http://lod.bco-dmo.org/id/dataset/948396
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
2025-01-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Dark DIC Fixation Rates collected from CliOMZ AT50-10 in the Eastern Pacific Ocean from May to June 2023 (CliOMZ project)
2025-08-05
publication
2025-08-05
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-02-27
publication
https://doi.org/10.26008/1912/bco-dmo.948396.1
Alyson E. Santoro
University of California-Santa Barbara
principalInvestigator
Barbara Bayer
University of Vienna
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) Dark DIC Fixation Rates collected from CliOMZ AT50-10 in the Eastern Pacific Ocean from May to June 2023 (CliOMZ project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 4) Version Date 2025-08-05 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.948396.4 [access date]
Methods and Sampling: <p>Water samples were collected during cruise 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 55 meters to 1500 meters. The sampling strategy focussed on targeting low oxygen zones within the water column. &nbsp;For depths where O2&nbsp;concentrations were above 20 µM, water was dispensed into 40 mL glass vials with teflon septa (TOC-certified, Fisher Scientific). For depths where&nbsp;in situ&nbsp;O2&nbsp;concentrations were&nbsp;≤20 µM, water was sampled directly from the Niskin bottle into 60 mL glass serum bottles using tygon tubing, allowing approximately three volumes of sample water to overflow the bottle prior to collection. Serum bottles were closed bubble-free with deoxygenated butyl rubber stoppers (De Brabandere et al. 2012) and sealed with aluminum crimps. A 20 mL helium (He) headspace was introduced to each serum bottle and oxygen was then added back to reach&nbsp;in situ&nbsp;concentrations by injecting air using gas-tight syringes (Hamilton) with volumes calculated using the solubility equations of Garcia and Gordon (1992).</p>
<p>For each depth, seven replicate bottles were filled, sealed&nbsp;and spiked with 50 µCi [14C]-bicarbonate (specific activity 56 mCi mmol−1/2.072 × 109 Bq mmol−1; PerkinElmer).&nbsp;To three bottles, 10 µM phenylacetylene dissolved in DMSO (0.01% final concentration) was added to inhibit ammonia oxidation activities as described in Bayer et al. 2024. One bottle served as killed control to which formaldehyde (3% vol/vol) was added at the start of incubation. Bottles were incubated in the dark at&nbsp;in situ&nbsp;temperature and live incubations terminated after 24-72 hours by adding formaldehyde (3% vol/vol). After 30–60 minutes, samples were filtered onto 0.2&nbsp;μm polycarbonate filters (GTTP, 25mm, Millipore) and rinsed with 10&nbsp;mL of artificial seawater at a vacuum pump pressure of&nbsp;~100 mbar. Incubation times were chosen according to the productivity of the sampling region (Bayer et al. 2024). The filters were transferred to scintillation vials, 10&nbsp;mL of scintillation cocktail (Ultima Gold; PerkinElmer) was added, samples were shaken for ca. 30 seconds&nbsp;and incubated in the dark for at least 24 hours prior to counting the disintegrations per minute (DPM) in a scintillation counter (Perkin-Elmer Tri-Carb 2910 TR) for 15 minutes. Total radioactivity measurements were performed to verify added [14C]-bicarbonate concentrations and DIC fixation rates were calculated as described previously (Bayer et al. 2022).</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 Vienna
Department of Microbiology and Ecosystem Science
Vienna
Austria
bbayer@ucsb.edu
pointOfContact
asNeeded
Dataset Version: 4
Unknown
Cruise
Date
Latitude
Longitude
Station
Cast
Depth
Treatment
DIC_fixation
Incubation_time
DIC_conc
Perkin-Elmer Tri-Carb 2910 TR
24x10 L Niskin Bottles
theme
None, User defined
Cruise identfier
date
latitude
longitude
station
cast
depth
treatment
dissolved inorganic Carbon
incubation time or duration
featureType
BCO-DMO Standard Parameters
Liquid Scintillation Counter
Niskin bottle
instrument
BCO-DMO Standard Instruments
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
-108.05027
-88.97095
-9.9999
16.07453
2023-05-04
2023-06-02
Eastern Tropical Pacific
0
BCO-DMO catalogue of parameters from Dark DIC Fixation Rates collected from CliOMZ AT50-10 in the Eastern Pacific Ocean from May to June 2023 (CliOMZ 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
http://lod.bco-dmo.org/id/dataset-parameter/952887.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise name from which sampling took place.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952888.rdf
Name: Date
Units: unitless
Description: <p>Date of sampling.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952890.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Sampling latitude in decimal degrees; a positive value indicates a northern coordinate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952889.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Sampling longitude in decimal degrees; a positive value indicates a western coordinate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952891.rdf
Name: Station
Units: unitless
Description: <p>Station number of cruise AT50-10.</p>
http://lod.bco-dmo.org/id/dataset-parameter/971949.rdf
Name: Cast
Units: unitless
Description: <p>Cast from which sample was taken.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952892.rdf
Name: Depth
Units: meters (m)
Description: <p>Sampling depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952893.rdf
Name: Treatment
Units: unitless
Description: <p>Additional amendments to incubation bottle; treatment options include, none, phenylacetylene addition, and DMSO.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952894.rdf
Name: DIC_fixation
Units: nanomoles per liter per day (nmol/L/d)
Description: <p>Dark DIC fixation rate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952895.rdf
Name: Incubation_time
Units: hours (h)
