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.

CCE LTER analyzes and determins total organic carbon (TOC) and total nitrogen (TN) in sea water, expressed as micromoles of carbon (nitrogen) per liter of sea water. TOC (<200 µmol·L-1) includes both dissolved and particulate organic carbon (DOC and POC, respectively). TN (<50 µmol·L-1) includes particulate and dissolved organic nitrogen as well as dissolved inorganic nitrogen species. The instruments employed are from the Aluwihare Laboratory at the Scripps Institution of Oceanography, and whenever possible, protocols closely follow those used by Jonathan Sharp (U. of Delware), Craig Carlson (U. of California, Santa Barbara) and Dennis Hansell (RMSAS). SIO has the Shimadzu TOC-VSN, normal sensitivity, with TN unit.

Complete methods of TOC and TN determination can be found here.

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.

CCE-LTER determines the size distribution of total chlorophyll a by filtering water though filters of differing pore sizes, extracting these in acetone and analyzing fluorometrically. Using size fractionation of chlorophyll a and taxon-specific pigments (chlorophylls and carotenoids) from HPLC analysis, the samples analyzed within the California Current Ecosystem are used to develop a metric for phytoplankton community structure that can be used to monitor its state and changes thereof over time.

Complete methods for chlorophyll a size fractionation can be found here.

CCE LTER measures particulate organic carbon (POC) and nitrogen (PON) by high-temperature combustion. Samples analyzed within the California Current Ecosystem constrain the mean C:N ratio of small particulates and by difference relative to measured living biomass, the biomass of suspended detritus.

Complete methods of POC and PON determination can be found here.

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.

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