http://lod.bco-dmo.org/id/dataset/970545
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
2025-08-01
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Nitrifier Abundances from R/V Atlantis AT50-10 in the Eastern Tropical and Subtropical Pacific Ocean from May 2023 (CliOMZ project)
2025-08-01
publication
2025-08-01
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-08-05
publication
https://doi.org/10.26008/1912/bco-dmo.970545.1
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) Nitrifier Abundances from R/V Atlantis AT50-10 in the Eastern Tropical and Subtropical Pacific Ocean from May 2023 (CliOMZ project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-08-01 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.970545.1 [access date]
Nitrifier abundances Dataset Description: Methods and Sampling: <p dir="ltr">Discrete water samples were collected using a rosette sampler equipped with 24×10 L Niskin bottles.&nbsp;Different depths were sampled, ranging from 45 meters to 600 meters.&nbsp;Seawater was collected into acid-washed 4 L polycarbonate bottles, biomass was filtered onto 0.22 µm (25mm, Supor PES, Pall) membrane filters, which were subsequently frozen at -80ºC until DNA extraction. DNA was extracted using the Qiagen DNeasy Blood &amp; Tissue kit with modifications as previously described (Santoro et al. 2010). Quantitative PCR assays were conducted using group-specific assays for the 16S ribosomal RNA (rRNA) gene of marine ammonia-oxidizing archaea of the Nitrosopumilaceae family and nitrite-oxidizing bacteria of the Nitrospinaceae family following established protocols and thermocycling conditions (Mincer et al. 2007; Santoro et al. 2010). We modified the previously published primer for marine ammonia-oxidizing archaea (Mincer et al. 2007) to increase the coverage of members of the Nitrosopumilus genus (MGI_F: 5’-GTC TAC CAG AAC ACG TYC-3’, MGI_R: 5’-WGG CGT TGA CTC CAA TTG-3’). Gene copies were quantified on a CFX96 qPCR machine (Bio-Rad) with SYBR Green chemistry. All samples were run in triplicate against a standard curve spanning approximately 10<sup>1</sup> – 10<sup>6</sup> template copies. Linearized plasmids containing cloned inserts of the target genes (TOPO pCR4 vector, Invitrogen) were used as standards as described in (Santoro et al. 2017).</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
Mean_Nitrosopumilaceae
SD_Nitrosopumilaceae
Mean_Nitrospinaceae
SD_Nitrospinaceae
Rosette Sampler equipped with 24x10 L Niskin Bottles
CFX96 Quantitative PCR Machine (Bio-Rad)
theme
None, User defined
Cruise identfier
date
latitude
longitude
station
cast
depth
abundance
featureType
BCO-DMO Standard Parameters
Niskin bottle
qPCR Thermal Cycler
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
-101.816
-90
-10
8.9009
2023-05-13
2023-05-29
Eastern Tropical Pacific
0
BCO-DMO catalogue of parameters from Nitrifier Abundances from R/V Atlantis AT50-10 in the Eastern Tropical and Subtropical Pacific Ocean from May 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/970578.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise name</p>
http://lod.bco-dmo.org/id/dataset-parameter/970579.rdf
Name: Date
Units: unitless
Description: <p>Date of sampling.</p>
http://lod.bco-dmo.org/id/dataset-parameter/970581.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/970580.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Sampling longitude in decimal degrees; a positive value indicates an eastern coordinate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/970582.rdf
Name: Station
Units: unitless
Description: <p>Station number of cruise AT50-10.</p>
http://lod.bco-dmo.org/id/dataset-parameter/970583.rdf
Name: Cast
Units: unitless
Description: <p>Cast number of cruise AT50-10.</p>
http://lod.bco-dmo.org/id/dataset-parameter/970584.rdf
Name: Depth
Units: meters (m)
Description: <p>Sampling depth in meters.</p>
http://lod.bco-dmo.org/id/dataset-parameter/970585.rdf
Name: Mean_Nitrosopumilaceae
Units: 16S rRNA gene copies per L
Description: <p>Nitrosopumilaceae abundances, mean of measurements from triplicate reactions.</p>
http://lod.bco-dmo.org/id/dataset-parameter/970586.rdf
Name: SD_Nitrosopumilaceae
Units: 16S rRNA gene copies per L
Description: <p>Nitrosopumilaceae abundances, standard deviation of measurements from triplicate reactions</p>
http://lod.bco-dmo.org/id/dataset-parameter/970587.rdf
Name: Mean_Nitrospinaceae
Units: 16S rRNA gene copies per L
Description: <p>Nitrospinaceae abundances, mean of measurements from triplicate reactions.</p>
http://lod.bco-dmo.org/id/dataset-parameter/970588.rdf
Name: SD_Nitrospinaceae
Units: 16S rRNA gene copies per L
Description: <p>Nitrospinaceae abundances, standard deviation of measurements from triplicate reactions</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
2811
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/f274cf88-cbf3-411f-9adf-b8a08b3f5536/content
download
https://doi.org/10.26008/1912/bco-dmo.970545.1
download
onLine
dataset
<p dir="ltr">Discrete water samples were collected using a rosette sampler equipped with 24×10 L Niskin bottles.&nbsp;Different depths were sampled, ranging from 45 meters to 600 meters.&nbsp;Seawater was collected into acid-washed 4 L polycarbonate bottles, biomass was filtered onto 0.22 µm (25mm, Supor PES, Pall) membrane filters, which were subsequently frozen at -80ºC until DNA extraction. DNA was extracted using the Qiagen DNeasy Blood &amp; Tissue kit with modifications as previously described (Santoro et al. 2010). Quantitative PCR assays were conducted using group-specific assays for the 16S ribosomal RNA (rRNA) gene of marine ammonia-oxidizing archaea of the Nitrosopumilaceae family and nitrite-oxidizing bacteria of the Nitrospinaceae family following established protocols and thermocycling conditions (Mincer et al. 2007; Santoro et al. 2010). We modified the previously published primer for marine ammonia-oxidizing archaea (Mincer et al. 2007) to increase the coverage of members of the Nitrosopumilus genus (MGI_F: 5’-GTC TAC CAG AAC ACG TYC-3’, MGI_R: 5’-WGG CGT TGA CTC CAA TTG-3’). Gene copies were quantified on a CFX96 qPCR machine (Bio-Rad) with SYBR Green chemistry. All samples were run in triplicate against a standard curve spanning approximately 10<sup>1</sup> – 10<sup>6</sup> template copies. Linearized plasmids containing cloned inserts of the target genes (TOPO pCR4 vector, Invitrogen) were used as standards as described in (Santoro et al. 2017).</p>
Specified by the Principal Investigator(s)
<p>16S rRNA gene copy numbers per liter&nbsp;were calculated by correcting for the amount of filtered seawater.</p>
Specified by the Principal Investigator(s)
- Date values in primary data file converted from %d.%m.%y to %Y-%m-%d format.
- Latitude and longitude values have been corrected and rounded to 6 degrees of precision.
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
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/
CFX96 Quantitative PCR Machine (Bio-Rad)
CFX96 Quantitative PCR Machine (Bio-Rad)
PI Supplied Instrument Name: CFX96 Quantitative PCR Machine (Bio-Rad) PI Supplied Instrument Description:16S rRNA gene abundances were quantified using a CFX96 quantitative PCR machine (Bio-Rad). Instrument Name: qPCR Thermal Cycler Instrument Short Name:qPCR Instrument Description: An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).
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