This abundance data was obtained from two week-long cruises (1301 in August and 1302 in September) during which MOCNESS samples were taken from the mid-bay of the Chesapeake from 9 stations in a box formation; 3 stations in a northern transect across the bay (N1-N3), 3 in a midline transect (M1-M3), and 3 in a southern transect (S1-S3).

The MOCNESS had a 0.5 meter square opening for each of 5 nets, which were 200um mesh. It was deployed from the aft A-frame of the RV Sharp, along with an array of sensors connected to the MOCNESS frame, including Sea-Bird temperature, salinity, and dissolved oxygen (SBE 43) sensors, a WetLabs FLNTU to measure chlorophyll a fluorescence and turbidity, and a LiCor 4π PAR sensor.

A CTD cast was done at each station prior to sampling with the MOCNESS. Sampling depths were determined based on the location of the pycnocline; the aim was to capture zooplankton below, within, and above the pycnocline. A drogue net (net 0) without a codend was used to deploy the MOCNESS to within 3m of the bottom. On the upcast, nets were triggered to close electronically from the wet lab so that they captured a depth range representing one of the three areas of interest.

Once brought on board, the nets were rinsed down with filtered seawater (provided by the Hugh R. Sharp) to collect plankton in the codend. Codends were filtered onto 64um sieves, then the samples were transferred to glass jars labeled on the inside and outside with the cast number, date, time, net number, and depth sampled. Sieves with 64um mesh were selected to catch all life stages of the copepod Acartia tonsa since Acartia tonsa eggs are about 75um in diameter and all subsequent life stages are larger. Buffered formalin was added to preserve the sample in a 4% solution, and then the jars were stores in labeled boxes.

After returning from the cruises, samples were stored indoors in climate-controlled laboratory space. To process the samples, the contents of the jars were filtered onto 64um mesh (to avoid loss of organisms), resuspended, and a subsample taken with a stemple pipette was transferred to a counting wheel where it was checked for density and diluted if necessary, the goal being at least 200 individuals of Acartia tonsa present but less than 300.

The sample was then examined for species composition under dissecting microscope with darkfield illumination. All organisms were identified to lowest possible taxonomic level. When species composition analysis was complete, the processed aliquot was photographed for size measurements and stored in 4% buffered formalin solution in a glass vial. The unused portion of the sample was returned to the original glass jar and returned to storage.

Abundance data were entered into Excel spreadsheets and checked for transcription errors, then imported into MatLab for data analysis.