http://lod.bco-dmo.org/id/dataset/959217
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
2025-04-15
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sediment porosity collected from R/V Oceanus cruise OC1906A and R/V Sikuliaq cruise SKQ202016S off the coast of California in 2019 and 2020
2025-04-16
publication
2025-04-16
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-05-06
publication
https://doi.org/10.26008/1912/bco-dmo.959217.1
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: Burdige, D. J. (2025) Sediment porosity collected from R/V Oceanus cruise OC1906A and R/V Sikuliaq cruise SKQ202016S off the coast of California in 2019 and 2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-04-16 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.959217.1 [access date]
California sediment porosity data Dataset Description: Methods and Sampling: <p>Sediment cores were collected using a gravity corer and a multicorer on both cruises. Following recovery, the gravity cores were secured horizontally on the ship's deck and sampled from the bottom of the core upwards. This was done by sequentially removing 10-centimeter (cm) sediment intervals by cutting the core liner using a pipe cutter. Freshly exposed sediment was placed in pre-weighed scintillation vials, and the vials were frozen on-board the ship.</p>
<p>Most multi cores were sectioned at intervals ranging from 1 to 5 cm over the 30-40 cm length of the core. Some cores were sampled using pre-drilled holes in multi-core tubes that were sealed with tape during deployment. Upon recovery of the cores, the holes were cut open to sample the sediment with open-faced syringes inserted horizontally into the holes in the core tube. In both cases, the collected sediment was again placed in pre-weighed scintillation vials, and the vials were frozen on-board the ship.</p>
<p>Frozen vials were returned to the shore-based lab at ODU where the samples&nbsp;were dried to constant weight, to obtain the wet-to-dry mass ratio of the sediment sample (±1% precision). A dry sediment density of 2.67 gr/cm3 and a pore water density of 1.024 gr/cm3 were used in the porosity calculations (cm3 pore water/cm3 total sediment). All values were corrected for the salt content of the pore water.</p>
<p>While it is possible to recover intact sediment-water interfaces using multi-corers, loss of surface sediments is typical during gravity coring, making it impossible to directly quantify absolute depths below the sediment-water interface in a gravity core. We therefore determined absolute depths of sediment sample intervals in gravity cores by aligning DIC, &nbsp;sulfate, ammonium, and porosity gravity core profiles to multicore profiles from the same site (Berelson et al., 2005; Iversen and Jørgensen, 1985; Komada et al., 2016).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756669 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756669
completed
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
Ship
Cruise_ID
St_ID
Station_Latitude
Station_Longitude
Date
Sa_ID
Core
samp
Depth
Err
Porosity
a standard lab drying oven
gravity corer
multicorer
top-loading balance
theme
None, User defined
ship
Cruise identfier
station
latitude
longitude
date
sample identification
instrument
sampling_method
depth core
sediment porosity
featureType
BCO-DMO Standard Parameters
Drying Oven
Gravity Corer
Multi Corer
scale or balance
instrument
BCO-DMO Standard Instruments
OC1906A
SKQ202016S
service
Deployment Activity
California coast
California Coast
place
Locations
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
California coast; California Coast
-122.186097
-118.6
33.3005
36.112556
2019-06-24
2020-12-09
California Borderland
0
BCO-DMO catalogue of parameters from Sediment porosity collected from R/V Oceanus cruise OC1906A and R/V Sikuliaq cruise SKQ202016S off the coast of California in 2019 and 2020
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/959232.rdf
Name: Ship
Units: unitless
Description: <p>Ship used: Oc = R/V Oceanus; Sk = R/V Sikuliaq</p>
http://lod.bco-dmo.org/id/dataset-parameter/959233.rdf
Name: Cruise_ID
Units: unitless
Description: <p>Cruise ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/959234.rdf
Name: St_ID
Units: unitless
Description: <p>Station ID: Cat = Catalina Basin; K = station K; D = station D.</p>
http://lod.bco-dmo.org/id/dataset-parameter/959235.rdf
Name: Station_Latitude
Units: decimal degrees
Description: <p>Station latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/959236.rdf
Name: Station_Longitude
Units: decimal degrees
Description: <p>Station longitude; negative values = West</p>
http://lod.bco-dmo.org/id/dataset-parameter/959237.rdf
Name: Date
Units: unitless
Description: <p>Date core was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/959238.rdf
Name: Sa_ID
Units: unitless
Description: <p>Individual sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/959239.rdf
Name: Core
Units: unitless
Description: <p>Type of core used to collect the sample: M = multi-core; G = gravity core</p>
http://lod.bco-dmo.org/id/dataset-parameter/959240.rdf
Name: samp
Units: unitless
Description: <p>How the sample was collected: cs = core sectioning; sp = pre-drilled holes in the multi-core tubes</p>
http://lod.bco-dmo.org/id/dataset-parameter/959241.rdf
Name: Depth
Units: centimeters (cm)
Description: <p>Depth of the sediment sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/959242.rdf
Name: Err
Units: centimeters (cm)
Description: <p>half-depth of the sampling interval</p>
http://lod.bco-dmo.org/id/dataset-parameter/959243.rdf
Name: Porosity
Units: cubic centimeters of porewater per cubic centimeters of total sediment (cm3pore water/cm3total sediment)
Description: <p>porosity of the sediment sample</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
12425
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/9de1fb17-1bdc-41ed-a220-9da019e51a2c/content
download
https://doi.org/10.26008/1912/bco-dmo.959217.1
download
onLine
dataset
<p>Sediment cores were collected using a gravity corer and a multicorer on both cruises. Following recovery, the gravity cores were secured horizontally on the ship's deck and sampled from the bottom of the core upwards. This was done by sequentially removing 10-centimeter (cm) sediment intervals by cutting the core liner using a pipe cutter. Freshly exposed sediment was placed in pre-weighed scintillation vials, and the vials were frozen on-board the ship.</p>
<p>Most multi cores were sectioned at intervals ranging from 1 to 5 cm over the 30-40 cm length of the core. Some cores were sampled using pre-drilled holes in multi-core tubes that were sealed with tape during deployment. Upon recovery of the cores, the holes were cut open to sample the sediment with open-faced syringes inserted horizontally into the holes in the core tube. In both cases, the collected sediment was again placed in pre-weighed scintillation vials, and the vials were frozen on-board the ship.</p>
<p>Frozen vials were returned to the shore-based lab at ODU where the samples&nbsp;were dried to constant weight, to obtain the wet-to-dry mass ratio of the sediment sample (±1% precision). A dry sediment density of 2.67 gr/cm3 and a pore water density of 1.024 gr/cm3 were used in the porosity calculations (cm3 pore water/cm3 total sediment). All values were corrected for the salt content of the pore water.</p>
<p>While it is possible to recover intact sediment-water interfaces using multi-corers, loss of surface sediments is typical during gravity coring, making it impossible to directly quantify absolute depths below the sediment-water interface in a gravity core. We therefore determined absolute depths of sediment sample intervals in gravity cores by aligning DIC, &nbsp;sulfate, ammonium, and porosity gravity core profiles to multicore profiles from the same site (Berelson et al., 2005; Iversen and Jørgensen, 1985; Komada et al., 2016).</p>
Specified by the Principal Investigator(s)
- Imported original file "porosity.txt" into the BCO-DMO system.
- Converted Date column to YYYY-mm-dd format.
- Added station latitude and longitude columns.
- Added cruise ID column.
- Replaced "MC" with "M" in the Core column for consistency.
- Saved final file as "959217_v1_sediment_porosity.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
a standard lab drying oven
a standard lab drying oven
PI Supplied Instrument Name: a standard lab drying oven Instrument Name: Drying Oven Instrument Short Name: Instrument Description: a heated chamber for drying
gravity corer
gravity corer
PI Supplied Instrument Name: gravity corer 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/
multicorer
multicorer
PI Supplied Instrument Name: multicorer 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/
top-loading balance
top-loading balance
PI Supplied Instrument Name: top-loading balance Instrument Name: scale or balance Instrument Short Name: Instrument Description: Devices that determine the mass or weight of a sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB13/
Cruise: OC1906A
OC1906A
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
OC1906A
Hussain Abdulla
Oregon State University
Cruise: SKQ202016S
SKQ202016S
R/V Sikuliaq
Community Standard Description
International Council for the Exploration of the Sea
R/V Sikuliaq
vessel
SKQ202016S
Hussain Abdulla
Texas A&M University
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
R/V Sikuliaq
Community Standard Description
International Council for the Exploration of the Sea
R/V Sikuliaq
vessel