http://lod.bco-dmo.org/id/dataset/954872
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
2025-02-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Nitrification and nitrite oxidation rate data collected during R/V Revelle cruise RR2104 and R/V Atlantis cruise AT50-10 in the Eastern Tropical and Subtropical Pacific Ocean from 2021 to 2023
2025-02-27
publication
2025-02-27
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-04-28
publication
https://doi.org/10.26008/1912/bco-dmo.954872.1
Alyson E. Santoro
University of California-Santa Barbara
principalInvestigator
Barbara Bayer
University of California-Santa Barbara
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: Santoro, A. E., Bayer, B. (2025) Nitrification and nitrite oxidation rate data collected during R/V Revelle cruise RR2104 and R/V Atlantis cruise AT50-10 in the Eastern Tropical and Subtropical Pacific Ocean from 2021 to 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-02-27 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.954872.1 [access date]
Nitrification and nitrite oxidation rate data Dataset Description: Methods and Sampling: <p dir="ltr">Water samples were collected during cruises&nbsp; RR2104 and AT50-10 in the eastern tropical and subtropical Pacific Ocean. Discrete water samples were obtained using a CTD rosette sampler equipped with 24 x 10 L Niskin bottles. Different depths were sampled, ranging from 35 meters to 300 meters.</p>
<p dir="ltr">Nitrification and nitrite oxidation rates were determined using&nbsp;<sup>15</sup>N isotope tracer methods.&nbsp;For oxygenated depths, incubations were conducted in 1L or 250 mL polycarbonate bottles (Nalgene) and for depths with low in situ O<sub>2</sub>&nbsp;concentrations (≤&nbsp;20 µM),&nbsp;incubations were conducted in 500 mL Tedlar bags (Restek) equipped with a septum injection port and three-way stopcocks, following the procedures described previously (Santoro et al. 2021).&nbsp;Each bottle or bag was spiked with&nbsp;[<sup>15</sup>N]-tracer&nbsp;(99 atm%&nbsp;<sup>15</sup>NH<sub>4</sub>Cl or 98 atm% Na<sup>15</sup>NO<sub>2</sub>-, Cambridge Isotope Laboratories) to a final label concentration of 70 to 200 nM (depending on the depth and productivity region the sample was collected from), and incubations were conducted as close to&nbsp;in situ&nbsp;temperature conditions as possible (±1.5°C).&nbsp;Phenylacetylene (10 µM) dissolved in dimethylsulfoxide (DMSO, 0.01%) was used to some bottles to test its efficiency in inhibiting ammonia oxidation activities.&nbsp;At timepoints of 0, 12, and 24 h, 50 mL samples were drawn from each bottle or bag, 0.2 µm syringe-filtered into a 20 mL HDPE bottle, and frozen at -20ºC. Frozen samples were transported to the laboratory, thawed, and prepared for&nbsp;δ<sup>15</sup>N<sub>NO2+NO3</sub>&nbsp;analysis using the ‘denitrifier method’ (Sigman et al. 2001). For nitrite oxidation rate samples, the added&nbsp;<sup>15</sup>NO<sub>2</sub>-&nbsp;tracer was removed using sulfamic acid addition and subsequent neutralization with NaOH prior to sample preparation (Granger et al. 2006). Samples were analyzed on a custom purge and trap system interfaced to a Thermo Delta Plus XP isotope ratio mass spectrometer (McIlvin and Casciotti 2011).&nbsp;δ<sup>15</sup>N<sub>NOx</sub>&nbsp;values were calibrated against NO<sub>3</sub>-&nbsp;isotope reference materials USGS 32, USGS 34, and USGS 35, analyzed in parallel.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924512 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924512
completed
Alyson E. Santoro
University of California-Santa Barbara
805-893-5318
2155 Marine Biotech Lab
Santa Barbara
CA
93106
USA
asantoro@ucsb.edu
pointOfContact
Barbara Bayer
University of California-Santa Barbara
Department of Microbiology and Ecosystem Science
Vienna
Austria
bbayer@ucsb.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Cruise
Date
Latitude
Longitude
Station
Cast
Depth
Nitrification
Nitrite_oxidation
Treatment
Thermo Delta Plus XP isotope ratio mass spectrometer
Rosette Sampler equipped with 24x10 L Niskin Bottles
theme
None, User defined
Cruise identfier
date
latitude
longitude
station id
cast
depth
Nitrite
treatment
featureType
BCO-DMO Standard Parameters
Mass Spectrometer
Niskin bottle
instrument
BCO-DMO Standard Instruments
RR2104
AT50-10
service
Deployment Activity
Eastern Tropical and Subtropical Pacific Ocean
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: Underexplored Connections between Nitrogen and Trace Metal Cycling in Oxygen Minimum Zones Mediated by Metalloenzyme Inventories
https://osprey.bco-dmo.org/project/806565
Collaborative Research: Underexplored Connections between Nitrogen and Trace Metal Cycling in Oxygen Minimum Zones Mediated by Metalloenzyme Inventories
<p><em>NSF abstract:</em><br />
