http://lod.bco-dmo.org/id/dataset/1002907
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
2026-07-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
In situ N2 production rates from the Eastern Tropical North Pacific Oxygen Deficient Zone on the R/V Sikuliaq cruise SKQ201617S in January 2017 and R/V Revelle in April 2018 cruise RR1805
2026-07-24
publication
2026-07-24
revision
BCO-DMO Linked Data URI
2026-07-24
creation
http://lod.bco-dmo.org/id/dataset/1002907
Allan Devol
University of Washington
principalInvestigator
Richard Keil
University of Washington
principalInvestigator
Clara Fuchsman
University of Maryland Center for Environmental Science
principalInvestigator
Wendi Ruef
University of Washington
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: Fuchsman, C., Duffy, M. E., Devol, A., Keil, R., Ruef, W. (2026) In situ N2 production rates from the Eastern Tropical North Pacific Oxygen Deficient Zone on the R/V Sikuliaq cruise SKQ201617S in January 2017 and R/V Revelle in April 2018 cruise RR1805. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-07-24 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/1002907 [access date]
In situ N2 production rates from the ETNP ODZ Dataset Description: Methods and Sampling: <p>In situ N<sub>2</sub> production rates with and without the addition of sinking particles were obtained&nbsp;from the Eastern Tropical North Pacific&nbsp;on the R/V <em>Sikuliaq</em> cruise SKQ201617S&nbsp;in January 2017, which sampled&nbsp;two stations: St P2 (16.5ºN 107ºW) and&nbsp;St P1 (20.1 ºN 106.2ºW), and the R/V <em>Revelle</em> cruise RR1805 sampled&nbsp;approximately the same two stations in 2018: St P2 (16.9ºN 107ºW) and&nbsp;St P1 (20.3 ºN 106.1ºW).</p>
<p>The unpoisoned trap-incubator design collected particles using either a hard plastic cone or mesh net design similar to (Peterson et al., 2005). &nbsp;Despite these differences, the plastic cone and mesh net trap styles were demonstrated to have similar collection efficiencies in the ETNP in 2017 (Cram et al., 2022). The gate valves at the tops and bottoms to incubation chambers, as well as the plungers of <sup>15</sup>N tracer-injecting syringes, were held open with tensioned rubber tubing restrained with nylon-jacketed electronic dissolving links (“burn wires”) prior to deployment. The chamber gate valves and syringes were controlled using a preprogrammed onboard Arduino microcontroller that directed current from two 9V alkaline batteries to individual electronic dissolving links. The nylon jacket on the electronic dissolving link was stripped at 1-cm wide sections which held open a gate valve or syringe plunger. When current was applied by the Arduino microcontroller, the electronic dissolving links corroded in seawater and released either the attached gate valves or syringe plungers. Sediment trap incubators were deployed with all gates open to facilitate the dissipation of any trapped air bubbles during an 8-hour acclimation period in anoxic waters at the target depth.&nbsp;</p>
<p>Particles collected in the trap fell into a vertically-oriented 1 L incubation chamber (“+particles chamber”) that was initially open on both ends. Another vertically-oriented 1 L incubation chamber (“water column chamber”)&nbsp; sat to the side of the sediment trap and was deployed open on both ends, but closed immediately before incubation.&nbsp; The bottom of the +particles chamber was programmed to close after the 8-hour acclimation period at the target depth, beginning a collection phase of 12-36 hours. After the collection phase, the top of the +particles closed, along with both top and bottom of the water column chamber. At the beginning of the incubation phase, <sup>15</sup>N-labeled nitrite was injected into both +particles and water column chambers. A second 500 mL collection chamber (“top collector”) immediately above the +particles chamber collected additional sinking particles during the incubation phase for use in flux calculations.&nbsp;</p>
<p>&nbsp;</p>
<p>Immediately after returning the sediment trap-<em>in situ</em> incubator systems shipboard, the experimental chambers were sampled using single-use needles into 12 mL septum-capped glass Exetainer vials (LabCo, UK) that had been purged with helium gas for 5 minutes. Duplicate vials were sampled for each incubation. Vials were poisoned with 50% (w/v) zinc chloride and stored in the dark at room temperature.&nbsp; Water from CTD casts was collected into Exetainers to measure the background isotopic composition of N<sub>2</sub> gas by overfilling the exetainer four times and closing the exetainer with a needle inserted to just below the septa, to cause any bubbles to be removed during closing. Each Exetainer was checked for bubbles. Exetainers were measured for <sup>29</sup>N<sub>2</sub> and <sup>30</sup>N<sub>2</sub> accumulation on a Thermo Delta V isotope ratio mass spectrometer in continuous flow mode using helium gas at the University of Washington. Each datapoint was background corrected. A tank of N<sub>2</sub> gas was the internal standard and was measured three times during each sample measurement. Each sample was in turn measured three times. Air was used as an external standard and was added to helium purged Exetainers using a range of volumes. These air standards were measured regularly throughout the run to quantify any drift.&nbsp; Rate measurements were calculated following de Brabandere et al. (2014) using incubation durations and the volumes of the experimental chambers.</p>
Funding provided by NSF Division of Environmental Biology (NSF DEB) Award Number: DEB-1542240 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1542240
onGoing
Allan Devol
University of Washington
206-543-1292
School of Oceanography University of Washington, Box 355351
Seattle
WA
98195
USA
devol@u.washington.edu
pointOfContact
Richard Keil
University of Washington
206-685-9994
School of Oceanography Box 355351
Seattle
WA
98195
USA
keil@u.washington.edu
pointOfContact
Clara Fuchsman
University of Maryland Center for Environmental Science
P. O. Box 775 2020 Horns Point Rd
Cambridge
MD
21613
USA
cfuchsman@umces.edu
pointOfContact
Wendi Ruef
University of Washington
wruef@uw.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
incubation_ID
date_deployed
station
latitude
longitude
depth
particle_collection_time
incubation_time
N_production_plus_P
N_production_WaterColumn
N_production_sinking_particles
Thermo Delta V
theme
None, User defined
sample identification
date begin
station
latitude
longitude
depth
duration
incubation time or duration
Nitrogen
featureType
BCO-DMO Standard Parameters
Isotope-ratio Mass Spectrometer
instrument
BCO-DMO Standard Instruments
SKQ201617S
RR1805
service
Deployment Activity
Eastern Tropical North Pacific Ocean
Eastern Tropical North Pacific Ocean 20N-14N, 105W-130W
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.
Dimensions of Biodiversity
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503446
Dimensions of Biodiversity
(adapted from the NSF Synopsis of Program)
Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program. [MORE from NSF]
The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes.
Dimensions of Biodiversity
largerWorkCitation
program
Dimensions: Diversity, assembly and function of microbial communities on suspended and sinking particles in a marine Oxygen Deficient Zone
https://osprey.bco-dmo.org/project/665101
Dimensions: Diversity, assembly and function of microbial communities on suspended and sinking particles in a marine Oxygen Deficient Zone
<p><em>Extracted from the NSF award abstract:</em></p>
<p>Marine oxygen deficient zones (ODZs) are waters that are functionally devoid of oxygen. Without oxygen, some microbes are capable of converting nitrogen in the water into N2 gas, which then leaves the ocean and enters the atmosphere. This loss of an important nutrient from the ocean has impacts on phytoplankton growth and marine food webs. While oxygen deficient zones occupy a very small percentage of the ocean, they account for as much as half of the oceanic loss of N as N2. Moreover, the size of these regions is predicted to expand during this century due to climate change. The microbes that are capable of producing N2 gas are extremely diverse, and use several different biochemical pathways to carry out this process. They may occur both free-floating in the water and attached to small particles that are suspended or sinking from the surface waters and providing them a carbon source. However the importance of these two lifestyles (free-living vs particle attached) in terms of contributions to N loss from the oceans is not well understood. This project will identify the major organisms that result in N2 gas production on both suspended and sinking particles, the chemical reactions they carry out, and the rates at which this occurs. This information will be used to improve global climate models to better predict rates of N loss in a future ocean. Elementary and middle school teachers enrolled in a Masters in Science for Science Teachers program will be involved in the project and the graduate students and post-doctoral researchers supported by the project will have opportunities to participate in their classrooms. Underserved populations will also be integrated into the research at the undergraduate and middle school level through a series of summer internships.</p>
<p>ODZs have very complex elemental cycles, implying great microbial diversity. Intertwined with the microbial complexity of ODZ regions is the relatively unexplored interplay between free-living bacteria and those living on either suspended or sinking particles. Determining how these communities and niches interact and relate is one of the most challenging components of ODZ system studies today. Current climate models portray the dynamics of particles in the ODZs and throughout the deep ocean through prescribed functions based on sparse data from the oxic ocean with microbes represented only by the net chemical reactions of the community. However, in reality a phylogenetically and metabolically diverse group of microbes, likely acting in consortia, are responsible for the nitrogen transformations that ultimately result in the production of N2. To explore the processes maintaining the genetic diversity and functional redundancy in N loss processes, four research areas will be integrated: the community phylogenetic diversity (both taxonomic and genomic diversity) the genetic diversity of the proteins that carry out key N transformation processes (as seen through quantitative proteomics), the resulting biogeochemical functions (15N labeled nitrogen transformation rate measurements) and predictions about how this diversity and corresponding function may change in response to climate change (biogeochemical modeling). The approach will be to assay both phylogenetic (16S rRNA tag sequencing) and functional genetic diversity (genomics) on sinking particles collected using large-volume sediment traps. Phylogenetic and genomic studies will be intimately tied to measurements of activity - who is doing key biogeochemical transformations (proteomics) and what are the in situ rates at which they are doing them (using novel incubation systems). Data will then be used to model how diversity and corresponding function change on a range of time and space scales, from the sinking of a single particle to seasonal cycles. To understand the relationship of community diversity and function on suspended and sinking particles, a series of three cruises will be conducted in the Eastern Tropical North Pacific ODZ.</p>
ETNP_ParticleOmics
largerWorkCitation
project
eng; USA
oceans
Eastern Tropical North Pacific Ocean; Eastern Tropical North Pacific Ocean 20N-14N, 105W-130W
-107.1392
-106.0001
16.5207
20.305
2017-01-01
2018-04-24
Eastern Tropical North Pacific
0
BCO-DMO catalogue of parameters from In situ N2 production rates from the Eastern Tropical North Pacific Oxygen Deficient Zone on the R/V Sikuliaq cruise SKQ201617S in January 2017 and R/V Revelle in April 2018 cruise RR1805
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/1002940.rdf
Name: incubation_ID
Units: unitless
Description: <p>Unique ID code for trap array and incubator depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/1002941.rdf
Name: date_deployed
Units: units
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1002942.rdf
Name: station
Units: unitless
Description: <p>station sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/1002943.rdf
Name: latitude
Units: decimal degrees (DD)
Description: <p>location deployed</p>
http://lod.bco-dmo.org/id/dataset-parameter/1002945.rdf
Name: longitude
Units: decimal degrees (DD)
Description: <p>location deployed</p>
http://lod.bco-dmo.org/id/dataset-parameter/1002947.rdf
Name: depth
Units: meters (m)
Description: <p>depth of trap-incubator system</p>
http://lod.bco-dmo.org/id/dataset-parameter/1002949.rdf
Name: particle_collection_time
Units: hours (hrs)
Description: <p>duration of sediment trap particles collection into plus particles (+P) chamber</p>
http://lod.bco-dmo.org/id/dataset-parameter/1002950.rdf
Name: incubation_time
Units: hours (hrs)
Description: <p>duration of incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/1002951.rdf
Name: N_production_plus_P
Units: nanomols nitrogen per day (nM N/d)
Description: <p>unadjusted N production rate in plus particles (+P) chamber</p>
http://lod.bco-dmo.org/id/dataset-parameter/1002952.rdf
Name: N_production_WaterColumn
Units: nanomols nitrogen per day (nM N/d)
Description: <p>unadjusted N production rate in water column chamber</p>
http://lod.bco-dmo.org/id/dataset-parameter/1002953.rdf
Name: N_production_sinking_particles
Units: nanomols nitrogen per day (nM N/d)
Description: <p>calculated N production rate due to sinking particles</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/1002907/data/download
download
onLine
dataset
<p>In situ N<sub>2</sub> production rates with and without the addition of sinking particles were obtained&nbsp;from the Eastern Tropical North Pacific&nbsp;on the R/V <em>Sikuliaq</em> cruise SKQ201617S&nbsp;in January 2017, which sampled&nbsp;two stations: St P2 (16.5ºN 107ºW) and&nbsp;St P1 (20.1 ºN 106.2ºW), and the R/V <em>Revelle</em> cruise RR1805 sampled&nbsp;approximately the same two stations in 2018: St P2 (16.9ºN 107ºW) and&nbsp;St P1 (20.3 ºN 106.1ºW).</p>
<p>The unpoisoned trap-incubator design collected particles using either a hard plastic cone or mesh net design similar to (Peterson et al., 2005). &nbsp;Despite these differences, the plastic cone and mesh net trap styles were demonstrated to have similar collection efficiencies in the ETNP in 2017 (Cram et al., 2022). The gate valves at the tops and bottoms to incubation chambers, as well as the plungers of <sup>15</sup>N tracer-injecting syringes, were held open with tensioned rubber tubing restrained with nylon-jacketed electronic dissolving links (“burn wires”) prior to deployment. The chamber gate valves and syringes were controlled using a preprogrammed onboard Arduino microcontroller that directed current from two 9V alkaline batteries to individual electronic dissolving links. The nylon jacket on the electronic dissolving link was stripped at 1-cm wide sections which held open a gate valve or syringe plunger. When current was applied by the Arduino microcontroller, the electronic dissolving links corroded in seawater and released either the attached gate valves or syringe plungers. Sediment trap incubators were deployed with all gates open to facilitate the dissipation of any trapped air bubbles during an 8-hour acclimation period in anoxic waters at the target depth.&nbsp;</p>
