http://lod.bco-dmo.org/id/dataset/995790
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
2026-04-01
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Oxygen, carbon, and 13C values from the deep-sea incubator (DSI) and parallel laboratory incubations with mesopelagic water from the same region and depth on May 12, 2023
2026-04-01
publication
2026-04-01
revision
BCO-DMO Linked Data URI
2026-04-01
creation
http://lod.bco-dmo.org/id/dataset/995790
Alexander Boris Bochdansky
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: Bochdansky, A. B. (2026) Oxygen, carbon, and 13C values from the deep-sea incubator (DSI) and parallel laboratory incubations with mesopelagic water from the same region and depth on May 12, 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-04-01 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/995790 [access date]
DSI deployment and lab incubation Dataset Description: Methods and Sampling: <p><strong>Cruise/Deployment Information:</strong><br />
Field samples were obtained using R/V Fay Slover (Ocean &amp; Earth Sciences, Old Dominion University).<br />
Deployment date of Deep-Sea Incubator: 2023-05-12<br />
Retrieval date of Deep-Sea Incubator: 2023-05-16<br />
Location: Continental shelf break off Virginia Beach, Virginia, USA<br />
Chief scientist: Alexander B. Bochdansky, Ocean &amp; Earth Sciences, Old Dominion University, abochdan@odu.edu</p>
<p><strong>In situ experiments with the DSI:</strong><br />
The deep-sea incubator (DSI) consists of 24 gas-tight glass syringes and a mechanism that fills the syringes to 42 milliliters (ml) with ambient water set on a timer with a 1-hour delay. This gives the DSI more than sufficient time to settle to the target depth and adjust to the in-situ temperature. The anchor depth was 600 meters (m) and the tether from the anchor to the DSI was 300 m resulting in a deployment depth of 300 m. The syringes were pre-filled with 2 ml of labeled algal phytodetritus from batch cultures of <em>Thalassiosira weissflogii</em> and <em>Tetraselmis</em> sp. The cultures were grown on a f/2+ (<em>T. weissflogii</em>) or f/2 (<em>Tetraselmis</em>) medium enriched with 13C-sodium bicarbonate, frozen at the late exponential stage, and then filtered onto a 0.2-micrometer (um) pore size polycarbonate filter. The particulate material (POC) was resuspended in a 50 ml centrifuge tube filled with the same volume of water as the original culture volume with artificial seawater. The filtrate was used as a source of 13C-labeled dissolved organic carbon (DOC). POC was dislodged from the filter by vigorous vortex mixing and shaking of the centrifuge tube. DOC was the filtrate. Two milliliters of the slurry of POC or the DOC filtrate were then injected into each syringe using an automatic pipette. Controls were poisoned with mercuric chloride (HgCl2). The four treatments were as follows:</p>
<p>1.) 3C labeled POC from <em>Thalassiosira weissflogii</em> (4 replicates)<br />
2.) 13C labeled DOC from <em>Thalassiosira weissflogii</em> (4 replicates)<br />
3.) 13C labeled POC from <em>Tetraselmis</em> sp. (4 replicates)<br />
4.) 13C labeled DOC from <em>Tetraselmis</em> sp. (4 replicates)<br />
5.) 13C labeled POC from <em>Thalassiosira weissflogii</em> with HgCl2 (duplicates)<br />
6.) 13C labeled DOC from <em>Thalassiosira weissflogii</em> with HgCl2 (duplicates)<br />
7.) 13C labeled POC from <em>Tetraselmis</em> sp. with HgCl2 (duplicates)<br />
8.) 13C labeled DOC from <em>Tetraselmis</em> sp. with HgCl2 (duplicates)</p>
<p>The incubation started on May 12, 2023 at 13:09. The syringes were processed (tfinal) on May 16, 2023 (i.e., 4.25 days later).</p>
<p><strong>Parallel laboratory incubations:</strong><br />
The laboratory incubations were set up in parallel using the exact same protocol as with the field incubations except they are filled with seawater from close to the same depth (300 m) as the deep-sea incubator collected with Niskin bottles. The water was returned to lab laboratory in a temperature controlled cool chest (11-12 degrees Celsius (C)) and experiments were started approximately 6.5 hours and after the syringes were filled with labeled material. They were placed in a cold room at 12 degrees C in the dark until retrieval.</p>
<p>The incubation interval for the laboratory experiments was 4 days.</p>
<p>The temperature of the DSI was unknown until retrieval. Because of the highly variable bathymetry at the deployment site (at the continental shelf break), the DSI landed in slightly deeper water than anticipated, which resulted in an average temperature of 8.2 degrees C (range 6.5 – 10.3 degrees C) according to an attached temperature logger.</p>
<p>Oxygen was measured by inserting a Unisense microprobe (a polargraphic oxygen sensor that is drawn out into a capillary) approximately 2 centimeters (cm) into the syringe immediately after removing the Luer-lock valve. A saturated oxygen standard and a NaOH-ascorbic acid standard (zero oxygen) at the same salinity and concentration were used as standards. A two-point calibration suffices as the polarographic sensor signal is strictly linear.</p>
<p>Five ml from each syringe was filtered onto a muffled GF/F filter and frozen until later processing. The filters were dried at 50 degrees C, acidified under HCl fumes to remove inorganic carbon, dried again and sent to the Stable Isotope Facility at UC Davis. There, the filters were encapsulated in tin capsules and processed in an elemental analyzer coupled to an isotope ratio mass spectrometer (EA-IRMS). Only the 13C and bulk particulate organic carbon values (12C + 13C) values were used for this analysis.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851368 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851368
onGoing
Alexander Boris Bochdansky
Old Dominion University
757-683-4933
Ocean, Earth and Atmospheric Sciences 4600 Elkhorn Ave.
Norfolk
VA
23529
USA
abochdan@odu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_ID
Description
Time_point
Date
Live_dead
Reading_Oxygen_units
Reading_Oxygen_saturation_average
Reading_zero_oxygen
Total_C_ug
Total_C_ug_L
Elapsed_time
Conc_13C
EA – IRMS at UC Davis
deep sea incubator (DSI)
Isoprime VisION IRMS or PDZ Europa 20-20
Niskin bottles
temperature logger
Unisense polarographic oxygen sensor type: MicroRespiration System
theme
None, User defined
sample identification
sample description
time_point
date
dissolved Oxygen
Elemental carbon (C)
time_elapsed
13C, stable isotope of C
featureType
BCO-DMO Standard Parameters
Elemental Analyzer
In-situ incubator
Isotope-ratio Mass Spectrometer
Niskin bottle
Temperature Logger
Unisense oxygen microsensor
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: Transforming Carbon in the Deep Sea
https://osprey.bco-dmo.org/project/817462
Collaborative Research: Transforming Carbon in the Deep Sea
<p><em>NSF Award Abstract:</em><br />
Through understanding the biological pump (the ocean's biologically driven sequestration of carbon from the atmosphere to the ocean interior and seafloor sediments), scientists know that the world's oceans absorb more carbon dioxide than it returns to the atmosphere. While much is known about the biological processes largely responsible for the transfer of carbon into the deep sea, very little is known about the microbial decay and subsequent remineralization processes that occur when the carbon reaches the deep sea. Using newly-designed deep-sea incubators deployed off the east coast of the United States, researchers will explore the microbial communities and remineralization processes that transform carbon in the deep sea. The incubators will be filled with tracer-labeled algae or fecal material mimicking the diet and waste products of animal plankton. The tracers allow the researchers to follow the material through the microbial food web, and simultaneously determine the net release of carbon dioxide during the incubations. Using a combination of genetic analysis and novel analytical techniques, the researchers will be able to identify the organisms involved in the decay processes and rates at which changes occur at the single-cell level. Results will shed light on these understudied biological phenomena and contribute to an improved understanding of the global carbon cycle. In addition to novel advancements in oceanographic technology, the research supports graduate and undergraduate student education, and public outreach through partnerships with the Virginia Aquarium and National Ocean Sciences Bowl to increase ocean science literacy.</p>