Though scarce and largely insoluble, trace metals are key components of sophisticated enzymes (protein molecules that speed up biochemical reactions) involved in biogeochemical cycles in the dark ocean (below 1000m). For example, metalloenzymes are involved in nearly every reaction in the nitrogen cycle. Yet, despite direct connections between trace metal and nitrogen cycles, the relationship between trace metal distributions and biological nitrogen cycling processes in the dark ocean have rarely been explored, likely due to the technical challenges associated with their study. Availability of the autonomous underwater vehicle (AUV) Clio, a sampling platform capable of collecting high-resolution vertical profile samples for biochemical and microbial measurements by large volume filtration of microbial particulate material, has overcome this challenge. Thus, this research project plans an interdisciplinary chemistry, biology, and engineering effort to test the hypothesis that certain chemical reactions, such as nitrite oxidation, could become limited by metal availability within the upper mesopelagic and that trace metal demands for nitrite-oxidizing bacteria may be increased under low oxygen conditions. Broader impacts of this study include the continued development and application of the Clio Biogeochemical AUV as a community resource by developing and testing its high-resolution and adaptive sampling capabilities. In addition, metaproteomic data will be deposited into the recently launched Ocean Protein Portal to allow oceanographers and the metals in biology community to examine the distribution of proteins and metalloenzymes in the ocean. Undergraduate students will be supported by this project at all three institutions, with an effort to recruit minority students. The proposed research will also be synergistic with the goals of early community-building efforts for a potential global scale microbial biogeochemistry program modeled after the success of the GEOTRACES program, provisionally called "Biogeoscapes: Ocean metabolism and nutrient cycles on a changing planet".</p>
<p>The proposed research project will test the following three hypotheses: (1) the microbial metalloenzyme distribution of the mesopelagic is spatially dynamic in response to environmental gradients in oxygen and trace metals, (2) nitrite oxidation in the Eastern Tropical Pacific Ocean can be limited by iron availability in the upper mesopelagic through an inability to complete biosynthesis of the microbial protein nitrite oxidoreductase, and (3) nitrite-oxidizing bacteria increase their metalloenzyme requirements at low oxygen, impacting the distribution of both dissolved and particulate metals within oxygen minimum zones. One of the challenges to characterizing the biogeochemistry of the mesopelagic ocean is an inability to effectively sample it. As a sampling platform, we will use the novel biogeochemical AUV Clio that enables high-resolution vertical profile samples for biochemical and microbial measurements by large volume filtration of microbial particulate material on a research expedition in the Eastern Tropical Pacific Ocean. Specific research activities will be orchestrated to test the hypotheses. Hypothesis 1 will be explored by comparison of hydrographic, microbial distributions, dissolved and particulate metal data, and metaproteomic results with profile samples collected by Clio. Hypothesis 2 will be tested by incubation experiments using 15NO2- oxidation rates on Clio-collected incubation samples. Hypothesis 3 will be tested by dividing targeted nitrite oxidoreductase protein copies by qPCR (quantitative polymerase chain reaction)-based nitrite oxidizing bacteria abundance (NOB) to determine if cellular copy number varies with oxygen distributions, and by metalloproteomic analyses of NOB cultures. The demonstration of trace metal limitation of remineralization processes, not just primary production, would transform our understanding of the role of metals in biogeochemical cycling and provide new ways with which to interpret sectional data of dissolved and particulate trace metal distributions in the ocean. The idea that oxygen may play a previously underappreciated role in controlling trace metals due not just to metals' physical chemistry, but also from changing biological demand, will improve our ability to predict trace metal distributions in the face of decreasing ocean oxygen content.</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>
CliOMZ
largerWorkCitation
project
eng; USA
oceans
Eastern Tropical and Subtropical Pacific Ocean
-124.7016
-90.0002
-9.9999
33.549
2021-06-16
2023-06-02
Eastern Tropical Pacific
0
BCO-DMO catalogue of parameters from Nitrification and nitrite oxidation rate data collected during R/V Revelle cruise RR2104 and R/V Atlantis cruise AT50-10 in the Eastern Tropical and Subtropical Pacific Ocean from 2021 to 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/956828.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/956829.rdf
Name: Date
Units: unitless
Description: <p>Date of sampling.</p>
