Methods:

Each survey was conducted onboard different research vessels. See the pictures below for an example of some of the vessels that have been used in these surveys. Likewise some differences in equipment and vessel capabilities have led to differences in the methods by which stations have been sampled on each cruise. The purpose of this methods section is to provide general information on how each station was sampled, without specific coverage of the differences in equipment that has been used. Therefore, this section should be treated as a general reference for the results of specific surveys presented in this website. In general, the sampling of a station can be divided into 5 categories; (1) CTD Profiles, (2) Current Profiles, (3) Secchi Disk Depths, (4) Water Sample Analysis, and (5) Plankton Analysis.

CTD Profiles:

At each station, a CTD (Conductivity, Temperature, and Density) was lowered to about 1 - 10 meters above the bottom (when possible) at the station and was then pulled back onboard. Different CTDs were used on each survey, and each CTD had different onboard components. Some typical components include a dissolved oxygen probe, pH probe, transmissometer, fluorometer, and light meter. In all cases, CTDs recorded data on the downcast and up cast, although only the data collected during the CTD's downcast are presented in this site given the fact that the instruments experience more turbulence on the ascent, which can lead to inaccurate readings. CTD data collected from each station was then used to create a variety of profile graphs. Also, Surfer V7.0 was used to plot contour maps of different parameters measured by the CTDs along transects within Commencement Bay.

Current Profiles:

Water current profiles were also obtained at each station sampled using an Aandera current meter when available. Different current probes were used on each survey in which they were used, however the general principle remains the same. A velocity probe with a built-in compass was lowered to several depths to obtain a profile of velocity and bearing within the water column.

Secchi Disk Depths:

Secchi disk depth was obtained by lowering a Secchi disk into the water at each station. The depth at which the disk was no longer visible was recorded by multiple observers. As with other equipment, different sized Secchi disks have been used, although the principle remains the same despite differences in equipment.

Water samples were also collected at each site. Samples were taken with a Niskin bottle, to allow for the collection of a water sample at a specific depth. At each station, at least one surface sample and one deep water sample was collected. The depths of these samples varied, given the depth of the water at each station. Water samples were used to obtain nutrient, dissolved oxygen, and chlorophyll concentrations. The following are the methods that were used to analyze water samples for these parameters when apllicable.

Nutrient samples were collected from the Niskin bottle into labeled Nalgene bottles. These bottles were rinsed three times prior to being filled ¾ full and capped. The bottle number, station, and sample depth were recorded on the master log for each cruise. After collection, nutrient samples were placed in a cooler with ice until the end of the survey. Nutrient samples were then placed in the freezer until they were shipped to the University of Washington's Marine Chemistry Lab for nutrient analysis. All nutrient samples were analyzed for phosphate, silicate, ammonium, nitrate, and nitrite.

Dissolved Oxygen:

Once the Niskin bottle was pulled onboard, a calibrated 125 mL glass flask with a ground glass stopper was filled with water from the Niskin bottle. The water was allowed to overflow to prevent the formation of and remove any present air bubbles from within the flask. Water was allowed to flow through the flask for a few seconds to rinse the flask. The tubing attached to the Niskin bottle was then slowly removed, taking care not to allow air bubbles to form within the flask. After the tubing was removed, 1 mL of manganese reagent and 1 mL of alkaline-iodide reagent was added to the sample using a pre-calibrated pipette head. The sample was then capped carefully with the ground glass stopper. The stopper was inserted at an angle to prevent air bubbles from being trapped inside the flask. With the lid securely in place, and no air bubbles being observed in the sample, the flask was then inverted several times and then placed into a dark staging area for 15 minutes. After the first 15 minutes following the initial mixing, the flask was then mixed again by inversion. After another 15 minutes, 1 mL of sulfuric acid reagent was added. The sample was then capped carefully, again making sure that no air bubbles become trapped in the sample, and was then placed into a dark staging area again. Following this procedure, the dissolved oxygen sample was then ready to be analyzed in the lab. All dissolved oxygen samples were processed within 6 hours of collection.

In the lab, the dissolved oxygen samples were analyzed using the Winkler Titration Method. To do this required the preparation of standards and a blank. To prepare the standards, a clean 125 mL flask was filled with about 80 mL of distilled water. 1 mL of H₂SO₄ reagent was added to the flask, which was then mixed with a stir bar. Following mixing, 1 mL NaOH-NaI reagent was then added and the sample was again mixed. Following mixing, 1 mL of MnCl₂ reagent solution was added and the sample was mixed once more. With a micropipetter, 1.0 mL of KIO₃ standard solution was added to the sample. With the dosimat reading 0.000 mL, thiosulfate reagent was added until the sample turned light yellow. 1 mL of starch was then added to the sample, turning the sample to a dark blue color. Titration with thiosulfate was continued until the sample was completely clear with no blue remaining. The volume of thiosulfate required to reach this endpoint are recorded. This process was repeated until at least two standard solutions were titrated to within 0.001 mL agreement.

A blank was then prepared by filling another clean 125 flask with about 80 mL of distilled water. 1 mL of H₂SO₄ reagent was added to the flask, which was then mixed with a stir bar. Following mixing, 1 mL NaOH-NaI reagent was then added and the sample was again mixed. Following mixing, 1 mL of MnCl₂ reagent solution was added and the sample was mixed once more. With a micropipetter, 1.0 mL of KIO₃ standard solution was added to the sample. With the dosimat reading 0.000 mL, thiosulfate reagent was added until the sample turned light yellow. 1 mL of starch was then added to the sample, turning the sample to a dark blue color. Titration with thiosulfate was continued until the sample was completely clear with no blue remaining. The volume of thiosulfate required to reach this endpoint was recorded. Another 1.0 mL of KIO₃ was added to the blank and then titrated until the sample was again clear. The difference between the volumes of thiosulfate required to reach each endpoint was then used as the correction factor. In this case, the correction factor was determined to be 0.000 mL.

Following the preparation and analysis of the standards and blank as outlined above, the samples from each station were analyzed. To process these samples, 1 mL of H₂SO₄ reagent was added to the flask and then mixed. The sample was titrated with thiosulfate until the sample became light yellow. 1 mL of starch was added to the sample, thus turning the sample dark blue. The sample was then titrated until the sample was clear, with no blue tint remaining. The volume of thiosulfate required to reach this endpoint was recorded. This process was repeated for each sample collected at each station. The dissolved oxygen concentration in each sample was calculated as follows:

[D.O.] = ((R - R_blk)559.8)/((R_std - R_blk)(V_b - 2)) - 0.018

Where:

[D.O.] = Dissolved Oxygen Concentration (mL/L)

R = Volume of Thiosulfate Needed in Titration (mL)

R_blk = Blank Correction Factor (0.000 mL)

R_std = Average Volume of Thiosulfate Needed in Standard Titration (mL)

V_b = Volume of Sample Bottle (mL)

Chlorophyll a:

Chlorophyll samples were collected from the Niskin bottle in a 1L Nalgene bottle. The bottle was rinsed three times to remove any potential contamination. The chlorophyll samples were stored in a cooler with ice until they were analyzed at UWT later that day. Each sample was analyzed using a modified version of the USGS Microbiological TWRI Manual. Each sample was filtered onto glass fiber filters, 25 mm in diameter. The filter was then placed into a tissue grinder tube, with 3 mL of 90% acetone. The sample was then grinded for about 3 minutes. The sample was then transferred to a labeled 15 mL graduated centrifuge tube. The grinder was then rinsed with two shots of 3 mL of 90% acetone, which was added to the centrifuge tube. The final volume was then adjusted to 10 mL with acetone, and placed in the dark for 10 minutes. After sitting for 10 minutes, the sample was then centrifuged at 3,500 rpm for 5 minutes. The sample was then transferred into a cuvete. The sample was then placed in the spectrophotometer, and the absorbance was read at 630, 647, 664, and 750 nm. The reading at 750 nm was subtracted from the values obtained at 630, 647, and 664 nm to correct for turbidity and colored materials within the sample. The chlorophyll a concentration was then calculated as follows: Ca (mg/mL) = (11.85 * A₆₆₄) - (1.54 * A₆₄₇) - (0.08 * A₆₃₀)

Chlorophyll a (mg/L) = (Ca)(Vext/Vsample)

Where:

A₆₆₄ = Absorbance at 664 nm

A₆₄₇ = Absorbance at 647 nm

A₆₃₀ = Absorbance at 630 nm

Vext = Acetone Extraction Volume (mL)

Vsample = Volume of Sample (L)

Plankton Analysis:

Plankton samples were obtained at each station by lowering a plankton net into the water to a predetermined depth, and then towing the net back onboard. The plankton entrained in the net's cup were then rinsed into a sample jar and labeled for further analysis in the lab. The net size and mesh sizes varied for each survey, although this information has been tracked. Each plankton sample was analyzed for both zooplankton and phytoplankton. Three 1 mL samples were obtained from each sample, which was then analyzed for zooplankton abundance. The total combined number of zooplankton observed in each 1 mL sample was then used to calculate the total projected density of zooplankton at that station. Each sample was also analyzed for phytoplankton by extracting three 0.1 mL samples from each station sample. The total combined number of phytoplankton observed in each 0.1 mL sample was then used to calculate the total projected density of zooplankton at that station. The density of zooplankton and phytoplankton was calculated as follows:

Dp = ((P_T/V_TS) V_S) / V_T)

Where:

Dp = Density of Plankton (Zooplankton or Phytoplankton/m³)

P_T = Total Number of Zooplankton or Phytoplankton Observed in all Sub-Samples

V_TS = Total Volume of All Sub-Samples for Zooplankton or Phytoplankton

V_S = Total Volume of Sample that was Collected by the Net

V_T = Total Volume of Water that was Towed by the Net

The volume of water towed by the net was calculated from the known area of the net opening used and the tow depth. The densities of phytoplankton and zooplankton were calculated separately, although the tow volume and sample volumes were the same.

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