Dataset: PAM Fluorescence Data

Name: Fluorescence from PAM fluorometer from fishing vessels in the Southern California Bight off Huntington Beach in 2012 (SoCalPlumeEx2012 project)
Published: 2014-11-04
Keywords: oceans

Cite This Dataset

Spatial Extent: N:33.617 E:-117.731 S:33.255 W:-118.059

Project:

Assessing the Ecophysiological and Biogeochemical Response to Deliberate Nutrient Loading in the Southern California Bight (SoCalPlumeEx2012)

Principal Investigator:

Raphael M. Kudela (University of California-Santa Cruz, UCSC)

Co-Principal Investigator:

Andrew J Lucas (University of California-San Diego, UCSD-SIO)

Contact:

Raphael M. Kudela (University of California-Santa Cruz, UCSC)

BCO-DMO Data Manager:

Stephen R. Gegg (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

04 November 2014

Version Date:

2014-11-04

Current State:

Preliminary and in progress

Fluorescence from PAM fluorometer from fishing vessels in the Southern California Bight off Huntington Beach in 2012 (SoCalPlumeEx2012 project)

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Description

PAM Fluorescence Data

Data are described in the following manuscript:
Kudela, R.M., Lucas, A.J., Negrey, K.H., Howard, M. McLaughlin, K. Submitted to Est. Coast. Shelf Sci. Death from below: Investigation of inhibitory factors in bloom development during a wastewater effluent diversion.

Methods & Sampling

Sampling and Analytical Methodology:
Water samples were collected from an instrumented rosette and dark adapted for 30 minutes. Samples were then analyzed using a Heinz-Walz WATER-PAM fluorometer, with 0.2 µm filtered seawater used as a blank. See references below for more details.

Data Processing Description

Data Processing:
PAM fluorescence data were fit to a 3-parameter photosynthesis versus irradiance curve (see references), using 3x replicate samples. Curve fit parameters are provided.

Data were processed using a 3-parameter curve fit as described in the following references:
Kudela RM, Ryan JP, Blakely MD, Lane JQ, Peterson TD (2008) Linking the physiology and ecology of Cochlodinium to better understand harmful algal bloom events: A comparative approach. Harmful Algae 7:278–292

Kromkamp JC, Forster RM (2003) The use of variable fluorescence measurements in aquatic ecosystems: differences between multiple and single turnover measuring protocols and suggested terminology. European Journal of Phycology 38:103–112

Jassby AD, Platt T (1976) Mathematical formulation of the relationship between photosynthesis and light for phytoplankton. Limnology and Oceanography 21:540–547

BCO-DMO Processing Notes
- Generated from original file: "SoCalPlumeEx2012_PAM.csv" contributed by Raphael Kudela
- Parameter names edited to conform to BCO-DMO naming convention found at Choosing Parameter Name
- Date reformatted from MM/DD/YY to YYYYMMDD

Data Files

File
PAM.csv (Comma Separated Values (.csv), 5.52 KB) MD5:ddfcae8042bd7c4d724b084f6ede9af9 Primary data file for dataset ID 537666

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1251547
NSF Division of Ocean Sciences	OCE-1251573

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
SoCalPlumeEx2012		2012-09-06	Fishing Vessels	Raphael M. Kudela (Principal Investigator)	data info

Instruments

CTD Sea-Bird SBE 911plus

Supplied Name: CTD SBE 911plus

Supplied Description:

Water samples were collected from an instrumented rosette

Instrument Type

Generic Name: CTD Sea-Bird SBE 911plus

Acronym: CTD SBE 911plus

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/

Generic Description:

The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics

Fluorometer

Supplied Name: Heinz-Walz WATER-PAM fluorometer

Supplied Description:

Samples were then analyzed using a Heinz-Walz WATER-PAM fluorometer, with 0.2 µm filtered seawater used as a blank

Instrument Type

Generic Name: Fluorometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/113/

Generic Description:

A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.

Niskin bottle

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Date	Date (GMT)	YYYYMMDD	date
Station_ID	Station Id	text	station
Latitude	Latitude Position (South is negative)	decimal degrees	lat
Longitude	Longitude Position (West is negative)	decimal degrees	lon
Depth	Depth	meters	depth
Yield	Yield (unitless)	unitless	no_bcodmo_term
PBs	PBs (maximum relative Electron Transport Rate; rETR)	(tbd)	no_bcodmo_term
a	a (initial slope of the rETR curve)	(tbd)	no_bcodmo_term
b	b (light-inhibition slope of the rETR curve)	(tbd)	no_bcodmo_term
r2	r2 (r2 value for the model fit)	(tbd)	no_bcodmo_term
PBm	PBm (maximum rETR with photo-inhibition included)	(tbd)	no_bcodmo_term
Em	Em (irradiance of maximum light inhibition; umol photons m-2 s-1)	umol photons m-2 s-1	no_bcodmo_term
Ek	Ek (irradiance of rETR half-saturation; umol photons m-2 s-1)	umol photons m-2 s-1	no_bcodmo_term

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Database

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Dataset: PAM Fluorescence Data