CCE-LTER samples picophytoplankton populations and non-pigmented prokaryotes within the California Current Ecosystem (CCE) are fixed in the field by the addition of paraformaldehyde and, in the laboratory, stained with Hoechst 33342 (a DNA specific dye). The cells are enumerated by an Altra flow cytometer and converted to biomass estimates

Complete methods for picoplankton and bacteria abundance and biomass determination can be found here.


Flow cytometric analyses of picoplankton populations (Prochlorococcus, Synechococcus, P-Euk and H-Bact) are preserved with paraformaldehyde, frozen in liquid nitrogen, and stored at -80°C. Prior to analysis, batches of thawed samples are stained to increase the precision of bacterial counts, relative to epifluorescence microscopy. Aliquots are analyzed using a Beckman-Coulter EPICS Altra flow cytometer with a Harvard Apparatus syringe pump for volumetric sample delivery.


Picoplankton and bacteria are sampled from 3 to 8 depths for each of the 66 CalCOFI stations located in the CCE. Seawater from the Niskin bottle is collected into a 600-ml sample bottle. When sampling, make sure the flow from the valves is low since no sample tubing is used. A 2-ml subsample is drawn from the sample bottle and placed into a properly labeled 2-ml cryovial, and 100 µl of prefiltered 10% paraformaldehyde is added (0.5% final v/v sample concentration). Samples are left out for 10 min and then stored in liquid nitrogen. At the shore-based laboratory, the samples are stored at -80°C. Samples are shipped overnight on dry ice to SOEST Flow Cytometry Facility, University of Hawaii at Manoa for flow cytometry analysis.

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