Data collection at sea is a complicated process, especially given that the science is done in a relatively small lab space on a rolling ship. Work at sea is usually conducted in shifts: on this cruise we had two teams that worked 12 hours per day, every day, during the 14-day voyage.
At each station, the instrument rosette containing Niskin bottles (tall grey cylinders, <<) was lowered to a designated depth (from 15 to 300 meters, depending on the ocean regime). Along the way, a fluorometer measured in-water chlorophyll concentrations and a "CTD" instrument provided temperature and salinity data. As the rosette was raised through the water column, the bottles were triggered to "grab" water at various depths. Once the rosette was hoisted on deck, Ilana gathered her water samples for subsequent in-lab analysis.
Water samples were filtered to concentrate cells into two size ranges: <3 micrometers and <20 micrometers. Renee then soaked the filters in acetone to extract chlorophyll from the cells. The acetone was then exposed to a beam of blue light: this excited the chlorophyll within the solution, causing it to emit red light. The red emisssion quantified the amount of chlorophyll in each sample.
Another important onboard activity was making nanoplankton and bacteria slides. Polly added stains to water samples, making identification of DNA and cytoplasm easier. The water was then filtered through a black membrane which was placed on a microscope slide, topped with a drop of oil and a cover slip. Thus these slides are not transparent: the microscope illuminates them from above (rather than below). The type of light (e.g., fluorescent blue, green, and ultraviolet) is specifically chosen to excite the slides' stained material.
Flow cytometry is used to measure the optical properties of cells in a flow stream. Plankton are naturally in suspension, thus flow cytometry is a good way to study them. Based on this technology, the FlowCAM instrument has a fluorescence detector that can pinpoint hundreds of cells per minute. It then counts and images those cells that contain photosynthetic pigments. At each station Nicole used FlowCAM to study plankton populations within water samples collected at various depths. In this way, she studied phytoplankton and some small zooplankton sized from 5 - 200 micrometers. Why might zooplankton have photosynthetic pigments?
Like the FlowCAM, the FACScan is a flow cytometer. This instrument, however, is designed to count (but not image) smaller phytoplankton cells. For this study, the FACScan was primarily being used to count bacteria and help determine what percentage of these cells are active. How is this done? Before Ed "ran his samples," he used a stain that indicates which bacteria are actively respiring. The FACScan also counts larger cells (e.g., up to 15 micrometers); this information helps to characterize the biological cycles where bacteria thrive. (See discussion on the Micobial Loop.)
A direct way of measuring bacterial growth rates is through the use of radioactive tracers. A radioactive substance was introduced into water samples, which were then incubated. Active cells took the tracer into their proteins, making it possible to calculate the percentage of active cells. David (>>) also stained water samples with a substance that adheres to nucleic acids (i.e., DNA or RNA) and filtered the stained water to allow only viruses through. Stained viruses were later analyzed under fluorescent light with a high-powered microscope. Andrew (<<) collected DNA samples to study the structure of the marine bacterial community. Lastly, dissolved organic carbon (DOC) was measured as carbon dioxide gas emitted from water samples that were heated to 680°C (1256°F).
All of these laboratory techniques were applied to our samples collected in various ocean regimes: from the "desert" of the Sargasso Sea to the high productivity of Georges Bank.