Photosynthetic data collected from the R/V Oceanus OC1504A in the Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W in 2015.

Website: https://www.bco-dmo.org/dataset/652739
Data Type: Cruise Results
Version: 1
Version Date: 2016-07-28

Project
» Linking physiological and molecular aspects of diatom silicification in field populations (Diatom Silicification)
ContributorsAffiliationRole
Thamatrakoln, KimberleeRutgers University (Rutgers IMCS)Principal Investigator, Contact
Brzezinski, Mark A.University of California-Santa Barbara (UCSB-LifeSci)Co-Principal Investigator
Ake, HannahWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Abstract
Photosynthetic data collected from the R/V Oceanus OC1504A in the Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W in 2015.


Coverage

Temporal Extent: 2015-04-20 - 2015-05-01

Dataset Description

Photosynthetic data on water collected by CTD and measured using fast repetition rate fluorometry.


Methods & Sampling

Photosynthetic parameters were measured using fast repetition rate fluorometry on whole seawater collected by CTD. See reference below for details on data analysis.


Data Processing Description

Photosynthetic parameters were corrected for background fluorescence by measuring 0.2 µm filtered seawater from 1-2 depths. Fo and Fm of background samples were subtracted from sample Fo and Fm and corrected values were used to calculate Fv/Fm, where Fv=Fm-Fo (Kolber et al. 1998)

DMO Notes:
-File was resubmitted by PI after some consultation with several columns and rows removed
-Column names were changed to meet BCO-DMO standards
- Some spaces were removed from cell contents
- cruise_id and ISO_DateTime_UTC column were added


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Data Files

File
photosynthetic_data.csv
(Comma Separated Values (.csv), 4.45 KB)
MD5:3a1d21a92492aafc6354c6ec2dcc10c8
Primary data file for dataset ID 652739

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Related Publications

Kolber, Z. S., Prášil, O., & Falkowski, P. G. (1998). Measurements of variable chlorophyll fluorescence using fast repetition rate techniques: defining methodology and experimental protocols. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1367(1-3), 88–106. doi:10.1016/s0005-2728(98)00135-2
General

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Parameters

ParameterDescriptionUnits
cruise_id

cruise identification where samples where collected

unitless
CTD

CTD cast

unitless
depth

depth at which samples were collected

meters
date_local

local date of sample collection; mm/dd/yy

unitless
time_local

local time of sample collection; HH:MM:SSpp

unitless
Fluor_min

minimal fluorescence yield corrected for background fluorescence. Fo

relative units
Fluor_max

maximal fluorescence yield corrected for background fluorescence. Fm

relative units
FvFm

maximum quantum yield corrected for background fluorescence; Fv divided by Fm

dimensionless
functional_absorption

Functional absorption cross-section of photosystem II (measured using 450 nm excitation; units A2); sigma

unitless
connectivity_p

connectivity factor defines the efficiency of exciton energy transfer between individual photosynthetic units; originally p

unitless
ISO_DateTime_UTC

DateTime (UTC) ISO formatted

unitless


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Instruments

Dataset-specific Instrument Name
Fast Repetition Rate Fluorometer
Generic Instrument Name
Fast Repetition Rate Fluorometer
Dataset-specific Description
Photosynthetic parameters were measured.
Generic Instrument Description
An FRRf is used for measuring the fluorescence of a sample of phytoplankton photosynthetic competency (Fv/Fm).


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Deployments

OC1504A

Website
Platform
R/V Oceanus
Report
Start Date
2015-04-19
End Date
2015-05-02
Description
Data for the project "Linking physiological and molecular aspects of diatom silicification in field populations" (PIs Kimberlee Thamatrakoln and Mark Brzezinski) were collected on this cruise.


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Project Information

Linking physiological and molecular aspects of diatom silicification in field populations (Diatom Silicification)

Coverage: Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W


Description from NSF award abstract:
Diatoms, unicellular, eukaryotic photoautotrophs, are among the most ecologically successful and functionally diverse organisms in the ocean. In addition to contributing one-fifth of total global primary productivity, diatoms are also the largest group of silicifying organisms in the ocean. Thus, diatoms form a critical link between the carbon and silicon (Si) cycles. The goal of this project is to understand the molecular regulation of silicification processes in natural diatom populations to better understand the processes controlling diatom productivity in the sea. Through culture studies and two research cruises, this research will couple classical measurements of silicon uptake and silica production with molecular and biochemical analyses of Silicification-Related Gene (SiRG) and protein expression. The proposed cruise track off the West Coast of the US will target gradients in Si and iron (Fe) concentrations with the following goals: 1) Characterize the expression pattern of SiRGs, 2) Correlate SiRG expression patterns to Si concentrations, silicon uptake kinetics, and silica production rates, 3) Develop a method to normalize uptake kinetics and silica production to SiRG expression levels as a more accurate measure of diatom activity and growth, 4) Characterize the diel periodicity of silica production and SiRG expression.

It is estimated that diatoms process 240 Teramoles of biogenic silica each year and that each molecule of silicon is cycled through a diatom 39 times before being exported to the deep ocean. Decades of oceanographic and field research have provided detailed insight into the dynamics of silicon uptake and silica production in natural populations, but a molecular understanding of the factors that influence silicification processes is required for further understanding the regulation of silicon and carbon fluxes in the ocean. Characterizing the genetic potential for silicification will provide new information on the factors that regulate the distribution of diatoms and influence in situ rates of silicon uptake and silica production. This research is expected to provide significant information about the molecular regulation of silicification in natural populations and the physiological basis of Si limitation in the sea.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)
NSF Division of Ocean Sciences (NSF OCE)

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