CRUISE INSTRUCTIONS
NOAA Ship: MILLER FREEMAN
Cruise No: MF9607
Area: Central and Eastern Bering Sea
Itinerary:
Depart Dutch Harbor April 17 Arrive Kodiak April 29
CRUISE DESCRIPTION:
Fisheries Oceanography Coordinated Investigations (FOCI) is a joint effort by scientists at PMEL and AFSC to understand the biological and physical processes which cause recruitment variability of commercially valuable fish and shellfish stocks in Alaskan waters. The Bering Sea FOCI program is presently studying the effects of the biotic and abiotic environment on the early life stages of walleye pollock spawned in the central and eastern Bering Sea. There are two aspects to the study: the acquisition and analysis of time-series data, and specific research topics to be covered on a cruise-by-cruise basis.
CRUISE OBJECTIVES:
We plan to obtain information on the inflow and outflow through Amukta Pass (near 172 degrees W) by use of CTD casts and a 25 - hour time series of ADCP measurements. Deep CTD casts will be made south of the Aleutian Islands to the east and west of Amukta Pass. Weather permitting, we will retrieve two subsurface moorings and deploy two surface moorings over the south eastern Bering Sea shelf. Various observations by net tows, water samples and a small surface buoy will be used to obtain information on plankton, chlorophyll, and sea color. Various measurements may be conducted in support of observations by a research aircraft. If time is available, a CTD grid near Unimak Pass will be occupied.
1.0. PERSONNEL
1.1. Chief Scientist: Ronald K. Reed / 526-6818
The Chief Scientist has the authority to revise or alter the technical portion of the instructions as work progresses provided that, after consultation with the Commanding Officer, it is ascertained that the proposed changes will not: (1) jeopardize the safety of personnel or the ship; (2) exceed the overall time allotted for the project; (3) result in undue additional expenses; (4) alter the general intent of these project instructions.
1.2 Participating Scientists
Ronald Reed M/USA PMEL William Parker M/USA PMEL Carol DeWitt F/USA PMEL Lisa Britt F/USA AFSC Aurea Ciotti F/Brazil Dalhousie University, Nova Scotia Gordana Lazin F/Brazil Dalhousie University, Nova Scotia Jen Patch F/USA University South Florida Engineer TBN M/USA PMEL
1.3 Ship Operations Contact:
Larry Mordock
(206) 553 - 4764
NOAA / PMC (PMC1x4)
1801 Fairview Ave. East
Seattle, WA 98102-3767
2.0. OPERATIONS
2.1. SUMMARY OF ACTIVITIES:
The ship will depart Dutch Harbor and steam directly to Amukta Pass and take a CTD section that was occupied during 1993 - 1995. A 25 - hour ADCP time series will be taken by steaming back and forth across the pass. At various sites Methot tows or Tucker sled trawls will be made; chlorophyll will be determined as well as ocean color from a small buoy. Deep CTD sections will be taken along 173.5 degrees W and approximately 170 degrees W. Some water samples from these casts will be analyzed for chlorophyll. Casts will be taken to near bottom or to approximately 3500 m in greater depths. After completion of this work, the ship will steam to the southeastern Bering shelf. Two subsurface current moorings will be recovered, and some of the equipment will be reused on two surface moorings (BSM2 and BSM3; Table 1) to be deployed at the same sites. A number of bongo tows for larvae and calVET tows will be made at these sites, as well as measurements of chlorophyll and ocean color. It there is time available, a grid of CTD stations near Unimak Pass will be occupied before departure for Kodiak.
2.2 PROCEDURES FOR OPERATIONS:
CTD/Water Sample Operations
PMC's Sea-Bird CTD will be the primary system used. (PMEL's CTD stand, which has been modified for the attachment of a Sea-Tech fluorometer, will be used). CTD data will be acquired on a PMEL computer using SEASOFT software. The capability to display CTD data using the SCS system and monitors will be available. Survey technicians and scientists will keep the "CTD Cast Information/Rosette Log" in addition to the wire usage log. The CTD should descend at a rate of 30m/min for the first 200m and 45m/min below that. The ascent rate should be 50m/min. The FOCI fluorometer, light meter, and chlorophyll absorbance meter (ChlAM) should be mounted on the rosette for all casts where possible. However, the ChlAM can not exceed 300m and the fluorometer and light meter cannot exceed 500 m. Water samples will be collected with 10-l Niskin bottles. Depth, fluorescence and light levels will be recorded on the "CTD Cast Information/Rosette Log" for all water bottle samples.
CTD Calibration: Salinity comparisons will be conducted on every cast (or as specified by the Chief Scientist). No reversing thermometers will be required. The CTD systems will be equipped with dual thermistors. A survey technician will run the AutoSal analysis during the cruise and record the readings on an AutoSal log.
Bongo Larval Condition Tows
A live tow for larval pollock uses the 60cm bongo with 0.333 mm or 0.505 mm net mesh with taped codends. The selection of the mesh size will depend on the time of field collections, larval size, amount of algae, etc. This is meant to be a vertical tow with ship speed used only to maintain a zero wire angle. The bongo is lowered at 50 m/min to a gear depth of 70 meters. The wire in speed should be 10 m/min, begin timing tow when net starts up. Do not rinse down the nets when they return to the deck, but do open the codends immediately into clean (live) 5 gallon buckets. The samples are carefully transferred into a bowl over ice and due to time restrictions are sorted quickly for live larvae (wigglers).
CalCOFI Vertical Egg Tow (CalVET)
Vertical tows to collect microzooplankton and free-floating copepod eggs will be conducted during patch studies, sometimes in conjunction with CTD/bottle casts. When done in conjunction with a CTD cast, the CTD will be stopped at 15 m during its descent, and the net frame's top and bottom will be attached to the wire so that the net flushes during its descent while the ship stands hove to. After standard descent to desired depth (usually 60 m), the net will then be retrieved at a rate of 60 m/min. The samples will be washed into the cod ends, then preserved in 32 oz. jars with formalin for later analysis. Once the net frame has been removed from the wire, then the CTD/bottle cast can begin. The CalVET net can also be deployed from the starboard quarter-deck.
Methot trawl
The Methot trawl is deployed using the Marco winch off the stern of the vessel (without the stern platform). A Scanmar acoustical depth sensor, with a readout in the trawl house (or alternatively, an electronic BKG or CTD), will be used to receive real-time depth information. A scientist or survey tech in the trawl house will relay orders for stopping and starting the winch to the winch operator based on trawl depth. The ship's speed should be 2.5 to 3.0 kts. This trawl will be deployed at 40 m/min and retrieved at 20 m/min. Tows will be oblique or stepped oblique from 100 m to the surface. Methot trawls may be conducted in daytime or at night with little or no advanced warning, as where and when they will be done depends on plankton catches or acoustic sign. Because this information is instantaneous, the trawl will need to be activated quickly with little time lost. Location and time of tows is at the discretion of the chief scientist or scientific watch leader.
Tucker trawls
The Tucker trawl will have 505 mm mesh netting and will be used in a standard manner. Depth of the net will be monitored with an electronic BKG or attached CTD. The net is deployed at constant wire speed of 40 m/min to a depth of 100 m. The winch is stopped and the net allowed to stabilize for 30 sec. A messenger is sent, opening the first net. The nets are retrieved at a wire speed of 20 m/min. The ship speed is adjusted to maintain a 45 degree wire angle during the entire tow. If both nets are to be used, at a predetermined depth, a second messenger is sent, closing the first net and opening the second, which is allowed to stabilize and then is retrieved as before. If the Tucker is used for the major part of the larval survey, it will probably be used in an oblique fashion, with only one net open. When the nets reach the surface, they are brought aboard and hosed down to wash the sample to the codend. Flow meters are read. Tows not meeting specifications may be repeated at the discretion of the scientific watch.
Chlorophyll Samples
Chlorophyll samples will be taken from the 2-l Niskin bottles. Sampling depths depend on the fluorescence profile. A typical strategy would be samples at 0, 10, 20, 30, 40, and 50 or 60 m depending upon which is closest to the fluorescence maximum. If the maximum is deeper, sampling should be moved deeper with less samples in the mixed layer.
When microzooplankton samples are to be collected from the same Niskin bottle, 500 ml of water is first removed from the water bottle using a graduated cylinder. Chlorophyll and nutrient samples are obtained from the 500 ml in the graduated cylinder. See the FOCI Field manual for sampling collection filtration and preserving details. The -70 degrees C freezer is required for sample storage.
Seachest and Uncontaminated Sea water
Sea surface temperature, conductivity and fluorescence will be continuously monitored. Data from the Sea-Bird thermosalinographinstalled in the sonar void seachest shall be sent to SCS. In addition, the uncontaminated sea water from this chest will be pumped to the Chemistry Laboratory and through a fluorometer. The scientists will be responsible for regularly cleaning the cuvette inside the fluorometer and obtaining and processing the calibration samples. Calibration samples will be taken at each bongo station or one hour apart, whichever is more frequent.
At the beginning of the cruise, the ship's chief survey technician will be responsible for ensuring that the data streams from the instruments are correctly logged by the SCS. During the cruise, the survey technicians are responsible for checking the logger once per watch to determine that the instruments are functioning, and for taking salinity calibration samples every other day. After the cruise, the chief survey technician should prepare an ASCII DOS formatted diskette that contains 1 minute averages of time, position, T, S, F and water depth.
ADCP
ADCP Observations:
The purpose of the Vessel-Mounted Acoustic Doppler Current Profiler (VM-ADCP) is to measure the ocean current velocity continuously over the upper 300 m of the water column, usually in 8 m depth increments. Current velocities relative to the earth at this spatial and temporal resolution cannot be measured by other methods: CTD sections, current meter moorings, or drifting buoys.
ADCP data is also used to estimate the abundance and distribution of biological scatterers over the same depth range and in the same depth increments.
ADCP Data Collection:
ADCP measurement requires four instruments working in concert: the ADCP, the ship's gyrocompass, a GPS receiver, and a GPS Attitude Determination Unit (ADU). The ADCP is connected to a dedicated PC and controlled by RD Instruments' Data Acquisition System (DAS) software. Version 2.48 of DAS software will be used as the controlling software. The DAS software shall be configured to use the user-exit programs AGCAVE.COM and UE4.EXE.. Separate written instructions detailing the ADCP setup and configuration files are kept in the ADCP notebook in the DataPlot compartment.
The ADCP PC is interfaced to the ship's gyrocompass, to the primary scientific GPS receiver, and to the GPS Attitude Determination Unit. The navigation GPS shall be configured to send only NMEA-0183 messages $GPGGA and $GPVTG at the maximum fix update rate for the receiver (usually 1 or 2 second rate), and with the maximum number of digits of precision (optimally 4). The Ashtech 3DF Attitude Determination Unit shall be configured to send the $PASHR,ATT message at least once, preferably twice, per second, and the NMEA-0183 message $GPGGA once each second. The user-exit program UE4.EXE shall be configured to control acquisition and processing of GPS and ADU messages, and to synchronize the PC clock with the time reported by the primary GPS.
The ADCP PC logs data from the profiler to SyQuest disks and optionally sends a complete data structure to SCS for logging on that system. This redundancy in data logging is desirable for post-cruise processing flexibility. The user-exit progam UE4.EXE should be configured to send an "RDI-style" ensemble to SCS.
PMEL supplies the SyQuest disks for FOCI projects. No more than one SyQuest disk will be required for the cruise. At the end of the cruise, a backup of the SyQuest should be made to a unique subdirectory of another disk maintained by the ship for this purpose until the original data is certified at PMEL.
Detailed, post-cruise processing of ADCP data is designed to take advantage of a higher quantity of navigation data than is retained by the ADCP acquisition software. Thus, the ship's SCS is relied on to log GPS navigation data at maximum available rates. The SCS system shall log output from the best two navigation receivers at all times during a cruise. For the purpose of designating a primary and secondary GPS system, precedence shall be assigned according to the following list of GPS receivers available on the Miller Freeman:
1. Trimble Centurion with encryption key installed and enabled (PPS-GPS)
2. Northstar 941X receiving differential corrections from radiobeacon (DGPS)
3. Trimble Centurion operating without encryption key (SPS-GPS)
4. Northstar 941X without differential corrections (SPS-GPS)
5. Magnavox MX-200 (SPS-GPS)
6. Ashtech 3DF ADU (SPS-GPS)
Changes in the availability of GPS equipment shall be communicated to PMEL to allow the above list to remain current. It is the responsibility of the ship to install and enable the appropriate encryption key for use of a PPS-GPS receiver.
The SCS file SENSOR.DAT should be configured to enable logging only of the NMEA-0183 format messages $GPGGA and $GPVTG from navigation sources; derived sensor messages are not desirable for post-cruise processing.
Similarly, only raw messages from the gyrocompass ($HEHDT) and GPS ADU ($PASHR,ATT) are desirable for logging.
SCS should log the primary GPS data at 1 second intervals, the secondary GPS data at 10 second intervals, gyro data at 10 second intervals, GPS ADU messages at 10 second intervals, and the temperature and input voltage of the ADCP electronics (deck unit) at 60 second intervals. The latter are used for adjusting the acoustic backscattered signal strength to absolute levels and relating the signal to biological scatterers.
ADCP Underway Operations:
The ADCP operates continuously during the entire cruise. At the start of a cruise, the system shall be configured and started according to the provided checklists "Before Leaving Port" and "Underway to Operations Area". The ADCP and its interface to the gyro and navigation must be checked daily by completing the "ADCP Daily Log" and also at the end of the cruise with the ship tied to the pier. The centerboard height affects the depth of sampling. The centerboard shall be lowered as soon as practical upon leaving port and remain lowered throughout the cruise. If it is necessary to raise the centerboard during the cruise, the times of raising and lowering must be logged in the Marine Operations Abstract (MOA).
In case of problems please describe the problem, error message numbers, flashing lights, etc. on the log sheets. Also contact Dan Dougherty (206-526-6844; e-mail DOUGHERTY@PMEL.NOAA.GOV) or Ned Cokelet (206-526-6820; e-mail COKELET@PMEL.NOAA.GOV) at PMEL as soon as possible.
Dedicated ADCP transects should be run at constant heading (not constant course-over-ground) if practicable, thus minimizing gyro lag. However, transects along lines of current-meter moorings should remain on the line with the ship's heading gradually adjusted to accomplish this. Sharp turns should be avoided. The ship's speed should be constant. 12 kts is often satisfactory, but the ship may have to slow down if the ADCP's percent good pings decreases below 75% in the upper 200-250 m due to sea state.
The ADCP should operate in bottom track mode when the water depth is less than about 500 m for more than a few hours. This gives currents better-compensated for transducer misalignment but somewhat lower in statistical significance because the number of pings is reduced. For extended periods in deeper water, an ADCP configuration without bottom tracking should be used.
ADCP Backtrack-L Calibration:
At least one backtrack-L calibration maneuver per cruise should be executed to test the instruments and to calibrate the transducer misalignment angle for which a 0.5 error can seriously bias the measurements. The "misalignment angle" may change with the ship's trim as well as with remounting the ADCP transducers. The basic idea is to measure the current twice on closely spaced parallel tracks of opposite heading when the ADCP and GPS are working well. The maneuver consists of 4 legs (N, S, E and W headings) connected by simple U-turns forming an L shape. Each leg should be 30 minutes long - the first 10 minutes are to allow the ship and instruments to stabilize on the new heading. The entire calibration should require about 2 1/2 hours with 5 minutes allowed for each turn. The following should be considered:
1. Negligible currents are best, but stronger currents are acceptable as long as they are reasonably uniform and steady. Avoid regions of strong horizontal shear due to topography, flow through passes, eddies and current boundaries. In tidal currents measure when the current is steadiest, often at maximum flood and ebb rather than at slack water.
2. Calibration legs can be done in any order provided opposite-headed legs are sequential.
3. Opposite-headed legs should be parallel and closely spaced, but not retraced. Use U-turns to minimize gyro oscillations. Avoid Williamson and hairpin turns.
4. The ADCP's PC screen should show at least 75%-good pings down to 250 m.
5. The ship should go fast enough to detect a misalignment error (over 5 kts), but slow enough to satisfy condition 4. This depends on sea conditions. 10-12 kts is often satisfactory.
6. Choose a time when GPS is navigating and is expected to remain so over the next 2 hours.
ADCP Absolute Backscatter Calibration:
A test to calibrate the absolute backscatter strength and to determine the background noise level of the ship-ADCP system may be performed once per cruise at the discretion of the Chief Scientist. Specific instructions in such event will be provided by PMEL personnel aboard, and cannot be anticipated in advance of the cruise.
Typically, such a test will be attempted in conditions when weather is relatively calm, and the water depth exceeds 250 m. This test may require that the main power plant, pumps, sonars, and other sources of acoustic and electronic noise be shut down. If conducted in the course of normal operations, the work will require about 1 hour. There may be opportunities for variations of the test any time the ship is at anchor, requiring the cooperation of the ship's officers and engineering watch.
Radiometer
The ship will be equipped with a radiometer to measure solar energy. The scientists will supply the calibrated instrument, mounting hardware and cable to run to DataPlot. We will need the assistance of the ship's Electronic Technician and SCS Manager to correctly install the instrument and make sure that the data stream is being logged by the SCS.
3.0. FACILITIES AND EQUIPMENT
The following systems and their associated support services are essential to the cruise. Sufficient consumables, back-up units, and on-site spares and technical support must be in place to assure that operational interruptions are minimal. All measurement instruments are expected to have current calibrations, and all pertinent calibration information shall be included in the data package.
3.1 Equipment and Capabilities to be Provided by the Ship