Documentation for Bio-Physical Cruise
CEAREX, RV Polarbjorn
April-May 1989
Dr. B. Greg Mitchell
1. Introduction and File Descriptions
1.1. Structure and Contents of This File
The Biological-Physical-Optical cruise was carried out aboard RV
POLARBJORN during April and May 1989 as part of the Coordinated Eastern
Arctic Experiment (CEAREX). The data base from the cruise consists of
6 separate files, in ASCII character format:
STADB.DAT the database of each station
DEPTHDB.DAT the database of all bottle samples
ZOOPLKT.DAT the database of the zooplankton sampling
BIOLUM1.DAT the database of bioluminescence profiles
BIOLUM2.DAT the database of bioluminescence values at
10-meter intervals
PROFK.DAT the database of optics profiles
A description of each data file, including variable names, formats,
and a brief description of each variable, is given in Section 1.2 of this
documentation file. Each description includes the name of the investigator
who provided the data and identifies the section of this document where the
methods and/or references for the variables are described.
Six sections (2 - 7) follow the initial file descriptions. These
sections contain the detailed descriptions of the methods and/or references,
provided by the individual investigators (PIs), used to determine each
variable type in the six data files listed above. The sections are:
2. Physical Oceanography, Dr. Thomas O. Manley, PI
3. Meteorological Data, Dr. Kenneth Davidson, PI
4. Nutrient Chemistry
4.1. Major Dissolved Nutrients, Dr. Louis Codispoti, PI
4.2. Biogenic and Lithogenic Silica, Dr. David Nelson, PI
5. Biological Analyses
5.1. Phytoplankton and Particulates, Dr. Walker O. Smith, Jr., PI
5.2. Zooplankton and Bioluminescence, Dr. Edward Buskey, PI
6. Optical Profiling and Particle Optics, Dr. R. Greg Mitchell, PI
7. Station Log Observations, Dr. H.J. Niebauer, PI
1.2. Description of the Data Base Files
Data format notes: Null values are provided in fields in the databases
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 Sections
1.2.1 through 1.2.5. Specified formats are for each field as written to the
ASCII files on this CD-ROM. At least one blank separates each field, but
there may be more than one blank between some fields.
1.2.1. Filename STADB.DAT - Station Log Data Base
These data are in the CD-ROM directory \BIOPHYS.
This file contains observations of data that have only one value at
each station. Variables include time, location, flags for occurrence (or
not) of ancillary data collection such as bioluminescence profiles,
zooplankton tows or optics profiles, or integrated values of biological
variables such as chlorophyll and primary production.
Field Null Fortran Description
Name Value Format
---------- ----- ------- ------------------------------------
STA N/A I3 Station number (see Manley, Section 2)
ZOOSTA N/A A1 Zooplankton station flag (y/n)
(see Buskey, Section 5.2)
BLSTA N/A A1 Bioluminescence station flag (y/n)
(see Buskey, Section 5.2)
OPTSTA N/A A1 Optics station flag (y/n)
(see Mitchell, Section 6)
MO N/A I2 Month of year (see Manley, Section 2)
DAY N/A I2 Day of month (see Manley, Section 2)
YR N/A I2 Year (see Manley, Section 2)
TIME -9:-9 I2:I2 Time of day (see Manley, Section 2)
JULDAY N/A I3 Julian day (see Manley, Section 2)
LAT -999 F8.4 Latitude (see Manley, Section 2)
LON -999 F4.4 Longitude (see Manley, Section 2)
IntCHL -9 F5.1 Chlorophyll-a integrated 0-150 m,
mg m-2 (see Smith, Section 5.1.1)
IntPH -9 F5.1 Phaeopigments integrated 0-150 m,
mg m-2 (see Smith, Section 5.1.1)
IntPROD -9 F6.1 Primary Production integrated from surface
to depth at which 0.1% of surface
irradiance penetrated (see Smith, Section
5.1.3)
AIRTEMP -999 F5.1 Air temp., degrees C. (see Davidson,
Section 3)
HUM -9 F5.1 Relative Humidity (see Davidson, Section 3)
WNDSPD -9 F5.1 Wind Speed, meters per sec. (see Davidson,
Section 3
WNDHEAD -9 F5.1 Wind Heading, degrees from true north (see
Davidson, Section 3)
PRESS -9 F6.1 Barometric Pressure, millibars (see Davidson,
Section 3)
GRPLOG -9 A37 Group station log (see Manley, Section 2)
HOOVLOG -9 A118 "Hoover" Log (see Niebauer, Section 7)
1.2.2. File DEPTHDB.DAT - Bottle Depths Data Base
These data are in the CD-ROM directory /BIOPHYS.
This file contains data collected by profiling with the CTD and
collecting water samples with the rosette. Values from the CTD include
salinity, temperature and fluorescence as well as discrete analyses for
biology, chemistry and particle optics.
Field Null Fortran Description
Name Value Format
---------- ------- -------- -----------------------------------------
STA N/A I3 Station # (see Manley, Section 2)
BOT -9 I2 CTD bottle number (see Manley, Section 2)
NBPR -9 F6.1 Neil Brown Pressure (see Manley, Section 2)
BioZ -9 I3 Biology "Nominal Depth"(see Smith,Section 5.1)
BioB -9 I3 Biology Bottle # (see Smith, Section 5.1)
NB_TE -9 F6.3 Neil Brown Temp. (see Manley, Section 2)
NB_SA -9 F6.3 Neil Brown Salinity (see Manley, Section 2)
NB_FL -9 F6.3 Neil Brown Fluorescence (see Manley,Section 2)
PO4 -.99 F4.2 Phosphate (see Codispoti, Section 4.1)
Si -9 F5.2 Silicate (see Codispoti, Section 4.1)
NO3 -9 F5.2 Nitrate (see Codispoti, Section 4.1)
NO2 -.99 F4.2 Nitrite (see Codispoti, Section 4.1)
BioSi -9 F8.3 Biogenic Silica (see Nelson, Section 4.2)
LithoSi -9 F8.3 Lithogenic Silica (see Nelson, Section 4.2)
CHLa -.99 F5.2 Chlorophyll-a (see Smith, Section 5.1)
PHEO -.99 F4.2 Phaeopigments (see Smith, Section 5.1)
POC -9 F7.2 Particulate organic carbon (see Smith,
Section 5.1.2)
PON -9 F6.2 Particulate organic nitrogen (see Smith,
Section 5.1.2)
PROD -9 F6.2 Primary Production (see Smith, Section 5.1.3)
AP410 -.99 F6.4 Particulate absorption at 410 nm (see
Mitchell, Section 6)
AP435 -.99 F6.4 Particulate absorption at 435 nm (see
Mitchell, Section 6)
AP441 -.99 F6.4 " 441 nm
AP488 -.99 F6.4 " 488 nm
AP520 -.99 F6.4 " 520 nm
AP565 -.99 F6.4 " 565 nm
AP633 -.99 F6.4 " 633 nm
AP675 -.99 F6.4 " 675 nm
AP683 -.99 F6.4 " 683 nm
STATION COMMENTS A40 General comments regarding a station
1.2.3. File ZOOPLKT.DAT - Zooplankton Data Base
These data are in the CD-ROM directory \BIOPHYS.
This file contains the results of enumeration of zooplankton collected
by net tows. The samples were collected with oblique tows with a .5 meter
diameter 153 um mesh net hauled between the surface and 150 meters. Values
in the data file are the mean densities for replicate tows. Heading titles
correspond to the categories in the table below; all values are 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 (m**3)
Field Name Description (See Buskey, Section 3, for details)
---------- --------------------------------------------------
Station CEAREX Station Number
Cff Calanus finmarchicus adult females (m**3)
Cfm Calanus finmarchicus adult males (m**3)
Cfj Calanus finmarchicus juveniles (copepodites) (m**3)
Cgf Calanus glacialis adult females (m**3)
Cgj Calanus glacialis juveniles (copepodites) (m**3)
Chf Calanus hyperboreus adult females (m**3)
ChCV Calanus hyperboreus copepodite 5 (m**3)
Chj C. hyperboreus juveniles (copepodites less than 5) (m**3)
Cbore Conchoecia borealis (m**3)
Eham Eukronia hamata (m**3)
Frit Fritillaria sp. (m**3)
Mlf Metridia longa adult females (m**3)
Mlm Metridia longa adult males (m**3)
Mlj Metridia longa juveniles (copepodites) (m**3)
Microf Microcalanus sp. adult females (m**3)
Microj Microcalanus sp. juveniles (copepodites) (m**3)
Oithf Oithona spp. adult females (m**3)
Oithm Oithona spp. adult males (m**3)
Oithj Oithona spp. juveniles (m**3)
Oiko Oikopleura spp. (m**3)
Para Parathemisto sp. (m**3)
Pseuf Pseudocalanus minutus adult females (m**3)
Pseuj Pseudocalanus minutus juveniles (m**3)
Thys Thysanoessa sp. (all developmental stages) (m**3)
Cnaup Copepod nauplii (m**3)
Cegg Copepod eggs (m**3)
OthCop Other copepods (m**3)
OthZoo Other zooplankton (m**3)
1.2.4. Files BIOLUM1.DAT and BIOLUM2.DAT - Bioluminescence Data Base
These data are in the CD-ROM directory \BIOPHYS.
1.2.4.1. BIOLUM1.DAT contains vertical profiles of mechanically stimulable
bioluminescence obtained using a High Input Defined Excitation (HIDEX) type
bathyphotometer. See Section 5.2.2 for details of the instrumentation and
sampling.
Data were averaged at 5 meter intervals. Data from the top five
meters were discarded. Values are in photons (*E10) per cubic meter.
There were no CEAREX 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.
Header records 1 through 3 have the Fortran format 21(A7,1X). Header
record 4 Fortran format is A7,161X. Data record Fortran format is
21(F6.1,1X). "1X" indicates one blank between each field in the headers
and data records.
Header:
Station -> Sta X Sta Y Sta Z...etc...
Date -> Date X Date Y Date Z...etc...
GMT -> GMT X GMT Y GMT Z...etc...
Data: Density of photoplankton group per cubic meter.
Depth Signal 1 Signal 2 Signal 3 ...etc...
F6.1 F6.1 F6.1 F6.1 ...etc...
F6.1 F6.1 F6.1 F6.1 ...etc...
F6.1 F6.1 F6.1 F6.1 ...etc...
.
.
etc.
1.2.4.2. The file BIOLUM2.DAT contains vertical profiles of mechanically
stimulable bioluminescence data from Stations 66, 69, 71 and 73. At these
stations, the BP was stopped at 10 meter intervals and the pump was run for
5 minutes at each depth. This is the only difference between the data for
these stations and the data in the file BIOLUM1.DAT. These four stations
are provided in a separate file because the significantly shorter record
length was difficult to integrate with the larger records in BIOLUM1.DAT.
The format of the header records 1 through 3 is 4(A7,1X); the format of
header record 4 is A7,25X. The data record format is 4(F6.1,1X).
1.2.5. File PROFK.DAT - Spectral K Data Base
These data are in the CD-ROM directory \BIOPHYS.
This file contains values for the spectral diffuse attenuation
coefficient (k per meter) derived from vertical profiles of downwelling
spectral irradiance. All optics data are in units per meter. The variable
'k' for all fields below is the diffuse attenuation coefficient for the
designated wavelength.
Field Null Fortran Description (see Mitchell, Section 5,
Name Value Format for details)
---------- ----- ------- ------------------------------------------
MERcast N/A A6 Station name of the optics profile
Sta N/A I3 CEAREX Biophys cruise station number
Zm N/A I3 Depth in meters from the surface
C N/A F6.3 Beam attenuation coefficient, per meter
k-410 -.99 F7.3 k at 410 nm, per meter
k-441 -.99 F7.4 k at 441 nm, per meter
k-488 -.99 F7.4 k at 488 nm, per meter
k-520 -.99 F7.4 k at 520 nm, per meter
k-565 -.99 F7.4 k at 565 nm, per meter
k-633 -.99 F7.4 k at 633 nm, per meter
k-683 -.99 F7.4 k at 683 nm, per meter
2. Physical Oceanography - Dr. T.O. Manley
2.1. CTD data collected and processed by Tom Manley were provided for
this CD-ROM volume. Comparison data used in quality control were extracted
from his file called COMPAR.LOG (on this CD-ROM in the directory
\HYDROG\BIOCTD), and were integrated into the bio-physical database for the
discrete depths sampled. The data were extracted at depths decimated at 1
meter, smoothed, and interpolated as described in Section 2.3 below.
For the bio-physical data base, 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 base, on this CD-ROM in the
directory \HYDROG\BIOCTD.
Variables (and their accompanying definitions) that were extracted from
COMPAR.LOG and subsequently used in this data base, file DEPTHDB.DAT, are
listed below.
NB_PR => Neil Brown PRessure - (final data) the closest Neil Brown
pressure to the actual pressure (TF_PR) at which the bottle was
actually tripped (e.g. TF_PR = 34.7 db; NB_PR = 38)
NB_TE => Neil Brown TEmperature (final data) at NB_PR
NB_SA => Neil Brown SAlinity (final data) at NB_PR
NB_FL => Neil Brown FLuorometer value (final data) at NB_PR
2.2. Documentation for Tom Manley's file COMPAR.LOG
The file COMPAR.LOG (on this CD-ROM in the directory \HYDROG\BIOCTD)
compares the trip log information obtained as each bottle was tripped
and reported in the file TAGNEW.DAT (on this CD-ROM in the directory
\HYDROG\BIOCTD) and bottle salinities with the final processed
CTD/fluorescence profiles. This file was used as a form of quality control
on the final data and did indeed reveal important information for the user.
The notes that follow are important to understanding and using the data.
2.2.1. Station 165 shows a trip-final temperature difference of 0.651
degrees C. This has NOT been modified for the following reasons.
Although the original log sheet and the trip file do confirm the 1.88
degree C temperature, the uptrace file shows no indication of such
temperatures. Looking at the original plot, it appears that the 1.8
degree C water is almost the last depth level plotted. All other
temperatures shown in the original plot are in the 1.2 degree C range
and agree with the Neil Brown final temperatures (NB_TE). This is not
a confusion of stations since the profiles (original and final) match
except for this upper level temperature of 1.8 degree C. I concede
that the high temperature was there, however, it must obviously be
slightly above where the uptrace profile was terminated by the
software. Further, one may want to show how different the surface
trips can be (perhaps due to the proximity of the ship and its engine
coolant outlets, on the same side as was used to lower the CTD) by
looking at station 168 results which had two duplicate trips at 2 db
with differences between the RECORD_TAG information of 0.4 deg. C!!!!
2.2.2. Stations 197 to 199 show the small but noticeable effect of a
broken thermistor in the differences (DEL_TE) between the record tag
observations (TF_TE) and the final data (NB_TE) when temperatures were
positive. This resulted in an offset of about 0.08 degree C that was
later corrected for in the final data.
2.2.3. When the thermistor was replaced after station 198, stations
199 to 212 show a rather obvious temperature mismatch of approximately
0.4 degree C between the record tag observations (TF_TE) and the final
data (NB_TE) when temperatures were positive. These varying offsets
were later corrected for in the final data.
2.3. CTD Data Processing - Tom Manley
Although this may appear to be a long document on how things were done,
I would strongly recommend that you read it in its ENTIRETY. If you are
knowledgeable about how the data were processed, you will better understand
what can and can not be 'obtained' from the data set.
2.3.1. Contents of the Data Set
2.3.1.1. All of the CEAREX bio-ctd stations are labeled XXX.BIO,
where XXX ranges from 002 to 212. Station 1 was not even considered
since it was an exceptionally bad TEST station.
2.3.1.2. The updated edition of the tagfile is \HYDROG\BIOCTD\TAGNEW.
Its first version was shipped out to everyone some time ago. All
modifications since the last issue of the file to this date (March 1991)
are labeled with the symbol '@' as the last character of the line.
2.3.1.3. The file \HYDROG\BIOCTD\COMPAR.LOG was used as one of the
quality control steps. This file may be of more use to you than TAGNEW
in that it incorporates the final data and compares it with the record
tag (bottle trip) information.
2.3.1.4. A station listing file called BIOSTA.LOG (on this CD-ROM in
the directory \HYDROG\BIOCTD) that lists all of the positions and times
of the stations, is more or less useful for quick reference.
2.3.2. Data Processing Steps
2.3.2.1. Downtrace processing was rejected due to too many
unexplainable hysteresis problems between the down and up traces.
Uptraces were chosen because they could be calibrated to much higher
standards since bottles were taken on these profiles.
2.3.2.2. Bulk salinity calibration was abandoned because of strong
variations between stations and because of the exceptional stability
of the temperature-salinity curve generated using calibrated Neil
Brown temperatures and BOTTLE salinities.
2.3.2.3. Temperature was entirely bulk-calibrated, since there was
no direct evidence of time variation, except when the first response
thermistor was replaced at station 197. A very small correction was
used for stations 2 through 196.
2.3.2.4. Pressure calibration equations were generated for both
uptrace and downtrace using a bulk processing method. However,
pressure offsets were calculated individually for each station to get
the best near surface information for the biological work as well as
to provide the best intercomparison with the MER (G. Mitchell's
bio-physical sensor, see Section 6 of this file) observations.
Station 196, due to its depth of approximately 2500 db, had its own
pressure calibration.
2.3.2.5. University of Rhode Island (URI) provided a week of
programming time and two weeks of microVAX time (at no cost) to
reprocess all of the up and down traces from the original digital
data. The reprocessing included temperature and pressure calibrations.
Salinity was then derived with the newly-calculated p, t and c.
Nothing was done to fluorometry or conductivity.
2.3.2.6. Station 151 was re-derived from audio data and was later
reprocessed by URI.
2.3.2.7. Processed uptraces were still quite noisy due to dragging
instrumentation through the water column (i.e. the sensors reading
some of the more nasty turbulent wake effects.) Filtering was done
to smooth out these turbulent effects.
2.3.2.8. Both the top and bottom of the profiles were inspected to
make sure that the data seemed reasonable. In several stations, a
bad point was included that would make a mess of the filtering process.
If bad data were observed, they were replaced with data along a
similar trend using the original plotted data and the uptrace plot
and/or, very rarely, the downtrace as a framework.
2.3.2.9. Two uptrace profiles were deemed unusable: station 117 and
station 164. Station 127 had a repairable section of data missing and
was salvaged using the downtrace information.
2.3.2.10. Initially, a median filter of 20 points and then a Gaussian
filter of 30 points was used. This turned out to be too `heavy-handed'
and a better method of 4 successive 10-point Gaussian passes was used.
Glen Cota and I agreed on this as the best compromise for fluorescence
as well as CTD work. Additionally, this provided a reasonable
fluorometry profile, as opposed to some of the original profiles that
looked more like a `shotgun' pattern. By the very nature of filtering,
top and bottom parts of the profile (if in high gradient regions) will
be off from the original characteristic conditions of the uptrace.
Deviations of this kind were checked at the very end of the processing
phase of quality control using the COMPAR.LOG file (i.e. comparing
final data against original record tag trips). Please read the
introduction to the COMPAR.LOG file to get an appreciation for these
errors (Section 2.2, above). In short, these errors were minimal
especially compared to the variability of the data within the record
tag file itself (see the FT_VAR column in the COMPAR.LOG file.) With
respect to the other high gradient regions such as the thermo/halo/
pycnoclines, there will be deviations. This is not totally desirable,
however it was a trade-off that I was willing to make to get the
hydrographic information into a more intelligible form. The deviations
in the `clines' can be also seen in the COMPAR.LOG file.
2.3.2.11. The correction of the `broken thermistor' data at Stations
197 through 212 was completed.
2.3.2.12. T,S, density and FL profiles were plotted for all of the
stations. Since many of the stations have very little density variation
in them, inversions, obviously a major source of problems, were easily
detected. Many of the inversions were created solely because of
a temperature/conductivity lagging mismatch. We did not have time to
investigate this at URI, so the data were processed using generic
lagging concepts. The lagging mismatch, the noisy nature of the data,
and the potential for bio-fouling (Phaeocystis) gumming up the
conductivity cell in certain high biomass regions, lead me to believe
that the density inversions were an artifact of the above-mentioned
problems and therefore COULD NOT BE CONSIDERED AS REAL PHYSICAL
PROCESSES occurring in the ocean. For this reason, all density
inversions were removed BY HAND to ensure the proper gradient
characteristics of the original density field were preserved.
2.3.2.13. A major problem was then discovered: There was an obvious
and CONSISTENT density inversion (approximately 0.006 sigma-0 units)
observed at the transition from positive to negative temperatures
(i.e. at 0 degrees C.) This problem should have been detected at the
beginning and corrected BEFORE all of the filtering since the 0
degree density shift was subsequently `smeared' by the filtering
process. Instead of starting from scratch, an attempt was made to
fix the `generic' problems with some creative software. Surprisingly
the program worked better than had been expected, and all of the
stations were realigned. Only stations 2 through 196 were done this
way. Stations 197 through 212 had already been (unwittingly) corrected
for this problem since it had manifested itself to extreme proportions
because of the broken thermistor. It should also be noted that the
temperature error that caused this 0.006 density inversion problem was
on the order of 0.005 degrees C, which upon recalculation of salinity
and then density (like a positive feedback loop) caused the observed
density problem. The opposite effect was also observed (i.e. - a
positive increase in density of 0.006 during the transition from
negative to positive temperatures). These were more difficult to find
since this transition was typically masked by the high gradient in the
thermocline/pycnocline but in several profiles where this was not the
case, it was observable. All positive temperatures were too warm
by 0.005 degree C so their salinity profiles, etc., were also off.
The program took all this into account so that ALL of the profiles can
be considered similar in their makeup.
2.3.2.14. After verification of acceptable density structure at both the
top and bottom of the profile, three techniques were tried for salinity
calibrations. These were: 1) calibrating the purely independent channel
of conductivity through the bottle salinity; 2) calibrating salinity as
a function of the bottle salinity; 3) calibration of salinity as a
function of pressure. Both 1 and 2 proved to be completely
unsatisfactory while 3 proved to be the most acceptable. Additionally,
the clean nature of the bottle salinity plotted against corrected Neil
Brown temperature on a T-S curve gave exceptionally high credibility to
the calibration of salinity on a per station basis. Of the DEEP bottles
that fell off of the tight T-S curve, all had justification for being
that way oceanographically (at virtually all points there was indication
of deep water ventilation - chimneys, cold pool survey, and the like).
