INTRODUCTION

The data in this report were collected during cruises 0704 of the California Cooperative Oceanic Fisheries Investigations (CalCOFI) program aboard the NOAA ship RV David Starr Jordan. The CalCOFI program was organized in the late 1940’s to study the causes of variations in population size of fishes of importance to the State of California.  It is carried out by NOAA’s National Marine Fisheries Service Southwest Fisheries Science Center, the California Department of Fish and Game, and the Integrative Oceanography Division (IOD) at Scripps Institution of Oceanography (SIO).  IOD contributes to this program by investigations of the physical, chemical and biological structure of the California Current. Data from the cruises were collected and processed by personnel of the Integrative Oceanography Division and the Southwest Fisheries Science Center.  Volunteers and other SIO staff members also assisted in the collection of data and chemical analyses at sea. CalCOFI data presented in this report and collected on previous cruises can be accessed at http://www.calcofi.org.

STANDARD PROCEDURES

CTD/Rosette Cast Data

    A Sea-Bird Electronics, Inc., Conductivity-Temperature-Depth (CTD) instrument with a rosette was deployed at each station on these cruises.  The rosette was equipped with 24 ten-liter plastic (PVC) bottles.  The CTD/rosette cast usually sampled 20 depths to a maximum sampling depth of 525 meters, bottom depth permitting.  Occasional stations have multiple bottles tripped at the same depth to provide more water for ancillary programs. The sample spacing was designed to sample depth intervals as close as 10 meters around the sharp upper thermocline features such as the chlorophyll, oxygen, nitrite maxima and the shallow salinity minimum.  Salinity, oxygen and nutrients were determined at sea for all depths sampled. Chlorophyll-a and phaeopigments were determined at sea within the top 200 meters, bottom depth permitting.

    Pressures and temperatures assigned to the water sample data were derived from the CTD signals recorded just prior to the bottle trip.  Pressures have been converted to depths by the Saunders (1981) pressure-to-depth conversion technique.  CTD temperatures reported with the bottle data have been rounded to the nearest hundredth of a degree Celsius.

    Salinity samples were collected from all rosette bottles and analyzed at sea using a Guildline model 8410 Portasal salinometer.  Salinity samples were drawn in to 200 ml Kimax high-alumina borosilicate bottles that were rinsed three times with sample prior to filling.  The results were compared with the CTD salinity in order to verify that the rosette bottle did not mis-trip or leak.  The salinometer was standardized before and after each group of samples with substandard seawater.  Periodic checks on the conductivity of the substandard were made by comparison with IAPSO Standard Seawater batch P144.  Salinity values have been calculated using the algorithms for the Practical Salinity Scale, 1978 (UNESCO, 1981a) and were reported to three decimal places, provided that accepted standards were met.

     Dissolved oxygen samples were collected in calibrated 100 ml iodine flasks, allowing at least 200% overflow.  The dissolved oxygen samples were analyzed at sea by the Winkler method, as modified by Carpenter (1965), using the equipment and procedure outlined by Anderson (1971).  Percent oxygen saturation was calculated from the equations of Weiss (1970).

     Nutrient samples were analyzed at sea for dissolved silicate, phosphate, nitrate and nitrite using procedures similar to those described in Gordon et al., 1993.  Samples were collected in 45 ml high-density polypropylene screw-capped tubes which were rinsed three times prior to filling.  Standardizations were done at the beginning and end of each group of samples with a set of mid-concentration  range standards prepared fresh for each run.  Samples

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* The first two digits represent the year and the last digits the month of the cruise.

not analyzed immediately after collection were refrigerated and run the following day.  Sets of six different concentration standards were analyzed periodically to determine the deviation from linearity as a function of concentration, primarily for the silicate and nitrate analyses.  Final sample concentrations were corrected for deviations from linearity.

     Samples for chlorophyll-a and phaeopigments were collected in calibrated 138 ml polyethylene bottles and filtered onto Whatman GF/F filters.  The pigments were extracted with a cold extraction technique in 90% acetone (Venrick and Hayward, 1984), and the fluorescence determined before and after acidification with a Turner Designs Fluorometer Model 10-AU-005-CE (Yentsch and Menzel, 1963; Holm-Hansen et al., 1965).

As part of broadening CalCOFI program, phytoplankton pigment concentrations have been added to the reugular sampling during cruises.  They were made by filtering sufficient 10m water samples to anlalyze pigments using HPLC and absorption coefficients of particulate soluble material.

    Evaluation of the water sample data involved comparisons with the CTD cast profiles, adjacent stations and consideration of the variation of a property as a function of density or depth and the relationships with other properties (Klein, 1973).  Precision estimates for the routine analyses were made on CalCOFI cruise 9003 and are reported in SIO Ref. 91-4.

Primary Productivity Sampling

    Primary productivity samples were taken each day shortly before local apparent noon (LAN). Primary production was estimated from ¹⁴C uptake using a simulated in situ technique.  Light penetration was estimated from the Secchi depth (assuming that the 1% light level is three times the Secchi depth).  The depths with ambient light intensities corresponding to light levels simulated by the on-deck incubators were identified and sampled on the up rosette cast.  Occasionally an extra bottle or two were tripped in addition to the usual 20 levels sampled in the combined rosette-productivity cast in order to maintain the normal sampling depth resolution.  The ten-liter bottles were equipped with epoxy-coated springs and Viton O-rings.  Triplicate samples (two light and one dark control) were drawn from each productivity sample depth into 250 ml polycarbonate incubation bottles.  Samples were inoculated with 53.14 µCi of ¹⁴C as NaHCO₃ (200 µl of 271.32 µCi/ml stock) prepared in a 0.3 g/liter solution of sodium carbonate (Fitzwater et al., 1982).  Samples were incubated from LAN to civil twilight in seawater-cooled incubators with neutral-density screens which simulate in situ light levels.  At the end of the incubation, the samples were filtered onto Millipore HA filters and placed in scintillation vials.  One half ml of 10% HCl was added to each sample.  The sample was then allowed to sit, without a cap, at room temperature for 12 hours (after Lean and Burnison, 1979).  Following this, 10 ml of scintillation fluor were added to each sample and the samples were returned to SIO where the radioactivity was determined with a scintillation counter.  Salinity, oxygen, nutrients, chlorophyll-a and phaeopigments were determined from all rosette productivity bottles.

Macrozooplankton Net Tows

    Macrozooplankton was sampled with a 71 cm mouth diameter paired net (bongo net) equipped with 0.505mm plankton mesh.  Bottom depth permitting, the nets were towed obliquely from 210 meters to the surface.  The tow time for a standard tow was 21.5 minutes.  Volumes filtered were determined from flowmeter readings and the mouth area of the net.  Only one sample of each pair was retained and preserved.  The biomass, as wet displacement volume, after removal of large (>5 ml) organisms, was determined in the laboratory ashore.  These procedures are summarized in greater detail in Kramer et al. (1972).  An Optical Plankton Counter (OPC) was routinely used in one side of the paired bongo net frame.  The purpose of the OPC is to obtain information on the vertical distributions of size categories of zooplankton, using data from the counter, without affecting the ongoing time series of data obtained from the catches of the integrative bongo net.

Avifauna Observations

Sea birds were counted within a 300-meter wide strip off to one side of the ship.  Counts were made while underway between stations during periods of daylight.  These counts were summed over 20 nautical mile (nm) intervals, or the distance between consecutive stations, whichever was less.  Included at the end of this report are individual maps of the most numerous bird species (individuals/nm).

Ancillary Programs

    Several ancillary programs produced data on these cruises that are not presented in this report. These programs include:  

1)    Underway Data.  Continuous near surface measurements of temperature, salinity and in vivo chlorophyll fluorescence were recorded from seawater pumped through the ship’s uncontaminated seawater system from a depth of approximately 3 meters.  The data were logged in one-minute averages using a Sea-Bird Electronics, Inc., SBE 45 MicroTSG Thermosalinograph and a Turner Designs SCUFAâII fluorometer.

2)      ADCP.  Continuous profiles of ocean currents and acoustic backscatter between 20 and 500 meters deep were measured along the shiptrack from a hull-mounted 150 kHz Acoustic Doppler Current Profiler (ADCP). The ADCP data were averaged over 5-minute intervals. Sixty 8-meter depth bins were recorded.

3)   Organic carbon: At each station several samples were drawn from the CTD for total organic carbon concentration profiles. At half of the stations 10 to 15L of surface water were filtered for stable isotope measurements of particulate organic carbon.  Several solid phase extracts from filtered seawater were taken for chemical and isotope analyses of dissolved organic carbon.

4)      California Current Ecosystem Long Term Ecological Research Program:  The CCE-LTER program augments standard CalCOFI measurements to further characterize the lower trophic levels as well as the carbon system.  These additional samples, taken at all CalCOFI stations, are for measurements of particulate organic carbon and nitrogen, dissolved organic carbon and nitrogen, taxon-specific phytoplankton pigments, flow-cytometric counts of bacteria and picoautotrophs, microscopic counts of nano- microplankton, determination of mesozooplankton size structure using a Laser Optical Plankton Counter, and mesozooplankton community structure. (M. Ohman, SIO)

5)      SCCOOS Nearshore and Bio-optical Observations: The objective of these observations is to extend CalCOFI time series to the nearshore and make bio-optical observations for the development of empirical proxies for particle size load and structure and phytoplankton biomass and rates of primary production.  The nearshore observations consist of 9 stations at the ends and interspersed with current CalCOFI lines on the 20 m isobath with a standard set of CalCOFI observations.  Bio-optical measurements at all CalCOFI and SCCOOS stations consist of irradiance at 9 wavelengths, light transmission at three wavelengths, fluorescence of Chl a, CDOM and phycoerythrin and light scattering at three wavelengths.

6)        Underway Sea Surface xCO2. Continuous measurements of the partial pressure of CO2 were made from the ship's uncontaminated seawater system. The seawater was equilibrated in a membrane contactor with a gas loop that was analyzed with a Licor 6262 infrared CO2/H2O analyzer. One-minute averages were recorded and the mole fraction of CO2 (xCO2) at sea surface temperature was calculated.  The system was calibrated with standard gases traceable to CMDL every two hours; at that time absolute zero and atmospheric samples were also collected. (G. Friederich, MBARI)

7)      Marine mammal observations. During daylight transits, visual line-transect surveys were conducted by marine mammal observers focusing on cetaceans.    Acoustic line-transect surveys were performed using a towed hydrophone array which consists of multiple hydrophone elements that sample sounds up to 100 kHz allowing for localization of calling animals.  Acoustic monitoring also takes place on individual stations using sonobuoys.

(J. Hildebrand, SIO)

TABULATED DATA

CTD/Rosette Cast Data

    The time reported is the Coordinated Universal Time (UTC) of the first rosette bottle trip on the up cast.  The rosette bottles tripped on the up cast are reported as cast 2, where cast 1 is considered to be the down CTD profile.  The sample number reported is the cast number followed by a two-digit rosette bottle number.  Bottom depths, determined acoustically, have been corrected using British Admiralty Tables (Carter, 1980) and are reported in meters.  Weather conditions have been coded using WMO code 4501.  Secchi depths are reported for most daylight stations. 

    Observed data from individual CTD/rosette trip levels are interpolated and reported for standard depths.   Interpolated or extrapolated standard level data are noted by the footnote “ISL” printed after the depth.  Multiple bottles tripped at the same depth to provide water for ancillary programs are not used in the calculation of standard depth data.  Density-related parameters have been calculated from the International Equation of State of Seawater 1980 (UNESCO, 1981b).  Computed values of potential temperature, sigma-theta, specific volume anomaly (SVA), and dynamic height or geopotential anomaly are included with both observed and interpolated standard depth levels.        

     On stations where primary productivity samples were drawn a footnote appears after each productivity depth sampled.  The corresponding primary productivity data are reported in a separate section following the tabulated rosette cast data.  

Primary Productivity Data

    In addition to the normal hydrographic data also reported in the rosette cast data section, the tabulated data include: the in situ light levels at which the samples were collected, the uptake from each of the replicate light bottles, uptake 1 and uptake 2 (which have been corrected for dark uptake by subtracting the dark value), the mean of the two uptake values and the dark uptake.  The uptake values are totals for the incubation period.  Also shown are the times of LAN, civil twilight, and the value of the mean uptake integrated from the surface to the deepest sample, assuming the shallowest value continues to the surface and that negative values (when dark uptake exceeds light

uptake) are zero.  The uptake data have been presented to two significant digits (values <1.00) or one decimal (values >1.00).  Precision of the higher production values  may not  warrant  all of  the  digits  presented.   Incubation

time, LAN, and civil twilight are given in local Pacific Standard Time (PST); to convert to UTC, add eight hours to the PST time.  Incubation light intensities are listed in a footnote at the bottom of each page.

Macrozooplankton Data

    Macrozooplankton biomass volumes are tabulated as total biomass volume (cm³/1000m³  strained) and as the total volume minus the volume of larger organisms under the heading “Small.”  Tow times are given in local PST (+8) time.

FOOTNOTES

In addition to footnotes, special notations are used without footnotes because the meaning is always the same:

 ISL: Values for standard levels from CTD sensors corrected as noted, nutrients calculated as double reciprocal regression.

CSL: Values for standard levels from CTD sensors corrected as noted, nutrients not calculated due to uncertainty.

    D: CTD values listed in place of ship board analysis, corrected as noted.

    U:  Uncertain value.  Values which are not used in interpolation because they seem to be in error without

         apparent reason.