Dataset: HPLC Pigments

Name: HPLC pigment analyses of CTD-collected samples from R/V Knorr cruise KN207-03 in the North Atlantic (transect from Ponta Delgada, Azores to Reykjavik, Iceland) in 2012 (NA-VICE project)
Published: 2014-09-17
License: https://creativecommons.org/licenses/by/4.0/
Keywords: oceans

Cite This Dataset

Project:

Lipid lubrication of oceanic carbon and sulfur biogeochemistry via a host-virus chemical arms race (NA-VICE)

Principal Investigator:

Giacomo DiTullio (Grice Marine Laboratory - College of Charleston, GML-CoC)

Contact:

Emily Cooper (Grice Marine Laboratory - College of Charleston, GML-CoC)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version Date:

2014-09-17

Validated:

Yes

Current State:

Final no updates expected

Data URL:

https://www.bco-dmo.org/dataset/517634/data

HPLC pigment analyses of CTD-collected samples from R/V Knorr cruise KN207-03 in the North Atlantic (transect from Ponta Delgada, Azores to Reykjavik, Iceland) in 2012 (NA-VICE project)

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Description

Dataset includes HPLC pigment analyses of CTD collected samples from the KN207-03 cruise (Northeast Atlantic Ocean transect from Azores to Iceland).

Acquisition Description

Water samples were collected from CTD Niskin bottles. Water samples for HPLC analyses were taken from one Niskin bottle per cast-depth combination included in the dataset. Note that the niskin_sampled column indicates which Niskin bottle the HPLC sample was taken from. The niskins_fired column indicates all Niskin bottle numbers fired at the specified depth, though the HPLC sample was taken from only one of those bottles.

Chlorophyll and accessory pigment composition was analyzed by high performance liquid chromatography (HPLC; Agilent 1100). Culture aliquots were filtered on Whatmann GF/F filters, flash frozen in liquid nitrogen, and stored at -80°C until analysis. Just prior to analysis, pigments were extracted overnight in acetone at -20°C. The following day extracted pigments were centrifuged and measured using a gradient elution method (DiTullio and Geesey, 2003), a modification of the Zapata et al 2000 method. Chromatographic separation was performed using a Waters C8 symmetry column, photodiode array and fluorescence detectors. The internal standard, β-Apo-8-carotenal-trans standard (Fluka Chemical Corp., USA) was added to extracted pigments as a peak reference. Individual pigment peaks were quantified with Chemstation software (revision B.03.01, Agilent) and our pigment action spectra library calibrated using pigment standards from DHI LABS (Hoersholm, Denmark) and in-house purifications of non-commercially available pigments. Coefficient of variation among replicate HPLC injections is < 3% and our limit of detection is approximately 1 ng L-1.

Processing Description

Response factors for pigments were performed using dilutions of calibration standards. Full details of data processing and methods used can be found in:
DiTullio, G. R. & Geesey, M. E. (2002) Photosynthetic pigments in marine algae and bacteria. In: BITTON, G. (ed.) The Encyclopedia of Environmental Microbiology. New York: John Wiley & Sons Inc.

BCO-DMO Processing Notes:
- Modified parameter names to conform to BCO-DMO conventions;
- Blanks (missing data) replaced with "nd" meaning "no data";
- Separated the original "niskin" column into two columns: "niskin_sampled" and "niskins_fired";
- Converted original longitude values provided as positive degrees West to negative degrees East;
- Added ISO_DateTime_UTC column from original date_gmt and time_gmt fields;
- Transposed data to convert columns containing pigment concentrations into rows.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1061876

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
KN207-03	NA-VICE	2012-06-15	R/V Knorr	Dr Kay D Bidle (Chief Scientist)	data info

Instruments

High Performance Liquid Chromatograph

(more info)

Short Name: HPLC

Community Standard Description

Generic Description

A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase. (http://www.files.chem.vt.edu/chem-ed/sep/lc/hplc.html)

PI supplied instrument name: HPLC

Dataset-specific description

Chlorophyll and accessory pigment composition was analyzed by high performance liquid chromatography (HPLC; Agilent 1100).

Niskin bottle

(more info)

Short Name: Niskin bottle

Community Standard Description

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.

PI supplied instrument name: Niskin bottle

Dataset-specific description

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
cast	Cast number.	alphanumeric	cast
station	Station name.	text	station
date_gmt	Date of cast (GMT).	mmddyyyy	date_gmt
time_gmt	Time of cast (GMT).	hhmmss	time_gmt
date_local	Date of cast (local time zone).	mmddyyyy	date_local
time_local	Time of cast (local time zone).	hhmmss	time_local
lat	Latitude. Positive values = North.	decimal degrees	lat
lon	Longitude. Positive values = East.	decimal degrees	lon
lat_deg	Degrees latitude.	degrees North	lat_degs
lat_min	Minutes latitude.	minutes North	lat_mins
lon_deg	Degrees longitude. Positive = West.	degrees West	lon_degs
lon_min	Minutes longitude. Positive = West.	minutes West	lon_mins
ISO_DateTime_UTC	Date and time of cast formatted to ISO8601 standard.	YYYY-mm-ddTHH:MM:SS.xx	ISO_DateTime_UTC
depth	Depth of Niskin bottle firing.	meters	depth
amb_bot	Amber bottle identification number.	integer	unknown
niskin_sampled	Niskin bottle number from which HPLC sample was taken.	integer	unknown
niskins_fired	Niskin bottle numbers fired at depth; HPLC sample was taken from one Niskin bottle.	range of integers	unknown
filt_vol	Volume of water filtered.	liters (L)	unknown
pigment	Name of the pigment measured: chl_c3 = Chlorophyll c3; chl_ide = Chlorophyllide a; mg_dvp = Magnesium-2;4-divinyl phaeoporphyrin a5 monomethyl ester; chl_c2 = Chlorophyll c2; chl_c1 = Chlorophyll c1; peridinin = Peridinin; but19 = 19-butanoyloxyfucoxanthin; fucox = Fucoxanthin; ph_ide = Pheophorbide a; neox = Neoxanthin; prasinox = Prasinoxanthin; violax = Violaxanthin; hex19 = 19'-hexanoyloxyfucoxanthin; diadinox = Diadinoxanthin; cis_fucox = cis-Fucoxanthin; allox = Alloxanthin; diatox = Diatoxanthin; monad = Monadoxanthin; zeax = Zeaxanthin; lutein = lutein; crocox = Crocoxanthin; chl_b = Chlorophyll b; dv_chl_a = Divinyl Chlorophyll a; chl_a = Chlorophyll a; p_phytin = Phaeophytin a; carotene_a = alpha Carotene; carotene_b = beta Carotene.	text	pigment_conc
concentration	Concentration of the pigment as determined by HPLC.	nanograms per liter (ng/L)	pigment_conc

Database

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Dataset: HPLC Pigments