http://lod.bco-dmo.org/id/dataset/986825
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
2025-10-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Compound-specific carbon stable isotopes of amino acids in planktic foraminifera from Santa Barbara Basin sediment traps from 2018 to 2021
2025-11-26
publication
2025-11-26
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2025-12-11
publication
https://doi.org/10.26008/1912/bco-dmo.986825.1
Catherine V. Davis
North Carolina State University
principalInvestigator
Matthew D. McCarthy
University of California-Santa Cruz
principalInvestigator
Shannon C. Doherty
North Carolina State University
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: Doherty, S. C., Christensen, S., Davis, C. V., McCarthy, M. D. (2025) Compound-specific carbon stable isotopes of amino acids in planktic foraminifera from Santa Barbara Basin sediment traps from 2018 to 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-11-26 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.986825.1 [access date]
Carbon CSI-AA SBB trap foraminifera Dataset Description: Methods and Sampling: <p>Samples were collected using a McLane Parflux 78H sediment trap deployed at depths &gt;400 meters (m) in the central Santa Barbara Basin (34.2450389, -120.0592917). The sampling interval was 10 to 14 days, and samples were preserved in borate-buffered formalin solution. A 1/16th split of the sediment trap sample was used. Samples were rinsed with tap water over a 125-micron sieve, and foraminifera tests were removed from other trap material using a fine paintbrush. Foraminifera tests were dried on a micropaleontology slide, then species were identified by test morphology and sorted. Tests of the three most abundant species were removed to separate micropaleontology slides. These tests were inspected under a dissecting microscope to ensure no organic particles were adhered to the exterior or interior of tests. Any organic particles were gently removed with a wet brush. The removed tests were counted and weighed on a microbalance. Tests from multiple sediment trap samples were combined to achieve a sample of 5-10 milligrams (mg). This combined sample was gently rinsed with methanol three times, then dried.</p>
<p>Compound-specific stable isotopes were measured at the UC Santa Cruz Stable Isotope Lab. Tests were demineralized by adding ~1 milliliter (mL) 1N HCl to dissolve carbonate, then stored at 4 degrees Celsius (°C) overnight to complete the demineralization reaction. The HCl was then evaporated under N<sub>2</sub>. The remaining organic matter was then hydrolyzed with ~ 1mL 6N HCl at 110°C for 20 hours after the vial was purged with N<sub>2</sub> to remove oxygen. Samples were purified by cation-exchange chromatography with DOWEX 50WX8-400 resin. Amino acids were measured as trifluoroacetyl isopropyl ester derivatives following Silfer et al. (1991). After drying under N<sub>2</sub>, samples were esterified with a 1:5 mixture of acetyl chloride:isopropanol at 110 °C for 60 minutes. Samples were dried again under N<sub>2</sub>, then trifluoroacetylation was completed using a 1:3 mixture of trifluoroacetic anhydride (TFAA) and dichloromethane (DCM) at 110 °C for 15 minutes. Inorganic salts were removed from samples by liquid-liquid extraction of derivatized amino acids in chloroform and an aqueous phosphate buffer. Trifluoroacetylation was completed again after liquid-liquid extraction. Samples were dried and dissolved in ethyl acetate for gas chromatography-isotope ratio mass spectrometry (GC-IRMS).</p>
<p>Amino acid stable isotopes were measured on a Thermo 1310 Trace gas chromatograph coupled to an Isolink II (Thermo combustion reactor 1000°C), Conflo IV, and Thermo Delta V Plus IRMS at the UCSC-SIL. Amino acids were separated for δ15N analyses using a BPX5 column (60 m×0.32 mm, 1 μm film thickness; SGE Analytical Science, Trajan, Austin, TX, USA) and for δ13C analyses using a DB-5 column (50 m× 0.32 mm 0.52 μm film thickness; Agilent Technologies, Santa Clara, CA, USA). Samples were analyzed alongside a set of amino acid standards of known δ13C and δ15N values. The injector temperature was 250°C with He column flow rate of 2 mL/min. The GC temperature program for carbon isotope analysis was: initial temp = 75°C hold for 2 min; ramp 1 = 4°C/min to 90°C, hold for 4 min; ramp 2 = 4°C/min to 185°C, hold for 5 min; ramp 3 = 10°C/min to 250°C, hold for 2 min; ramp 4 = 20°C/min to 300°C, hold for 5 min.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2303608 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2303608
