CCE-LTER asseses the microbial community assemblages of the California Current ecosystem (CCE) for abundance and biomass using high-throughput digital epifluorescence microscopy. Samples to estimate the nano- and microplankton (0.2-2.0-µm and 2.0-20-µm size, respectively) are collected, preserved, stained, and filtered onto a membrane filter and mounted on a glass microscope slide in the field. Slides are then frozen at -80°C for subsequent imaging and analysis in the laboratory onshore.

Complete methods for microbial community assemblage assessment can be found here.


Microscopical assessment of nano- and microplankton: Aliquots of 50- and 500-ml are collected for analyses of nano- and microplankton by digitally enhanced epifluorescence microscopy. Samples for nano- and microplankton abundance and biomass are preserved and then stained. Preserved samples are allowed to fix prior to gentle filtration onto 0.8-µm (nano) or 8.0-µm (micro) pore size filters. Filters are mounted onto glass slides with immersion oil and cover slip. Slides are stored at -80°C for analysis back on shore.


Nano- and microplankton 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.

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