http://lod.bco-dmo.org/id/dataset-parameter/956830.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sampling location in decimal degrees; a positive value indicates a northern coordinate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/956831.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sampling location in decimal degrees; a negative value indicates a western coordinate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/956832.rdf
Name: Station
Units: unitless
Description: <p>Station number of cruises RR2104 and AT50-10.</p>
http://lod.bco-dmo.org/id/dataset-parameter/956833.rdf
Name: Cast
Units: unitless
Description: <p>Cast number of cruises RR2104 and AT50-10.</p>
http://lod.bco-dmo.org/id/dataset-parameter/956834.rdf
Name: Depth
Units: meters (m)
Description: <p>Sampling depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/956835.rdf
Name: Nitrification
Units: nanomoles per Liter per day (nmol/L/day)
Description: <p>Nitrite oxidation rate from sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/956836.rdf
Name: Nitrite_oxidation
Units: nanomoles per Liter per day (nmol/L/day)
Description: <p>Nitrite oxidation rate from sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/956837.rdf
Name: Treatment
Units: unitless
Description: <p>Additional amendments to incubation bottle; (none; phenylacetylene addition).</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
6698
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/b3826fa7-d96f-470d-84a7-badbda61dec5/content
download
https://doi.org/10.26008/1912/bco-dmo.954872.1
download
onLine
dataset
<p dir="ltr">Water samples were collected during cruises&nbsp; RR2104 and AT50-10 in the eastern tropical and subtropical Pacific Ocean. Discrete water samples were obtained using a CTD rosette sampler equipped with 24 x 10 L Niskin bottles. Different depths were sampled, ranging from 35 meters to 300 meters.</p>
<p dir="ltr">Nitrification and nitrite oxidation rates were determined using&nbsp;<sup>15</sup>N isotope tracer methods.&nbsp;For oxygenated depths, incubations were conducted in 1L or 250 mL polycarbonate bottles (Nalgene) and for depths with low in situ O<sub>2</sub>&nbsp;concentrations (≤&nbsp;20 µM),&nbsp;incubations were conducted in 500 mL Tedlar bags (Restek) equipped with a septum injection port and three-way stopcocks, following the procedures described previously (Santoro et al. 2021).&nbsp;Each bottle or bag was spiked with&nbsp;[<sup>15</sup>N]-tracer&nbsp;(99 atm%&nbsp;<sup>15</sup>NH<sub>4</sub>Cl or 98 atm% Na<sup>15</sup>NO<sub>2</sub>-, Cambridge Isotope Laboratories) to a final label concentration of 70 to 200 nM (depending on the depth and productivity region the sample was collected from), and incubations were conducted as close to&nbsp;in situ&nbsp;temperature conditions as possible (±1.5°C).&nbsp;Phenylacetylene (10 µM) dissolved in dimethylsulfoxide (DMSO, 0.01%) was used to some bottles to test its efficiency in inhibiting ammonia oxidation activities.&nbsp;At timepoints of 0, 12, and 24 h, 50 mL samples were drawn from each bottle or bag, 0.2 µm syringe-filtered into a 20 mL HDPE bottle, and frozen at -20ºC. Frozen samples were transported to the laboratory, thawed, and prepared for&nbsp;δ<sup>15</sup>N<sub>NO2+NO3</sub>&nbsp;analysis using the ‘denitrifier method’ (Sigman et al. 2001). For nitrite oxidation rate samples, the added&nbsp;<sup>15</sup>NO<sub>2</sub>-&nbsp;tracer was removed using sulfamic acid addition and subsequent neutralization with NaOH prior to sample preparation (Granger et al. 2006). Samples were analyzed on a custom purge and trap system interfaced to a Thermo Delta Plus XP isotope ratio mass spectrometer (McIlvin and Casciotti 2011).&nbsp;δ<sup>15</sup>N<sub>NOx</sub>&nbsp;values were calibrated against NO<sub>3</sub>-&nbsp;isotope reference materials USGS 32, USGS 34, and USGS 35, analyzed in parallel.</p>
Specified by the Principal Investigator(s)
<p>Nitrification and nitrite oxidation rates were calculated using the basic equations of Dugdale and Goering (1967).</p>
Specified by the Principal Investigator(s)
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 Plus XP isotope ratio mass spectrometer
Thermo Delta Plus XP isotope ratio mass spectrometer
PI Supplied Instrument Name: Thermo Delta Plus XP isotope ratio mass spectrometer PI Supplied Instrument Description:d15N values were measured on a Thermo Delta Plus XP isotope ratio mass spectrometer. Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Rosette Sampler equipped with 24x10 L Niskin Bottles
Rosette Sampler equipped with 24x10 L Niskin Bottles
PI Supplied Instrument Name: Rosette Sampler equipped with 24x10 L Niskin Bottles PI Supplied Instrument Description:Discrete water samples were collected using a rosette sampler equipped with 24×10 L 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/
Cruise: RR2104
RR2104
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel
RR2104
C. Anela Choy
University of California-San Diego
Cruise: AT50-10
AT50-10
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT50-10
Mak A. Saito
Woods Hole Oceanographic Institution
https://www.rvdata.us/search/cruise/AT50-10
Report describing AT50-10
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel