http://lod.bco-dmo.org/id/dataset/905161
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
2023-07-25
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Stable carbon isotope data for thirteen individual amino acids from twelve species of eukaryotic microalgae and four species of eukaryotic microalgae
2023-07-25
publication
2023-07-25
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-07-28
publication
https://doi.org/10.26008/1912/bco-dmo.905161.1
Kelton W. McMahon
University of Rhode Island
principalInvestigator
Tatiana A. Rynearson
University of Rhode Island
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: McMahon, K. W., Rynearson, T. A. (2023) Stable carbon isotope data for thirteen individual amino acids from twelve species of eukaryotic microalgae and four species of eukaryotic microalgae. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-07-25 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.905161.1 [access date]
Primary producer amino acid carbon isotopes Dataset Description: Methods and Sampling: <p>This study was conducted at the University of Rhode Island (URI) Phytoplankton Culture Laboratory and Ocean Ecogeochemistry Isotope Laboratory.</p>
<p>A library of three species from each of four major eukaryotic microalgae classes - diatoms (Class Bacillariophyceae), dinoflagellates (Class Dinophyceae), raphidophytes (Class Raphidophyceae), and prasinophytes (Class Mamiellophyceae) - was generated from established laboratory culture lines in the URI microalgal libraries and the National Center for Marine Algae and Microbiota (NCMA; formerly CCMP). Cultures were grown in triplicate in either f/2 or L1 media created using 0.22-micrometer (µm) filtered, autoclaved Narragansett Bay, Rhode Island seawater. All seawater was collected at the same time and location to ensure consistent water conditions for all cultures. Cultures were grown in climate-controlled incubators under a light intensity of 55 ± 10 micromoles photons per square meter per second (µmol photons m-2 s-1) on a 12-hours:12-hours light:dark cycle. One species from each of the four Classes was grown in triplicate under three temperature treatments: 15° Celsius (C), 20°C, and 25°C. A microplate reader was used to obtain growth rates to target biomass collection. The Supplemental File "Stahl_et_al_2023_L&amp;O_BCO-DMO_Supplemental_DataSet.pdf" contains the identification and laboratory culture conditions for the four major groups of eukaryotic microalgae.</p>
<p>Once cultures reached sufficient density to obtain ~5 milligrams (mg) of dry weight needed for amino acid isotope analysis, cultures were gently vacuum filtered onto either 5 µm PETE membrane filters (Sterlitech), 2 µm PETE membrane filters (Sterlitech), or 0.22 µm PES membrane filters (Millipore Express PLUS) depending on the size of the species being filtered. Filtered biomass was frozen at -20°C, freeze dried for 72 hours, and homogenized prior to isotope analysis. Dried, homogenized samples were acid hydrolyzed in 6 N hydrochloric acid at 110°C for 20 hours, filtered through a 0.45 µm nylon syringe filter (Restek), and evaporated to dryness under a gentle stream of N₂. Five µl of nor-leucine (Sigma-Aldrich) with a known δ13C value was added to each sample and standard as an internal calibration. Acid hydrolyzed samples were derivatized to N-trifluoroacetic acid isopropyl esters and the carbon isotope values of 13 individual amino acids were separated and analyzed on a BPX5 column (60 meters length, 0.32 millimeters internal diameter (ID), 1 µm film thickness) in a Thermo Trace 1310 gas chromatograph (GC) and analyzed on a Finnegan MAT Delta V Plus Isotope Ratio Mass Spectrometer (IRMS) interfaced to the GC through a GC-IsoLink II and reduction furnace (1000°C) at the University of Rhode Island, Graduate School of Oceanography. Standardization of runs was achieved using intermittent pulses of a CO₂ reference gas of known isotopic value. Amino acid standards of known isotopic value were derivatized concurrently with samples and analyzed bracketing each sample. All samples were analyzed minimally in triplicate along with the amino acid mixed standard and a cyanobacteria working lab standard. Normalized <em>δ</em><sup>13</sup>C<sub>AAnorm</sub> values were calculated using the following equation: <em>δ</em><sup>13</sup>C<sub>AAnorm</sub> = <em>δ</em><sup>13</sup>C<sub>AA</sub> - <em>δ</em><sup>13</sup>C<sub>AAmean</sub></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2049307 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2049307
completed
Kelton W. McMahon
University of Rhode Island
401-874-6944
Graduate School of Oceanography, URI 215 South Ferry Rd
Narragansett
RI
02882
United States
kelton_mcmahon@uri.edu
pointOfContact
Tatiana A. Rynearson
University of Rhode Island
401-874-6022
Graduate School of Oceanography, University of Rhode Island 215 South Ferry Rd.
Narragansett
RI
02882
USA
rynearson@uri.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
SampleID
Group
Genus_Species
Temperature
Gly
Ser
Ala
Asx
Glx
Pro
Thr
Ile
Lys
Met
Val
Phe
Leu
Thermo Trace 1310 gas chromatograph (GC)
Finnegan MAT Delta V Plus Isotope Ratio Mass Spectrometer (IRMS)
SpectraMax M5 Series microplate reader (Molecular Devices)
theme
None, User defined
sample identification
taxon
water temperature at measurement depth
amino acid concentration
featureType
BCO-DMO Standard Parameters
Gas Chromatograph
Isotope-ratio Mass Spectrometer
plate reader
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.
Collaborative Research: Sources and transformations of export production: A novel 50-year record of pelagic-benthic coupling from coral and plankton bioarchives
https://osprey.bco-dmo.org/project/833411
Collaborative Research: Sources and transformations of export production: A novel 50-year record of pelagic-benthic coupling from coral and plankton bioarchives
<p><em>NSF Award Abstract:</em><br />
Changes in ocean life, the environment, and the climate can influence the timing and composition of biological material that sinks to the sea floor. As this material sinks it is consumed by bottom-dwelling organisms such as deep-sea corals. Similar to tree rings, corals preserve a history of growth embedded in their skeletons, which can be analyzed using a new technique called microgeochemistry. This project is compiling a historic dataset from deep-sea corals spanning 50 years in the Gulf of Maine to understand how biological material sinking to the bottom has changed with time. Results from the coral analysis are being compared with archival samples of small planktonic crustaceans, copepods, to better understand the connection between productivity in the surface waters and the geochemical record in the coral tissue. A complementary modeling approach is identifying environmental and climatic drivers of decadal-scale oceanographic change with the sources and transformations of organic matter that connect the surface and the deep ocean. This cross-disciplinary project is unifying transformational research with broader impacts focused on science education and outreach that broaden the understanding of the links between climate, oceanography, and marine ecosystem response using a 50-year historical context. Two open-access, media-enhanced, and National curriculum standards-aligned educational lessons plans are being developed through partnerships with a science documentary filmmaker, K-12 teachers from RI and ME, and the PBS LearningMedia Program. The topics of these lesson plans are: 1) Deep-sea exploration: A window into the past and future, and 2) Changing food webs on a changing planet. The project's educational goals include training of three graduate students, career development of five early career researchers, and research experiences for undergraduates from underrepresented groups in STEM. The multi-faceted research and education effort is addressing a question described as highest priority in the Ocean Sciences by the National Research Council: How are ocean biogeochemical and physical processes linked to today's climate and its variability?</p>
<p>Pelagic-benthic coupling regulates ocean production and food web dynamics, biogeochemical cycling, and climate feedback mechanisms through the export of surface production to the ocean interior. Yet access to long-term data sets of export production are scarce and urgently needed to test assumptions about 1) the sources and transformations of organic matter through different food web pathways, and 2) the variability of these processes across climatic, oceanographic, and ecological changes through time. The proposed work is testing key hypotheses about bottom-up mechanisms that link decadal-scale oceanographic changes in hydrography and biogeochemical cycling with phytoplankton community composition, zooplankton abundance and trophic dynamics, and the resulting composition of export production. Complementary approaches are generating multiple and independent 50+ year, annually resolved time series of phytoplankton community composition, zooplankton trophic dynamics, and export composition. Coral tissue and archived zooplankton samples are being analyzed using pioneering molecular geochemistry approaches to assess changes in diet related variation in primary production. Deep-sea corals are being collected using a remotely operated vehicle (ROV), and zooplankton are available through archival samples from a Gulf of Maine long-term monitoring program managed by NOAA. The stable isotope data are being integrated with additional data from existing long-standing ocean monitoring programs and incorporated into a unifying modeling approach to identify unique ecosystem states and their environmental drivers. The project is focused on Jordan Basin in the Gulf of Maine, which has a long history of oceanographic study and is experiencing significant changes due to climate warming, making it an ideal natural laboratory for testing hypotheses on drivers of change in the composition of exported organic matter, and the relative importance of primary (e.g., phyto-detritus) vs. secondary production (e.g., copepod fecal pellets), and large vs. small pelagic plankton dynamics.</p>
