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

Website: https://www.bco-dmo.org/dataset/889930
Data Type: Cruise Results
Version: 1
Version Date: 2023-02-24

Project
» Island mass effects on planktonic communities in the open ocean (Island Mass Effect)
ContributorsAffiliationRole
Karp-Boss, LeeUniversity of MainePrincipal Investigator
Bourdin, GuillaumeTara Ocean FoundationStudent
Rauch, ShannonWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

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).


Coverage

Spatial Extent: N:51.5538 E:179.384 S:-35.6093 W:-179.101
Temporal Extent: 2016-05-30 - 2018-10-26

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


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Data Files

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

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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.



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Related Publications

Lombard, F., Bourdin, G., Pesant, S., Agostini, S., Baudena, A., Boissin, E., Cassar, N., Clampitt, M., Conan, P., Silva, O. D., Dimier, C., Douville, E., Elineau, A., Fin, J., Flores, J. M., Ghiglione, J. F., Hume, B. C. C., Jalabert, L., John, S. G., … Gorsky, G. (2022). Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems. https://doi.org/10.1101/2022.05.25.493210
Methods
Ras, J., Claustre, H., & Uitz, J. (2008). Spatial variability of phytoplankton pigment distributions in the Subtropical South Pacific Ocean: comparison between in situ and predicted data. Biogeosciences, 5(2), 353–369. https://doi.org/10.5194/bg-5-353-2008
Methods

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Parameters

ParameterDescriptionUnits
Event

Event identifier

unitless
Sample_ID

Sample identifier

unitless
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
Depth_top_m

Depth top/min

meters (m)
Depth_bot_m

Depth bottom/max

meters (m)
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)
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_comment

Sample comment

unitless
Env_feature

Description of sampling environment

unitless
Sampling_protocol

Sampling protocol or method

unitless
Sample_replicates

Sample replicates (filtration replicates of the same water sample)

unitless
Technical_replicate

Technical replicates (measurement replicates performed during the sample analysis in the lab)

unitless
Analysis

Analysis date

unitless
Analysis_comment

Analysis comment

unitless
Chl_c3

Chlorophyll c3 (Chl c3) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Chlc3

Quality flag for Chl_c3

unitless
Chl_c1_c2

Chlorophyll c1+c2 (Chl c1+c2) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Chlc2

Quality flag for Chl_c1_c2

unitless
Chlide_a

Chlorophyllide a (Chlide a) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Chlda

Quality flag for Chlide_a

unitless
Perid

Peridinin (Perid) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Peri

Quality flag for Perid

unitless
Phaeopho_a

Phaeophorbide a (Phaeopho a) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Phda

Quality flag for Phaeopho_a

unitless
But_fuco

19-Butanoyloxyfucoxanthin (But-fuco) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_But

Quality flag for But_fuco

unitless
Fuco

Fucoxanthin (Fuco) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Fuco

Quality flag for Fuco

unitless
Neo

Neoxanthin (Neo) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Neo

Quality flag for Neo

unitless
Hex19_4_kfuco

19'-Hexanoyloxy-4-ketofucoxanthin (19Hex-4-kfuco) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Hex4K

Quality flag for Hex19_4_kfuco

unitless
Pras

Prasinoxanthin (Pras) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Pras

Quality flag for Pras

unitless
Viola

Violaxanthin (Viola) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Viola

Quality flag for Viola

unitless
Hex_fuco

19-Hexanoyloxyfucoxanthin (Hex-fuco) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Hex

Quality flag for Hex_fuco

unitless
Myxox

Myxoxanthophyll (Myxox) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Myxo

Quality flag for Myxox

unitless
Diadino

Diadinoxanthin (Diadino) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Diadino

Quality flag for Diadino

unitless
Anthera

Antheraxanthin (Anthera) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Anthera

Quality flag for Anthera

unitless
Allo

Alloxanthin (Allo) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Allo

Quality flag for Allo

unitless
Diato

Diatoxanthin (Diato) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Diato

Quality flag for Diato

unitless
Zea

Zeaxanthin (Zea) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Zea

Quality flag for Zea

unitless
Lut

Lutein (Lut) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Lut

Quality flag for Lut

unitless
BChl_a

Bacteriochlorophyll a (BChl a) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Bchla

Quality flag for BChl_a

unitless
DV_chl_a_1

Divinyl chlorophyll a (DV chl a) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_DVChlb

Quality flag for DV_chl_a_1

unitless
Chl_b

Chlorophyll b (Chl b) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Chlb

Quality flag for Chl_b

unitless
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)
QA_TChlb

Quality flag for Chl_b_DV_chl_b

unitless
DV_chl_a_2

Divinyl chlorophyll a (DV chl a) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_DVChla

Quality flag for DV_chl_a_2

unitless
Chl_a

Chlorophyll a (Chl a) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Chla

Quality flag for Chl_a

unitless
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)
QA_Tchla_QA

Quality flag for Chl_a_DV_chla_chlide_a

unitless
Phaeophytin_a

Phaeophytin a (Phaeophytin a) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Phytna

Quality flag for Phaeophytin_a

unitless
Carotene

Carotene (Carotene) determined by HPLC

milligrams per cubic meter (mg/m^3)
QA_Tcar

Quality flag for Carotene

unitless
Latitude_Start

Latitude at start of sampling event

decimal degrees North
Longitude_Start

Longitude at start of sampling event

decimal degrees East
Latitude_End

Latitude at end of sampling event

decimal degrees North
Longitude_End

Longitude at end of sampling event

decimal degrees East
DateTime_Start

Date and time at start of sampling event

unitless
DateTime_End

Date and time at end of sampling event

unitless
Location

Location of cruise (Pacific Ocean)

unitless
Campaign

Name of campaign/expedition (TARA_PACIFIC_2016-2018)

unitless
Basis

Name of vessel (SV Tara)

unitless
Method_or_Device

Name of sampling method or instrument

unitless


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Instruments

Dataset-specific Instrument Name
Aligent 1200 Series Gradient HPLC System
Generic Instrument Name
High-Performance Liquid Chromatograph
Dataset-specific 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.
Generic Instrument 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.


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Deployments

Tara Pacific Expedition

Website
Platform
Tara
Description
The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58,000 samples. Tara is a 36-meter aluminum-hulled schooner, formerly named "Antarctica" then "Seamaster". 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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Project Information

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


Coverage: South Pacific


NSF Award Abstract:

This study is using existing data to characterize the Island Mass Effect (IME) at 20 locations across the Pacific Ocean. The Island Mass Effect occurs when islands and atolls alter atmospheric and oceanic circulation, resulting in local enrichment of surface waters with nutrients. Local fertilization, in turn, promotes phytoplankton blooms and high plankton biomass that can be advected into the surrounding open ocean and enhance regions of low nutrient availability and low plankton biomass. The Island Mass Effect (IME) is thought to be sufficiently important to affect regional fisheries and biogeochemical processes, but most of our current understanding of this phenomenon comes from satellite remote sensing observations of elevated chlorophyll concentrations that serve as a proxy for phytoplankton biomass. This project entails a systematic, basin-scale evaluation of changes in phytoplankton and zooplankton biomass and composition along environmental gradients from the lagoons and coastal water of islands into the open ocean. The study is making use of a large dataset collected during the TARA Pacific expedition (2016-2018), and results are providing new information about marine ecological responses to IME and the plankton inventories needed to improve ecosystem models for under sampled regions of the world’s oceans. In addition to supporting graduate and undergraduate students, this project offers a training workshop for early career scientists on best practices for the collection and processing of ship-based underway data.

Islands in the oligotrophic gyres of the Pacific Oceans alter oceanic and atmospheric circulation and provide sources of fertilization to promote local phytoplankton blooms. This so-called Island Mass Effect (IME) is a ubiquitous phenomenon in the Pacific Ocean where vast areas are known to be limited by the availability of macro- and micro-nutrients, yet it is mostly understood from satellite remote sensing observations of elevated chlorophyll concentrations. Beyond remote sensing of chlorophyll, concurrent changes in plankton community composition and structure have been examined for only a small number of islands, limiting our understanding of the biological responses to IME. In this project, the investigators are examining the IME at 20 locations by evaluating phytoplankton community composition, mesozooplankton biomass, and plankton diversity. The investigators are making use of a comprehensive data set collected during the TARA Pacific expedition (2016-2018) that includes: environmental measurements (temperature, salinity, nutrients and trace metals), plankton samples (flow cytometry, plankton imaging, pigments, and genomics), high resolution measurements of optical properties from which biogeochemical proxies are derived, satellite remote sensing data (chlorophyll, temperature, sea surface height), and currents from an ocean circulation model (Mercator Oceans).

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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