http://lod.bco-dmo.org/id/dataset/814713
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
2020-06-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Intracellular sulfonate metabolites measured in a variety of eukaryotic and prokaryotic phytoplankton and heterotrophic bacteria using liquid chromatography-mass spectrometry-based metabolomics
2020-06-10
publication
2020-06-10
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-06-10
publication
https://doi.org/10.26008/1912/bco-dmo.814713.1
Bryndan P. Durham
University of Washington
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: Durham, B. (2020) Intracellular sulfonate metabolites measured in a variety of eukaryotic and prokaryotic phytoplankton and heterotrophic bacteria using liquid chromatography-mass spectrometry-based metabolomics. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-06-10 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.814713.1 [access date]
Dataset Description: <p>Intracellular sulfonate metabolites were measured in a variety of eukaryotic and prokaryotic phytoplankton and heterotrophic bacteria using liquid chromatography-mass spectrometry-based metabolomics. These data have been published in Durham et al. (2019).&nbsp;Raw data are available at Metabolomics Workbench under Project ID PR000797.</p> Methods and Sampling: <p>Pure cultures of bacteria and phytoplankton were grown in artificial seawater medium, and cells were collected during mid-to-late exponential phase by gentle filtration onto 0.2 micron Durapore filters. All filters were flash frozen in liquid nitrogen and stored at -80 degrees Celsius until further processing. Frozen filters of cells and media blanks were extracted and analyzed using a targeted liquid chromatography-mass spectrometry-based metabolomics method according to the protocols in Boysen and Heal et al., 2018. Briefly, metabolites were extracted using a modified Bligh–Dyer extraction using 1:1 methanol/water (aqueous phase) and dichloromethane (organic phase). Targeted metabolomics data were generated using a Waters Xevo TQ-S triple quadrupole with both reverse-phase and hydrophilic interaction liquid chromatography (HILIC). Taurine, isethionate, sulfolactate, and cysteate were quantified using isotopically-labeled internal standards that were added prior to extraction. DHPS was quantified by generating standard addition curves.</p>
<p>Instruments: Targeted metabolomics data were generated using a Waters Xevo TQ-S triple quadrupole (TQS) with electrospray ionization (ESI) in selected reaction monitoring mode (SRM) with polarity switching. SRM conditions for each compound (collision energy, cone voltage, precursor, and product ions) were optimized by infusion of each metabolite standard. For most metabolites, two SRM transitions were selected based on maximum peak areas. All chromatographic separations were carried out on a Waters Acquity I-Class UPLC (Waters Corporation, Milford, MA).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1521564 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1521564
completed
Bryndan P. Durham
University of Washington
352-294-6312
2033 Mowry Rd. Cancer & Genetics Research Complex 415
Gainesville
FL
32610
USA
b.durham@ufl.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Organism
replicate
cells_filtered
DHPS
cysteic_acid
sulfolactate
isethionic_acid
taurine
Waters Xevo TQ-S triple quadrupole
theme
None, User defined
taxon
replicate
number
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Mass Spectrometer
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.
OCE-PRF Track 1 (Broadening Participation): Cryptic Sulfonate Cycling between Marine Phytoplankton and Heterotrophic Bacterioplankton
https://osprey.bco-dmo.org/project/718131
OCE-PRF Track 1 (Broadening Participation): Cryptic Sulfonate Cycling between Marine Phytoplankton and Heterotrophic Bacterioplankton
<p><em>NSF Award Abstract:</em><br />
Information in the form of chemicals and energy flows constantly through complex networks of marine microbes. In the surface ocean, sunlight and atmospheric carbon dioxide are captured by autotrophic unicellular phytoplankton and transformed into a vast pool of organic matter that microbes use as metabolic currencies and signaling molecules to form the basis for different trading alliances. Several little-known sulfonate compounds have recently been identified as key currencies underlying marine bacterial-phytoplankton mutualisms and appear to be widespread in coastal communities. In this project, the fellow will investigate the prevalence and role of sulfonates in marine microbial interactions and their resulting impact on the Earth's biogeochemistry. With sponsor Dr. E. Virginia Armbrust at the University of Washington, the fellow will advance professionally through interdisciplinary training in microbial ecology and marine biogeochemistry. Broadening participation activities include mentorship of an undergraduate and development of an outreach program for a local minority-serving high school where students will conduct classroom laboratory exercises using microbiological and bioinformatics concepts.</p>