<p>Particles collected in the trap fell into a vertically-oriented 1 L incubation chamber (“+particles chamber”) that was initially open on both ends. Another vertically-oriented 1 L incubation chamber (“water column chamber”)&nbsp; sat to the side of the sediment trap and was deployed open on both ends, but closed immediately before incubation.&nbsp; The bottom of the +particles chamber was programmed to close after the 8-hour acclimation period at the target depth, beginning a collection phase of 12-36 hours. After the collection phase, the top of the +particles closed, along with both top and bottom of the water column chamber. At the beginning of the incubation phase, <sup>15</sup>N-labeled nitrite was injected into both +particles and water column chambers. A second 500 mL collection chamber (“top collector”) immediately above the +particles chamber collected additional sinking particles during the incubation phase for use in flux calculations.&nbsp;</p>
<p>&nbsp;</p>
<p>Immediately after returning the sediment trap-<em>in situ</em> incubator systems shipboard, the experimental chambers were sampled using single-use needles into 12 mL septum-capped glass Exetainer vials (LabCo, UK) that had been purged with helium gas for 5 minutes. Duplicate vials were sampled for each incubation. Vials were poisoned with 50% (w/v) zinc chloride and stored in the dark at room temperature.&nbsp; Water from CTD casts was collected into Exetainers to measure the background isotopic composition of N<sub>2</sub> gas by overfilling the exetainer four times and closing the exetainer with a needle inserted to just below the septa, to cause any bubbles to be removed during closing. Each Exetainer was checked for bubbles. Exetainers were measured for <sup>29</sup>N<sub>2</sub> and <sup>30</sup>N<sub>2</sub> accumulation on a Thermo Delta V isotope ratio mass spectrometer in continuous flow mode using helium gas at the University of Washington. Each datapoint was background corrected. A tank of N<sub>2</sub> gas was the internal standard and was measured three times during each sample measurement. Each sample was in turn measured three times. Air was used as an external standard and was added to helium purged Exetainers using a range of volumes. These air standards were measured regularly throughout the run to quantify any drift.&nbsp; Rate measurements were calculated following de Brabandere et al. (2014) using incubation durations and the volumes of the experimental chambers.</p>
Specified by the Principal Investigator(s)
<p>The goal in the incubations was to arrive at N<sub>2</sub> production rate values that represented 1) the overall N<sub>2</sub> production rate in the water column, which was obtained from the water column chambers; and 2) the N<sub>2</sub> production rate due solely attributed to the sinking particles in the water column. Because the incubations occurred with particles that had been collected over a 12 hour period, we thus adjusted the initial rates in the +particles chambers to account for this concentration factor and arrive at an adjusted rate relevant to the actual concentration of particles in the water column. To do this, we adjusted the labeled N<sub>2</sub> accumulation rate in the +particles chamber to be the rate for the mass concentration (m/V, in mol organic C/m<sup>3</sup>) for sinking particles in the water column at the target depth. This concentration (mol C m<sup>-3 </sup>) was determined using the calculated fluxes of organic carbon in sinking particles (mol C m<sup>-2</sup> day<sup>-1</sup>) derived from the sediment traps and the average sinking rate of particles (m day<sup>-1</sup>). While particle sinking rates were not directly measured during our cruises; we used a value for sinking particles in the ETNP ODZ determined with a particle settling column from Cavan et al. (2017) who reported the ratio of slow sinking vs. fast sinking particle flux to be 18:0.6, with sinking rates measured at a range from 6.5 m day<sup>-1</sup> and 69 m day<sup>-1</sup>. We therefore used an average sinking rate value of 8.45 m day<sup>-1</sup> in these adjustments. The mass concentration of organic carbon in sinking particles at depth (mol C m<sup>-3</sup>) was then used with the actual concentration organic carbon in the top collector chamber (umol C m<sup>-3</sup>) to calculate a unitless "concentration factor" that was used to adjust the initial N<sub>2</sub> production rates (nmol N day<sup>-1</sup>) to account for this factor and arrive at the N<sub>2</sub> production rate due to sinking particles (nmol N day<sup>-1</sup>).&nbsp;</p>
Specified by the Principal Investigator(s)
- Converted NA values to blank values (=missing values).
- Converted date_deployed from format "%m/%d/%Y" to ISO date format "%Y-%m-%d"
- Renamed column N_production_+P to N_production_plus_P
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 Delta V
Thermo Delta V
PI Supplied Instrument Name: Thermo Delta V PI Supplied Instrument Description:Thermo Delta V Isotope Ratio Mass Spectrometer was used to measure 15N of N2 gas. 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/
Cruise: SKQ201617S
SKQ201617S
R/V Sikuliaq
Community Standard Description
International Council for the Exploration of the Sea
R/V Sikuliaq
vessel
SKQ201617S
Gabrielle Rocap
University of Washington
Cruise: RR1805
RR1805
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel
RR1805
Richard Keil
University of Washington
R/V Sikuliaq
Community Standard Description
International Council for the Exploration of the Sea
R/V Sikuliaq
vessel
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel