California Current Ecosystem LTER

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  3. ALF Active and Passive Fluorescence Measurements – UW Data (CalCOFI Cruise)

ALF Active and Passive Fluorescence Measurements – UW Data (CalCOFI Cruise)

Title
Continuous passive and active fluorescence measurements of chlorophyll-a (Chl), phycoerythrin (PE), chromophoric dissolved organic matter (CDOM), and variable fluorescence (Fv/Fm) from CCE-CalCOFI Augmented cruises in the California Current System, 2012 - 2020

Abstract
Active and passive fluorescence measurements are made using the ALFA5 system (Chekalyuk and Hafez, 2013) on water from the ship’s underway system during CalCOFI cruises. The instrument uses excitation at 405 and 510 nm to measures passively the fluorescence of chlorophyll-a (Chl), three different phycoerythrins (PE1, PE2 and PE3) and chromophoric dissolved organic matter (CDOM). Variable fluorescence (Fv/Fm) is measured actively using pump-during-probe (PDP) measurements of Chl a fluorescence induction. Fluorescence measurements are normalized to the water’s Raman fluorescence.
Keywords
biomass, carbon, chlorophyll, fluorescence, marine, physiology, phytoplankton, Fv/Fm, CDOM, colored dissolved organic carbon, phycobiliproteins, phycoerythrin, physiological state, pump-during-Probe

LTER Data System Record
http://dx.doi.org/10.6073/pasta/90024f2e913653d14eee2f4eea5f313d
Projects
California Current Ecosystem LTER

Creators
Goericke, Ralf (rgoericke@ucsd.edu)

Contact
CCE LTER Information Manager (ccelter.im@gmail.com)

Data

table ALF Active and Passive Fluorescence Measurements Underway Data
Primary data table 		Rows: 341240
Columns: 18 		View / Download

Methods

Methods
The instrument used is described by Chekalyuk and Hafez (2013). A blue (b – 405 nm) and a green (g - 510 nm) laser is used to acquire data ~ four times per min. Data from files *_m.txt, *_s.txt are read into Matlab and are available for each cruise as a raw data table. Pump-During-Probe (PDP) data (*_pm.txt) are reanalyzed using a robust curve fitting procedure to generate Fv/Fm data corresponding to Fv/FmC which is generated by the ALFA5 software. Data processing involves the following: Unrealistic data (e.g. < 0 or extremely high values) are removed (set to NaN). Sections of the data that are affected by stopped flow in the UW-water system are removed as well. Data are further filtered for outliers (Matlab: isoutlier(Data.Value, 'movmean', 100, 'SamplePoints', Data.ID). Calibrations between Chl a fluorescence (CF_Rb and CF_Rg) and CalCOFI surface bottle Chl a are used to convert Chl-fluorescence measurements into predicted values of Chl a (ug-Chl/L), i.e. PredChl_b and PredChl_g. As part of this process a data file is generated that lists CalCOFI CTD and bottle data and corresponding ALFA5 data. This file is available as a separate data product. The four/min data are reduced to one/per min data, the final data product. These data are plotted against distance from shore for all CalCOFI lines covered and as property maps for the whole region covered during a cruise. These plots are available upon request.

References

A. M. Chekalyuk and M. Hafez, "Next generation Advanced Laser Fluorometry (ALF) for characterization of natural aquatic environments: new instruments," Opt. Express 21, 14181-14201 (2013).

A. M. Chekalyuk and M. Hafez, “Advanced laser fluorometry of natural aquatic environments,” Limnol. Oceanogr. Methods 6, 591–609 (2008).

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