CCE-LTER uses a high-performance liquid chromatographic (HPLC) method with a reverse phase C8 column to measure concentrations of chlorophylls and carotenoids in samples of particulate matter from the California Current Ecosystem (CCE). Concentrations of chlorophyll a are used as a proxy for phytoplankton biomass and concentrations of other taxon-specific pigments are used to determine contributions of phytoplankton taxa to total phytoplankton biomass.

Complete methods for taxon-specific phyto-pigments determination can be found here.


Chlorophylls and carotenoids are extracted from samples collected on CalCOFI (California Cooperative Oceanic Fisheries Investigations) cruises with acetone. The extracts are analyzed on an Agilent 1100 series HPLC with a thermostatted autosampler derived from the method described in Zapata et al. (2000).


HPLC samples are collected at CalCOFI and SCCOOS (Southern California Coastal Observing System) stations located within the CCE. Samples are collected from three to eight different depths in the photic zone. Samples are drawn from the niskin bottles using 0.5, 1.04 or 2.2 liter brown polypropylene bottles, depending on the chlorophyll concentration measured by the fluorometer on the CTD. For the higher chlorophyll values, typically the coastal stations, less water is sampled. Samples (0.5, 1.04, or 2.2 L) are filtered onto 25 mm GF/F filters (Whatman) under a low vacuum pressure (≤ 40 mm Hg). 2.4. Once the sample has finished filtering, the filter is carefully folded in half, and blotted on a paper towel to remove excess water. The folded filter is placed in a labeled 2 ml cryovial and stored in liquid nitrogen for analysis ashore.

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