Sea Elsa Stuber.
What is collected at each station: A CTD measures specific properties of seawater including salinity, temperature and fluorescence as it is lowered off the stern of the ship. The CTD descends under the supervision of the CTD technician, crane operator and assisting crew member to the prescribed depth while generating real-time data in graph form through the descent. Once at depth, the technician is in radio contact with the crane operator who raises the CTD to prescribed depths where bottles are tripped to collect water samples at stated intervals. Generally the prescribed depth is 1000 meters with exceptions at the near shore stations where the depth is less than 1000 meters. Other data is collected from HyperPro Optical sensor casts, made at midday stations and Secchi disk casts made at all daytime stations following CTD casts. Oblique bongo net tows for zooplankton are made after the CTD casts at a depth of 200 meters. As the water is collected, several chemical tests are performed, including dissolved oxygen and nutrients. Dissolved oxygen is tested from each cast using a set of chemicals that is very similar to ones I have used in fresh water chemical analysis as well as nutrients to assess the changes in sediment load. Phytoplankton samples are collected for processing and culturing. In addition, a surface observer is stationed on the flying bridge to document all marine mammals and birds that are encountered. There is an interest in cetaceans, specifically beaked whales.
Marguerite Blum models under the Bay Bridge while loading science gear.
Personal Log
I found a ship’s billet on my door to tell me where to muster for fire, man overboard, and abandon ship. I made sure to visit all the locations to ensure that I knew where to go. The “plan of the day” is posted in convenient locations by ship’s personnel and is required reading in order to know what activities and meetings, are planned. I was able to try on my “gumby” suit and heavy PFD. I identified what is now called the “Leedo Deck” reminiscent of the television show Love Boat where science team members have placed a few lawn chairs for relaxing on aft section of deck one, near the phytoplankton incubation trays. As we depart San Francisco, we will sail out of the Golden Gate, under the Golden Gate Bridge. Although I had hoped for clear weather for the trip under the bridge, it was foggy.
Dr. Kurt Collins listening to the ball game on the “Lido deck” off watch.
Question of the Day
How does the collection and evaluation of phytoplankton assist with monitoring oceanic primary production and our understanding of the role the ocean plays as a global carbon sink?
I need to read more about the total project and perform more interviews of the cooperating scientists to better answer this.
Exclusive Economic Zone – extends for 200 nautical miles (370 km) beyond the baselines of the territorial sea.
Territorial Waters or sea-an area of coastal waters that extends at most twelve nautical miles from the mean low water mark of a littoral state that is regarded as the sovereign territory of the state.
Nautical Mile – is 1852 meters.
Erich Rienecker sets up the filter system to process phytoplankton from the CTD casts.
CTD – A CTD recorder, which stands for Conductivity-Temperature-Depth recorder, measures salinity, the amount of seawater conductivity in practical salinity units. It also measures pressure recorded in decibars. Since depth and pressure are directly related, a measurement in decibars can be converted to depth in meters. Temperature is measured as well and other sensors may be placed on the device as well. The one used had an altimeter to compare to the ships depth sounder and deployed cable for an accurate measure of the depth of the device.
HyperPro Optical sensor – measures light refraction at different wavelengths through the water column as compared to the surface measurement. This device is lowered by hand to a set depth. It is a hyperspectral radiometer, recording optical data in the wavelength region between 350 and 800 nanometers.
Oblique bongo net – a set of rings (thus the name bongo as it looks like a bongo drum) designed for oblique plankton tows. The rings are connected to nets which cone into two catch devices at the ends. Bongos are towed at 200 meters , devised by allowing 300 meters of cable out and towing it at an angle of 45-degrees. Adjustments in cable length are made depending on the angle reached.
NOAA Teacher at Sea Elsa Stuber prepares the seawater phytoplankton incubation trays.
Secchi disk – is used to measure how deep a person can see into the water. It is lowered into the ocean by unwinding the waterproof tape to which it is attached and until the observer loses sight of it. The disk is then raised until it reappears. The depth of the water where the disk vanishes and reappears is the Secchi disk reading. The depth level reading on the tape at the surface level of the ocean is recorded to the nearest foot.
Sea Level Pressure (from Wikipedia) Also referred to as Mean sea level pressure (MSLP or QFF) is the pressure at sea level or (when measured at a given elevation on land) the station pressure reduced to sea level assuming an isothermal layer at the station temperature. This is the pressure normally given in weather reports on radio, television, and newspapers or on the Internet. When barometers in the home are set to match the local weather reports, they measure pressure reduced to sea level, not the actual local atmospheric pressure. Average sea-level pressure is 101.325 kPa (mbar) or 29.921 inches of mercury (inHg).
Visibility – how far in front, or around the ship one can see. In this case, using the marine mammal observer’s scale, based on nautical miles.
Wind Direction- Which direction the wind is blowing FROM. 0 is north, 180 is south, 270 is west. This may also be recorded using the abbreviation of the direction in capital letters.
Sea Wave Height and Swell Height – estimates (based on an average of waves passing under buoys) the height of a wave (from crest to trough) of individual waves and larger waves.
Dissolved oxygen- the amount of oxygen that is available in the water for organisms to use for ventilation, typically referred to in parts per million, or ppm.
Phytoplankton – (from Wikipedia) are the autotrophic component of the plankton that drift in the water column. The name comes from the Greek terms, phyton or “plant” and πλαγκτος (“planktos”), meaning “wanderer” or “drifter”. Most phytoplankton are too small to be individually seen with the unaided eye. However, when present in high enough numbers, they may appear as a green discoloration of the water due to the presence of chlorophyll within their cells (although the actual color may vary with the species of phytoplankton present due to varying levels of chlorophyll or the presence of accessory pigments such as phycobiliproteins).
Zooplankton – (from Wikipedia) are the heterotrophic (or detritivorous) component of the plankton that drift in the water column of oceans, seas, and bodies of fresh water. The name is derived from the Greek terms, ζῴον (“zoon”) meaning “animal”, and πλαγκτος (“planktos”) meaning “wanderer” or “drifter”[1]. Many zooplankton are too small to be individually seen with the unaided eye. Zooplankton is a broad categorisation spanning a range of organism sizes that includes both small protozoans and large metazoans. It includes holoplanktonic organisms whose complete life cycle lies within the plankton, and meroplanktonic organisms that spend part of their life cycle in the plankton before graduating to either the nekton or a sessile, benthic existence. Through their consumption and processing of phytoplankton (and other food sources), zooplankton play an important role in aquatic food webs, both as a resource for consumers on higher trophic levels and as a conduit for packaging the organic material in the biological pump.
Gumby Suit – big, plastic, orange suits that are designed to protect a person from the cold water. Made of a material similar to what scuba divers wear. The suit is thicker, more buoyant and designed to remain dry inside. Suits are very bulky and are supposed to cover the entire body except the face.
PFD – personal floatation device, lifejacket, or “puff-duh”
Flying Bridge – located on the very top and most forward deck of the ship. On the MCARTHUR II, the flying bridge is above, or on top of the bridge. All ship personnel and crew when engaging in science activities keep in contact through the bridge with radios. Radio protocol requires the location being called to be stated first, followed by the calling location. For example,” bridge, flying bridge” If one is calling the bridge from the flying bridge.
Plan of the Day – is posted throughout the ship in common locations. This bulletin informs both crew and science personnel as to ship activities, wave height and safety issues.
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 3, 2007
Weather DAY 1: San Francisco, Pier 30/32
Visibility: 10 nautical miles
Wind direction: 270 NW
Wind Speed: 8 knots
Sea wave height in harbor: 1′
Seawater temperature: 15.129 C.
Sea level pressure: 1016.4
Air temperature: 15.2
Cloud cover: 1/4 cumulus
Science and Technology Log
The day began @ 07:30 picking up equipment at Moss Landing and riding up to San Francisco in van with other MCARTHUR II cruise members: Chief Scientist Tim Pennington, Biological Oceanographers-Marguerite Blum, Kit Clark, Erich Rienecker, Troy Benbow, Charlotte Hill; Physical Oceanographer, Dr. Curt Collins; CTD technician, Doug Conlin. At Pier 30/32, Marine Mammal Biologist, Katherine Whitaker, joined us and the other Teacher at Sea participant, Turtle Haste.
Tim Pennington coordinated the staging operation with the (FOO) Field Operation Officer Lt. Amanda Middlemiss. The large equipment for the cruise was at the pier on a flat bed truck and was loaded by crane on the ship’s deck with the assistance of the ship’s crew. All scientists were involved in unpacking the gear and setting up the wet lab and dry lab for the Time Series study work. As these labs have been physically updated since the last MBARI cruise on MCARTHUR II, set up in these labs required some modifications. All staff commented on the benefits and advantages of the lab improvements.
I reviewed material I researched on line prior to cruise about the Monterey Bay Aquarium Research Institute (MBARI) Time Series program. The focus is on the relations between oceanic carbon and nitrogen cycles and climate variability with emphasis on measuring the primary phytoplankton production. The research involves both observational and experimental studies with shipboard measurements of physical, chemical and biological parameters during cruises in Monterey Bay (since 1989) and offshore into the California Current (since 1997) at different seasons of the year. The data collected over this time span is being used to construct synthetic views of the oceanographic system dynamics of the California Current. The work has documented seasonal cycles, El Ninos and La Ninas and longer decade-scale cycles (e.g., Pacific Decadal Oscillation). The overall goal is to learn as much as possible about the earth’s climate and ocean systems, and therefore it is important to understand these cycles. Beyond construction of views of the California Current cycles and understanding the causation of them, will scientists determine that the directions show potential effects of global warming?
As stated in the summary of the MBARI Time Series Program report 2007: “Is this a local-or remotely-driven effect? We are uncertain. Is it important? You bet. Why? Because we area certain that (1) conclusions about global climate change begin with local observations, and (2) unusual conditions are often highly informative.”
Chief Scientist (CS) Tim Pennington went over the wet lab organization with the three of us new to working there, defining the different sample bottles and chemicals used in collecting and processing the sea water samples. He showed us which type of samples were stored in the freezer or in the liquid nitrogen, and which were placed in the seawater bath on the back deck. We signed up for our individual research tasks, my assignment is seawater sample collection from the rosette bottles of the CTD and processing in the wet lab. When filtered samples are ready, to process with the flurometer for chlorophyll level. My shift is 08:00 – 12:00 and 20:00-24:00. I work with CS Tim. Then we are free to study/work in other areas as you would like or as you are needed. We put duct tape ridge along front edge of wet lab tables to help stop materials from sliding off counter if ship is rolling.
At 16:00 we moved our personal belongings to our assigned quarters and then were free to explore the set-up of the MCARTHUR II. Important to note were the areas where one must wear a hard hat and a PFD. No open toed footwear outside your quarters. Pay attention to stay far away from winches when they are being used.
FOO Lt. Middlemiss requested that we review the safety instructions packet found in our quarters and that we should be ready for the safety drill to take place the next day.
