Dataset: AE1913 Clio pigments

Name: Pigment concentration data from AUV Clio dives conducted during R/V Atlantic Explorer cruise AE1913 in the Sargasso Sea in June of 2019
Published: 2024-05-03
Keywords: pigments, microeukaryotes, metaproteomics, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.926546.1

Spatial Extent: N:38.528372 E:-65.976848 S:32.995067 W:-70.84278

Sargasso Sea, beginning at Bermuda Atlantic Time-series Station (BATS) and ending in the northeast shelf of Woods Hole Oceanographic Institution (WHOI)

Temporal Extent: 2019-06

Project:

Collaborative Research: Direct Characterization of Adaptive Nutrient Stress Responses in the Sargasso Sea using Protein Biomarkers and a Biogeochemical AUV (Nutrient Stress Responses and AUV Clio)

Principal Investigator:

Mak A. Saito (Woods Hole Oceanographic Institution, WHOI)

Scientist:

Natalie Cohen (Woods Hole Oceanographic Institution, WHOI)

Rodney J. Johnson (Bermuda Institute of Ocean Sciences, BIOS)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-05-03

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Pigment concentration data from AUV Clio dives conducted during R/V Atlantic Explorer cruise AE1913 in the Sargasso Sea in June of 2019

Abstract:

Pigment concentration data from R/V Atlantic Explorer cruise AE1913 (June 2019) in which seawater was collected across a 1,050 km section in the western North Atlantic.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2024-05-03	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.926546.1	2024-10-30

Description

See the "Related Datasets" section on this page for the ELOG from cruise AE1913 and other closely related data.
* Also see all datasets related to the same cruise AE1913: https://www.bco-dmo.org/deployment/916412

Methods & Sampling

Oceanographic samples were collected onboard the R/V Atlantic Explorer between June 16th - 28th 2019, along a transect beginning at the Bermuda Atlantic Time-series Study (BATS) site and terminating in northeast US continental shelf waters (Woods Hole Oceanographic Institution [WHOI]). Biomass was collected using the biogeochemical AUV Clio. Clio payloads contained SUPR cartridges housing 142 mm combusted GFF filters for pigment collection. GFF filter fractions were additionally preserved for high performance liquid chromatography pigment analyses throughout the surface transect.

Pigments were collected onto 142 mm GFF filters by AUV Clio at the same depths that proteins were collected on Supor filters. GFF 25 mm punchouts were used for the pigment analysis, and the estimated volume filtered through 25 mm was used to quantify pigments per volume. Concentrations are reported as ng/kg assuming the standard density of seawater (1025 kg/m3). At stations 1 and 3, GFF fractions for pigments were not collected by Clio. Instead, pigments were analyzed from the CTD rosette at these stations (though deployments and recoveries were the same) whereby samples (4 L) were filtered directly onto 25 mm GFF glass fiber filters and immediately frozen in liquid nitrogen. Samples were analyzed on an Agilent 1100 series high performance liquid chromatography (HPLC) using the method of Bidigare et al. 2005 and instrument calibration was performed with certified pigment standards from the Danish Hydraulic Institute.

Abbreviation,Pigment Name:

ChlC3, Chlorophyll C3
ChlC2, Chlorophyll C2
Per, Peridinin
NBut, 19'But-Fucoxanthin
Fux, Fucoxanthin
NHex, 19'Hex-Fucoxanthin
Prx, Prasinoxanthin
Vix, Violoxanthin
Ddx, Diadinoxanthin
Alx, Alloxanthin
Dtx, Diatoxanthin
Lut, Lutein
Zex, Zeaxanthin
ChlB, Chlorophyll b
DvA, Divinyl Chlorophyll a
Chla, Chlorophyll a
ABCar, Alpha & Beta Carotene

BCO-DMO Processing

* Sheet 1 of submitted file "CLIO_BV55.xls" was imported into the BCO-DMO data system for this dataset. Values "NA" imported as missing data values. Sheet 2 containing pigment abbreviations and names was added to Methods & Sampling section.
* Imported rows did not include comment outside of the data table "Pigment concentrations are reported in ng/kg", that information was added to the "parameters" section of metadata.
** Missing data values are displayed differently based on the file format you download. They are blank in csv files, "NaN" in MatLab files, etc.

* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]

* question mark in Depth value for CLIO_023_13 "110?" was removed after verification by the data submitter.

* After importing the table, a transformation to the long form of the table was made (going from column per pigment to one column for pigment_name, one column for pigment_conc). The long form was added to the dataset page as the primary form of the dataset, and the supplemental files section include the wide form as an alternate format of the same data.

Data Files

File

Pigment data (long form)
filename: 926546_v1_ae1913-clio-pigments.csv

(Comma Separated Values (.csv), 26.25 KB)
MD5:f894485b42a5c7a5426e13c86cb6529b

Primary data file for dataset ID 926546, version 1. This is form of the data includes a column containing the pigment name, and a column containing the pigment concentration. See the Supplemental Files section for data in alternate format (wide form) which includes a separate column for each pigment type which contains the pigment concentration.

Supplemental Files

File

Pigment data (wide form)
filename: 926546_v1_AE1913-clio-pigments-wideform.csv

(Comma Separated Values (.csv), 4.38 KB)
MD5:47fb27d47f0c5db201792619d8b44b7c

Data in alternate format (wide form). This form of the data includes a separate column for each pigment type which contains the pigment concentration.  This table contains the same data provided in the primary data file for this dataset "926546_v1_ae1913-clio-pigments.csv." 

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1658030

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AE1913	Clio-BATS-WHOI AE1913	2019-06-16	R/V Atlantic Explorer	Mak A. Saito (Chief Scientist)	data info

Instruments

AUV Clio

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: AUV Clio

Generic Description:

Clio is an autonomous underwater vehicle (AUV) created to accomplish the dual goals of global ocean mapping and biochemistry sampling. The ability to sample dissolved and particulate seawater biochemistry across ocean basins while capturing fine-scale biogeochemical processes sets it apart from other AUVs. Clio is designed to efficiently and precisely move vertically through the ocean, drift laterally to observe water masses, and integrate with research vessel operations to map large horizontal scales up to a depth of 6,000 meters. More information is available at https://www2.whoi.edu/site/deepsubmergencelab/clio/

High-Performance Liquid Chromatograph

Supplied Name: Agilent 1100 series high performance liquid chromatography (HPLC)

Supplied Description:

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.

Niskin bottle

Supplied Name: X-Niskin bottles

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
SampleName	Sample identifier (e.g. CLIO_020_10) which includes the dive (station) and the pump filter number.	unitless	sample
Latitude	latitude. Obtained from the trace metal rosette	decimal degrees	lat
Longitude	longitude. Obtained from the trace metal rosette.	decimal degrees	lon
Depth	sample depth	meters (m)	depth
pigment_abbr	Pigment abbreviation (See "Methods & Sampling" for list of abrreviations and full pigment name).	unitless	sample_descrip
pigment_conc	Pigment concentration	nanograms per kilogram (ng/kg)	pigment_conc