Sample Analysis

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. Sample collection and analysis have evolved over time and the methods described are the ones currently practiced (2004). Data from the cruises are collected and processed by personnel of the Integrative Oceanography Division and the Southwest Fisheries Science Center. Volunteers, CDF&G and other SIO staff members also assisted in the collection of data and chemical analyses at sea.

STANDARD PROCEDURES

CTD/Rosette Cast Data

Sea-Bird Electronics, Inc., Conductivity-Temperature-Depth (CTD) instrument with rosette is deployed at each station. The aluminum frame rosette is equipped with 24 ten-liter plastic (PVC) bottles. Bottle springs are plastic-coated and viton o-rings are used to minimize metal and rubber contamination. The CTD/rosette cast usually samples 20 depths to a maximum sampling depth of 525 meters, bottom depth permitting. Occasionally, multiple bottles are tripped at the same depth to provide more water for ancillary projects. The sample spacing is 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 are determined at sea for all depths sampled. Chlorophyll-a and phaeopigments are determined at sea within the top 200 meters, depth permitting.
Pressures and temperatures assigned to the water sample data are 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 are collected from all rosette bottles and analyzed at sea using a Guildline model 8410 Portasal salinometer. Salinity samples are drawn in to 200 ml Kimax high-alumina borosilicate bottles that are rinsed three times with sample prior to filling. The results are compared with the CTD salinity in order to verify that the rosette bottle did not mis-trip or leak. The salinometer is standardized before and after each group of samples with substandard seawater. Periodic checks on the conductivity of the substandard are made by comparison with IAPSO Standard Seawater batch P134. Salinity values are calculated using the algorithms for the Practical Salinity Scale, 1978 (UNESCO, 1981a) and are reported to three decimal places, provided that accepted standards are met.
Dissolved oxygen samples are collected in calibrated 100 ml iodine flasks, allowing at least 200% overflow. Prior to 2003, 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). Since then an Oxygen Autotitrator with computer interface detects the titration end-point, records the value and derives a temperature-corrected oxygen. Percent oxygen saturation is calculated from the equations of Weiss (1970).
Nutrient samples are analyzed at sea for dissolved silicate, phosphate, nitrate and nitrite using procedures similar to those described in Gordon et al., 1993. Samples are collected in 45 ml high-density polypropylene screw-capped tubes which are rinsed three times prior to filling. Standardizations are 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 not analyzed immediately after collection are refrigerated and run the following day. Sets of six different concentration standards are analyzed periodically to determine the deviation from linearity as a function of concentration, primarily for the silicate and nitrate analyses. Final sample concentrations are corrected for deviations from linearity.
Chlorophyll-a and phaeopigments samples are collected in calibrated 138 ml polyethylene bottles and filtered onto Whatman GF/F filters. The pigments are 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).
Primary productivity samples are taken each day shortly before local apparent noon (LAN). Primary production is estimated from 14C uptake using a simulated in situ technique. Light penetration is 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 are identified and sampled on the rosette upcast. Occasionally extra bottles are 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 are equipped with epoxy-coated springs and Viton O-rings. Triplicate samples (two light and one dark control) are drawn from each productivity sample depth into 250 ml polycarbonate incubation bottles. Samples are inoculated with 10 µCi of 14C as NaHCO3 (200 µl of 50 µCi/ml stock) prepared in a 0.3 g/liter solution of sodium carbonate (Fitzwater et al., 1982). Samples are incubated from LAN to civil twilight (calculated using Nautical Almanac tables) in seawater-cooled incubators with neutral-density screens which simulate in situ light levels. At the end of the incubation, the samples are filtered onto Millipore HA filters and placed in scintillation vials. One half ml of 10% HCl is added to each sample 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 are added to each sample and the samples are returned to SIO where the radioactivity is determined with a scintillation counter. Salinity, oxygen, nutrients, chlorophyll-a and phaeopigments are determined from all rosette productivity bottles.

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 are made on CalCOFI cruise 9003 and are reported in SIO Ref. 91-4.

Macrozooplankton Net Tows
Macrozooplankton are sampled with a 71 cm mouth diameter paired net (bongo net) equipped with 0.505mm plankton mesh. Bottom depth permitting, the nets are towed obliquely from 210 meters to the surface (300m wire 45deg wire angle). The tow time for a standard tow is 21.5 minutes. Volumes filtered are determined from flowmeter readings and the area of the net opening. One codend is buffered formalin preserved and the other is alcohol preserved or frozen. The biomass, as wet displacement volume, after removal of large (>5 ml) organisms, is determined in the laboratory ashore. These procedures are summarized in greater detail in Kramer et al. (1972). An Optical Plankton Counter (OPC) is routinely used in one side of the paired bongo net frame. The OPC measures and records 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 are counted within a 300-meter wide strip off to one side of the ship. Counts are made while underway between stations during periods of daylight. These counts are summed over 20 nautical mile intervals, or the distance between consecutive stations, whichever was less.

Ancillary Programs
Several ancillary programs produced data on these cruises that are not presented in our Data Report. These programs include:

Underway Data - Continuous near surface measurements of temperature, salinity and in vivo chlorophyll fluorescence are recorded from seawater pumped through the ship’s uncontaminated seawater system from a depth of approximately 3 meters. The data are logged in one-minute averages using a Sea-Bird Electronics, Inc., SBE 45 MicroTSG Thermosalinograph and a Turner Designs SCUFA II fluorometer.
ADCP - Continuous profiles of ocean currents and acoustic backscatter between 20 and 500 meters deep are measured along the shiptrack from a hull-mounted 150 kHz Acoustic Doppler Current Profiler (ADCP). The ADCP data are averaged over 3-minute intervals. Sixty 8-meter depth bins are recorded.
Bio-optics - In-situ measurements of apparent and inherent optical properties of seawater are obtained daily using a bio-optical package consisting of a MER-2040 (Multi-channel Environmental Radiometer), a Sea-Bird SeaCAT CTD, and two transmissometers. Also integrated into the profiling system is a Hydroscat-6 that measured spectral backscattering at six wavelengths. Measurements are obtained daily at the primary productivity station in the upper 300 meters of the water column. Phytoplankton pigment concentrations are made using HPLC in addition to determination of particulate organic carbon, nitrogen, phycoerythrin concentrations and particle size distribution using flow-cytometry and Coulter Counter techniques.
Atmospheric and Marine Optics - Datasets of spectral water leaving radiance and aerosol optical thickness are acquired during daylight hours en route and on stations using hand held SIMBAD radiometers. The SIMBAD radiometer measures both variables in typical spectral bands of satellite ocean color sensors, namely bands centered at 443, 490, 560, 670 and 870 nm. The instrument was designed for evaluation of satellite derived ocean color. In sun viewing mode the instrument operates like a classic sun photometer. In sea viewing mode a vertical polarizer reduces sky light reflection in the instrument's field of view. Water samples are collected from the CTD/Rosette casts to determine particulate, detrital, and soluble absorption as well as phytoplankton pigment concentrations. (data collection currently suspended as of 2003)