<p>In this project, researchers will study the organisms, mechanisms, and physical and ecological factors that modulate the remineralization of organic material in the deep sea. The methods include using in situ incubations of well-defined and stable isotope-labeled sources of organic carbon (live and dead phytoplankton and fecal pellets of zooplankton) with natural microbial communities. The incubations will take place northeast of Cape Hatteras, a region characterized by strong offshore transport of phytoplankton carbon. Net carbon dioxide release rates will be measured over time by conversion of Carbon-13 labeled organic carbon to 13CO2 . The dependence of degradation rates on the source material, seasonality, oxygen concentration, and the type of microbial colonizers will be assessed. Parallel laboratory experiments will elucidate the exact shape of the time course of carbon release by phytoplankton into dissolved organic and inorganic fractions as well as determine how representative laboratory and ship-board generated values are relative to those obtained in situ. Target eukaryotic and prokaryotic taxa are identified by fluorescence in-situ hybridization (FISH) after the incubations and individually interrogated using Raman microspectrometry to investigate the relative Carbon-13-enrichment rates in organisms assimilating labeled detrital carbon. This multi-faceted approach will provide better constrained parameters for ecosystem and biological pump models and shed light on carbon balances of the deep sea. The research contributes to the development of new oceanographic technology, including new deep-sea incubators and application of single-cell Raman microspectrometry to natural microbial communities.</p>
Carbon in the Deep Sea
largerWorkCitation
project
eng; USA
oceans
-74.629
-74.629
36.788
36.788
2023-05-12
2023-05-16
Mesopelagic North Atlantic
0
BCO-DMO catalogue of parameters from Oxygen, carbon, and 13C values from the deep-sea incubator (DSI) and parallel laboratory incubations with mesopelagic water from the same region and depth on May 12, 2023
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/995805.rdf
Name: Sample_ID
Units: unitless
Description: <p>Unique sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/995806.rdf
Name: Description
Units: unitless
Description: <p>TW is Thalassiosira weissflogii, Tetra is Tetrasellmis sp., POC is particulate organic carbon, T0 and Tfin are times zero and times final of the experiment, respectively</p>
http://lod.bco-dmo.org/id/dataset-parameter/995807.rdf
Name: Time_point
Units: unitless
Description: <p>t0 beginning of experiment, tfin end of the experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/995808.rdf
Name: Date
Units: unitless
Description: <p>Date at which the individual syringes were processed</p>
http://lod.bco-dmo.org/id/dataset-parameter/995809.rdf
Name: Live_dead
Units: unitless
Description: <p>Live: no preserved; dead: preserved with HgCl2 </p>
http://lod.bco-dmo.org/id/dataset-parameter/995810.rdf
Name: Reading_Oxygen_units
Units: picoAmps
Description: <p>Reading of polarographic oxygen sensor</p>
http://lod.bco-dmo.org/id/dataset-parameter/995811.rdf
Name: Reading_Oxygen_saturation_average
Units: picoAmps
Description: <p>Average reading of polarographic oxygen sensor at oxygen saturation</p>
http://lod.bco-dmo.org/id/dataset-parameter/995812.rdf
Name: Reading_zero_oxygen
Units: picoAmps
Description: <p>Reading of polarographic oxygen sensor at zero oxygen saturation</p>
http://lod.bco-dmo.org/id/dataset-parameter/995813.rdf
Name: Total_C_ug
Units: milligrams (mg)
Description: <p>IRMS measurement of carbon on filter</p>
http://lod.bco-dmo.org/id/dataset-parameter/995814.rdf
Name: Total_C_ug_L
Units: milligrams per liter (mg/L)
Description: <p>Carbon of sample per liter</p>
http://lod.bco-dmo.org/id/dataset-parameter/995815.rdf
Name: Elapsed_time
Units: days
Description: <p>Incubation period</p>
http://lod.bco-dmo.org/id/dataset-parameter/995816.rdf
Name: Conc_13C
Units: milligrams per liter (mg/L)
Description: <p>13C-carbon concentration of the sample (IRMS)</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://osprey.bco-dmo.org/dataset/995790/data/download
download
onLine
dataset
<p><strong>Cruise/Deployment Information:</strong><br />
Field samples were obtained using R/V Fay Slover (Ocean &amp; Earth Sciences, Old Dominion University).<br />
Deployment date of Deep-Sea Incubator: 2023-05-12<br />
Retrieval date of Deep-Sea Incubator: 2023-05-16<br />
Location: Continental shelf break off Virginia Beach, Virginia, USA<br />
Chief scientist: Alexander B. Bochdansky, Ocean &amp; Earth Sciences, Old Dominion University, abochdan@odu.edu</p>
<p><strong>In situ experiments with the DSI:</strong><br />
The deep-sea incubator (DSI) consists of 24 gas-tight glass syringes and a mechanism that fills the syringes to 42 milliliters (ml) with ambient water set on a timer with a 1-hour delay. This gives the DSI more than sufficient time to settle to the target depth and adjust to the in-situ temperature. The anchor depth was 600 meters (m) and the tether from the anchor to the DSI was 300 m resulting in a deployment depth of 300 m. The syringes were pre-filled with 2 ml of labeled algal phytodetritus from batch cultures of <em>Thalassiosira weissflogii</em> and <em>Tetraselmis</em> sp. The cultures were grown on a f/2+ (<em>T. weissflogii</em>) or f/2 (<em>Tetraselmis</em>) medium enriched with 13C-sodium bicarbonate, frozen at the late exponential stage, and then filtered onto a 0.2-micrometer (um) pore size polycarbonate filter. The particulate material (POC) was resuspended in a 50 ml centrifuge tube filled with the same volume of water as the original culture volume with artificial seawater. The filtrate was used as a source of 13C-labeled dissolved organic carbon (DOC). POC was dislodged from the filter by vigorous vortex mixing and shaking of the centrifuge tube. DOC was the filtrate. Two milliliters of the slurry of POC or the DOC filtrate were then injected into each syringe using an automatic pipette. Controls were poisoned with mercuric chloride (HgCl2). The four treatments were as follows:</p>
<p>1.) 3C labeled POC from <em>Thalassiosira weissflogii</em> (4 replicates)<br />
2.) 13C labeled DOC from <em>Thalassiosira weissflogii</em> (4 replicates)<br />
3.) 13C labeled POC from <em>Tetraselmis</em> sp. (4 replicates)<br />
4.) 13C labeled DOC from <em>Tetraselmis</em> sp. (4 replicates)<br />
5.) 13C labeled POC from <em>Thalassiosira weissflogii</em> with HgCl2 (duplicates)<br />
6.) 13C labeled DOC from <em>Thalassiosira weissflogii</em> with HgCl2 (duplicates)<br />
7.) 13C labeled POC from <em>Tetraselmis</em> sp. with HgCl2 (duplicates)<br />
8.) 13C labeled DOC from <em>Tetraselmis</em> sp. with HgCl2 (duplicates)</p>
<p>The incubation started on May 12, 2023 at 13:09. The syringes were processed (tfinal) on May 16, 2023 (i.e., 4.25 days later).</p>
<p><strong>Parallel laboratory incubations:</strong><br />
The laboratory incubations were set up in parallel using the exact same protocol as with the field incubations except they are filled with seawater from close to the same depth (300 m) as the deep-sea incubator collected with Niskin bottles. The water was returned to lab laboratory in a temperature controlled cool chest (11-12 degrees Celsius (C)) and experiments were started approximately 6.5 hours and after the syringes were filled with labeled material. They were placed in a cold room at 12 degrees C in the dark until retrieval.</p>
<p>The incubation interval for the laboratory experiments was 4 days.</p>
<p>The temperature of the DSI was unknown until retrieval. Because of the highly variable bathymetry at the deployment site (at the continental shelf break), the DSI landed in slightly deeper water than anticipated, which resulted in an average temperature of 8.2 degrees C (range 6.5 – 10.3 degrees C) according to an attached temperature logger.</p>
<p>Oxygen was measured by inserting a Unisense microprobe (a polargraphic oxygen sensor that is drawn out into a capillary) approximately 2 centimeters (cm) into the syringe immediately after removing the Luer-lock valve. A saturated oxygen standard and a NaOH-ascorbic acid standard (zero oxygen) at the same salinity and concentration were used as standards. A two-point calibration suffices as the polarographic sensor signal is strictly linear.</p>
<p>Five ml from each syringe was filtered onto a muffled GF/F filter and frozen until later processing. The filters were dried at 50 degrees C, acidified under HCl fumes to remove inorganic carbon, dried again and sent to the Stable Isotope Facility at UC Davis. There, the filters were encapsulated in tin capsules and processed in an elemental analyzer coupled to an isotope ratio mass spectrometer (EA-IRMS). Only the 13C and bulk particulate organic carbon values (12C + 13C) values were used for this analysis.</p>
Specified by the Principal Investigator(s)
- Imported original file "PO13C FIGURES for DSI drop 12May2023 Version 2.csv" into the BCO-DMO processing system.