<p>Sulfonates are produced and degraded by several important phytoplankton and heterotrophic bacterial taxa, respectively. Yet, these compounds represent a poorly understood component of the marine organic matter pool. To the extent that sulfonates account for an unquantified flux of carbon and sulfur that supports mutualisms between bacteria and phytoplankton, sulfonates represent cryptic missing links in both carbon and sulfur transformations in the ocean. In this study, the fellow will use laboratory-based approaches to examine physiological and ecological controls on sulfonate production in model phytoplankton species and field-based approaches to examine taxonomically driven dynamics of sulfonate pools in the coastal waters of Puget Sound and surrounding North Pacific. Specifically, the fellow will perform metabolic profiling of model sulfonate-producing phytoplankton taxa (Aim I) and measure spatiotemporal gradients and turnover rates of sulfonates in the ocean environment using targeted in situ metabolite surveys (II) and stable isotope incubations (III), respectively, together with transcriptomics-based identification of marine microbes that control the fate of sulfonate-derived carbon (IV). The planned experiments will provide the first intensive characterization of sulfonates in the environment in terms of their contribution to the marine organic matter pool, their taxonomically driven spatiotemporal dynamics, and their roles in ocean ecosystem interdependencies.</p>
Sulfonate Cycling
largerWorkCitation
project
eng; USA
oceans
2020-06-10
University of Washington
0
BCO-DMO catalogue of parameters from Intracellular sulfonate metabolites measured in a variety of eukaryotic and prokaryotic phytoplankton and heterotrophic bacteria using liquid chromatography-mass spectrometry-based metabolomics
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/814722.rdf
Name: Organism
Units: unitless
Description: <p>name and strain number</p>
http://lod.bco-dmo.org/id/dataset-parameter/814723.rdf
Name: replicate
Units: unitless
Description: <p>biological replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/814724.rdf
Name: cells_filtered
Units: unitless
Description: <p>number of cells extracted</p>
http://lod.bco-dmo.org/id/dataset-parameter/814725.rdf
Name: DHPS
Units: amol per cell
Description: <p>sulfonate</p>
http://lod.bco-dmo.org/id/dataset-parameter/814726.rdf
Name: cysteic_acid
Units: amol per cell
Description: <p>sulfonate</p>
http://lod.bco-dmo.org/id/dataset-parameter/814727.rdf
Name: sulfolactate
Units: amol per cell
Description: <p>sulfonate</p>
http://lod.bco-dmo.org/id/dataset-parameter/814728.rdf
Name: isethionic_acid
Units: amol per cell
Description: <p>sulfonate</p>
http://lod.bco-dmo.org/id/dataset-parameter/814729.rdf
Name: taurine
Units: amol per cell
Description: <p>sulfonate</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
6716
https://darchive.mblwhoilibrary.org/bitstream/1912/25847/1/dataset-814713_sulfonates-plankton-cultures__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.814713.1
download
onLine
dataset
<p>Pure cultures of bacteria and phytoplankton were grown in artificial seawater medium, and cells were collected during mid-to-late exponential phase by gentle filtration onto 0.2 micron Durapore filters. All filters were flash frozen in liquid nitrogen and stored at -80 degrees Celsius until further processing. Frozen filters of cells and media blanks were extracted and analyzed using a targeted liquid chromatography-mass spectrometry-based metabolomics method according to the protocols in Boysen and Heal et al., 2018. Briefly, metabolites were extracted using a modified Bligh–Dyer extraction using 1:1 methanol/water (aqueous phase) and dichloromethane (organic phase). Targeted metabolomics data were generated using a Waters Xevo TQ-S triple quadrupole with both reverse-phase and hydrophilic interaction liquid chromatography (HILIC). Taurine, isethionate, sulfolactate, and cysteate were quantified using isotopically-labeled internal standards that were added prior to extraction. DHPS was quantified by generating standard addition curves.</p>
<p>Instruments: Targeted metabolomics data were generated using a Waters Xevo TQ-S triple quadrupole (TQS) with electrospray ionization (ESI) in selected reaction monitoring mode (SRM) with polarity switching. SRM conditions for each compound (collision energy, cone voltage, precursor, and product ions) were optimized by infusion of each metabolite standard. For most metabolites, two SRM transitions were selected based on maximum peak areas. All chromatographic separations were carried out on a Waters Acquity I-Class UPLC (Waters Corporation, Milford, MA).</p>
Specified by the Principal Investigator(s)
<p>Data processing: Peak integration was performed using Skyline for small molecules. After integration, data were passed through an in-house quality control (QC) filter to ensure proper metabolite identification as described in Boysen et al. (2018).</p>
<p>BCO-DMO Processing:<br />
- modified parameter names</p>
Specified by the Principal Investigator(s)
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
Waters Xevo TQ-S triple quadrupole
Waters Xevo TQ-S triple quadrupole
PI Supplied Instrument Name: Waters Xevo TQ-S triple quadrupole PI Supplied Instrument Description:Targeted metabolomics data were generated using a Waters Xevo TQ-S triple quadrupole with both reverse-phase and hydrophilic interaction liquid chromatography (HILIC). 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/