<p>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.</p>
GoME Copepod Coral Export
largerWorkCitation
project
eng; USA
oceans
2019-01-01
2019-12-31
Jordan Basin, Gulf of Maine (43 to 44.25N, 68.5 to 66.5W)
0
BCO-DMO catalogue of parameters from Stable carbon isotope data for thirteen individual amino acids from twelve species of eukaryotic microalgae and four species of eukaryotic microalgae
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/905184.rdf
Name: SampleID
Units: unitless
Description: <p>Unique ID for each species of eukaryotic microalgae. Integers reflect separate species and decimal numbers reflect replicate number of that species.</p>
http://lod.bco-dmo.org/id/dataset-parameter/905185.rdf
Name: Group
Units: unitless
Description: <p>Taxonomic group of eukaryotic microalgae</p>
http://lod.bco-dmo.org/id/dataset-parameter/905186.rdf
Name: Genus_Species
Units: unitless
Description: <p>Genus and species of eukaryotic microalgae</p>
http://lod.bco-dmo.org/id/dataset-parameter/905187.rdf
Name: Temperature
Units: degrees Celsius
Description: <p>Incubation temperature for that culture of eukaryotic microalgae</p>
http://lod.bco-dmo.org/id/dataset-parameter/905188.rdf
Name: Gly
Units: per mil
Description: <p>Carbon isotope value of Glycine measured in this culture of eukaryotic microalgae</p>
http://lod.bco-dmo.org/id/dataset-parameter/905189.rdf
Name: Ser
Units: per mil
Description: <p>Carbon isotope value of Serine measured in this culture of eukaryotic microalgae</p>
http://lod.bco-dmo.org/id/dataset-parameter/905190.rdf
Name: Ala
Units: per mil
Description: <p>Carbon isotope value of Alanine measured in this culture of eukaryotic microalgae</p>
http://lod.bco-dmo.org/id/dataset-parameter/905191.rdf
Name: Asx
Units: per mil
Description: <p>Carbon isotope value of Aspartic acid and Arginine measured in this culture of eukaryotic microalgae</p>
http://lod.bco-dmo.org/id/dataset-parameter/905192.rdf
Name: Glx
Units: per mil
Description: <p>Carbon isotope value of Glutamic acid and Glutamine measured in this culture of eukaryotic microalgae</p>
http://lod.bco-dmo.org/id/dataset-parameter/905193.rdf
Name: Pro
Units: per mil
Description: <p>Carbon isotope value of Proline measured in this culture of eukaryotic microalgae</p>
http://lod.bco-dmo.org/id/dataset-parameter/905194.rdf
Name: Thr
Units: per mil
Description: <p>Carbon isotope value of THreonine measured in this culture of eukaryotic microalgae</p>
http://lod.bco-dmo.org/id/dataset-parameter/905195.rdf
Name: Ile
Units: per mil
Description: <p>Carbon isotope value of Isoleucine measured in this culture of eukaryotic microalgae</p>
http://lod.bco-dmo.org/id/dataset-parameter/905196.rdf
Name: Lys
Units: per mil
Description: <p>Carbon isotope value of Lysine measured in this culture of eukaryotic microalgae</p>
http://lod.bco-dmo.org/id/dataset-parameter/905197.rdf
Name: Met
Units: per mil
Description: <p>Carbon isotope value of Methionine measured in this culture of eukaryotic microalgae</p>
http://lod.bco-dmo.org/id/dataset-parameter/905198.rdf
Name: Val
Units: per mil
Description: <p>Carbon isotope value of Valine measured in this culture of eukaryotic microalgae</p>
http://lod.bco-dmo.org/id/dataset-parameter/905199.rdf
Name: Phe
Units: per mil
Description: <p>Carbon isotope value of Phenylalanine measured in this culture of eukaryotic microalgae</p>
http://lod.bco-dmo.org/id/dataset-parameter/905200.rdf
Name: Leu
Units: per mil
Description: <p>Carbon isotope value of Leucine measured in this culture of eukaryotic microalgae</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
7964
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/4664206e-8b08-4ac2-adcb-8b142c98dc9f/content
download
https://doi.org/10.26008/1912/bco-dmo.905161.1
download
onLine
dataset
<p>This study was conducted at the University of Rhode Island (URI) Phytoplankton Culture Laboratory and Ocean Ecogeochemistry Isotope Laboratory.</p>
<p>A library of three species from each of four major eukaryotic microalgae classes - diatoms (Class Bacillariophyceae), dinoflagellates (Class Dinophyceae), raphidophytes (Class Raphidophyceae), and prasinophytes (Class Mamiellophyceae) - was generated from established laboratory culture lines in the URI microalgal libraries and the National Center for Marine Algae and Microbiota (NCMA; formerly CCMP). Cultures were grown in triplicate in either f/2 or L1 media created using 0.22-micrometer (µm) filtered, autoclaved Narragansett Bay, Rhode Island seawater. All seawater was collected at the same time and location to ensure consistent water conditions for all cultures. Cultures were grown in climate-controlled incubators under a light intensity of 55 ± 10 micromoles photons per square meter per second (µmol photons m-2 s-1) on a 12-hours:12-hours light:dark cycle. One species from each of the four Classes was grown in triplicate under three temperature treatments: 15° Celsius (C), 20°C, and 25°C. A microplate reader was used to obtain growth rates to target biomass collection. The Supplemental File "Stahl_et_al_2023_L&amp;O_BCO-DMO_Supplemental_DataSet.pdf" contains the identification and laboratory culture conditions for the four major groups of eukaryotic microalgae.</p>
<p>Once cultures reached sufficient density to obtain ~5 milligrams (mg) of dry weight needed for amino acid isotope analysis, cultures were gently vacuum filtered onto either 5 µm PETE membrane filters (Sterlitech), 2 µm PETE membrane filters (Sterlitech), or 0.22 µm PES membrane filters (Millipore Express PLUS) depending on the size of the species being filtered. Filtered biomass was frozen at -20°C, freeze dried for 72 hours, and homogenized prior to isotope analysis. Dried, homogenized samples were acid hydrolyzed in 6 N hydrochloric acid at 110°C for 20 hours, filtered through a 0.45 µm nylon syringe filter (Restek), and evaporated to dryness under a gentle stream of N₂. Five µl of nor-leucine (Sigma-Aldrich) with a known δ13C value was added to each sample and standard as an internal calibration. Acid hydrolyzed samples were derivatized to N-trifluoroacetic acid isopropyl esters and the carbon isotope values of 13 individual amino acids were separated and analyzed on a BPX5 column (60 meters length, 0.32 millimeters internal diameter (ID), 1 µm film thickness) in a Thermo Trace 1310 gas chromatograph (GC) and analyzed on a Finnegan MAT Delta V Plus Isotope Ratio Mass Spectrometer (IRMS) interfaced to the GC through a GC-IsoLink II and reduction furnace (1000°C) at the University of Rhode Island, Graduate School of Oceanography. Standardization of runs was achieved using intermittent pulses of a CO₂ reference gas of known isotopic value. Amino acid standards of known isotopic value were derivatized concurrently with samples and analyzed bracketing each sample. All samples were analyzed minimally in triplicate along with the amino acid mixed standard and a cyanobacteria working lab standard. Normalized <em>δ</em><sup>13</sup>C<sub>AAnorm</sub> values were calculated using the following equation: <em>δ</em><sup>13</sup>C<sub>AAnorm</sub> = <em>δ</em><sup>13</sup>C<sub>AA</sub> - <em>δ</em><sup>13</sup>C<sub>AAmean</sub></p>
Specified by the Principal Investigator(s)
<p>All statistical analyses were performed in R version 3.6.3 with RStudio interface version 1.1.456.</p>
Specified by the Principal Investigator(s)
- imported original file named "Stahl_et_al_2023_L&O_BCO-DMO_DataSet.xlsx" into the BCO-DMO system;
- renamed fields to comply with BCO-DMO naming conventions;
- named the final data file "905161_v1_pp_amino_acid_c_isotopes.csv";
- converted original file named "Stahl_et_al_2023_L&O_BCO-DMO_Supplemental_DataSet.xlsx" into PDF format and attached as a Supplemental File.
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
Thermo Trace 1310 gas chromatograph (GC)
Thermo Trace 1310 gas chromatograph (GC)
PI Supplied Instrument Name: Thermo Trace 1310 gas chromatograph (GC) PI Supplied Instrument Description:Thermo Trace 1310 gas chromatograph (GC) and analyzed on a Finnegan MAT Delta V Plus Isotope Ratio Mass Spectrometer (IRMS) interfaced to the GC through a GC-IsoLink II and reduction furnace (1000°C) used to separate and analyze the carbon isotope values of 13 individual amino acids from each sample and standard. Instrument Name: Gas Chromatograph Instrument Short Name:Gas Chromatograph Instrument Description: Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB02/
Finnegan MAT Delta V Plus Isotope Ratio Mass Spectrometer (IRMS)
Finnegan MAT Delta V Plus Isotope Ratio Mass Spectrometer (IRMS)
PI Supplied Instrument Name: Finnegan MAT Delta V Plus Isotope Ratio Mass Spectrometer (IRMS) PI Supplied Instrument Description:Thermo Trace 1310 gas chromatograph (GC) and analyzed on a Finnegan MAT Delta V Plus Isotope Ratio Mass Spectrometer (IRMS) interfaced to the GC through a GC-IsoLink II and reduction furnace (1000°C) used to separate and analyze the carbon isotope values of 13 individual amino acids from each sample and standard. Instrument Name: Isotope-ratio Mass Spectrometer Instrument Short Name:IR Mass Spec; IRMS Instrument Description: The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
SpectraMax M5 Series microplate reader (Molecular Devices)
SpectraMax M5 Series microplate reader (Molecular Devices)
PI Supplied Instrument Name: SpectraMax M5 Series microplate reader (Molecular Devices) PI Supplied Instrument Description:Microplate reader (SpectraMax M5 Series, Molecular Devices) - used to obtain growth rates to target biomass collection approximately during exponential growth or early in the stationary phase. Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.