So they remained as part of the calibration. Calibration for most of
the stations was calculated using linear regression of the difference
between the bottle salinity and the filtered and corrected Neil Brown
data against their respective pressures, which of course provides a
perfect fit given two x,y pairs. Only Station 196 had three salinity
bottles taken. Using this station as a test case, a linear equation was
generated with only the top and bottom information. The intermediate
value was then solved for and compared with the actual value. The
resulting error of 0.005 psu (see COMPAR.LOG Station 196 for this result)
confirmed the linear method and additionally gave the best indication of
accuracy of the data, this being less than 0.006 psu. Note that the
0.006 psu accuracy is ONLY for those stations that had both bottom and
top bottle salinities available. About 82% of the data fall within
these conditions. Those stations that have only one bottle or no bottles
were provided extra information from the bounding stations (in time) to
come up with the required equation. For those stations that had one
bottle, accuracy is estimated to be on the order of 0.015 psu. For
stations that had no bottles, accuracy would be on the order of 0.025
psu.
The stations that fall into the 0.015 psu accuracy are 19, 46, 47, 57,
73, 102, 105, 106, 107, 114, 127, 129, 152, 153, 154, 155, 156, 165,
168, 190, 195, 201, and 202.
The stations that fall into the 0.025 psu accuracy are 2, 3, 11, 15,
29, 30, 40, 49, 60, 67, 82, 92, 94, 103, and 104.
All remaining stations have the higher 0.006 psu accuracy.
2.3.2.15. After salinity calibration was applied, plots were then made
to verify the validity of the equation for each station. Several
stations were found to have bad (primarily surface) bottle data when
compared to the bounding station information and were therefore
discarded. New equations were then made and retried. This iterative
method was only used on about 8 stations and each was correctly
calibrated on the second pass.
2.3.2.16. All profiles went though visual editing to insure the removal
of all density inversions. If I don't believe them, I won't let other
people suffer through them! New salinities were then 'back-solved'
from the corrected density and unaltered pressure and temperature
values.
2.3.2.17. T-S plots of all of the stations proved to be another quality
control technique. Station 212 was found to be in error serendipitously.
An autosal typographical error was found that gave the low salinity that
in turn made the delta S look like all of the other `normal' stations.
This was taken care of. Freezing temperature quality control also proved
to be exceptionally useful in that no data values fell below the freezing
point.
2.3.2.18. All of the station headers were redone to reflect the start
time and position of the uptrace (or downtrace where applicable.) This
was done on the basis of the original log sheets. Uptrace position was
defined to be the average of the beginning and ending latitude and
longitude.
2.3.2.19. The COMPAR.LOG file was the last quality control check (see
the file for details) which also turned up one station, or I should say
the lack of one station, in error. Station 151 was actually Station 150!
Since Station 151 was the audio tape station and was difficult to get
reprocessed (and I didn't want to hold the data back any more - at least
not for one station), I decided to use the downtrace version and apply
salinity calibration to the data based on the uptrace tag file
information. This also proved to be acceptable. As it turns out,
Station 151 did not have that large a deviation from the uptrace.
2.3.2.20. The parameters of potential temperature and dynamic height
were added to each station.
2.3.2.21. The station file headers are explained below. The example
shown here is for Station 002.BIO, with the actual data values at the
beginning of the station given in the example.
CPB32 2 2 78.5403 9.3690 89/04/10 100 12:29 PB5
PR TE SA FL PT S0 HZ
7.0 0.140 34.214 1.206 0.140 27.464 0.004
8.0 0.145 34.216 1.271 0.145 27.466 0.005
9.0 0.150 34.218 1.339 0.150 27.467 0.005
The first line (a traditional file header) can be broken down as:
CPB32 - ship id code
2 - station number
2 - uptrace cast used; if value is 1, a downtrace was used
78.5403 - decimal latitude
9.3690 - decimal longitude (East is positive, West is negative)
89/04/10 - year/month/day
100 - relative Julian day (year-day)
12:29 - recorded log sheet time at beginning of uptrace or downtrace
PB5 - CEAREX cruise number id for the bio/phys/oceanog phase
The second line (data column headers) can be broken down as:
PR - pressure in db
TE - temperature in degrees C
SA - salinity in psu
FL - uncalibrated, but very close to correct, according to Glen Cota;
units are mg/l
PT - potential temperature in degrees C
S0 - Sigma-0 or potential density
HZ - dynamic height anomaly in dyn. m. using the surface (0 db) as the
reference level; the first value in the data (if not at 0 db) is
used to represent the surface parameters.
2.4. Conclusion
Time, and use of the data, will find any remaining errors. Please let
me [T. Manley] know of any problems that are encountered so they can be
investigated and corrected in later versions of the data set.
3. Meteorological Data for Bio-Physical Stations - Dr. K. Davidson
3.1. Meteorological Data Description
Note: ONLY DATA FROM THE POLARBJORN AT THE TIME OF THE BIO-PHYSICAL
STATIONS WERE EXTRACTED AND INCLUDED IN THIS DATA BASE. A PC diskette
containing the CEAREX hourly meteorological data is available from NSIDC.
The complete CEAREX ten-minute meteorological data are contained on this
CD-ROM in the directory \METEOR.
The file provided by K. Davidson contains observations taken during the
Coordinated Eastern ARctic EXperiment (CEAREX). The data consist of hourly
averaged observations of wind speed, wind direction, air temperature,
relative humidity and sea level pressure. 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.
Note: THE FOLLOWING VARIABLE SYMBOLS ARE DIFFERENT THAN THOSE ORIGINALLY
PROVIDED BY K. DAVIDSON. THE FOLLOWING SYMBOLS ARE THE ONES USED IN THE
BIO-PHYSICAL DATABASE, FILE STADB.DAT:
WNDSPD = wind speed in meters per second;
WNDHEAD = wind direction in degrees from true north;
AIRTEMP = air temperature in degrees C;
HUM = relative humidity in percent;
PRESS = sea level in millibars.
Missing values are coded as -9, except AIRTEMP, coded as -99 if missing.
Note that there are gaps in the data records where observations are missing
and there is no entry for one or more date/time group.
3.2. Reference
Lackmann, G.M.; P.S. Guest; K.L. Davidson; R.J. Lind and J. Gonzales (1989)
CEAREX/POLARBJOERN Meteorology Atlas. Naval Postgraduate School,
NPS-63-89-005, 545 p.
4. Nutrient Chemistry
4.1. Major Dissolved Nutrients - Dr. L. Codispoti
4.1.1. Data Description
These 1980 CEAREX nutrient observations were taken in Fram Strait from
the R/V POLARBJORN between 10 April and 17 May 1989. The samples whose
concentrations are reported here were obtained during the biological Niskin
bottle casts. A six-channel Alpkem Rapid Flow Analyzer "mated" to a
computer-controlled (HP Vectra ES/12) data acquisition system performed the
nutrient analyses. The methods used for the ammonium, nitrate, nitrite,
phosphate and silicate analyses were slight modifications of the methods
described by Sakamoto et al., 1990 ("MBARI procedures for automated nutrient
analyses using a modified APKEM Series 300 Rapid Flow Analyzer," MBARI
Technical Report 90-2).
Some problems were encountered with the ammonium method, so we have not
included these data here. These data, although useful, require additional
editing. Consequently, investigators wishing to use the ammonium data should
contact us directly. The nitrate, nitrite, phosphate and silicate data are
reported as NO2, NO3, PO4, and Si in micromolar.
So far, the nutrient data have gone through three stages of editing,
but some errors may remain. We urge the user to contact us if they encounter
suspicious values, and we are continuing to improve the already-acceptable
quality of these data. At the present stage of editing, we estimate the
accuracy of the PO4 data to be plus or minus 0.06 micromolar, and the nitrite
data to be plus or minus 0.04 micromolar. We estimate the accuracy of the
silicate and nitrate data to be plus or minus about 4%. These accuracy
estimates are for the entire suite of data. Precision within any given cast
is considerably better. The accuracy estimates may improve with further
editing.
A pumping system based on the system described by Friederich et al.,
1989 ("Bottle and pumpcasts data from the 1988 Black Sea Expedition," MBARI
Technical Report 90-3) and Codispoti et al., 1991 ("Chemical Variability in
the Black Sea: Implications of Continuous Vertical Profiles that Penetrated
the Oxic/Anoxic Interface," Deep Sea Research) was used to obtain a few continuous
vertical nutrient profiles. These data require further editing before they can be
distributed, but interested parties can
contact us directly for preliminary copies.
4.1.2. References
Codispoti, L.A., G.E. Friederich, J.W. Murray, and C.M. Sakamoto. 1991.
Chemical variability in the Black Sea: Implications of continuous
vertical profiles that penetrated the oxic/anoxic interface. Deep-Sea
Research 38 (Sup 2A): S691-S710.
Friederich, G.E., L.A. Codispoti and C.M. Sakamoto. 1990. Bottle and
pumpcasts data from the 1988 Black Sea expedition. MBARI Technical Report
90-3.
Sakamoto, C.M., G.E. Friederich and L.A. Codispoti. 1990. MBARI procedures
for automated nutrient analyses using a modified Alpkem Series 300 rapid flow
analyzer. MBARI Technical Report 90-2.
4.2. Biogenic and Lithogenic Silica - Dr. D. Nelson
4.2.1. Procedures
Biogenic silica was determined by filtering seawater through 0.6 um
Nuclepore filters, drying them and returning them to OSU for analysis. Back
in the lab, the filters were digested in hot NaOH to dissolve the biogenic
silica (Paasche, 1973, Marine Biology, 19(2), p. 117-126; and Krausse, et al.,
1983, Freshwater Biology, 13(1), p. 73-81) and the resulting solution was
analyzed for reactive silicate by the acid-molybdate method of Strickland and
Parsons (Practical Handbook of Seawater Analysis, 1972). These same filters
were subsequently digested in 0.2 mls of 2.9M HF acid in order to dissolve the
lithogenic silica (Eggimann and Betzer, 1976, Analytical Chemistry, 48(6),
p. 886-890). This solution was diluted to an HF concentration of less than
8mM and analyzed by the above acid-molybdate method.
4.2.2. References
Eggimann, D.W. and P.R. Betzer. 1976. Decomposition and analysis of refractory
oceanic suspended materials. Analytical Chemistry 48(6): 886-890.
Krausse, G.L.; C.L. Schelske and C.O. Davis. 1983. Comparison of three
wet-alkaline methods of digestion of biogenic silica in water. Freshwater
Biology 13(1): 73-81.
Paasche, E. 1973. Silicon and the ecology of marine plankton diatoms. I.
Thalassiosira pseudonana (Cyclotella nana) grown in a chemostat with
silicate as limiting nutrient. Marine Biology 19(2): 117-126.
Strickland, J.D.H. and T.R. Parsons 1972. Practical Handbook of Seawater
Analysis. Canada. Fisheries Research Board. Bulletin 167: 311.
5. Biological Analyses
5.1. Phytoplankton and Particle Analysis - Dr. W.O. Smith, Jr.
Data collected during CEAREX included variables which describe
phytoplankton and particulate matter concentrations. They include pigment
(chlorophyll and phaeophytin) concentrations, particulate carbon, and
particulate nitrogen. Also measured was the rate of primary productivity.
Variables in the data file are:
CHL Variable 1 is chlorophyll concentration in ug/l
PHEO Variable 2 is phaeophytin concentration in ug/l
POC Variable 3 is particulate organic carbon in ug/l
PON Variable 4 is particulate organic nitrogen in ug/l
PROD Variable 5 is primary productivity in ug C/l/d.
Following are brief descriptions of the procedures used for each analysis.
5.1.1. Pigments: Chlorophyll and phaeophytin were determined
fluorometrically on a Turner Designs Fluorometer Model 10 (Holm-Hansen et al.,
1967, "Fluorometric determination of chlorophyll," J. Cons. Perm. Int. Explor.
Mer, 30, p. 3-15; Parsons et al., 1984, Manual of Chemical and Biological
Methods for Seawater Analysis, NY, Pergamon Press), which had been calibrated
with commercially purified chlorophyll-a (Sigma Chemical). Filters were
extracted in 90% acetone, sonicated for 10 minutes, and the fluorescence was
assayed before and after acidification.
5.1.2. Particulate carbon and nitrogen: Particulate matter concentrations
were determined by pyrolysis of filtered samples in a Perkin Elmer Model 240B
elemental analyzer. Samples (ca. 0.3-1.1 l) were filtered through
precombusted (450 C for 4 h) 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, "Particulate matter and nutrient
distributions in the ice-edge zone of the Weddell Sea: Relationship to
hydrography during late summer," Deep Sea Research, 36, p. 191-209).
5.1.3. Primary productivity: Rates of primary productivity were determined
using simulated in situ 14C-incorporation experiments (Smith and Nelson,
1990, "Phytoplankton growth and new production in the Weddell Sea marginal
ice zone in the austral spring and autumn," Limnol. Oceanogr., 35, p.
809-821). 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 ca. 20 uCi of HCO3 and
incubated on deck for ca. 24 h. 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,
"Susceptibility of some marine phytoplankton species to cell breakage
during filtration and post-filtration rinsing". J.Exp. Mar. Biol. Ecol.,
86, p. 47-58). 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% of surface
irradiance penetrated. This depth varies for each station.
5.1.4. References
Goldman, J.C. and M.R. Dennett. 1985. Susceptibility of some marine
phytoplankton species to cell breakage during filtration and post-filtration
rinsing. J. Exp. Mar. Biol. Ecol. 86: 47-58.
Holm-Hansen, O., C.J. Lorenzen, R.W. Holmes and J.D.H. Strickland. 1965
Fluorometric determination of chlorophyll. J. Cons. Perm. Int. Explor. Mer
30: 3-15.
Nelson, D.M., W.O. Smith, Jr., R. Muench, L.I. Gordon, D. Husby and C.W.
Sullivan. 1989. Particulate matter and nutrient distributions in the ice-edge
zone of the Weddell Sea: Relationship to hydrography during late summer.
Deep-Sea Research 36: 191-209.
Parsons, T.R., Y. Maita and C.M. Lalli. 1984 Manual of Chemical and
Biological Methods for Seawater Analysis. NY: Pergamon Press.
Smith, W.O., Jr. and D.M. Nelson 1990. Phytoplankton growth and new
production in the Weddell Sea marginal ice zone in the austral spring and
autumn. Limnol. Oceanogr 35: 809-821.
5.2. Zooplankton and Bioluminescence - Dr. E. Buskey
5.2.1. The file ZOOPLKT.DAT contains the results of enumeration of
zooplankton obtained by net tows. The samples were collected with oblique
tows with a 0.5 meter diameter 153 um mesh net hauled between the surface
and 150 m. 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 Section 1.2.3, "File
ZOOPLKT.DAT - Zooplankton Data Base".
5.2.2. The files BIOLUM1.DAT and BIOLUM2.DAT contain vertical profiles of
mechanically stimulable bioluminescence data obtained using a High Input
Defined Excitation (HIDEX) type bathyphotometer. The design was based on the
NORDA HIDEX. A 220 volt stainless steel well pump (Crown pumps) was used to
pump 100 gallons per minute through our detection chamber. Bioluminescence
was stimulated by the shear created as the flow of seawater passed through a
1 cm**2 grid at the intake to the detection chamber. The walls of the
detection chamber are 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.
The file BIOLUM1.DAT contains data averaged at 5 meter intervals. Data
from the top five meters were discarded. Values are in photons (*E10) per
cubic meter. The variables in this file are defined in Section 1.2.4,
"Files BIOLUM1.DAT and BIOLUM2.DAT, Bioluminescence Data Base".
The file BIOLUM2.DAT contains data from Stations 66, 69, 71 and 73. At
these stations the BP was stopped at 10 m intervals and the pump was run for
5 minutes at each depth. The variables in this file are also defined in
Section 1.2.4, "Files BIOLUM1.DAT and BIOLUM2.DAT - Bioluminescence Data
Base".
6. Optics - Dr. G. Mitchell
6.1. Particle Optics
Marine particulate absorption and fluorescence excitation spectra were
determined according to the methods of Mitchell and Kiefer, 1984
("Determination of absorption and fluorescence excitation spectra for
phytoplankton." In: Marine Phytoplankton and Productivity, L. Bolis et al.,
Springer-Verlag; and, "Chlorophyll-a specific absorption and fluorescence
excitation spectra for light limited phytoplankton," Deep Sea Research, 35,
p. 639-663, 1988) and Mitchell, 1990 ("Algorithms for determining the
absorption coefficient of aquatic particulates using the quantitative filter
technique (QFT)". In: Ocean Optics X, R. Spinrad, ed., SPIE). Briefly, from
0.5 to 2.0 liters of seawater collected in the rosette Niskin bottles (see
Section 1.2.2) was filtered through Whatman GF/F filters. The particles
concentrated on the filters were then analyzed in a spectrophotometer and
spectrofluorometer. The analysis using the spectrophotometer provided the
raw absorbance which was then corrected according to Mitchell, 1990
("Algorithms for determining ...," In: Ocean Optics X, R. Spinrad, ed.,
SPIE) to determine the absorption coefficient of the particles in the sea
water suspension. The method is considered to have an accuracy of +/- 15%.
