http://lod.bco-dmo.org/id/dataset/948411
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)
Heterotrophic Production Rates collected from CliOMZ AT50-10 in the Eastern Pacific Ocean from May to June 2023 (CliOMZ project)
2025-01-13
publication
2025-01-13
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-02-27
publication
https://doi.org/10.26008/1912/bco-dmo.948411.1
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) Heterotrophic Production 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 1) Version Date 2025-01-13 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.948411.1 [access date]
Methods and Sampling: <p>Discrete water samples were collected using a rosette sampler equipped with 24×10 L Niskin bottles.&nbsp;<span style="font-size:1rem">Different depths were sampled ranging from 55 meters to 1500 meters. The sampling strategy specifically focused on targeting low oxygen zones within the water column.&nbsp;</span><span style="font-size:1rem">Water was dispensed into 2 mL microcentrifuge tubes in the laboratory.&nbsp;</span><span style="font-size:1rem">Microbial heterotrophic production was measured via the incorporation of [</span><span style="font-size:1rem">3</span><span style="font-size:1rem">H]-leucine into microbial biomass using a modified version of the microcentrifuge method</span><span style="font-size:1rem">&nbsp;(Baetge et. al., 2021).&nbsp;</span><span style="font-size:1rem">[</span><span style="font-size:1rem">3</span><span style="font-size:1rem">H]-leucine (specific activity 44.9 Ci mmol</span><span style="font-size:1rem">-1</span><span style="font-size:1rem">; Perkin Elmer) was added to 1.7 mL of sample at a final concentration of 20 nM and incubated for 2-3 h at in situ temperature. For each depth and station, triplicate live incubations and one killed control, to which 100 µL of trichloroacetic acid (TCA) was added immediately, were carried out.&nbsp;</span><span style="font-size:1rem">At one station, the effect of phenylacetylene and DMSO additions on heterotrophic production activities was tested over a time-span of 24h as described in detail in Bayer et al. 2024.</span></p>
<p><span style="font-size:1rem">Incubations were terminated by addition of cold 100 µL 100% TCA and stored at 4°C until extraction following established procedures&nbsp;</span><span style="font-size:1rem">(Baetge et. al., 2021)</span><span style="font-size:1rem">. DPM were measured on a scintillation counter (Perkin-Elmer Tri-Carb 2910 TR) for 2 min, and [</span><span style="font-size:1rem">3</span><span style="font-size:1rem">H]-leucine incorporation rates were converted to units of carbon using a conversion factor of 1.5 kg C (mol leucine incorporated)</span><span style="font-size:1rem">-1&nbsp;</span><span style="font-size:1rem">(Simon and Azam 1989).</span></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: 1
Unknown
Cruise
Date
Latitude
Longitude
Station
Cast
Depth
Het_production
Treatment
Incubation_time
Perkin-Elmer Tri-Carb 2910 TR
24x10 L Niskin Bottles
theme
None, User defined
Cruise identfier
date
latitude
longitude
station
cast
depth
leucine incorporation rate
treatment
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
-101.4507
-90.0002
-9.9999
9.181
2023-05-04
2023-05-28
Eastern Tropical Pacific
0
BCO-DMO catalogue of parameters from Heterotrophic Production 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/952844.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise name from which sampling took place.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952845.rdf
Name: Date
Units: unitless
Description: <p>Date of sampling.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952846.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Sampling location in decimal degrees; a positive value indicates a Northern coordinate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952847.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Sampling location in decimal degrees; a positive value indicates an Eastern coordinate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952848.rdf
Name: Station
Units: unitless
Description: <p>Station number of cruise AT50-10.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952849.rdf
Name: Cast
Units: unitless
Description: <p>Cast number of cruise AT50-10.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952850.rdf
Name: Depth
Units: meters (m)
Description: <p>Sampling depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952851.rdf
Name: Het_production
Units: nanomoles carbon per liter per day (nmol C/L/d)
Description: <p>Leucine incorporation rate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/952852.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/952853.rdf
Name: Incubation_time
Units: hours (h)
Description: <p>Length of incubation with 3H-Leucine.</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
8653
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/2f147187-0e35-41a3-9566-2683594597c4/content
download
https://doi.org/10.26008/1912/bco-dmo.948411.1
download
onLine
dataset
<p>Discrete water samples were collected using a rosette sampler equipped with 24×10 L Niskin bottles.&nbsp;<span style="font-size:1rem">Different depths were sampled ranging from 55 meters to 1500 meters. The sampling strategy specifically focused on targeting low oxygen zones within the water column.&nbsp;</span><span style="font-size:1rem">Water was dispensed into 2 mL microcentrifuge tubes in the laboratory.&nbsp;</span><span style="font-size:1rem">Microbial heterotrophic production was measured via the incorporation of [</span><span style="font-size:1rem">3</span><span style="font-size:1rem">H]-leucine into microbial biomass using a modified version of the microcentrifuge method</span><span style="font-size:1rem">&nbsp;(Baetge et. al., 2021).&nbsp;</span><span style="font-size:1rem">[</span><span style="font-size:1rem">3</span><span style="font-size:1rem">H]-leucine (specific activity 44.9 Ci mmol</span><span style="font-size:1rem">-1</span><span style="font-size:1rem">; Perkin Elmer) was added to 1.7 mL of sample at a final concentration of 20 nM and incubated for 2-3 h at in situ temperature. For each depth and station, triplicate live incubations and one killed control, to which 100 µL of trichloroacetic acid (TCA) was added immediately, were carried out.&nbsp;</span><span style="font-size:1rem">At one station, the effect of phenylacetylene and DMSO additions on heterotrophic production activities was tested over a time-span of 24h as described in detail in Bayer et al. 2024.</span></p>
<p><span style="font-size:1rem">Incubations were terminated by addition of cold 100 µL 100% TCA and stored at 4°C until extraction following established procedures&nbsp;</span><span style="font-size:1rem">(Baetge et. al., 2021)</span><span style="font-size:1rem">. DPM were measured on a scintillation counter (Perkin-Elmer Tri-Carb 2910 TR) for 2 min, and [</span><span style="font-size:1rem">3</span><span style="font-size:1rem">H]-leucine incorporation rates were converted to units of carbon using a conversion factor of 1.5 kg C (mol leucine incorporated)</span><span style="font-size:1rem">-1&nbsp;</span><span style="font-size:1rem">(Simon and Azam 1989).</span></p>
Specified by the Principal Investigator(s)
<div class="field" id="form_data_processing" style="box-sizing: inherit; margin-bottom: 0.75rem; color: rgb(68, 68, 68); font-family: Lato, sans-serif; font-size: 15px;">
<p>The mean DPM of the samples were corrected for the DPM of the blank and converted into leucine incorporation over time.&nbsp;Leucine incorporation rates were converted to units of carbon using a conversion factor of 1.5 kg C (mol leucine incorporated)-1&nbsp;(Simon and Azam 1989).</p>
</div>
Specified by the Principal Investigator(s)
- Converted the primary data file from a variable width plain text file to a CSV 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 to 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