- Treated "NaN" as a missing data value (missing data are empty/blank in the final CSV file).
- Renamed fields to comply with BCO-DMO naming conventions.
- Saved the final file as "995790_v1_dsi_o2_c_13c.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
EA – IRMS at UC Davis
EA – IRMS at UC Davis
PI Supplied Instrument Name: EA – IRMS at UC Davis PI Supplied Instrument Description:13C and 15N isotopes using an Elementar Vario EL Cube or Micro Cube elemental analyzer (Elementar Analysensysteme GmbH, Hanau, Germany) interfaced to either an Isoprime VisION IRMS (Elementar UK Ltd, Cheadle, UK) or a PDZ Europa 20-20 isotope ratio mass spectrometer (Sercon Ltd., Cheshire, UK) Instrument Name: Elemental Analyzer Instrument Short Name: Instrument Description: Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB01/
deep sea incubator (DSI)
deep sea incubator (DSI)
PI Supplied Instrument Name: deep sea incubator (DSI) PI Supplied Instrument Description:The deep sea incubator (DSI) consists of 24 gas-tight glass syringes and a mechanism that fills the syringes to 42 ml with ambient water set on a timer with a 1-hour delay. Instrument Name: In-situ incubator Instrument Short Name:in-situ incubator Instrument Description: A device on a ship or in the laboratory that holds water samples under controlled conditions of temperature and possibly illumination. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/82/
Isoprime VisION IRMS or PDZ Europa 20-20
Isoprime VisION IRMS or PDZ Europa 20-20
PI Supplied Instrument Name: Isoprime VisION IRMS or PDZ Europa 20-20 PI Supplied Instrument Description:13C and 15N isotopes using an Elementar Vario EL Cube or Micro Cube elemental analyzer (Elementar Analysensysteme GmbH, Hanau, Germany) interfaced to either an Isoprime VisION IRMS (Elementar UK Ltd, Cheadle, UK) or a PDZ Europa 20-20 isotope ratio mass spectrometer (Sercon Ltd., Cheshire, UK) 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/
Niskin bottles
Niskin bottles
PI Supplied Instrument Name: Niskin bottles Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
temperature logger
temperature logger
PI Supplied Instrument Name: temperature logger Instrument Name: Temperature Logger Instrument Short Name: Instrument Description: Records temperature data over a period of time.
Unisense polarographic oxygen sensor type: MicroRespiration System
Unisense polarographic oxygen sensor type: MicroRespiration System
PI Supplied Instrument Name: Unisense polarographic oxygen sensor type: MicroRespiration System PI Supplied Instrument Description:Oxygen was measured by inserting a Unisense microprobe. Instrument Name: Unisense oxygen microsensor Instrument Short Name:Unisense O2 Instrument Description: The Unisence oxygen microsensor is a miniaturized Clark-type dissolved oxygen instrument, including glass micro-sensors with minute tips (diameters ranging from 1 to 800 um). A gold sensing cathode is polarized against an internal reference and, driven by external partial pressure, oxygen from the environment penetrates through the sensor tip membrane and is reduced at the sensing cathode surface. A picoammeter converts the resulting reduction current to a signal. The sensor also includes a polarized guard cathode, which scavenges oxygen in the electrolyte, thus minimizing zero-current and pre-polarization time. See more on the manufacturer's website: https://www.unisense.com/