Absorption coefficients at selected wavelengths corresponding to the
channels of the optical profiler (described in Section 6.2) are included
in the data base. The spectral fluorescence data are not included in the
data base.
6.2. Optical Profiling
6.2.1. Data Description
A bio-optical-physical profiler was deployed at approximately 25% of the
CEAREX stations. The system is an integrated in situ profiler capable of
measuring the following variables in continuous profile mode:
Auxiliary sensors:
Temperature Sea Bird Electronics
Salinity Sea Bird Electronics
Fluorescence Sea Tech, Inc.
Transmission Sea Tech, Inc.
Optics sensors:
Surface PAR Biospherical Instruments QSR-100
Profiled PAR Biospherical Instruments MER 1012
Downwelling Irradiance Biospherical Instruments MER 1012
410 nm
441 nm
488 nm
520 nm
565 nm
633 nm
683 nm
Upwelling radiance Biospherical Instruments MER 1012
441 nm
488 nm
520 nm
565 nm
683 nm
All data from the profiler and the deck PAR sensor 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 ("Bio-optical
properties of Antarctic waters: Differentiation from temperate ocean
models," Deep Sea Research, in press) or Mitchell, 1991 ("Predictive
bio-optical relationships for polar oceans and marginal ice zones," Journal
of Marine Systems, in press.)
6.3. References
Mitchell, B. G. 1991. Predictive bio-optical relationships for polar oceans
and marginal ice zones. Journal of Marine Systems, in press.
Mitchell, B. G. 1990. Algorithms for determining the absorption coefficient
of aquatic particulates using the quantitative filter technique (QFT).
Ocean Optics X Bellingham, WA: Society of Photo-optical Instrumentation Engineers.
Mitchell, B. G. and O. Holm-Hansen. 1991. Bio-optical properties of Antarctic
waters: Differentiation from temperate ocean models. Deep-Sea Research, in
press.
Mitchell, B. G. and D. A. Kiefer. 1988. Chlorophyll a specific absorption
and fluorescence excitation spectra for light limited phytoplankton.
Deep-Sea Research 35: 639-663.
Mitchell, B. G. and D. A. Kiefer. 1984. Determination of absorption and
fluorescence excitation spectra for phytoplankton. In: Marine Phytoplankton
and Productivity, L. Bolis, R. Giles and O. Holm-Hansen, eds. Berlin:
Springer-Verlag.
7. Station Observational Log - H.J. Niebauer
At each station notes on sea ice, sea state, cloud state and station
type were recorded by a watch person. The data were entered into a personal
computer file for subsequent qualitative assessment of each station.
*************
8. Contact Information
If you encounter any problems with data in the files on this CD-ROM,
please contact the CEAREX Bio-Optics Data Set Manager:
Dr. B. Greg Mitchell
Marine Research Division 0218
Scripps Institution of Oceanography
La Jolla, CA 92093-0218 USA
Phone: 619-534-8947
Telemail: G.MITCHELL/Omnet
The Physical Oceanography data described in Section 2 were provided and
documented by:
Dr. Thomas O. Manley
Marine Research Corporation
8 Nedde Lane - Battell Hill
Middlebury, VT 05753
Phone: 802-338-6884
Telemail: T.MANLEY/OMNET
The Meteorological data described in Section 3 were provided and
documented by:
Dr. Kenneth Davidson and Dr. Peter Guest
Naval Postgraduate School
Monterey, CA 93943-5000 USA
Phone: 408-646-2451
Telemail: K.DAVIDSON/Omnet
The Major Dissolved Nutrient data described in Section 4.1 were provided
and documented by:
Dr. Louis Codispoti
Monterey Bay Aquarium Research Institute (MBARI)
P.O. Box 20, 160 Central Avenue
Pacific Grove, CA 93950-0020 USA
Phone: 408-647-3710
Telemail: L.CODISPOTI/Omnet
The Biogenic and Lithogenic Silica data described in Section 4.2 were
provided and documented by:
Dr. David Nelson
College of Oceanography
Oregon State University
Corvallis, OR 97331 USA
Phone: 503-737-3962
Telemail: D.NELSON/Omnet
The Biological Analyses described in Section 5.1 were provided and
documented by:
Dr. Walker O. Smith, Jr.
Graduate Program in Ecology
University of Tennessee
Knoxville, TN 37916 USA
Phone: 615-974-5226
Telemail: W.SMITH/Omnet
The Zooplankton and Bioluminescence data described in Section 5.2 were
provided and documented by:
Dr. Edward Buskey
Marine Science Institute
University of Texas at Austin
Port Aransas, TX 78373-1267 USA
Phone: 512-749-6794
Telemail: E.BUSKEY/Omnet
The Optics data described in Section 6 were provided and documented by:
Dr. B. Greg Mitchell
Marine Research Division 0218
Scripps Institution of Oceanography
University of California, San Diego
La Jolla, CA 92093-0218 USA
Phone: 619-534-8967
Telemail: G.MITCHELL/Omnet
The Station Observational Log described in Section 7 was provided and
documented by:
Dr. H. J. Niebauer
Institute of Marine Science
University of Alaska
Fairbanks, AK 99775-1080 USA
Phone: 907-474-7832
Telemail: J.NIEBAUER/Omnet
Acknowledgments
The data files for this CD-ROM were compiled at Scripps Institution
of Oceanography under Office of Naval Research grant N00014-89-J-1077.
The bio-physical investigators gratefully acknowledge the support of the
Office of Naval Research under the Coordinated Eastern Arctic Experiment ARI.
March 1991 (rev. July 1991)
