Dataset: HPLC pigment data collected during the Tara Pacific expedition

Name: Pigment concentrations derived from High-Performance Liquid Chromatography (HPLC) analysis from samples collected during the Tara Pacific expedition from 2016-2018
Published: 2023-02-24
Keywords: HPLC, pigments, Pacific Ocean, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.889930.1

Spatial Extent: N:51.5538 E:179.384 S:-35.6093 W:-179.101

Temporal Extent: 2016-05-30 - 2018-10-26

Project:

Island mass effects on planktonic communities in the open ocean (Island Mass Effect)

Principal Investigator:

Lee Karp-Boss (University of Maine)

Student:

Guillaume Bourdin (Tara Ocean Foundation)

BCO-DMO Data Manager:

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

Version:

Version Date:

2023-02-24

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Pigment concentrations derived from High-Performance Liquid Chromatography (HPLC) analysis from samples collected during the Tara Pacific expedition from 2016-2018

Abstract:

The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean. Here we provide pigment concentration data originating from 545 stations that were sampled during the expedition in the Pacific and during transit across the Atlantic. Pigment concentrations were derived from High-Performance Liquid Chromatography (HPLC) analysis. This data set provides high-quality measurements of major pigments including chlorophylls a, b, and c, peridinin, 19'-butanoyloxyfucoxanthin, fucoxanthin, neoxanthin, prasinoxanthin, violaxanthin, 19'-hexanoyloxyfucoxanthin, diadinoxanthin, antheraxanthin, alloxanthin, diatoxanthin, zeaxanthin, lutein, divinyl chlorophyll b, chlorophyll b, divinyl chlorophyll a, chlorophyll a, carotene, and bacteriochlorophyll a, which can be used to estimate phytoplankton community composition. More details on the Tara Pacific expedition and its sampling program can be found in Lombard et al., 2022 (doi: 10.1101/2022.05.25.493210).

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2023-02-24	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.889930.1	2023-04-26

Methods & Sampling

Water samples (volume: 5 liters) for High-Performance Liquid Chromatography (HPLC) analysis were collected from surface water using a custom-made, underway pumping system (nicknamed "Dolphin"; Lombard et al., 2022) and filtered onto 25 millimeter (mm) diameter, 0.7 micrometer (um) pore glass fiber filters. Filters were flash frozen and stored in liquid nitrogen until arrival to the Laboratoire d'Oceanographie de Villefranche (LOV) where they were stored in -80 degrees Celsius (C) until analysis. Samples were analyzed as described in Ras et al., 2008. Pigment extraction was carried out in 3 milliliters (mL) Methanol containing an internal standard (Vitamin E acetate, Sigma). Methanol and Vitamin E acetate were injected regularly during each run to check for retention time reproducibility, peak area precision (<1%), and instrument stability.

Data Processing Description

Data Processing:
Data were processed with the ChemStation software. Zeros were replaced by <<LOD>>. All pigment peaks were inspected and quality controlled as good, acceptable, or qualitative (based on peak symmetry and purity, spectral shape, signal to noise ratio, and calibrated compounds), and any measurements below the detection limit were discarded.

Quality Flag Descriptions:
[0] below detection limit
[1] good
[2] acceptable
[3] qualitative

BCO-DMO Processing:
- renamed fields to comply with BCO-DMO naming conventions;
- added the following columns by joining to the event log: Latitude_Start, Longitude_Start, Latitude_End, Longitude_End, DateTime_Start, DateTime_End, Location, Campaign, Basis, Method_or_Device

Data Files

File
pigments.csv (Comma Separated Values (.csv), 582.50 KB) MD5:7de2876f5807f26dffc1967534152680 Primary data file for dataset ID 889930.

Supplemental Files

File

tara_pacific_event_log.csv

(Comma Separated Values (.csv), 132.65 KB)
MD5:b1ff3318210d345b2da9be1eef2ebda1

Tara Pacific expedition event log. Supplemental File for dataset ID 889930. 

Column names, descriptions, and units:
Event = identifier for sampling event.
Latitude_Start = latitude at start of event in decimal degrees North.
Longitude_Start = longitude at start of event in decimal degrees East.
Latitude_End = latitude at end of event in deicmal degrees North.
Longitude_End = longitude at end of event in decimal degrees East.
DateTime_Start = date and time at start of event in ISO 8601 format (YYYY-MM-DDThh:mm:ss).
DateTime_End = date and time at end of event in ISO 8601 format (YYYY-MM-DDThh:mm:ss).
Location = location of cruise (Pacific Ocean).
Campaign = name of campaign/expedition.
Basis = name of vessel.
Method_or_Device = name of sampling method or instrument.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-2025402

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Tara Pacific Expedition			Tara		data info

Instruments

High-Performance Liquid Chromatograph

Supplied Name: Aligent 1200 Series Gradient HPLC System

Supplied Description:

Instrument calibration is done once per year using standards from DHI Water and Environment (Denmark) and Sigma Aldrich (Chla and Chlb). Preventive maintenance of the instrument is done once per year (seal replacements, window detectors, injection valve, and worn parts). Long-term quality control of the instrument's performance is done by injecting mixed pigment standards from DHI several times a year.

Instrument Type

Generic Name: High-Performance Liquid Chromatograph

Acronym: HPLC

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/

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.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Event	Event identifier	unitless	event
Sample_ID	Sample identifier	unitless	sample
Sampling_event_label	Event label, follows Tara Pacific data conventions: TARA_EVENT_[sampling-event_date_time-utc]_[sampling-design label]_[sampling-day-night_label]_[sampling-environment_feature_label]_[sample- material_label]_[sampling-protocol_label]_[sample-storage_container-label] Refer to Lombard et al. (2022) for more information on the labeling protocols.	unitless	sample
Depth_top_m	Depth top/min	meters (m)	depth
Depth_bot_m	Depth bottom/max	meters (m)	depth
Depth_water_m	The mid-depth at which the water was sampled. (Note: the min and max depth associated with the samples take into account the potential variability in sampling depth, but Depth_water_m would be considered the sampling depth.)	meters (m)	depth
Sampling_design_label	Sampling design label, follows Tara Pacific data conventions. Provided to facilitate the identification and integration of data that originate from the same open ocean station (OA###), island (I##), site (S##) or coral colony (C###), and hence share provenance and environmental context. Refer to Lombard et al. (2022) for more information on the labeling protocols.	unitless	sample
Sample_comment	Sample comment	unitless	comment
Env_feature	Description of sampling environment	unitless	site_descrip
Sampling_protocol	Sampling protocol or method	unitless	sampling_method
Sample_replicates	Sample replicates (filtration replicates of the same water sample)	unitless	replicate
Technical_replicate	Technical replicates (measurement replicates performed during the sample analysis in the lab)	unitless	replicate
Analysis	Analysis date	unitless	date
Analysis_comment	Analysis comment	unitless	comment
Chl_c3	Chlorophyll c3 (Chl c3) determined by HPLC	milligrams per cubic meter (mg/m^3)	chl_c3
QA_Chlc3	Quality flag for Chl_c3	unitless	q_flag
Chl_c1_c2	Chlorophyll c1+c2 (Chl c1+c2) determined by HPLC	milligrams per cubic meter (mg/m^3)	chl_c1_c2
QA_Chlc2	Quality flag for Chl_c1_c2	unitless	q_flag
Chlide_a	Chlorophyllide a (Chlide a) determined by HPLC	milligrams per cubic meter (mg/m^3)	chlide_a
QA_Chlda	Quality flag for Chlide_a	unitless	q_flag
Perid	Peridinin (Perid) determined by HPLC	milligrams per cubic meter (mg/m^3)	peridinin
QA_Peri	Quality flag for Perid	unitless	q_flag
Phaeopho_a	Phaeophorbide a (Phaeopho a) determined by HPLC	milligrams per cubic meter (mg/m^3)	p_phorbide_a
QA_Phda	Quality flag for Phaeopho_a	unitless	q_flag
But_fuco	19-Butanoyloxyfucoxanthin (But-fuco) determined by HPLC	milligrams per cubic meter (mg/m^3)	fucox_but
QA_But	Quality flag for But_fuco	unitless	q_flag
Fuco	Fucoxanthin (Fuco) determined by HPLC	milligrams per cubic meter (mg/m^3)	fucox
QA_Fuco	Quality flag for Fuco	unitless	q_flag
Neo	Neoxanthin (Neo) determined by HPLC	milligrams per cubic meter (mg/m^3)	neox
QA_Neo	Quality flag for Neo	unitless	q_flag
Hex19_4_kfuco	19'-Hexanoyloxy-4-ketofucoxanthin (19Hex-4-kfuco) determined by HPLC	milligrams per cubic meter (mg/m^3)	hex_kfuco
QA_Hex4K	Quality flag for Hex19_4_kfuco	unitless	q_flag
Pras	Prasinoxanthin (Pras) determined by HPLC	milligrams per cubic meter (mg/m^3)	prasinox
QA_Pras	Quality flag for Pras	unitless	q_flag
Viola	Violaxanthin (Viola) determined by HPLC	milligrams per cubic meter (mg/m^3)	violax
