SPOT Methods

The CTD is operated per Sea-Bird’s suggested methods. The CTD is powered up and allowed to stabilize at approximately 0-5 m prior to profiling. The instrument is lowered at 40 m per minute (maximum rate) for the entire depth of the sampling site (0-890 m). Descent rates are adjusted depending on weather, ranging between 10 and 40 m/min. Sensor data are collected during the downcast, and water samples are collected during the upcast. Analysis of the temperature and conductivity data at the time of the bottle closure generally show good agreement with the downcast data, and are otherwise noted on cruise logs.

The following Sea-Bird data acquisition and processing programs are used during the cruise for preliminary observations of raw CTD and other sensor data: SEASAVE v.7.2 (to display, record and playback data) and SEACON (to enter calibration coefficients and configuration records). Data are recorded using the Sea-Bird software Seasoft at the full scan rate of 24 Hz. The data are stored directly on a PC.

Water samples are collected in twelve 12-L Niskin bottles. Before water samples are collected, the CTD is kept at the desired depth for a minimum of 120 seconds (which ensures entrainment from the CTD wake has been removed). Seawater samples are drained from the Niskin bottles according to protocols for various biological, physical and chemical measurements.

Cruise log sheets are filled out with the ship’s position when the CTD first goes in to the water and recorded when the CTD comes out of the water using a DGPS. Relevant information such as weather conditions are also added on the cruise sheets. Notes on hydrographic parameters at depths that the bottles are fired are also included.

SPOT cruises typically include 1 to 5 CTD casts per cruise, depending on sampling needs.

Equipment Specifications: CTD and Other Sensors

1. Pressure: SBE 9plus. Range: 0-10,000 psia (6,800 m). Depth resolution: 0.001% of full scale at 24 Hz. Response time: 0.015 seconds. Accuracy: 0.015% of full scale. Typical stability: 0.02% of full scale per year.
2. Temperature: SBE 9plus (SBE 3plus). Range: -5.0 to +35 ˚C. Accuracy: ±0.001 ˚C. Resolution: 0.0003 ˚C at 24 samples per second. Response time: 0.065 ± 0.010 seconds. Typical stability: 0.0002 ˚C per month.
3. Conductivity: SBE 9plus (SBE 4C). Range: 0-7.0 Siemens/meter. Accuracy: ±0.0003 S/m. Resolution: 0.00004 at 24 Hz. response time: 0.060 seconds (pumped). Typical stability: 0.003 S/m per month.
4. Pump: SBE 5T submersible pump. The pump flushes water through the conductivity cell at a constant rate, independent of the CTD’s motion, improving dynamic performance. Typical flow rate for the model is approximately 30-50 ml/sec.
5. Dissolved Oxygen: SBE 43 Dissolved Oxygen Sensor. Range: 0-7,000 m. Resolution: ± 2% of saturation. Response time: 2-5 seconds for 0.5-mil membrane, 8-20 seconds for 1.0-mil membrane.
6. Beam Transmission: WET Labs C-Star Transmissometer, 25 cm path-length. Light source wavelength= 650 nm (red). Depth range: 0-6,000 m.
7. Fluorescence: WET Labs ECO-AFL-FL, Deep Chlorophyll & Turbidity sensor. Chl Range: 0-50 µg/l. Sensitivity: 0.025 µg/l. Excitation: 470 nm. Emission: 695 nm. Depth range: 0-6,000 m. Turbidity wavelength: 700 nm, Range: 0-25 NTU, Sensitivity: 0.01 NTU.
   Note: WET Labs ECO-AFL-FL was installed in June 2012
   Aug 2000-Mar 2003 – WET Labs Fluorometer
   May 2003-May 2012 – SeaPoint Fluorometer
8. Colored Dissolved Organic Matter: WET Labs ECO-CD(RT)D, Deep CDOM fluorometer, Sensitivity: 0.09 ppb, Range: 0-500 ppb, Light source wavelength=470 nm, Depth range: 0-6,000 m.
9. PAR meter: Biospherical/Licor, installed June 2013

In June 2012, a new CTD and additional sensors were installed.  The current sampling rosette includes replicate temperature, conductivity, and oxygen sensors, a PAR sensor and in vivo fluorescence sensor.

The temperature sensors, conductivity cells and dissolved oxygen sensor are returned to Sea-Bird approximately every year for routine factory calibration.  The pressure sensor is calibrated approximately every 2 years.

CTD Data Processing Protocol (adapted from ‘SeaSoft-Win32: SBE Data Processing’)

The Sea-Bird software produces four files for each cast:
.bl – Bottle file, a record of time and scan number range (1.5 seconds) when bottle is fired
.hdr – header file, lat, long, time, etc.
.hex – raw 24 Hz data file, binary
.XMLCON – configuration file, containing instrument configuration and calibrations used by the software

The SPOT program’s naming convention for raw CTD data from the Sea-Bird software is as follows:

YYYYMMDDA
Where: YYYY is the year, MM is the month, DD is the day, and the following letter (A-F) denotes cast number (A is the first cast).

The following items are provided to cruise participants:

• Raw CTD files
• .asc files (tab delimited) – CTD and other sensor data
• .hdr files (text file) – UTC Time, header information (including units)

Processing Raw CTD Files using the SBE Data Processing Software v7.225

1. Data Conversion: convert binary voltages to engineering units.
2. Window Filter:  smooth profiles and remove spikes.  We apply a median filter of 9 for all parameters.
3. Filter:  Low-pass filter (0.15) on Pressure only.
4. Alignctd:aligns Conductivity, Temperature and Oxygen data to ensure that the sensors are measuring the same parcel of water.
   1. Oxygen:Pressure advancement: 3.0 sec
   2. Secondary conductivity advancement:  0.073 sec
      Note: For an SBE 9plus with TC-ducted temperature and conductivity sensors and a 3000-rpm pump, the typical lag of conductivity relative to temperature is 0.073 seconds. The Deck Unit is programmed to advance conductivity relative to pressure, eliminating the need to run Align CTD.). Corrects for the different response times and physical alignment of the CTD sensors so that all sensors are measuring the same parcel of water.
   3. Temperature and Salinity profiles are checked for alignment.
5. Celltm: correct for thermal mass of conductivity cell. We apply 0.03 for alpha and 7 for 1/beta.
6. Derive: potential temperature, salinity, density, oxygen.
7. Loopedit: apply a minimum CTD velocity of 0.1 m/s (fixed) and use a window size of 300s.  Loop Edit marks scans that have pressure slowdowns or reversals (typically caused by ship heave) with a ‘badflag’ value. The ‘badflag’ value is documented in the input .cnv header.  The SPOT CTD is operated at a maximum speed of 40 m/min (0.67 m/sec) and a minimum of 10 m/min (0.17 m/sec), depending on weather.
8. Binavg: convert data to 1 m depth averages
9. Split: create separate downcast and upcast data (denoted with a ‘d’ or ‘u’ prefix in file name for downcast or upcast, respectively)
10. Sea Plot:  create preliminary plots for temperature, salinity, conductivity, fluorescence, oxygen, and PAR (100 m and max depth plots)
11. Bottle summary:  create bottle summary file to provide hydrographic information at depths that bottles were fired (.btl file; can open using standard text editor).  This information can also be found in the provided excel sheet.
12. AscII Out:  create a file containing CTD data (.asc contains CTD data and the .hdr file is the associated header data).  CTD data can also be found in the provided excel sheet (along with the bottle summary file).

Chlorophyll-a 

Nutrients (nitrate, nitrite, phosphate, silicate)

Dissolved Oxygen

Salinity