http://lod.bco-dmo.org/id/dataset/964221
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
2025-06-09
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
1H NMR spectra of whole porewater dissolved organic matter (DOM) samples from California margin sediments sampled in 2020 onboard the R/V Sikuliaq
2025-09-11
publication
2025-09-11
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-09-12
publication
https://doi.org/10.26008/1912/bco-dmo.964221.1
Tomoko Komada
San Francisco State University
principalInvestigator
Hussain Abdulla
Texas A&M, Corpus Christi
principalInvestigator
David J. Burdige
Old Dominion 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: Komada, T., Abdulla, H., Burdige, D. J. (2025) 1H NMR spectra of whole porewater dissolved organic matter (DOM) samples from California margin sediments sampled in 2020 onboard the R/V Sikuliaq. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-09-11 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.964221.1 [access date]
Porewater DOM NMR spectra Dataset Description: Methods and Sampling: <p>Porewater samples from gravity cores were collected as described in Komada et al. (2016) Geochim. Cosmochim. Acta, 176:259-278. Briefly, sediment cores were sectioned within hours of retrieval, then centrifuged, filtered (0.2 micron pore size). Porewater samples from multicores were extracted using Rhizon samplers (Seeberg-Elverfeldt et al., Limnol. Oceanogr. Meth., 8:361-371, 2005) to prevent contamination from squashed benthic macrofauna during centrifugation. Samples from multicores (MC) were retrieved using Rhizon samplers (5 cm, 0.15 micron pore size). Samples from BB gravity cores were collected by centrifugation, then filtered through 0.2 miron filters.&nbsp;Samples were immediately poisoned with HgCl2 and flame-sealed under a stream of high-purity nitrogen gas and refrigerated until analysis.&nbsp;</p>
<p>Blank samples: MQ_blank samples =&nbsp;UV-irradiated MQ water collected on the ship in parallel with porewater samples; Rhizon_blank samples =&nbsp;UV-irradiated MQ water collected on in the laboratory after passing it through a Rhizon sampler.</p>
<p>1H NMR spectra were acquired in 5-mm O.D. thin-wall precision NMR tube (Bel-Art Wilmad part #528-PP-7-5) in 5% D2O (Sigma Aldrich part #151882) using a Bruker Avance NEO 500 MHz instrument with Prodigy cryoprobe using W5-WATERGATE solvent suppression method (Lam and Simpson, Analyst, 133:263-269, 2008).&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756686 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756686
completed
Tomoko Komada
San Francisco State University
415-338-3748
3150 Paradise Drive
Tiburon
CA
94920
USA
tkomada@sfsu.edu
pointOfContact
Hussain Abdulla
Texas A&M, Corpus Christi
361-825-6050
6300 Ocean Drive
Corpus Christi
TX
78412-5503
USA
hussain.abdulla@tamucc.edu
pointOfContact
David J. Burdige
Old Dominion University
757-683-4930
Dept. of Ocean, Earth and Atmospheric Sciences
Norfolk
VA
23529
USA
dburdige@odu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
station
latitude
longitude
sampling_date
sample_type
core_type
sample_ID
sediment_depth
chemical_shift
nmr_value
Bruker Avance NEO 500 MHz
theme
None, User defined
station
latitude
longitude
date
sample type
sample identification
depth core
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Gravity Corer
Multi Corer
Nuclear Magnetic Resonance Spectrometers
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: Peptide Deamination as a Source of Refractory Dissolved Organic Matter in Marine Sediments
https://osprey.bco-dmo.org/project/906864
Collaborative Research: Peptide Deamination as a Source of Refractory Dissolved Organic Matter in Marine Sediments
<p><strong>NSF Award Abstract:</strong><br />
Dissolved organic matter (DOM) in the ocean is one of the largest carbon reservoirs on Earth. Much of this DOM is highly resistant to degradation (refractory) and aged, but the nature and reasons behind the accumulation of refractory DOM in the ocean is one of the unresolved mysteries of the marine carbon cycle. While marine sediments have been shown to be a globally important source of DOM to the ocean, the connection between sediment DOM dynamics and the oceanic DOM cycle remains elusive, because information is lacking on the molecular composition and reactivity of pore water DOM. To fill this knowledge gap, this project will address the question of how refractory DOM is produced in sediments and the fate of benthic DOM in the water column. The research will focus on the relationship between protein/peptide dynamics and sediment DOM cycling, examining peptide deamination as an important pathway for the production of refractory and 14C-depleted DOM in continental margin sediments. These objectives will be met through a combination of geochemical profiling of sediment cores collected across a range of redox conditions, and long-term sediment incubation studies conducted under controlled laboratory conditions. At the heart of this proposed work is structural elucidation and quantification of intact and deaminated peptides in pore-water DOM using state-of-the-art analytical techniques. The study will help better understand how the present-day carbon cycle operates, as well as how it may respond in the future. The proposed work will integrate research and education using several approaches. All PIs routinely integrate their research into their classes, which range from introductory-undergraduate to advanced-graduate courses and will continue to do so here. All three PIs are also committed to engaging women and underrepresented minority students.</p>
<p>Marine sediments are a globally important source of dissolved organic matter (DOM) to the ocean. However, the connection between sediment DOM dynamics and the oceanic DOM cycle remains elusive because information about the molecular composition and reactivity of pore water DOM is lacking. To help fill this knowledge gap, this project will address the question of how refractory DOM is produced in sediments and the fate of the benthic DOM flux in the water column. The proposed study explores a novel and potentially transformative idea that deamination of peptides in sediments is a source of refractory and 14C-depleted DOM in seawater. This idea is consistent not only with the fact that the majority of seawater dissolved organic nitrogen occurs in amide form, but also with recent reports about the widespread occurrence of nitrogen-bearing formulas in deep-sea refractory DOM. The central hypothesis will be tested through a unique blend of bottom-up (molecular level DOM analyses) and top-down (bulk-level elemental and isotopic analyses, and numerical modeling) approaches. This work will involve a combination of geochemical profiling of sediment cores collected across a range of redox conditions, and long-term sediment incubation studies conducted under controlled laboratory conditions. At the heart of the proposed work is structural elucidation and quantification of intact and deaminated peptides in pore-water DOM using a state-of-the-art liquid chromatography-mass spectrometry system (ultra-high performance liquid chromatography coupled to an Orbitrap Fusion Tribrid Mass Spectrometer), which is expected to provide an unprecedented wealth of molecular-level information about pore water DOM. The proposed work will lead to an improved mechanistic understanding of organic matter decomposition and benthic DOM cycling and shed light on the connections between the modern-day oceanic and sedimentary carbon and nitrogen cycles as they relate to the formation of refractory DOM.</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>
Peptide Deamination
largerWorkCitation
project
eng; USA
oceans
-122.31074
-121.83534
35.62588
36.1875
2020-12-04
2020-12-09
California Borderland
0
BCO-DMO catalogue of parameters from 1H NMR spectra of whole porewater dissolved organic matter (DOM) samples from California margin sediments sampled in 2020 onboard the R/V Sikuliaq
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/983021.rdf
Name: station
Units: unitless
Description: <p>D and K represent Station D (36.1875 latitude, -122.31074 longitude) and Station K (35.62588 latitude, -121.83534 longitude). Further details can be found in Reimers et al. (1992) Global Biogeochem. Cycles, 6:199-224.</p>
http://lod.bco-dmo.org/id/dataset-parameter/983022.rdf
Name: latitude
Units: decimal degrees
Description: <p>Latitude of sampling station, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/983023.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude of sampling station, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/983024.rdf
Name: sampling_date
Units: unitless
Description: <p>Sampling date</p>
http://lod.bco-dmo.org/id/dataset-parameter/983025.rdf
Name: sample_type
Units: unitless
Description: <p>Porewater samples = whole samples without pre-extraction or concentration. Blanks = test samples processed in similar manner to porewater samples to assess contamination.</p>
http://lod.bco-dmo.org/id/dataset-parameter/983026.rdf
Name: core_type
Units: unitless
Description: <p>MC = multicores. BB = Big Bertha gravity core operated by Oregon State University Marine Rock and Sediment Sampling Group</p>
http://lod.bco-dmo.org/id/dataset-parameter/983027.rdf
Name: sample_ID
Units: unitless
Description: <p>sample ID: combination of station, core type, analysis date = last 6 digits of sample ID mmddyy)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983028.rdf
Name: sediment_depth
Units: centimeters (cm)
Description: <p>Depth of sediment in core</p>
http://lod.bco-dmo.org/id/dataset-parameter/983029.rdf
Name: chemical_shift
Units: parts per million (ppm)
Description: <p>1H chemical shift relative to tetramethylsilane</p>
http://lod.bco-dmo.org/id/dataset-parameter/983030.rdf
Name: nmr_value
Units: unitless
Description: <p>Area-normalized intensity</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
87269231
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/be037d62-507f-4beb-a727-83bfc337740e/content
download
https://doi.org/10.26008/1912/bco-dmo.964221.1
download
onLine
dataset
<p>Porewater samples from gravity cores were collected as described in Komada et al. (2016) Geochim. Cosmochim. Acta, 176:259-278. Briefly, sediment cores were sectioned within hours of retrieval, then centrifuged, filtered (0.2 micron pore size). Porewater samples from multicores were extracted using Rhizon samplers (Seeberg-Elverfeldt et al., Limnol. Oceanogr. Meth., 8:361-371, 2005) to prevent contamination from squashed benthic macrofauna during centrifugation. Samples from multicores (MC) were retrieved using Rhizon samplers (5 cm, 0.15 micron pore size). Samples from BB gravity cores were collected by centrifugation, then filtered through 0.2 miron filters.&nbsp;Samples were immediately poisoned with HgCl2 and flame-sealed under a stream of high-purity nitrogen gas and refrigerated until analysis.&nbsp;</p>
<p>Blank samples: MQ_blank samples =&nbsp;UV-irradiated MQ water collected on the ship in parallel with porewater samples; Rhizon_blank samples =&nbsp;UV-irradiated MQ water collected on in the laboratory after passing it through a Rhizon sampler.</p>
<p>1H NMR spectra were acquired in 5-mm O.D. thin-wall precision NMR tube (Bel-Art Wilmad part #528-PP-7-5) in 5% D2O (Sigma Aldrich part #151882) using a Bruker Avance NEO 500 MHz instrument with Prodigy cryoprobe using W5-WATERGATE solvent suppression method (Lam and Simpson, Analyst, 133:263-269, 2008).&nbsp;</p>
Specified by the Principal Investigator(s)
<p>NMR spectra were normalized by the total area under the spectra after removing the residual water peak (4.2-5.0 ppm).</p>
Specified by the Principal Investigator(s)
* Converted original data that was in wide format to long format. Both files are part of this dataset.
* Added sampling latitude and logitude to dataset
* Adjusted parameter names to comply with database requirements (no periods, spaces or special characters)
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: Gravity Corer Instrument Short Name:Gravity Corer Instrument Description: The gravity corer allows researchers to sample sediment layers at the bottom of lakes or oceans. The coring device is deployed from the ship and gravity carries it to the seafloor. (http://www.whoi.edu/instruments/viewInstrument.do?id=1079). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
PI Supplied Instrument Name: Instrument Name: Multi Corer Instrument Short Name:Multi Corer Instrument Description: The Multi Corer is a benthic coring device used to collect multiple, simultaneous, undisturbed sediment/water samples from the seafloor. Multiple coring tubes with varying sampling capacity depending on tube dimensions are mounted in a frame designed to sample the deep ocean seafloor. For more information, see Barnett et al. (1984) in Oceanologica Acta, 7, pp. 399-408. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
Bruker Avance NEO 500 MHz
Bruker Avance NEO 500 MHz
PI Supplied Instrument Name: Bruker Avance NEO 500 MHz PI Supplied Instrument Description:Bruker Avance NEO 500 MHz instrument with Prodigy cryoprobe using W5-WATERGATE solvent suppression method Instrument Name: Nuclear Magnetic Resonance Spectrometers Instrument Short Name:NMR Instrument Description: Instruments that identify and quantify magnetically active chemical entities by subjecting a sample to orthogonal magnetic and electrical fields. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB18/