CEAREX Biophysical Data


Data Description
Data Acquisition
Data Processing
Data Organization
Data Format

Data Description:

The Biological-Physical-Optical cruise was carried out aboard RV POLARBJORN during April and May 1989. The bio-physical data variables and their accompanying definitions are listed in the data processing section of the CD-ROM documentation file.

The meteorology data consist of hourly averaged observations of wind speed, wind direction, air temperature, relative humidity and sea level pressure made from the CEAREX biophysical stations. All optics profile data are in units per meter. The variable 'k' for all fields is the diffuse attenuation coefficient for the designated wavelength. All bioluminescence data values are in photons (*E10) per cubic meter. Values in the zooplankton data file are the mean densities for replicate tows. The phytoplankton and particulate matter variables from the biological analyses include:

  • chlorophyll concentration (ug/l)
  • phaeophytin concentration (ug/l)
  • particulate organic carbon (ug/l)
  • particulate organic nitrogen (ug/l)
  • primary productivity (ug C/l/d)

Data Acquisition:

Biological Analyses - Bioluminescence

Vertical profiles of mechanically stimulable bioluminescence were obtained using a High Input Defined Excitation (HIDEX) type bathyphotometer. Please refer to the CD-ROM documentation file for details of the instrumentation and sampling.

The design was based on the NORDA HIDEX. A 220 volt stainless steel well (Crown) pump was used to pump 100 gallons per minute through a detection chamber. Bioluminescence was stimulated by the shear created as the flow of seawater passed through a 1-cm x 1-cm grid at the intake to the detection chamber. The walls of the detection chamber were lined with optical fibers that collect light from the entire detection chamber and direct it to the photomultiplier tube (PMT) in the MER-2050 profiling bioluminescence photometer (BP) (Biospherical Instruments, Inc.). This instrument samples voltages at the photomultiplier tube at a sampling interval of 1 microsecond. Through a shipboard computer, the instrument is directed to sample the PMT a specified number of times, and then to sample any other sensors. In this case, the only other parameters sampled were voltage to the PMT and depth. Typically, these parameters were sampled at 1-second intervals. The MER-2050 allows for the high voltage to the PMT to be set at four levels: off (0 volts), low (500 volts), medium (700 volts) and high (900 volts), with higher voltages resulting in increased sensitivity. The BP was usually operated at its highest sensitivity, except in highly bioluminescent waters where bioluminescence was too bright to be accurately measured at the highest sensitivity.

One bioluminescence data file contains data averaged at 5 m intervals. Data from the top 5 meters were discarded. Values are in photons (*E10) per cubic meter. Another data file contains data from four stations (66, 69, 71 and 73) at which the BP was stopped at 10 m intervals and the pump was run for five minutes at each depth. The variables in these files are defined in the CD-ROM documentation file.

Biological Analyses - Phytoplankton and Particulate Matter

Pigments: Chlorophyll and phaeophytin were determined fluorometrically on a Turner Designs Fluorometer Model 10 (Holm-Hansen et al. 1967; Parsons et al. 1984), which had been calibrated with commercially purified chlorophyll-a (Sigma Chemical). Filters were extracted in 90 percent acetone, sonicated for ten minutes, and the fluorescence was assayed before and after acidification.

Particulate carbon and nitrogen: Particulate matter concentrations were determined by pyrolysis of filtered samples in a Perkin Elmer Model 240B elemental analyzer. Samples (approximately 0.3-1.1 l) were filtered through precombusted (450 C for four hours) GF/F filters, rinsed with a few ml of weak (0.01 N) HCl, placed in precombusted glass vials and covered with aluminum foil, and dried at 60 C. Blanks were filters placed under another filter and processed as above (Nelson et al. 1989).

Primary productivity: Rates of primary productivity were determined using simulated in situ 14C-incorporation experiments (Smith and Nelson 1990). Samples were collected from depths which corresponded to known percentages of surface irradiance and placed in bottles covered with neutral density screens. The samples were inoculated with approximately 20 uCi of HCO3 and incubated on deck for approximately 24 hours. Incubations were terminated by filtering the samples through GF/F filters, which were rinsed with 5 ml 0.1N HCl just prior to the completion of the filtration (Goldman and Dennett 1985). All samples were counted on a liquid scintillation counter, and counting efficiencies determined by the external standard method. Total added isotope was determined by counting 0.5 ml of unfiltered sample directly.

Integration was from the surface to the depth at which 0.1 percent of surface irradiance penetrated. This depth varies for each station.

Biological Analyses - Zooplankton

The results of enumeration of zooplankton obtained by net tows are contained in a separate data file. The samples were collected with oblique tows with a 0.5 m diameter 153 um mesh net hauled between the surface and 150 meters. Numbers included in the database are the mean densities for replicate tows. Each field represents the results for a species, a species developmental stage, or an aggregate of organisms not identified to the species level. All variable symbols are defined in the CD-ROM documentation file.

Nutrient Chemistry - Major Dissolved Nutrients

All major dissolved nutrient observations were taken in Fram Strait between April 10 and May 17, 1989. Nutrient observation samples whose concentrations are reported in the data file were obtained during the biological Niskin bottle casts. The nutrient analyses were performed using a six-channel Alpkem Rapid Flow Analyzer "mated" to a computer-controlled (HP Vectra ES/12) data acquisition system. The methods used for the ammonium, nitrate, nitrite, phosphate and silicate analyses were slight modifications of the methods described by Sakamoto et al. (1990).

Please refer to the CD-ROM documentation file for discussions of the continuous vertical nutrient profiles obtained, ammonium method problems encountered, and nutrient data errors detected.

Nutrient Chemistry - Biogenic and Lithogenic Silica

Biogenic silica was determined by filtering seawater through 0.6 um Nuclepore filters, drying them and returning them to Oregon State University for analysis. Back in the lab, the filters were digested in hot NaOH to dissolve the biogenic silica (Paasche 1973, Krausse et al. 1983) and the resulting solution was analyzed for reactive silicate by the acid-molybdate method of Strickland and Parsons (1972). These same filters were subsequently digested in 0.2 ml of 2.9M HF acid in order to dissolve the lithogenic silica (Eggimann and Betzer 1976). This solution was diluted to an HF concentration of less than 8 mm and analyzed by the above acid-molybdate method.


A bio-optical-physical profiler was deployed at approximately 25 percent of the CEAREX stations. The system is an integrated in situ profiler capable of measuring the variables in continuous profile mode that are identified in the CD-ROM documentation file.

Marine particulate absorption and fluorescence excitation spectra were determined according to the methods of Mitchell and Kiefer (1984) and Mitchell (1990). Briefly, from 0.5 to 2.0 liters of seawater collected in rosette Niskin bottles were filtered through Whatman GF/F filters. The particles concentrated on the filters were then analyzed in a spectrophotometer and spectrofluorometer. An analysis using the spectrophotometer provided the raw absorbance, which was then corrected according to Mitchell (1990) to determine the absorption coefficient of the particles in the sea water suspension. The method is considered to have an accuracy of +/- 15 percent. Absorption coefficients at selected wavelengths corresponding to the channels of the optical profiler are included in the data files. The spectral fluorescence data are not included in the data base.

Station Observational Log

Notes on sea ice, sea state, cloud state and station type were recorded by a watch person at each station. The data were entered into a personal computer file for subsequent qualitative assessment of each station.

Data Processing:

Bioluminescence Data

Data were averaged at 5 m intervals. Data from the top 5 meters were discarded. Values are in photons (*E10) per cubic meter. There were no CEAREX conductivity-temperature-depth (CTD) stations numbered bp1700 and bp2300 for the second and third casts during the second drift. These station numbers in the data set refer to times when the BP and nets were deployed but no CTD was operating. At four stations, the BP was stopped at 10 m intervals and the pump was run for five minutes at each depth. Data from these four stations are provided in a separate file because the significantly shorter record length was difficult to integrate with the larger records in the other bioluminescence data file.

Physical Oceanography Data

CTD data were collected and processed by Tom Manley. Comparison data used in quality control were extracted from a file on the CEAREX CD-ROM and integrated into the bio-physical data for the discrete depths sampled. The data were extracted at depths decimated at 1 meter, smoothed, and interpolated as described in the physical oceanography data processing section of the CD-ROM documentation file. Please read it in its entirety to better understand what can and cannot be 'obtained' from the data set.

For the biophysical data files, ONLY CTD DATA FOR THE DEPTHS OF THE WATER SAMPLES ARE INCLUDED. The final CTD data set for the bio-physical cruise is included in the hydrography data files.

The quality control file used on the final data file is available in the CD-ROM documentation file. The file compares the trip log information obtained as each bottle was tripped and reported and bottle salinities with the final processed CTD/fluorescence profiles. The contents of the physical oceanography data files are also discussed in CD-ROM documentation file. For a discussion of the errors associated with the physical oceanography data, please refer to the data processing section of the CD-ROM documentation file.

Meteorology Data

The hourly averaged values were calculated from ten minute averaged values. Wind data were converted into u and v components, averaged, and then converted back into speed and direction. Missing values were coded as -9, except AIRTEMP, which was coded as -99 if missing. There are gaps in the data records where observations are missing, and there is no entry for one or more date/time group.

Only bio-physical station data from the POLARBJORN Cruise were extracted and are included. A PC diskette containing the CEAREX hourly meteorological data is available from NSIDC User Services. The complete CEAREX ten minute meteorological data are contained on the CEAREX CD-ROM.

Optics Data

All data from the deck PAR sensor and the bio-optical-physical profiler deployed at CEAREX stations were integrated using a Biospherical Instruments multiplexing deck box. The digitized signal was transferred by RS-232 interface to an IBM-AT compatible computer. A complete description of the profiler, data sampling and data processing can be found in Mitchell and Holm-Hansen (1991) or Mitchell (1991).

Data Organization:

The bio-physical cruise data are presented in six ASCII data files on the CEAREX CD-ROM including:

  • two bioluminescence data files
  • a data file of all bottle samples and bottle depths
  • a zooplankton sampling data file
  • an optics profiles data file
  • a station log data file

Tables describing the data files are provided in the CD-ROM documentation file. Each table includes variable names, formats, and a brief variable descriptions.

Data Format:

Null values are provided in data file fields that may in some cases contain no data. The null value varies depending on the field. The null value for each field is given in the tables in the CEAREX CD-ROM documentation files. Formats are specified are for each field. At least one blank separates each field, but there may be more than one blank between some fields.

In the larger bioluminescence data file, the first three header records have the FORTRAN format 21(A7,1X). The FORTRAN format for the fourth header record is A7,161X. The data record FORTRAN format is 21(F6.1,1X). "1X" indicates one blank between each field in the headers and data records. For the smaller bioluminescence data file, the format of the first three header records is 4(A7,1X), the format of the fourth header record is A7,25X, and the data record format is 4(F6.1,1X).

Heading titles in the zooplankton data file correspond to categories in a table in the documentation files on the CEAREX CD-ROM that shows all values in floating point format. The FORTRAN format of the header record is 29(A10,1X). The format of the data records is 29(F10.2,1X). Values are number of observations of zooplankton groups per cubic meter.


The following Principal Investigators (PIs) provided the data file/methods and/or references description for the CD-ROM documentation files (and this document):

Edward Buskey, University of Texas at Austin - biological analyses zooplankton and bioluminescence
Louis Codispoti, Monterey Bay Aquarium Research Institute (MBARI) - nutrient chemistry, dissolved nutrients
Kenneth Davidson, Naval Postgraduate School - meteorological data
Peter Guest, Naval Postgraduate School - meteorological data
Thomas O. Manley, Marine Research Corporation - meteorological data
R. Greg Mitchell, Scripps Institution of Oceanography - optical profiling and particle optics
David Nelson, Oregon State University - nutrient chemistry, biogenic and lithogenic silica
H. J. Niebauer, University of Alaska - station log observations
Walker O. Smith, Jr., University of Tennessee - biological analyses, phytoplankton and particulates

For a complete list of all CEAREX investigators, please refer to the CEAREX Investigator Address List.