completed
Catherine V. Davis
North Carolina State University
267-438-2198
701 Sumter St.
Columbia
SC
29208
USA
cdavis24@ncsu.edu
pointOfContact
Matthew D. McCarthy
University of California-Santa Cruz
831-459-1533
1156 High Street
Santa Cruz
CA
95064
USA
mdmccar@ucsc.edu
pointOfContact
Shannon C. Doherty
North Carolina State University
907-474-5713
2150 Koyukuk Drive 209B O'Neill
Fairbanks
AK
99775
USA
scdoherty@alaska.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample
Start_date
End_date
Latitude
Longitude
Ala
Gly
Thr
Ser
Val
Leu
Ile
Pro
Asp
Glu
Phe
Tyr
Lys
Ala_sd
Gly_sd
Thr_sd
Ser_sd
Val_sd
Leu_sd
Ile_sd
Pro_sd
Asp_sd
Glu_sd
Phe_sd
Tyr_sd
Lys_sd
Thermo 1310 Trace gas chromatograph coupled to an Isolink II and Conflo IV
Thermo Delta V Plus IRMS
dissecting microscope
McLane PARFLUX 78HW-13 sediment trap
theme
None, User defined
sample identification
date
latitude
longitude
d13C
featureType
BCO-DMO Standard Parameters
Gas Chromatograph Mass Spectrometer
Isotope-ratio Mass Spectrometer
Microscope - Optical
Sediment Trap
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: Constraining Planktic Foraminiferal Ecology Using Compound Specific Isotope Analysis of Amino Acids
https://osprey.bco-dmo.org/project/982734
Collaborative Research: Constraining Planktic Foraminiferal Ecology Using Compound Specific Isotope Analysis of Amino Acids
<p><em>NSF Award Abstract:</em><br />
Current climate change is unique in human history. To understand how the Earth and life on it responds to comparable change it is necessary to look millions of years in the past. A huge amount of what we know about past climate comes from the fossils of marine plankton. Specifically, a group of single-celled organisms called foraminifera. Foraminifera make tiny fossil shells which capture the chemistry of the water they grew in. As a result, they can be used to reconstruct ancient ocean waters and climate. To use the fossil shells of foraminifera to their greatest effect, the ecology of the living creature must be understood. Variables like what the foraminifera ate, what depth it lived at, and whether it had symbionts will all impact how shell chemistry is interpreted. Compound-specific nitrogen and carbon isotopes of specific amino acids (CSI-AA) represent a unique approach to study these variables in living plankton. This proposal would test how well this approach can be applied to fossil shells. If successful, this would provide powerful ways to describe the ecology of long extinct planktic foraminifera. In doing so, one may better understand the records they hold of Earth’s past. The project broader impacts include support for a postdoctoral researcher, development of a career-opportunities workshop to introduce students from Primarily Undergraduate Institutions to geoscience research, and content contributions to a summer program for at-risk STEM transfer students at UC Santa Cruz.</p>
<p>Specifically, this project will investigate and develop multiple aspects of CSI-AA to better understand the species-level ecology of planktic foraminifera. This is key to generating paleoclimate and paleoceanographic records that can contextualize the Ocean’s future climate and trajectory. The proposed project will use CSI-AA to constrain three key aspects of planktic foraminiferal ecology: depth habitat, diet, and symbiosis. CSI-AA from shell-bound organics will be used in foraminifera for the first time to refine species-level inferences about these ecological traits. First CSI-AA applications in extant species will be ground-truthed using plankton tows, sediment traps, and recent sedimentary samples from the Santa Barbara Basin. Lessons learned will then be applied deeper into the fossil record to elucidate the trophic ecology of extinct foraminifera. Finally, amino acid molar ratios and racemization (the diagnostic shift between amino acid forms which occurs with fossil age) will be used to assess amino acid preservation in fossils and ultimately test the limits of this approach by targeting a suite of abundant species from the Miocene, Eocene, and Cretaceous.</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>
Planktic Foraminiferal Ecology Using CSIA-AA
largerWorkCitation
project
eng; USA
oceans
-120.0592917
-120.0592917
34.2450389
34.2450389
2018-11-17
2021-10-28
0
BCO-DMO catalogue of parameters from Compound-specific carbon stable isotopes of amino acids in planktic foraminifera from Santa Barbara Basin sediment traps from 2018 to 2021
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/989808.rdf
Name: Sample
Units: unitless
Description: <p>Sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/989809.rdf
Name: Start_date
Units: unitless
Description: <p>Date when sample collection started</p>
http://lod.bco-dmo.org/id/dataset-parameter/989810.rdf
Name: End_date
Units: unitless
Description: <p>Date when sample collection ended</p>
http://lod.bco-dmo.org/id/dataset-parameter/989811.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sample collection site</p>
http://lod.bco-dmo.org/id/dataset-parameter/989812.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sample collection site</p>
http://lod.bco-dmo.org/id/dataset-parameter/989813.rdf
Name: Ala
Units: permille
Description: <p>Alanine d13C</p>
http://lod.bco-dmo.org/id/dataset-parameter/989814.rdf
Name: Gly
Units: permille
Description: <p>Glycine d13C</p>
http://lod.bco-dmo.org/id/dataset-parameter/989815.rdf
Name: Thr
Units: permille
Description: <p>Threonine d13C</p>
http://lod.bco-dmo.org/id/dataset-parameter/989816.rdf
Name: Ser
Units: permille
Description: <p>Serine d13C</p>
http://lod.bco-dmo.org/id/dataset-parameter/989817.rdf
Name: Val
Units: permille
Description: <p>Valine d13C</p>
http://lod.bco-dmo.org/id/dataset-parameter/989818.rdf
Name: Leu
Units: permille
Description: <p>Leucine d13C</p>
http://lod.bco-dmo.org/id/dataset-parameter/989819.rdf
Name: Ile
Units: permille
Description: <p>Isoleucine d13C</p>
http://lod.bco-dmo.org/id/dataset-parameter/989820.rdf
Name: Pro
Units: permille
Description: <p>Proline d13C</p>
http://lod.bco-dmo.org/id/dataset-parameter/989821.rdf
Name: Asp
Units: permille
Description: <p>Aspartic acid d13C</p>
http://lod.bco-dmo.org/id/dataset-parameter/989822.rdf
Name: Glu
Units: permille
Description: <p>Glutamic acid/glutamine d13C</p>
http://lod.bco-dmo.org/id/dataset-parameter/989823.rdf
Name: Phe
Units: permille
Description: <p>Phenylalanine d13C</p>
http://lod.bco-dmo.org/id/dataset-parameter/989824.rdf
Name: Tyr
Units: permille
Description: <p>Tyrosine d13C</p>
http://lod.bco-dmo.org/id/dataset-parameter/989825.rdf
Name: Lys
Units: permille
Description: <p>Lysine d13C</p>
http://lod.bco-dmo.org/id/dataset-parameter/989826.rdf
Name: Ala_sd
Units: permille
Description: <p>Alanine standard deviation of replicate injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/989827.rdf
Name: Gly_sd
Units: permille
Description: <p>Glycine standard deviation of replicate injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/989828.rdf
Name: Thr_sd
Units: permille
Description: <p>Threonine standard deviation of replicate injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/989829.rdf
Name: Ser_sd
Units: permille
Description: <p>Serine standard deviation of replicate injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/989830.rdf
Name: Val_sd
Units: permille
Description: <p>Valine standard deviation of replicate injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/989831.rdf
Name: Leu_sd
Units: permille
Description: <p>Leucine standard deviation of replicate injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/989832.rdf
Name: Ile_sd
Units: permille
Description: <p>Isoleucine standard deviation of replicate injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/989833.rdf
Name: Pro_sd
Units: permille
Description: <p>Proline standard deviation of replicate injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/989834.rdf
Name: Asp_sd
Units: permille
Description: <p>Aspartic acid standard deviation of replicate injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/989835.rdf
Name: Glu_sd
Units: permille
Description: <p>Glutamic acid/glutamine standard deviation of replicate injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/989836.rdf
Name: Phe_sd
Units: permille
Description: <p>Phenylalanine standard deviation of replicate injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/989837.rdf
Name: Tyr_sd
Units: permille
Description: <p>Tyrosine standard deviation of replicate injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/989838.rdf
Name: Lys_sd
Units: permille
Description: <p>Lysine standard deviation of replicate injections</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
https://doi.org/10.26008/1912/bco-dmo.986825.1
download
onLine
dataset
<p>Samples were collected using a McLane Parflux 78H sediment trap deployed at depths &gt;400 meters (m) in the central Santa Barbara Basin (34.2450389, -120.0592917). The sampling interval was 10 to 14 days, and samples were preserved in borate-buffered formalin solution. A 1/16th split of the sediment trap sample was used. Samples were rinsed with tap water over a 125-micron sieve, and foraminifera tests were removed from other trap material using a fine paintbrush. Foraminifera tests were dried on a micropaleontology slide, then species were identified by test morphology and sorted. Tests of the three most abundant species were removed to separate micropaleontology slides. These tests were inspected under a dissecting microscope to ensure no organic particles were adhered to the exterior or interior of tests. Any organic particles were gently removed with a wet brush. The removed tests were counted and weighed on a microbalance. Tests from multiple sediment trap samples were combined to achieve a sample of 5-10 milligrams (mg). This combined sample was gently rinsed with methanol three times, then dried.</p>
<p>Compound-specific stable isotopes were measured at the UC Santa Cruz Stable Isotope Lab. Tests were demineralized by adding ~1 milliliter (mL) 1N HCl to dissolve carbonate, then stored at 4 degrees Celsius (°C) overnight to complete the demineralization reaction. The HCl was then evaporated under N<sub>2</sub>. The remaining organic matter was then hydrolyzed with ~ 1mL 6N HCl at 110°C for 20 hours after the vial was purged with N<sub>2</sub> to remove oxygen. Samples were purified by cation-exchange chromatography with DOWEX 50WX8-400 resin. Amino acids were measured as trifluoroacetyl isopropyl ester derivatives following Silfer et al. (1991). After drying under N<sub>2</sub>, samples were esterified with a 1:5 mixture of acetyl chloride:isopropanol at 110 °C for 60 minutes. Samples were dried again under N<sub>2</sub>, then trifluoroacetylation was completed using a 1:3 mixture of trifluoroacetic anhydride (TFAA) and dichloromethane (DCM) at 110 °C for 15 minutes. Inorganic salts were removed from samples by liquid-liquid extraction of derivatized amino acids in chloroform and an aqueous phosphate buffer. Trifluoroacetylation was completed again after liquid-liquid extraction. Samples were dried and dissolved in ethyl acetate for gas chromatography-isotope ratio mass spectrometry (GC-IRMS).</p>
<p>Amino acid stable isotopes were measured on a Thermo 1310 Trace gas chromatograph coupled to an Isolink II (Thermo combustion reactor 1000°C), Conflo IV, and Thermo Delta V Plus IRMS at the UCSC-SIL. Amino acids were separated for δ15N analyses using a BPX5 column (60 m×0.32 mm, 1 μm film thickness; SGE Analytical Science, Trajan, Austin, TX, USA) and for δ13C analyses using a DB-5 column (50 m× 0.32 mm 0.52 μm film thickness; Agilent Technologies, Santa Clara, CA, USA). Samples were analyzed alongside a set of amino acid standards of known δ13C and δ15N values. The injector temperature was 250°C with He column flow rate of 2 mL/min. The GC temperature program for carbon isotope analysis was: initial temp = 75°C hold for 2 min; ramp 1 = 4°C/min to 90°C, hold for 4 min; ramp 2 = 4°C/min to 185°C, hold for 5 min; ramp 3 = 10°C/min to 250°C, hold for 2 min; ramp 4 = 20°C/min to 300°C, hold for 5 min.</p>
Specified by the Principal Investigator(s)
<p>The δ<sup>13</sup>C of amino acids was corrected for carbon added during derivatization using standards and following the methods of Silfer et al. (1991). Reproducibility was estimated by the standard deviation of triplicate injections of each sample. Accuracy was checked by analyzing an in-house long-term lab reference material (cyanobacteria) with every sample set.</p>
Specified by the Principal Investigator(s)
- Imported original file "BCO-DMO_SBB_foram_CSI-AA_C.csv" into the BCO-DMO system.
- Added the following columns and populated with values provided in the metadata: Start_date, End_date, Lat, Lon.
- Saved the final file as "986825_v1_csi-aa_sbb_carbon.csv".
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 1310 Trace gas chromatograph coupled to an Isolink II and Conflo IV
Thermo 1310 Trace gas chromatograph coupled to an Isolink II and Conflo IV
PI Supplied Instrument Name: Thermo 1310 Trace gas chromatograph coupled to an Isolink II and Conflo IV PI Supplied Instrument Description:Amino acid stable isotopes were measured on a Thermo 1310 Trace gas chromatograph coupled to an Isolink II (Thermo combustion reactor 1000°C), Conflo IV, and Thermo Delta V Plus IRMS at the UCSC-SIL. Instrument Name: Gas Chromatograph Mass Spectrometer Instrument Short Name: Instrument Description: Instruments 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 by a mass spectrometer.
Thermo Delta V Plus IRMS
Thermo Delta V Plus IRMS
PI Supplied Instrument Name: Thermo Delta V Plus IRMS PI Supplied Instrument Description:Amino acid stable isotopes were measured on a Thermo 1310 Trace gas chromatograph coupled to an Isolink II (Thermo combustion reactor 1000°C), Conflo IV, and Thermo Delta V Plus IRMS at the UCSC-SIL. 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/
dissecting microscope
dissecting microscope
PI Supplied Instrument Name: dissecting microscope PI Supplied Instrument Description:Tests were inspected under a dissecting microscope. Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
McLane PARFLUX 78HW-13 sediment trap
McLane PARFLUX 78HW-13 sediment trap
PI Supplied Instrument Name: McLane PARFLUX 78HW-13 sediment trap PI Supplied Instrument Description:A McLane PARFLUX 78HW-13 sediment trap was used to collect samples. Instrument Name: Sediment Trap Instrument Short Name:Sediment Trap Instrument Description: Sediment traps are specially designed containers deployed in the water column for periods of time to collect particles from the water column falling toward the sea floor. In general a sediment trap has a jar at the bottom to collect the sample and a broad funnel-shaped opening at the top with baffles to keep out very large objects and help prevent the funnel from clogging. This designation is used when the specific type of sediment trap was not specified by the contributing investigator. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/33/