SIMBIOS METHODS Flow-Through System Our flow-through system is equipped with several sensors, with data integration and logging performed by National Instruments LabVIeW software run on two pentium processor computers. The system receives time and the ship's geographic position continually from a Garmin 220 global positioning system, the antenna of which is mounted outside of the ship. Seawater first enters a 4 foot tall de-bubbler, then into an InterOcean thermal conductivity sensor. It measures salinity with an accuracy of +0.05 Practical Salinity Units and temperature to an accuracy of +0.1oC. Following the temperature/salinity measurements, the flow bifurcates into a Turner 111 fluorometer for monitoring underway fluorescence and a secondary debubbler to prepare the water for light scatter measurements. The fluorometer is equipped with a Turner Designs cool white F4T5 lamp, blue-violet excitation filter (peak excitation 438nm with half band pass of 418-458nm) and red emission filter (high pass interference filter passing all wavelengths >650nm). It is zeroed with a black piece of cardboard inserted over the excitation and emission windows. Due to fast growing bio-fouling organisms in the Gulf of Maine, the fluorometer needs to be cleaned regularly. As for the light scattering measurements, the water passes from the secondary debubbler, via peristaltic pump, into a Wyatt Technologies Model Dawn laser light scattering photometer at a flow-rate of ~11ml min-1. The photometer operates with an 30 mW Argon ion laser (514 nm) which is directed into the center of a flow-through cuvette, whereupon, seawater is viewed by 18 photodiodes arranged between 21.54o and 158.14o. Included in the 18 detectors are two photodiodes for laser power monitoring. The laser beam has a 1/e2 gaussian beam profile radius of 0.39 mm which makes the effective viewing volume of the light-scattering photometer 0.25 ml. All detectors are scanned at rates up to 400 HZ. In fact, for most flow-through applications, we slow the scanning rate to 200 HZ in order to not sample the same seawater volume twice. The LabView software, which controls the Wyatt light scattering photometer, can be programmed to calculate averages and standard deviations of seawater volume scattering data to any desired time period. For field applications, we typically average the data for about 50 seconds (which then represents an effective volume viewed of 9ml). The statistics are highly informative for understanding the variance of the optics due to particle types. Because of our interest in calcite, we also measure seawater pH to verify that the pH is sufficiently high such that calcite cannot dissolve. Following the first 50s of measurements done on each raw seawater sample, another peristaltic pump is activated by the LabView control system, which injects 1.2% glacial acetic acid into the flow stream, and mixes it by running it through a Teflon mixing column. This drops the pH to about 5.8 to dissolve any calcium carbonate. Once the pH stabilizes at the more acidic value, volume scattering is re-sampled, and average backscattering re-calculated. The difference between the raw and acidified backscattering values represents the "acid-labile" backscattering. Using field measurements, we have calibrated this acid-labile backscattering to atomic absorption estimates of suspended calcite concentration (r2=0.83). The time for a complete acidification cycle can be adjusted, but we have preferred to collect average backscattering values such that one complete raw/acidification cycle takes 4 minutes. This means that during any passage, we would be logging a data point about once every 2000 meters. For sea-truth measurements, this is adequate since typically a 3 pixel by 3 pixel area from SeaWiFS is viewed (10.9 km2). Water next flows into an AC-9 (Wet Labs, Oregon). This instrument simultaneously measures spectral beam attenuation and spectral absorption at nine wavelengths using a dual path optical scheme. Fundamentally, this consists of two pressure housings, with the absorption and attenuation beam paths in between. The absorption light path passes through a reflective tube while the the attenuation light path passes through a non-reflective tube. A rotating filter wheel provides the 9 different wavelengths, between 412-715 nm. The accuracy of the attenuation and absorption measurements are +0.005m-1 with linearity error of +0.1%. With access to attenuation (c) and absorption (a) information, we calculate b (= c - a). Water-leaving radiance and downwelling irradiance (for calculating remote sensing reflectance) were measured from the Scotia Prince ferry. A Satlantic SeaWiFS Aircraft Simulator (SAS) was used. This consisted of a radiance sensor mounted on the port bridge wing, and an irradiance sensor mounted on the compass deck, aft of the bridge, as far from any potentially shading structures as possible. The radiance detector viewed the water forward of any shipwake, at ~20-30o from nadir. The distance of the sensor to the water was ~30m. The direction of the sensor was changed periodically, as the sun's position changed, so, when possible, the sensor was viewing the water 90o from the sun's azimuth, free from any sun glint. Protocols for operation and plaque calibration were made according to SeaWiFS technical memorandum #25. Data in real time are filtered for sun glint and sea foam by eliminating data with irradiance reflectance >15%. Between the hours of 1000 and 1400, all data are logged at 10Hz. Outside of this time, averages of the glint and foam filtered data are logged every 16 seconds. Discrete Samples: Every hour a water sample was taken for suspended CaCO3, particulate organic carbon, chlorophyll, and microscope counts. The technique of Fernandez et al. (1993) was used to measure CaCO3 concentrations. Briefly, 100 ml samples were filtered onto 0.4um pore-size polycarbonate filters, and rinsing first with filtered sea water, then borate buffer (pH=8) to remove seawater calcium chloride. Filters were placed in trace metal free centrifuge tubes with 5 ml 0.5% Optima grade Nitric acid (this will also drive off any 14C activity of the coccoliths). Next, the Ca concentration was measured using graphite furnace atomic absorption spectrometry. The sensitivity of the technique, after correction to the volume of seawater filtered, was about 2ng Ca l-1. Chlorophyll and particulate organic carbon were measured according to the JGOFS protocols (JGOFS, 1996) using GFF and Millipore .45um membrane filters respectively. A 60ml water sample was taken for coccolithophore and coccolith counts. Brown glass bottles were rinsed 3X with each sample prior to final filling. Samples were preserved with 4% buffered formalin and, after the cruise, settled in 10 ml counting chambers prior to counting detached coccoliths and plated coccolithophores (Utermöhl, 1931, 1958). Microscope enumeration of detached coccoliths and plated coccolithophores was made using an Olympus BH2 microscope with polarization optics which allows quantification of birefringent CaCO3 coccoliths, and coccospheres. For statistical reasons, 200 coccoliths or cells were counted from each sample, when available. Data manipulation The data produced by this system are: time latitude longitude upwelling radiance (uW cm-2 nm-1 sr-1; at 412, 443, 490, 510, 555, 670 & 685 nm) downwelling irradiance (uW cm-2 nm-1; at 412, 443, 490, 510, 555, 670 & 685 nm) fluorescence (volts) calibrated to hourly discrete chlorophyll samples backscattering (m-1; at 515nm) absorption (m-1; at 412, 440, 488, 510, 555, 630, 650, 676 and 715 nm) attenuation (m-1; at 412, 440, 488, 510, 555, 630, 650, 676 and 715 nm) In addition, we also take Microtops sun photometer measurements when the sun was visible, and the data are offloaded for distribution to SEABASS. Discrete samples for suspended calcite, POC, PON, and coccolith counts are also taken hourly along with an XBT temperature profile, and are processed over subsequent months. Hourly XBT profiles are used to construct one temperature section per trip from which we can calculate isotherm slope (strongly related to gradients in integrated primary production and chlorophyll).