Flow-through bio-optical system This system operates semi-continuously with water from the ship's seachest. The water is first debubbled with a vortex debubbler. Approximately every 2 minutes it measures temperature, salinity, chlorophyll fluorescence, CDOM fluoresence, total backscattering at 532nm (bbptot), acidified backscattering (bbpacid; backscattering of the seawater suspension after the pH has been lowered to dissolve calcium carbonate), acid-labile backscattering (bb'; the difference between the bbptot and bbpacid), absorption and attenuation at 9 visible wavelengths (made every 128 seconds), absorption and attenuation at 9 visible wavelengths after water was routed serially through a 1.0um then a 0.2um cartridge filter (during intervening 128 second segments). Absorption and attenuation values are averaged over their respective 128 second segments after the first ~30 seconds of each segment is discarded to eliminate noise induced by switching from unfiltered to filtered or back. Backscatter values (bbptot and bbpacid) are the average of 20 samples taken once the pH values have stabilized at either nominal seawater pH or at the dissolution point for calcium carbonate. Temperature, Salinity, chlorophyll fluoresence and CDOM fluoresence are single value measurements taken at the beginning of the bbptot measurement period. Above-Water Radiance Measurements In order to check ocean color algorithm performance, free of atmospheric error, water-leaving radiance, sky radiance and downwelling irradiance were measured from the bow of the ship using a Satlantic SeaWiFS Aircraft Simulator (SAS or MicroSAS). The system consists of a down-looking radiance sensor and a sky-viewing radiance sensor, both mounted on the bow. A downwelling irradiance sensor is mounted as far as practical from any potentially shading structures. These data were then used to estimate normalized water-leaving radiance as a function of wavelength. The radiance detector was set to view the water at 40o from nadir as recommended by Mueller et al. (2003b). The water radiance sensor is able to view over an azimuth range of at least 120o and occasionally as much as 180o, depending on the vessel, across the ship's heading with no contamination from the ship's wake. The direction of the sensor was adjusted regularly to view the water at as close to 120o from the sun's azimuth as possible, to minimize sun glint. This is done either manually roughly every 30 minutes or, on more recent cruises, using a computer-based system that calculated the sun's azimuth angle relative to the ship's heading and elevation constantly. The computer controlls a stepping motor that turns the sensors to the proper viewing angle depending on the ship's course. Protocols for operation and calibration are performed according to Mueller (Mueller et al. 2003a; Mueller et al. 2003b; Mueller et al. 2003c). Before 1000h and after 1400h local time, data quality is poorer as the solar elevation decreases. The data are filtered to remove as much residual white cap and glint as possible (we accept the lowest 5% of the data). When weather permits, a plaque calibration is performed, using a 2% spectralon plaque, to check for instrument drift. Description of measurements made During cruises, underway samples are typically collected about every 30km, except sampling points are modified as needed to optimize for satellite overpass matchups. Samples are taken for particulate inorganic carbon and biogenic silica, particulate organic carbon/nitrogen and chlorophyll a. Coccolith counts were performed using the technique of Haidar and Thierstein (2000; 2001) except optical adhesive was substituted for Canada Balsam. Discrete samples were taken for measuring surface maximum primary production (Pm; units mg C m^-3 day^-1). Water samples were prefiltered through 200 mm Nitex mesh to remove large grazers, then maintained in surface light conditions in a temperature-controlled incubator until returning to the laboratory (~1/2 day). Note, there was a single incubation temperature for all productivity samples during each cruise, the average temperature as determined from ship based measurements at the time each sample was taken. The full temperature range across the GNATS transect was typically 4–6oC, thus at any one station, the in situ temperature varied by +2–3oC from the incubation temperature. After each trip, samples were inoculated with 14C-HCO3 near local apparent midnight, for 1/2 day incubations (Mantyla et al., 1995) then filtered onto 0.4 mm polycarbonate filters at local apparent noon of the following day. The 14C microdiffusion technique was used for sample preparation and analysis (Paasche and Brubak, 1994; Balch et al., 2000). Triplicate primary production values were processed for each station along with a formalin-killed blank. Conversion of the 12 day rates to full day rates was based on ratios of 12 and 24 h incubations. The half-day 14C incubation insured that the total time that samples were in bottles was <1 day, thus minimizing bottle effects. References: Haidar A.T., Thierstein H.R., Deuser W.G. 2000. Calcareous phytoplankton standing stocks, fluxes and accumulation in Holocene sediments off Bermuda (N. Atlantic). Deep Sea Research 47(9-11), 1907-1938. Haidar A.T., Thierstein H.R. 2001. Coccolithophore dynamics off Bermuda (N. Atlantic). Deep Sea Research 48(8-9), 1925-1956. Mueller J.L., Austin R.W., Morel A., Fargion G.S., McClain C.R. 2003a. Ocean optics protocols for satellite ocean color sensor validation, Revision 4, Volume I: Introduction, background, and conventions. Greenbelt, MD: Goddard Space Flight Center. 50 p. Mueller J.L., Morel A., Frouin R., Davis C., Arnone R., Carder K., Lee Z.P., Steward R.G., Hooker S.B., Mobley C.D., McLean S., Holben B., Miller M., Pietras C., Knobelspiesse K.D., Fargion G.S., Porter J., Voss K. 2003b. Ocean optics protocols for satellite ocean color sensor validation, Revision 4, Volume III: Radiometric measurements and data analysis protocols. Greenbelt, MD: Goddard Space Flight Center. 78 p. Mueller J.L., Pietras C., Hooker S.B., Austin R.W., Miller M., Knobelspiesse K.D., Frouin R., Holben B., Voss K. 2003c. Ocean optics protocols for satellite ocean color sensor validation, Revision 4, Volume II: Instrument specifications, characterisation and calibration. Greenbelt, MD: Goddard Space Flight Center. Mantyla, A. W., Venrick, E. L. and Hayward, T. L. (1995) Primary production and chlorophyll relationships, derived from ten years of CalCOFI Measurements. CalCOFI Rep., 36, 159–166. Paasche, E. and Brubak, S. (1994) Enhanced calcification in the coccolithophorid Emiliania huxleyi (Haptophyceae) under phosphorus limitation. Phycologia, 33, 324–330. Balch, W. M., Drapeau, D. and Fritz, J. (2000) Monsoonal forcing of calcification in the Arabian Sea. Deep-Sea Res. II, 47, 1301–1337.