http://lod.bco-dmo.org/id/dataset/931516
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
2024-07-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Ammonium (NH4) and Nitrite (NO2) concentrations from R/V Roger Revelle cruise RR2311 in the Eastern Tropical South Pacific from November to December 2023
2024-07-31
publication
2024-07-31
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-08-22
publication
https://doi.org/10.26008/1912/bco-dmo.931516.1
Bess B. Ward
Princeton 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: Ward, B. B. (2024) Ammonium (NH4) and Nitrite (NO2) concentrations from R/V Roger Revelle cruise RR2311 in the Eastern Tropical South Pacific from November to December 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-07-31 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.931516.1 [access date]
RR2311 NH4 and NO2 Dataset Description: Methods and Sampling: <p><strong>Water Sample Collection</strong></p>
<p>Water samples for both NO2 and NH4 analyses were collected using a 24 x 10-liter Niskin bottle rosette sampler equipped with a conductivity, temperature, and pressure instrument package (SBE9, Sea-Bird Electronics, Bellevue, Washington, U.S.A.). The sampler was also equipped with sensors for dissolved oxygen (SBE43, Sea-Bird) and chlorophyll fluorescence (FluoroSeatechWetlabsFLF Sensor). NH4 and NO2 were measured on board immediately after sample collection.</p>
<p><strong>NO2 Analysis</strong></p>
<p>Nitrite concentration was measured manually colorimetrically using standard methods (Hansen and Koroleff, 1999).</p>
<p><strong>NH4 Analysis</strong></p>
<p>Duplicate samples for ammonium concentration were measured immediately upon retrieval and were not filtered prior to analysis. Ammonium concentration was measured manually fluorometrically using standard methods (Holmes et al. 1999).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1946516 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1946516
completed
Bess B. Ward
Princeton University
609-258-5150
Geosciences Department 217 Guyot Hall
Princeton
NJ
08544-1003
USA
bbw@princeton.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
CTD_ISO_DateTime_UTC
Date_Local
CTD_Latitude
Lat_Deg
Lat_Min
CTD_Longitude
Long_Deg
Long_Min
Station
Cast_Number
Niskin_Bottle
CTD_Depth
Target_Depth
Nitrite
NH4
SBE9 Sea-Bird Electronics
FluoroSeatechWetlabsFLF_Sensor
10-liter Niskin bottle
SBE43, Sea-Bird
GENESYS 150 UV-VIS Spectrophotometer
Turner Designs fluorometer Model: 7200-000
theme
None, User defined
ISO_DateTime_UTC
date_local
latitude
lat_degs
lat_mins
longitude
lon_degs
lon_mins
station
cast
bottle
depth
Nitrite
Ammonium
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird SBE 911plus
CTD-fluorometer
Niskin bottle
Sea-Bird SBE 43 Dissolved Oxygen Sensor
Spectrophotometer
Turner Designs Trilogy fluorometer
instrument
BCO-DMO Standard Instruments
RR2311
service
Deployment Activity
Eastern Tropical South Pacific
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.