Description: <p>Length of incubation with 14C-bicarbonate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952896.rdf
Name: DIC_conc
Units: micromoles per liter (umol/L)
Description: <p>Concentration of dissolved inorganic carbon.</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
18076
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/bbe9a575-605f-48ce-95a8-1b745fa65c64/content
download
18033
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/abc07cf4-f7a8-4266-a449-59db694e5d3b/content
download
18003
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/df1c90f9-957d-44eb-ba0e-dfeda7d87495/content
download
18031
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/462668ce-ce1d-466c-a5a8-9d9dc1a127a5/content
download
18031
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/4d770ae6-b0d0-4aba-a495-75af0d407837/content
download
https://doi.org/10.26008/1912/bco-dmo.948396.1
download
onLine
dataset
<p>Water samples were collected during cruise 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 55 meters to 1500 meters. The sampling strategy focussed on targeting low oxygen zones within the water column. &nbsp;For depths where O2&nbsp;concentrations were above 20 µM, water was dispensed into 40 mL glass vials with teflon septa (TOC-certified, Fisher Scientific). For depths where&nbsp;in situ&nbsp;O2&nbsp;concentrations were&nbsp;≤20 µM, water was sampled directly from the Niskin bottle into 60 mL glass serum bottles using tygon tubing, allowing approximately three volumes of sample water to overflow the bottle prior to collection. Serum bottles were closed bubble-free with deoxygenated butyl rubber stoppers (De Brabandere et al. 2012) and sealed with aluminum crimps. A 20 mL helium (He) headspace was introduced to each serum bottle and oxygen was then added back to reach&nbsp;in situ&nbsp;concentrations by injecting air using gas-tight syringes (Hamilton) with volumes calculated using the solubility equations of Garcia and Gordon (1992).</p>
<p>For each depth, seven replicate bottles were filled, sealed&nbsp;and spiked with 50 µCi [14C]-bicarbonate (specific activity 56 mCi mmol−1/2.072 × 109 Bq mmol−1; PerkinElmer).&nbsp;To three bottles, 10 µM phenylacetylene dissolved in DMSO (0.01% final concentration) was added to inhibit ammonia oxidation activities as described in Bayer et al. 2024. One bottle served as killed control to which formaldehyde (3% vol/vol) was added at the start of incubation. Bottles were incubated in the dark at&nbsp;in situ&nbsp;temperature and live incubations terminated after 24-72 hours by adding formaldehyde (3% vol/vol). After 30–60 minutes, samples were filtered onto 0.2&nbsp;μm polycarbonate filters (GTTP, 25mm, Millipore) and rinsed with 10&nbsp;mL of artificial seawater at a vacuum pump pressure of&nbsp;~100 mbar. Incubation times were chosen according to the productivity of the sampling region (Bayer et al. 2024). The filters were transferred to scintillation vials, 10&nbsp;mL of scintillation cocktail (Ultima Gold; PerkinElmer) was added, samples were shaken for ca. 30 seconds&nbsp;and incubated in the dark for at least 24 hours prior to counting the disintegrations per minute (DPM) in a scintillation counter (Perkin-Elmer Tri-Carb 2910 TR) for 15 minutes. Total radioactivity measurements were performed to verify added [14C]-bicarbonate concentrations and DIC fixation rates were calculated as described previously (Bayer et al. 2022).</p>
Specified by the Principal Investigator(s)
<p>The mean DPM of the samples were corrected for the DPM of the blank, converted into organic carbon fixed over time and corrected for the ambient seawater DIC concentration.&nbsp;</p>
Specified by the Principal Investigator(s)
Version 1 (948396_v1_dark_dic_fixation_rates.csv)
- Converted the primary data file from a variable-width plain text file to a CSV file.
- Dates converted from %d/%m/%Y to %Y-%m-%d.
- Latitude and longitude values corrected (original file contained transcription errors).
- This version contains altered (incorrect and inconsistent) data values caused by Excel. These errors have been corrected in Version 2 of the data.
Version 2 (948396_v2_dark_dic_fixation_rates.csv)
- Removed blank rows from the provided data file.
- Dates converted from %d/%m/%Y to %Y-%m-%d.
- NA "no data" values in data file have been replaced with blank values.
- Version 2 of this dataset includes data corrections to the original file.
Version 3 (948396_v3_dark_dic_fixation_rates.csv)
- Latitude and longitude values were corrected (previous version contained flipped coordinate values).
- Latitude and longitude values were rounded to 6 degrees of precision.
Version 4 (948396_v4_dark_dic_fixation_rates.csv)
- Latitude and longitude values were corrected further.
- Latitude and longitude values were rounded to 6 degrees of precision.
- Missing measurement values were added to the primary data file.
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
Perkin-Elmer Tri-Carb 2910 TR
Perkin-Elmer Tri-Carb 2910 TR
PI Supplied Instrument Name: Perkin-Elmer Tri-Carb 2910 TR PI Supplied Instrument Description:Disintegrations per minute (DPM) were counted in a scintillation counter (Perkin-Elmer Tri-Carb 2910 TR). Instrument Name: Liquid Scintillation Counter Instrument Short Name:LSC Instrument Description: Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used the quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.
Liquid scintillation counters are instruments assaying alpha and beta radiation by quantitative detection of visible light produced by the passage of rays or particles through a suitable scintillant incorporated into the sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB21/
24x10 L Niskin Bottles
24x10 L Niskin Bottles
PI Supplied Instrument Name: 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: 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 Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel