http://lod.bco-dmo.org/id/dataset/926546
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2024-05-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Pigment concentration data from AUV Clio dives conducted during R/V Atlantic Explorer cruise AE1913 in the Sargasso Sea in June of 2019
2024-05-03
publication
2024-05-03
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-10-30
publication
https://doi.org/10.26008/1912/bco-dmo.926546.1
Mak A. Saito
Woods Hole Oceanographic Institution
principalInvestigator
Natalie Cohen
Woods Hole Oceanographic Institution
principalInvestigator
Rodney J. Johnson
Bermuda Institute of Ocean Sciences
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Saito, M. A., Cohen, N., Johnson, R. J. (2024) Pigment concentration data from AUV Clio dives conducted during R/V Atlantic Explorer cruise AE1913 in the Sargasso Sea in June of 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-05-03 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.926546.1 [access date]
Dataset Description: <p>See the "Related Datasets" section on this page for the ELOG from cruise AE1913 and other closely related data.<br />
*&nbsp;Also see all datasets related to the same cruise AE1913:&nbsp;https://www.bco-dmo.org/deployment/916412</p> Methods and Sampling: <p>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.&nbsp;</p>
<p>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)&nbsp;whereby samples (4 L) were filtered directly onto 25 mm GFF glass fiber filters and immediately frozen in liquid nitrogen.&nbsp;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.&nbsp;<br />
&nbsp;</p>
<p><strong>Abbreviation,Pigment Name:</strong></p>
<div>ChlC3, Chlorophyll C3<br />
ChlC2, Chlorophyll C2<br />
Per, Peridinin<br />
NBut, 19'But-Fucoxanthin<br />
Fux, Fucoxanthin<br />
NHex, 19'Hex-Fucoxanthin<br />
Prx, Prasinoxanthin<br />
Vix, Violoxanthin<br />
Ddx, Diadinoxanthin<br />
Alx, Alloxanthin<br />
Dtx, Diatoxanthin<br />
Lut, Lutein<br />
Zex, Zeaxanthin<br />
ChlB, Chlorophyll b<br />
DvA, Divinyl Chlorophyll a<br />
Chla, Chlorophyll a<br />
ABCar, Alpha &amp; Beta Carotene</div>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1658030 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1658030
completed
Mak A. Saito
Woods Hole Oceanographic Institution
508-289-2393
266 Woods Hole Rd. MS #51 Watson Lab
Woods Hole
MA
02543
USA
msaito@whoi.edu
pointOfContact
Natalie Cohen
Woods Hole Oceanographic Institution
919-519-8297
10 Ocean Science Circle
Savannah
GA
31411
USA
cohen@uga.edu
pointOfContact
Rodney J. Johnson
Bermuda Institute of Ocean Sciences
441-297-1880
7 Biological Station
St. Georges
GE 01
Bermuda
rod.johnson@bios.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
SampleName
Latitude
Longitude
Depth
pigment_abbr
pigment_conc
Agilent 1100 series high performance liquid chromatography (HPLC)
X-Niskin bottles
theme
None, User defined
sample identification
latitude
longitude
depth
sample description
pigment concentration
featureType
BCO-DMO Standard Parameters
AUV Clio
High-Performance Liquid Chromatograph
Niskin bottle
instrument
BCO-DMO Standard Instruments
AE1913
service
Deployment Activity
St. George's, Bermuda to Woods Hole, MA
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Research: Direct Characterization of Adaptive Nutrient Stress Responses in the Sargasso Sea using Protein Biomarkers and a Biogeochemical AUV
https://osprey.bco-dmo.org/project/765945
Collaborative Research: Direct Characterization of Adaptive Nutrient Stress Responses in the Sargasso Sea using Protein Biomarkers and a Biogeochemical AUV
<p><em>NSF Award Abstract:</em><br />
Microscopic communities in the ocean can be surprisingly diverse. This diversity makes it difficult to study the individual organisms and reactions that control specific reactions controlling nutrient cycles. Past studies confirm that iron and nitrogen are vital elements for biological growth. There is increasing evidence, however, that other chemicals such as silica, zinc, cobalt, and vitamin B12 may be just as important. This project will provide an unprecedented view of community distributions using new molecular methods to isolate and link active proteins to specific chemical cycles during the very first research deployment of a brand-new autonomous underwater vehicle (AUV). The AUV will collect samples in programed patterns by pumping water directly into its filtering mechanism and then return the samples to the ship for analysis. The Bermuda Atlantic Time-series Study (BATS) station, which provides abundant supporting data, is the site for this innovative investigation into the microbial ecology and chemistry of the open oceans. Additionally, data will be widely distributed to other scientists through the Ocean Protein Portal website being developed by the Woods Hole Oceanographic Institute (WHOI) and the Biological and Chemical Oceanography Data Management Office. Data will also contribute a new teaching module in the Marine Bioinorganic Chemistry course at WHOI.</p>
<p>This first scientific deployment of the newly engineered and constructed biogeochemical AUV, Clio, will generate a novel dataset to examine marine microbial biogeochemical cycles in the Northwestern Atlantic oligotrophic ocean in unprecedented detail and at high vertical resolution. First the project proposes to understand if the microbial community reflects the varying chemical composition and cyanobacterial species through nutrient response adaptations. Additionally, the research will determine if iron stress in the low light Prochlorococcus ecotyope found in the deep chlorophyll maximum is a persistent feature influenced by seasonal dust fluxes. The highly resolved vertical data from the in situ pumping capabilities of Clio are fundamental to a rigorous examination of these biogeochemical questions. This highly transformative dataset will greatly advance understanding of the nutrient and trace element cycling of this region and will be the first field validation of the potentially revolutionary capability these new approaches represent for the study of marine microbial biogeochemistry.</p>
Nutrient Stress Responses and AUV Clio
largerWorkCitation
project
eng; USA
oceans
St. George's, Bermuda to Woods Hole, MA
-70.84278
-65.976848
32.995067
38.528372
2019-06-01
2019-06-01
Bermuda Atlantic Time Series
0
BCO-DMO catalogue of parameters from Pigment concentration data from AUV Clio dives conducted during R/V Atlantic Explorer cruise AE1913 in the Sargasso Sea in June of 2019
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/926615.rdf
Name: SampleName
Units: unitless
Description: <p>Sample identifier (e.g. CLIO_020_10) which includes the dive (station) and the pump filter number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926616.rdf
Name: Latitude
Units: decimal degrees
Description: <p>latitude. Obtained from the trace metal rosette</p>
http://lod.bco-dmo.org/id/dataset-parameter/926617.rdf
Name: Longitude
Units: decimal degrees
Description: <p>longitude. Obtained from the trace metal rosette.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926618.rdf
Name: Depth
Units: meters (m)
Description: <p>sample depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/926619.rdf
Name: pigment_abbr
Units: unitless
Description: <p>Pigment abbreviation (See "Methods & Sampling" for list of abrreviations and full pigment name).</p>
http://lod.bco-dmo.org/id/dataset-parameter/926620.rdf
Name: pigment_conc
Units: nanograms per kilogram (ng/kg)
Description: <p>Pigment concentration</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
26875
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/a960c389-9679-49c2-b2eb-5d0999077b6d/content
download
https://doi.org/10.26008/1912/bco-dmo.926546.1
download
onLine
dataset
<p>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.&nbsp;</p>
<p>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)&nbsp;whereby samples (4 L) were filtered directly onto 25 mm GFF glass fiber filters and immediately frozen in liquid nitrogen.&nbsp;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.&nbsp;<br />
&nbsp;</p>
<p><strong>Abbreviation,Pigment Name:</strong></p>
<div>ChlC3, Chlorophyll C3<br />
ChlC2, Chlorophyll C2<br />
Per, Peridinin<br />
NBut, 19'But-Fucoxanthin<br />
Fux, Fucoxanthin<br />
NHex, 19'Hex-Fucoxanthin<br />
Prx, Prasinoxanthin<br />
Vix, Violoxanthin<br />
Ddx, Diadinoxanthin<br />
Alx, Alloxanthin<br />
Dtx, Diatoxanthin<br />
Lut, Lutein<br />
Zex, Zeaxanthin<br />
ChlB, Chlorophyll b<br />
DvA, Divinyl Chlorophyll a<br />
Chla, Chlorophyll a<br />
ABCar, Alpha &amp; Beta Carotene</div>
Specified by the Principal Investigator(s)
* 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.
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
PI Supplied Instrument Name: Instrument Name: AUV Clio Instrument Short Name: Instrument 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/
Agilent 1100 series high performance liquid chromatography (HPLC)
Agilent 1100 series high performance liquid chromatography (HPLC)
PI Supplied Instrument Name: Agilent 1100 series high performance liquid chromatography (HPLC) Instrument Name: High-Performance Liquid Chromatograph Instrument Short Name:HPLC 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/
X-Niskin bottles
X-Niskin bottles
PI Supplied Instrument Name: X-Niskin bottles Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Cruise: AE1913
AE1913
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1913
Mak A. Saito
Woods Hole Oceanographic Institution
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel