http://lod.bco-dmo.org/id/dataset/843270
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
2021-03-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sampling and accession information for extracellular reef seawater metabolites collected from the Jardines de la Reina reef-system, Cuba in November of 2017
2023-10-20
publication
2023-10-20
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-10-26
publication
https://doi.org/10.26008/1912/bco-dmo.843270.1
Amy Apprill
Woods Hole Oceanographic Institution
principalInvestigator
Elizabeth Kujawinski
Woods Hole Oceanographic Institution
principalInvestigator
Laura Gray
Woods Hole Oceanographic Institution
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: Apprill, A., Kujawinski, E., Gray, L. (2023) Sampling and accession information for extracellular reef seawater metabolites collected from the Jardines de la Reina reef-system, Cuba in November of 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-10-20 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.843270.1 [access date]
Dataset Description: <p>Funding Description:</p>
<p>Dalio Foundation (now ‘OceanX’) (awarded to Amy Apprill)<br />
National Science Foundation (OCE-1736288) (awarded to Amy Apprill)</p>
<p>Mass spectrometry samples were analyzed at the WHOI FT-MS Users’ Facility using instruments funded by the National Science Foundation (grant OCE-1058448 awarded to Elizabeth B. Kujawinski and Melissa Kido Soule) and the Simons Foundation (Award ID #509042, awarded to Elizabeth B. Kujawinski)</p> Methods and Sampling: Location: Jardines de la Reina reef system south of the island of Cuba; General location: 20.8333° N, 78.9167° W
Sampling and analytical procedure summary:
Reef seawater microbial biogeochemistry and extracellular metabolite compositions were surveyed at nine, shallow (6 – 14 m in depth) forereef sites during a cruise to Jardines de la Reina (JR), Cuba in November of 2017. Seawater was also collected from two surface ‘off reef’ sites (800 – 1600 m depth).
Methods and data access for the biogeochemistry data are available from Related Dataset "Extracellular reef seawater biogeochemistry from the Jardines de la Reina reef-system" (see "Related Datasets" section).
Surface and reef depth seawater samples were also collected to quantify concentrations of known metabolites using a targeted metabolomics method and survey trends in untargeted metabolite feature composition using an untargeted method. Exometabolite extracts were subjected to reverse-phase liquid chromatography mass spectrometry after filtering and solid-phase- extraction.
Note: term "benthic" and "reef depth" are used interchangeably in columns "reef" and "Depth"
Targeted metabolomics analysis was completed using a UPLC (Accela Open Autosampler and Accela 1250 Pump, Thermo ScientificTM) coupled to a heated electrospray ionization source (H-ESI) and a triple stage quadrupole mass spectrometer (TSQ Vantage, Thermo Fisher ScientificTM), operated in selective reaction monitoring (SRM) mode. For chromatography, a Waters Acquity HSS T3 column (2.1 mm × 100 mm, 1.8 μm), equipped with a Vanguard pre-column, was used for chromatographic separation at 40 °C.
Untargeted metabolomics analysis was completed using an ultra-high performance liquid chromatography system (Vanquish UHPLC, Thermo ScientificTM) coupled with an Orbitrap Fusion Lumos Tribid mass spectrometer (Thermo ScientificTM) using the same chromatographic conditions as used for targeted metabolomics.
Detailed methods are included on the MetaboLights project page (Project MTBLS1820) and within the open access paper, Weber et al. (2020).
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1736288 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1736288
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1058448 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1058448
completed
Amy Apprill
Woods Hole Oceanographic Institution
508-289-2649
Marine Chemistry and Geochemistry Department 266 Woods Hole Road, MS# 4
Woods Hole
MA
02543
USA
aapprill@whoi.edu
pointOfContact
Elizabeth Kujawinski
Woods Hole Oceanographic Institution
508-289-3493
266 Woods Hole Rd. MS #4
Woods Hole
MA
02543
USA
ekujawinski@whoi.edu
pointOfContact
Laura Gray
Woods Hole Oceanographic Institution
508-289-2981; 301-602-1540
Marine Chemistry and Geochemistry Department 266 Woods Hole Road, Mailstop 4
Woods Hole
MA
02543
USA
laura.gray@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
MetaboLights_Study_Number
Sample_Name
reef
site
Seawater_collection_date
Latitude
Longitude
Sample_type
Seawater_sampling_location
Depth
Replicate
Profiling_mode
Ion_mode
raw_file_name
derived_file_name
Orbitrap Fusion Lumos (Thermo Fisher Scientific)
Thermo Scientific TSQ Vantage Triple Stage Quadrupole Mass Spectrometer
Vanquish UHPLC system (Thermo Fisher Scientific)
theme
None, User defined
accession number
sample identification
Site_ID
site
date
latitude
longitude
sample description
depth nominal
replicate
sampling_method
file_name
featureType
BCO-DMO Standard Parameters
Mass Spectrometer
Mass Spectrometer
Ultra-high-performance liquid chromatography
instrument
BCO-DMO Standard Instruments
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.
Signature exometabolomes of Caribbean corals and influences on reef picoplankton
https://osprey.bco-dmo.org/project/746196
Signature exometabolomes of Caribbean corals and influences on reef picoplankton
<p><em>NSF Award Abstract:</em><br />
Coral reefs are some of the most diverse and productive ecosystems in the ocean. Globally, reefs have declined in stony (reef-building) coral abundance due to environmental variations, and in the Caribbean this decline has coincided with an increase in octocoral (soft coral) abundance. This phase shift occurring on Caribbean reefs may be impacting the interactions between the sea floor and water column and particularly between corals and picoplankton. Picoplankton are the microorganisms in the water column that utilize organic matter released from corals to support their growth. These coral-picoplankton interactions are relatively unstudied, but could have major implications for reef ecology and coral health. This project will take place in the U.S. territory of the Virgin Islands (USVI) and will produce the first detailed knowledge about the chemical diversity and composition of organic matter released from diverse stony coral and octocoral species. This project will advance our understanding of coral reef microbial ecology by allowing us to understand how different coral metabolites impact picoplankton growth and dynamics over time. The results from this project will be made publically accessible in a freely available online magazine, and USVI minority middle and high school students will be exposed to a lesson about chemical-biological interactions on coral reefs through established summer camps. This project will also contribute to the training of USVI minority undergraduates as well as a graduate student.</p>
<p>Coral exometabolomes, which are the sum of metabolic products of the coral together with its microbiome, are thought to structure picoplankton communities in a species-specific manner. However, a detailed understanding of coral exometabolomes, and their influences on reef picoplankton, has not yet been obtained. This project will utilize controlled aquaria-based experiments with stony corals and octocorals, foundational species of Caribbean reef ecosystems, to examine how the exometabolomes of diverse coral species differentially influence the reef picoplankton community. Specifically, this project will capitalize on recent developments in mass spectrometry-based metabolomics to define the signature exometabolomes of ecologically important and diverse stony corals and octocorals. Secondly, this project will determine how the exometabolomes of these corals vary with factors linked to coral taxonomy as well as the coral-associated microbiome (Symbiodinium algae, bacteria and archaea). With this new understanding of coral exometabolomes, the project will then apply a stable isotope probe labeling approach to the coral exometabolome and will examine if and how (through changes in growth and activity) the seawater picoplankton community incorporates coral exometabolomes from different coral species over time. This project will advance our ability to evaluate the role that coral exometabolomes play in contributing to benthic-picoplankton interactions on changing Caribbean reefs.</p>
Coral Exometabolomes
largerWorkCitation
project
RAPID/MRI: Acquisition of a Triple-Quad Mass Spectrometer for Quantitative Identification of Dispersants and Water-Soluble Oil in the Gulf of Mexico
https://osprey.bco-dmo.org/project/843277
RAPID/MRI: Acquisition of a Triple-Quad Mass Spectrometer for Quantitative Identification of Dispersants and Water-Soluble Oil in the Gulf of Mexico
<p>The PI's request MRI RAPID funding to acquire a triple-quad Mass Spectrometer for quantitative identification of dispersants and water-soluble oil in the Gulf of Mexico. Dispersants were applied to the leak at the bottom of the ocean. Preliminary results using the PI's Fourier-transform ion cyclotron resonance (FT) mass spectrometer show that is possible identify the active ingredient of this dispersant in samples collected during research cruises in the Gulf of Mexico. Components of the dispersant have even been found in samples taken from within the underwater oil plume deep below the ocean's surface (~1100 m). Now the PI's would like to quantify this compound in order to assess its environmental fate in this environment.</p>
<p>In order to quantify these marker compounds, a mass spectrometer designed for sensitive and accurate quantification of targeted compounds is required. The PI's have identified a triple-quadrupole mass spectrometer (triple-Q-MS) as the most appropriate instrument for their needs. With the help of the EPA, the PI's now have the appropriate method ready and have been running samples on a triple-Q-MS in a colleague's lab. The increased sensitivity and quantitative accuracy of the triple-Q-MS will allow them to quantify dispersant components and other target compounds at lower concentrations, thus providing important constraints on modeling and predictive efforts underway in other research groups.</p>
<p>Broader Impacts</p>
<p>This research has the potential to provided unprecedented data on the environmental fate of both petroleum and dispersant components as they interact with the extant biological, chemical, and physical processes of the Gulf of Mexico. Beyond the immediate needs of the Gulf oil spill the development of the methods described in the proposal will have broad applications not only in oil spill research but also in marine organic matter characterization and its interactions with biological, chemical and physical processes. The instrument will be available for Gulf oil spill related research in a timeframe consistent with the intent of the RAPID funding mechanism.</p>
RAPID Mass Spec for Dispersants
largerWorkCitation
project
eng; USA
oceans
-79.5911
-78.3811
20.5065
21.3033
2017-11-05
2017-11-20
From projects that focused on the following 2 locations: 1. U.S. Virgin Islands 2. Gulf of Mexico
0
BCO-DMO catalogue of parameters from Sampling and accession information for extracellular reef seawater metabolites collected from the Jardines de la Reina reef-system, Cuba in November of 2017
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/913860.rdf
Name: MetaboLights_Study_Number
Units: unitless
Description: <p>MetaboLights study number</p>
http://lod.bco-dmo.org/id/dataset-parameter/913861.rdf
Name: Sample_Name
Units: unitless
Description: <p>Name of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/913862.rdf
Name: reef
Units: unitless
Description: <p>sample name of reef (site identifier and sample depth; "surf" for surface or "benthic" for reef depth).</p>
http://lod.bco-dmo.org/id/dataset-parameter/913863.rdf
Name: site
Units: unitless
Description: <p>Site identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/913864.rdf
Name: Seawater_collection_date
Units: unitless
Description: <p>Date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/913865.rdf
Name: Latitude
Units: decimal degrees
Description: <p>sampling location latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/913866.rdf
Name: Longitude
Units: decimal degrees
Description: <p>sampling location longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/913867.rdf
Name: Sample_type
Units: unitless
Description: <p>sample type</p>
http://lod.bco-dmo.org/id/dataset-parameter/913868.rdf
Name: Seawater_sampling_location
Units: unitless
Description: <p>description of sampling location relative to the coral reef</p>
http://lod.bco-dmo.org/id/dataset-parameter/913869.rdf
Name: Depth
Units: unitless
Description: <p>categorical sampling depth (e.g. pooled QC, reef depth, surface)</p>
http://lod.bco-dmo.org/id/dataset-parameter/913870.rdf
Name: Replicate
Units: unitless
Description: <p>Indicates if a duplicate sample was collected for this location and depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/913871.rdf
Name: Profiling_mode
Units: unitless
Description: <p>Type of method used - either targeted or untargeted</p>
http://lod.bco-dmo.org/id/dataset-parameter/913872.rdf
Name: Ion_mode
Units: unitless
Description: <p>Type of ionization used - either positive or negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/913873.rdf
Name: raw_file_name
Units: unitless
Description: <p>full file name for the raw data file that can be downloaded from MetaboLights (extension .raw)</p>
http://lod.bco-dmo.org/id/dataset-parameter/913874.rdf
Name: derived_file_name
Units: unitless
Description: <p>full file name for the derived data file that can be downloaded from MetaboLights (extension .mzML)</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
25445
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/d44f858c-d30e-43f3-a514-ecf1cf63c3ae/content
download
https://doi.org/10.26008/1912/bco-dmo.843270.1
download
onLine
dataset
Location: Jardines de la Reina reef system south of the island of Cuba; General location: 20.8333° N, 78.9167° W
Sampling and analytical procedure summary:
Reef seawater microbial biogeochemistry and extracellular metabolite compositions were surveyed at nine, shallow (6 – 14 m in depth) forereef sites during a cruise to Jardines de la Reina (JR), Cuba in November of 2017. Seawater was also collected from two surface ‘off reef’ sites (800 – 1600 m depth).
Methods and data access for the biogeochemistry data are available from Related Dataset "Extracellular reef seawater biogeochemistry from the Jardines de la Reina reef-system" (see "Related Datasets" section).
Surface and reef depth seawater samples were also collected to quantify concentrations of known metabolites using a targeted metabolomics method and survey trends in untargeted metabolite feature composition using an untargeted method. Exometabolite extracts were subjected to reverse-phase liquid chromatography mass spectrometry after filtering and solid-phase- extraction.
Note: term "benthic" and "reef depth" are used interchangeably in columns "reef" and "Depth"
Targeted metabolomics analysis was completed using a UPLC (Accela Open Autosampler and Accela 1250 Pump, Thermo ScientificTM) coupled to a heated electrospray ionization source (H-ESI) and a triple stage quadrupole mass spectrometer (TSQ Vantage, Thermo Fisher ScientificTM), operated in selective reaction monitoring (SRM) mode. For chromatography, a Waters Acquity HSS T3 column (2.1 mm × 100 mm, 1.8 μm), equipped with a Vanguard pre-column, was used for chromatographic separation at 40 °C.
Untargeted metabolomics analysis was completed using an ultra-high performance liquid chromatography system (Vanquish UHPLC, Thermo ScientificTM) coupled with an Orbitrap Fusion Lumos Tribid mass spectrometer (Thermo ScientificTM) using the same chromatographic conditions as used for targeted metabolomics.
Detailed methods are included on the MetaboLights project page (Project MTBLS1820) and within the open access paper, Weber et al. (2020).
Specified by the Principal Investigator(s)
BCO-DMO Data Manager Processing Notes:
* Sheet 1 of file "Cuba2017_metabdata_BCODMO_date_latlong.xlsx" was imported into the BCO-DMO data system with values "NaN" as missing data values. This file version was submitted to BCO-DMO 2023-09-06.
** 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]
* date format changed to ISO format
* Column "MetaboLights_Study_Number" was added with value "MTBLS1820" as discussed with submitter.
* Column "reef" and "site" added to correspond to related dataset, biogeochemistry data column "reef". See related dataset description. Reef values added from information in the sample identifier. Logic and the resulting reef column was reviewed by the submitter.
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
Orbitrap Fusion Lumos (Thermo Fisher Scientific)
Orbitrap Fusion Lumos (Thermo Fisher Scientific)
PI Supplied Instrument Name: Orbitrap Fusion Lumos (Thermo Fisher Scientific) PI Supplied Instrument Description:Mass spectrometry samples were analyzed on a Vanquish UHPLC system (Thermo Fisher Scientific) coupled via heated electrospray ionization (H-ESI) to an ultrahigh resolution tribrid mass spectrometer, the Orbitrap Fusion Lumos (Thermo Fisher Scientific). Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Thermo Scientific TSQ Vantage Triple Stage Quadrupole Mass Spectrometer
Thermo Scientific TSQ Vantage Triple Stage Quadrupole Mass Spectrometer
PI Supplied Instrument Name: Thermo Scientific TSQ Vantage Triple Stage Quadrupole Mass Spectrometer PI Supplied Instrument Description:Extracts prepared for targeted metabolomics were analyzed using UPLC (Accela Open Autosampler and Accela 1250 Pump, Thermo Scientific) coupled to a heated electrospray ionization source (H-ESI) and a triple stage quadrupole mass spectrometer (TSQ Vantage, Thermo Fisher Scientific), operated in selective reaction monitoring (SRM) mode. Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Vanquish UHPLC system (Thermo Fisher Scientific)
Vanquish UHPLC system (Thermo Fisher Scientific)
PI Supplied Instrument Name: Vanquish UHPLC system (Thermo Fisher Scientific) PI Supplied Instrument Description:Mass spectrometry samples were analyzed on a Vanquish UHPLC system (Thermo Fisher Scientific) coupled via heated electrospray ionization (H-ESI) to an ultrahigh resolution tribrid mass spectrometer, the Orbitrap Fusion Lumos (Thermo Fisher Scientific). Instrument Name: Ultra-high-performance liquid chromatography Instrument Short Name:UHPLC Instrument Description: Ultra high-performance liquid chromatography: Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small (< 2 microm) particles and the inlet pressure is relatively high.