Nitrite Oxidation in Oxygen Minimum Zones
https://osprey.bco-dmo.org/project/831333
Nitrite Oxidation in Oxygen Minimum Zones
<p><em>NSF Award Abstract:</em><br />
This research is grounded in the fundamental role of nitrogen in limiting production in the ocean. Nitrite is a pivotal compound in the nitrogen cycle: it can be oxidized to nitrate, and thus retained as an available nutrient, or it can be reduced to dinitrogen gas, and thus lost from the bioavailable nitrogen pool. Oxidation of nitrite by nitrite oxidizing bacteria (NOB) is the only biological pathway by which nitrate is produced, and all known NOB require oxygen for life. The reduction pathway is also carried out by microbes, in this case, bacteria that thrive only in the absence of oxygen. In previous experiments, however, both oxidation and reduction of nitrite were detected in the same samples from ocean waters in the absence of oxygen. We will investigate three explanations for the apparent oxidation of nitrite in the absence of oxygen on a research cruise to the low oxygen waters off the coast of Peru: 1) The presence of unknown kinds of NOB that do not require oxygen; 2) a new reaction called dismutation, which is possible but never detected in nature; 3) an artifact associated with oxygen stress in NOB. This research could lead to discovery of novel mechanisms and or novel organisms that determine the fate of nitrite and the availability of nitrogen to support primary production in the long run. This project will advance discovery and understanding while promoting teaching, training and learning by providing opportunities for Princeton students to get involved in and have hands on experience in research in the lab and potentially at sea. Both undergraduate and graduate students will participate in the research through internships and field experiences. We will also integrate our work at sea into teaching in the classroom via videos and assignments based on data collected during the cruise.</p>
<p>Nitrite oxidation is the only known biological process that produces nitrate, which comprises the largest fixed nitrogen reservoir in the ocean. Nitrite oxidation is carried out by nitrite oxidizing bacteria (NOB), and all known species are obligate aerobes. Nitrite reduction to N2 occurs in multiple microbial pathways, generally under anoxic conditions. Despite their apparent incompatibility regarding oxygen, both processes are detected in the low oxygen or anoxic waters of oxygen minimum zones (OMZs). Thus, the fate of nitrite in OMZs has implications for the global fixed N budget. Nitrite oxidation is detected at high rates in essentially zero oxygen water in the most oxygen depleted depth intervals in OMZ regions, which suggests that some nitrite oxidizers might possess anaerobic metabolic capabilities. Nitrite disproportionation (or dismutation), in which nitrite is simultaneously oxidized to nitrate and reduced to N2, is a thermodynamically favorable reaction, which would link the two processes in one organism – but it has never been observed in nature. The research proposed here will address two big questions about nitrite in the ocean: 1) How does anaerobic nitrite oxidation work? 2) What determines the fate of nitrite? The experimental approach will investigate three possible explanations for anaerobic nitrite oxidation: 1) Nitrite is oxidized to nitrate by different clades of NOB, which exhibit different tolerances/requirements for oxygen; 2) Nitrite dismutation, also performed by NOB, partially explains the cooccurrence of oxidation and reduction of nitrite; 3) Apparently anaerobic nitrite oxidation is indeed biologically mediated but does not always represent net production of nitrate from nitrite; rather it results from isotopic equilibration during enzyme-catalyzed interconversion of nitrite and nitrate. These questions will be addressed by performing a suite of 15N-tracer incubations at stations located within and outside of one of the major OMZs in the ocean, the Eastern Tropical South Pacific. The dependence of the rate processes on oxygen concentrations will be determined, and the composition of the microbial assemblages will be assessed in order to determine whether different microbial components are involved under different environmental conditions. The expression of genes involved in oxidation/reduction/ respiratory metabolisms at low oxygen concentrations will be measured across oxygen gradients and in oxygen manipulations to identify their potential role in supporting “anaerobic” nitrite oxidation. The possibility that the apparently anaerobic nitrite oxidation is due to an enzyme level interconversion between nitrite and nitrate, which does not lead to net nitrate production and is not linked to growth of nitrite oxidizing bacteria, will also be investigated.</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>