QA_Viola	Quality flag for Viola	unitless	q_flag
Hex_fuco	19-Hexanoyloxyfucoxanthin (Hex-fuco) determined by HPLC	milligrams per cubic meter (mg/m^3)	fucox_hex
QA_Hex	Quality flag for Hex_fuco	unitless	q_flag
Myxox	Myxoxanthophyll (Myxox) determined by HPLC	milligrams per cubic meter (mg/m^3)	myxox
QA_Myxo	Quality flag for Myxox	unitless	q_flag
Diadino	Diadinoxanthin (Diadino) determined by HPLC	milligrams per cubic meter (mg/m^3)	diadinox
QA_Diadino	Quality flag for Diadino	unitless	q_flag
Anthera	Antheraxanthin (Anthera) determined by HPLC	milligrams per cubic meter (mg/m^3)	antherax
QA_Anthera	Quality flag for Anthera	unitless	q_flag
Allo	Alloxanthin (Allo) determined by HPLC	milligrams per cubic meter (mg/m^3)	allox
QA_Allo	Quality flag for Allo	unitless	q_flag
Diato	Diatoxanthin (Diato) determined by HPLC	milligrams per cubic meter (mg/m^3)	diatox
QA_Diato	Quality flag for Diato	unitless	q_flag
Zea	Zeaxanthin (Zea) determined by HPLC	milligrams per cubic meter (mg/m^3)	zeax
QA_Zea	Quality flag for Zea	unitless	q_flag
Lut	Lutein (Lut) determined by HPLC	milligrams per cubic meter (mg/m^3)	lutein
QA_Lut	Quality flag for Lut	unitless	q_flag
BChl_a	Bacteriochlorophyll a (BChl a) determined by HPLC	milligrams per cubic meter (mg/m^3)	bchl_a
QA_Bchla	Quality flag for BChl_a	unitless	q_flag
DV_chl_a_1	Divinyl chlorophyll a (DV chl a) determined by HPLC	milligrams per cubic meter (mg/m^3)	chl_a2
QA_DVChlb	Quality flag for DV_chl_a_1	unitless	q_flag
Chl_b	Chlorophyll b (Chl b) determined by HPLC	milligrams per cubic meter (mg/m^3)	chl_b
QA_Chlb	Quality flag for Chl_b	unitless	q_flag
Chl_b_DV_chl_b	Chlorophyll b plus divinyl chlorophyll b (Chl b+DV chl b) determined by HPLC	milligrams per cubic meter (mg/m^3)	chl_b_tot
QA_TChlb	Quality flag for Chl_b_DV_chl_b	unitless	q_flag
DV_chl_a_2	Divinyl chlorophyll a (DV chl a) determined by HPLC	milligrams per cubic meter (mg/m^3)	chl_a2
QA_DVChla	Quality flag for DV_chl_a_2	unitless	q_flag
Chl_a	Chlorophyll a (Chl a) determined by HPLC	milligrams per cubic meter (mg/m^3)	chl_a
QA_Chla	Quality flag for Chl_a	unitless	q_flag
Chl_a_DV_chla_chlide_a	Chlorophyll a plus divinyl chlorophyll a plus chlorophyllide a (Chl a+DV chla+chlide a) determined by HPLC	milligrams per cubic meter (mg/m^3)	chl_a_tot
QA_Tchla_QA	Quality flag for Chl_a_DV_chla_chlide_a	unitless	q_flag
Phaeophytin_a	Phaeophytin a (Phaeophytin a) determined by HPLC	milligrams per cubic meter (mg/m^3)	p_phytin
QA_Phytna	Quality flag for Phaeophytin_a	unitless	q_flag
Carotene	Carotene (Carotene) determined by HPLC	milligrams per cubic meter (mg/m^3)	carotene
QA_Tcar	Quality flag for Carotene	unitless	q_flag
Latitude_Start	Latitude at start of sampling event	decimal degrees North	lat
Longitude_Start	Longitude at start of sampling event	decimal degrees East	lon
Latitude_End	Latitude at end of sampling event	decimal degrees North	lat
Longitude_End	Longitude at end of sampling event	decimal degrees East	lon
DateTime_Start	Date and time at start of sampling event Format: %Y-%m-%dT%H:%M:%S	unitless	date
DateTime_End	Date and time at end of sampling event Format: %Y-%m-%dT%H:%M:%S	unitless	date
Location	Location of cruise (Pacific Ocean)	unitless	region
Campaign	Name of campaign/expedition (TARA_PACIFIC_2016-2018)	unitless	cruise_name
Basis	Name of vessel (SV Tara)	unitless	ship
Method_or_Device	Name of sampling method or instrument	unitless	sampling_method

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Dataset: HPLC pigment data collected during the Tara Pacific expedition