NO2Ox_OMZs
largerWorkCitation
project
eng; USA
oceans
Eastern Tropical South Pacific
-81.0005
-71.10026
-22.90058
-13.99992
2023-11-18
2023-12-20
Eastern Tropical South Pacific and Chesapeake Bay
0
BCO-DMO catalogue of parameters from Ammonium (NH4) and Nitrite (NO2) concentrations from R/V Roger Revelle cruise RR2311 in the Eastern Tropical South Pacific from November to December 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/934662.rdf
Name: CTD_ISO_DateTime_UTC
Units: unitless
Description: <p>Date and time (UTC) of the cast/event in ISO 8601 format (source: CTD)</p>
http://lod.bco-dmo.org/id/dataset-parameter/934663.rdf
Name: Date_Local
Units: unitless
Description: <p>Local date of cast/event in UTC-3</p>
http://lod.bco-dmo.org/id/dataset-parameter/934664.rdf
Name: CTD_Latitude
Units: decimal degrees
Description: <p>Latitude, N is positive (source: Ship)</p>
http://lod.bco-dmo.org/id/dataset-parameter/934665.rdf
Name: Lat_Deg
Units: degrees
Description: <p>Latitude degrees, N is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/934666.rdf
Name: Lat_Min
Units: minutes
Description: <p>Latitude minutes</p>
http://lod.bco-dmo.org/id/dataset-parameter/934667.rdf
Name: CTD_Longitude
Units: decimal degrees
Description: <p>Longitude, E is positive (source: Ship)</p>
http://lod.bco-dmo.org/id/dataset-parameter/934668.rdf
Name: Long_Deg
Units: degrees
Description: <p>Longitude degrees, E is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/934669.rdf
Name: Long_Min
Units: minutes
Description: <p>Longitude minutes</p>
http://lod.bco-dmo.org/id/dataset-parameter/934670.rdf
Name: Station
Units: unitless
Description: <p>Station identifier, project-specific, PS = Process stations, T = Transect station</p>
http://lod.bco-dmo.org/id/dataset-parameter/934671.rdf
Name: Cast_Number
Units: unitless
Description: <p>CTD cast number</p>
http://lod.bco-dmo.org/id/dataset-parameter/934672.rdf
Name: Niskin_Bottle
Units: unitless
Description: <p>Niskin bottle number</p>
http://lod.bco-dmo.org/id/dataset-parameter/934673.rdf
Name: CTD_Depth
Units: meters (m)
Description: <p>Depth (source: CTD)</p>
http://lod.bco-dmo.org/id/dataset-parameter/934674.rdf
Name: Target_Depth
Units: meters (m)
Description: <p>Target depth of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/934675.rdf
Name: Nitrite
Units: micromolar (uM)
Description: <p>Nitrite (NO2) concentration in µM</p>
http://lod.bco-dmo.org/id/dataset-parameter/934676.rdf
Name: NH4
Units: micromolar (uM)
Description: <p>Ammonium (NH4) concentration in µM</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
32218
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/06dc1db7-308c-4485-83d2-437ca43f35a7/content
download
https://doi.org/10.26008/1912/bco-dmo.931516.1
download
onLine
dataset
<p><strong>Water Sample Collection</strong></p>
<p>Water samples for both NO2 and NH4 analyses were collected using a 24 x 10-liter Niskin bottle rosette sampler equipped with a conductivity, temperature, and pressure instrument package (SBE9, Sea-Bird Electronics, Bellevue, Washington, U.S.A.). The sampler was also equipped with sensors for dissolved oxygen (SBE43, Sea-Bird) and chlorophyll fluorescence (FluoroSeatechWetlabsFLF Sensor). NH4 and NO2 were measured on board immediately after sample collection.</p>
<p><strong>NO2 Analysis</strong></p>
<p>Nitrite concentration was measured manually colorimetrically using standard methods (Hansen and Koroleff, 1999).</p>
<p><strong>NH4 Analysis</strong></p>
<p>Duplicate samples for ammonium concentration were measured immediately upon retrieval and were not filtered prior to analysis. Ammonium concentration was measured manually fluorometrically using standard methods (Holmes et al. 1999).</p>
Specified by the Principal Investigator(s)
<p>Measurements were compiled in Excel with CTD collection metadata.</p>
Specified by the Principal Investigator(s)
- Imported submitter files "RR2311_ETSP_2023_NO2andNH4data.xlsx", "rr2311_nh4_no2_check depths_corrected.xlsx", and "924943_v1_rr2311_bottle.csv" into the BCO-DMO system.
- Joined tables to include relevant CTD metadata, including collection time in UTC and location information in decimal degrees.
- Joined tables to include corrected target depths.
- Changed local date format from m-d-y to yyyy-mm-dd (ISO Date 8601 format).
- Renamed fields to comply with BCO-DMO naming conventions.
- Saved the final file as "931516_v1_rr2311_no2_nh4.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
SBE9 Sea-Bird Electronics
SBE9 Sea-Bird Electronics
PI Supplied Instrument Name: SBE9 Sea-Bird Electronics PI Supplied Instrument Description:Water samples were collected using a 24 x 10-liter Niskin bottle rosette sampler equipped with a conductivity, temperature, and pressure instrument package (SBE9, Sea-Bird Electronics, Bellevue, Washington, U.S.A.), a sensor for dissolved oxygen (SBE43, Sea-Bird), and a sensor for chlorophyll fluorescence (FluoroSeatechWetlabsFLF_Sensor). Instrument Name: CTD Sea-Bird SBE 911plus Instrument Short Name:CTD SBE 911plus Instrument Description: The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/
FluoroSeatechWetlabsFLF_Sensor
FluoroSeatechWetlabsFLF_Sensor
PI Supplied Instrument Name: FluoroSeatechWetlabsFLF_Sensor PI Supplied Instrument Description:Water samples were collected using a 24 x 10-liter Niskin bottle rosette sampler equipped with a conductivity, temperature, and pressure instrument package (SBE9, Sea-Bird Electronics, Bellevue, Washington, U.S.A.), a sensor for dissolved oxygen (SBE43, Sea-Bird), and a sensor for chlorophyll fluorescence (FluoroSeatechWetlabsFLF_Sensor). Instrument Name: CTD-fluorometer Instrument Short Name:CTD-fluorometer Instrument Description: A CTD-fluorometer is an instrument package designed to measure hydrographic information (pressure, temperature and conductivity) and chlorophyll fluorescence. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
10-liter Niskin bottle
10-liter Niskin bottle
PI Supplied Instrument Name: 10-liter Niskin bottle PI Supplied Instrument Description:10-liter Niskin bottle 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/
SBE43, Sea-Bird
SBE43, Sea-Bird
PI Supplied Instrument Name: SBE43, Sea-Bird PI Supplied Instrument Description:Water samples were collected using a 24 x 10-liter Niskin bottle rosette sampler equipped with a conductivity, temperature, and pressure instrument package (SBE9, Sea-Bird Electronics, Bellevue, Washington, U.S.A.), a sensor for dissolved oxygen (SBE43, Sea-Bird), and a sensor for chlorophyll fluorescence (FluoroSeatechWetlabsFLF_Sensor). Instrument Name: Sea-Bird SBE 43 Dissolved Oxygen Sensor Instrument Short Name:SBE-43 DO Instrument Description: The Sea-Bird SBE 43 dissolved oxygen sensor is a redesign of the Clark polarographic membrane type of dissolved oxygen sensors. more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0036/
GENESYS 150 UV-VIS Spectrophotometer
GENESYS 150 UV-VIS Spectrophotometer
PI Supplied Instrument Name: GENESYS 150 UV-VIS Spectrophotometer Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/
Turner Designs fluorometer Model: 7200-000
Turner Designs fluorometer Model: 7200-000
PI Supplied Instrument Name: Turner Designs fluorometer Model: 7200-000 PI Supplied Instrument Description:Fluorescence was measured on a Turner Designs fluorometer Model: 7200-000 using a 1 cm cell. Instrument Name: Turner Designs Trilogy fluorometer Instrument Short Name:Turner Trilogy Instrument Description: The Trilogy Laboratory Fluorometer is a compact laboratory instrument for making fluorescence, absorbance, and turbidity measurements using the appropriate snap-in application module. Fluorescence modules are available for discrete sample measurements of various fluorescent materials including chlorophyll (in vivo and extracted), rhodamine, fluorescein, cyanobacteria pigments, ammonium, CDOM, optical brighteners, and other fluorescent compounds.
Cruise: RR2311
RR2311
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel
RR2311
Bess B. Ward
Princeton University
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel