http://lod.bco-dmo.org/id/dataset/1005611
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
2026-08-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Depth profiles of nutrients and dark carbon fixation rates collected from the San Pedro Ocean Time-series (SPOT) R/V Yellowfin cruise in the San Pedro Basin on February 19, 2025
2026-08-19
publication
2026-08-19
revision
BCO-DMO Linked Data URI
2026-08-19
creation
http://lod.bco-dmo.org/id/dataset/1005611
David A. Hutchins
University of Southern California
principalInvestigator
Wei Qin
University of Oklahoma
principalInvestigator
Feixue Fu
University of Southern California
principalInvestigator
Seth G. John
University of Southern California
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: Qin, W., Hutchins, D. A., Fu, F., John, S. G. (2026) Depth profiles of nutrients and dark carbon fixation rates collected from the San Pedro Ocean Time-series (SPOT) R/V Yellowfin cruise in the San Pedro Basin on February 19, 2025. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-08-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/1005611 [access date]
Depth profiles of nutrients and dark carbon fixation rates SPOT 2025 Dataset Description: Methods and Sampling: <p>Water samples for nutrient analyses were collected from CTD Niskin bottles at discrete depths (15–100 m) from a single CTD cast. Approximately 40 mL of seawater was filtered onboard through 0.22 μm sterile syringe filters (Basix™ PES) and immediately frozen using an ethanol and dry ice bath prior to storage. Ammonia concentrations were determined using the o-phthaldialdehyde (OPA) fluorescence method following Holmes et al. (1999). Nitrite concentrations were measured spectrophotometrically using the sulfanilamide–NED method as described in Grasshoff et al. (1999). Nitrate concentrations were determined using the vanadium(III) chloride reduction method following García-Robledo et al. (2014).</p>
<p>For dark carbon fixation measurements, seawater was collected from CTD Niskin bottles from the same CTD cast and maintained in the dark at near in situ temperature. Four subsamples (90 mL each) were transferred into separate 110 mL acid-cleaned HDPE brown bottles. All subsamples were collected from the same Niskin bottle at each depth and divided into replicate incubations. All bottles were amended with approximately 6 μCi of 14C-labeled bicarbonate. One subsample was treated with 2.5% glutaraldehyde as a killed control, while the remaining three subsamples were incubated as biological replicates. Incubations were conducted in the dark at temperatures approximating in situ conditions (~15 °C for the 15m sample and ~11 °C for deeper samples). After ~60 hours of incubation, samples were processed following standard 14C carbon fixation protocols, including filtration and radioactivity measurement by liquid scintillation counting.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2336534 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2336534
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2610907 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2610907
onGoing
David A. Hutchins
University of Southern California
213-740-5616
Department of Biological Sciences 3616 Trousdale Parkway, AHF 20
Los Angeles
CA
90089
USA
dahutch@usc.edu
pointOfContact
Wei Qin
University of Oklahoma
601 S Goodwin Ave Room C205 CLSL
Urbana
IL
61801
USA
weiqin@illinois.edu
pointOfContact
Feixue Fu
University of Southern California
2137403188
Department of Biology, MC 0371, University of Southern California 3616 Trousdale Pkwy
Los Angeles
CA
90089
USA
ffu@usc.edu
pointOfContact
Seth G. John
University of Southern California
213-740-0696
USC ZHS 117 2651 Trousdale Pkwy.
Los Angeles
CA
90089
USA
sethjohn@usc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Date_of_sampling
Latitude
Longitude
Depth
Ammonia
Nitrite
Nitrate
DCF
DCF_stdev
Wallac System 1400 liquid scintillation counter
Niskin bottles
Sea-Bird Electronics SBE 9plus
Shimadzu UV-1800 UV–Vis spectrophotometer
Turner Designs Trilogy fluorometer
theme
None, User defined
date
latitude
longitude
depth
Ammonia
Nitrite
Nitrate
No BCO-DMO term
standard deviation
featureType
BCO-DMO Standard Parameters
Liquid Scintillation Counter
Niskin bottle
Sea-Bird SBE 9plus CTD
Spectrophotometer
Turner Designs Trilogy fluorometer
instrument
BCO-DMO Standard Instruments
SPOT_20250219
service
Deployment Activity
San Pedro Basin
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: The impact of ocean warming on bioactive trace metal requirements and use efficiencies of marine nitrifying microorganisms
https://osprey.bco-dmo.org/project/921937
Collaborative Research: The impact of ocean warming on bioactive trace metal requirements and use efficiencies of marine nitrifying microorganisms
<p><em>NSF Award Abstract:</em></p>
<p>This project seeks to provide a deeper understanding of how major biogeochemical cycles that support all living marine resources will respond to climate warming in a changing ocean environment. It will train one postdoctoral researcher and three graduate students, and provides research training opportunities for undergraduate students in microbial physiology and ecology, bioinformatics, trace metal biogeochemistry, and oceanography. Project personnel also conduct K-12 education and outreach activities. All data is freely available through the Biological and Chemical Oceanographic Data Management Office (BCO-DMO).</p>
<p>This project investigates how climate warming will interact with the unique trace metal requirements of marine nitrifying microorganisms (nitrifiers) to affect ammonia and nitrite oxidation pathways in the rapidly changing ocean. Four investigators with diverse expertise in microbial global change physiology, nitrogen and trace metal biogeochemistry, and mechanistic transcriptomics and proteomics combine their efforts, using well-controlled pure culture-based laboratory studies along with field incubation experiments with natural communities to systematically investigate 1) thermal effects on iron (Fe) and copper (Cu) requirements and use efficiencies in isolated cultures and natural populations of marine ammonia-oxidizing archaea and bacteria (AOA, AOB) and nitrite-oxidizing bacteria (NOB), 2) the underlying molecular and biochemical mechanisms that facilitate such thermally-driven adaptive responses, and 3) system-level feedbacks between global change, trace metal biogeochemistry, and marine nitrifiers and their associated microbial communities in diverse marine environments. Together, these studies enhance our understanding of the marine nitrogen cycle and trace metal biogeochemistry, and ultimately contribute to a more detailed understanding of the impact of rapid ocean warming on critical major nutrient and micronutrient cycles.</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>
Nitrifiers_TMReqs_OceanWarming
largerWorkCitation
project
eng; USA
biota
oceans
San Pedro Basin
-118.4
-118.4
33.55
33.55
2025-02-19
2025-02-19
Eastern North Pacific: HNLC and subtropical gyre; SPOT time-series station; HOT time-series station.
0
BCO-DMO catalogue of parameters from Depth profiles of nutrients and dark carbon fixation rates collected from the San Pedro Ocean Time-series (SPOT) R/V Yellowfin cruise in the San Pedro Basin on February 19, 2025
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/1005823.rdf
Name: Date_of_sampling
Units: unitless
Description: <p>Date of sampling in Pacific Standard Time</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005824.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sampling location, positive is North</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005826.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sampling location, negative is West</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005828.rdf
Name: Depth
Units: meters (m)
Description: <p>Sampling depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005830.rdf
Name: Ammonia
Units: nanomole per liter (nM)
Description: <p>Ammonia concentration in seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005831.rdf
Name: Nitrite
Units: nanomole per liter (nM)
Description: <p>Nitrite concentration in seawater. Nitrite values not detected or below the detection limit are not included in the dataset.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005832.rdf
Name: Nitrate
Units: micromole per liter (μM)
Description: <p>Nitrate concentration in seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005833.rdf
Name: DCF
Units: nanomole carbon per liter per day (nM C d⁻¹)
Description: <p>Dark carbon fixation rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005834.rdf
Name: DCF_stdev
Units: nanomole carbon per liter per day (nM C d⁻¹)
Description: <p>Standard deviation of dark carbon fixation rate across three replicates</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
https://osprey.bco-dmo.org/dataset/1005611/data/download
download
onLine
dataset
<p>Water samples for nutrient analyses were collected from CTD Niskin bottles at discrete depths (15–100 m) from a single CTD cast. Approximately 40 mL of seawater was filtered onboard through 0.22 μm sterile syringe filters (Basix™ PES) and immediately frozen using an ethanol and dry ice bath prior to storage. Ammonia concentrations were determined using the o-phthaldialdehyde (OPA) fluorescence method following Holmes et al. (1999). Nitrite concentrations were measured spectrophotometrically using the sulfanilamide–NED method as described in Grasshoff et al. (1999). Nitrate concentrations were determined using the vanadium(III) chloride reduction method following García-Robledo et al. (2014).</p>
<p>For dark carbon fixation measurements, seawater was collected from CTD Niskin bottles from the same CTD cast and maintained in the dark at near in situ temperature. Four subsamples (90 mL each) were transferred into separate 110 mL acid-cleaned HDPE brown bottles. All subsamples were collected from the same Niskin bottle at each depth and divided into replicate incubations. All bottles were amended with approximately 6 μCi of 14C-labeled bicarbonate. One subsample was treated with 2.5% glutaraldehyde as a killed control, while the remaining three subsamples were incubated as biological replicates. Incubations were conducted in the dark at temperatures approximating in situ conditions (~15 °C for the 15m sample and ~11 °C for deeper samples). After ~60 hours of incubation, samples were processed following standard 14C carbon fixation protocols, including filtration and radioactivity measurement by liquid scintillation counting.</p>
Specified by the Principal Investigator(s)
<p>Carbon fixation rates were calculated from 14C incorporation measurements. Measured disintegrations per minute (DPM) were converted to carbon fixation rates using the known activity of added 14C-bicarbonate and the ambient dissolved inorganic carbon (DIC) pool. Background activity was corrected using the killed control sample. Rates are reported as carbon fixed per unit volume per day.</p>
Specified by the Principal Investigator(s)
This section documents curation actions performed prior to publication review with the submitter, and additional information relevant to understanding and reusing this dataset. It distinguishes changes made to the submitted (meta)data from unresolved issues and/or enhancements that improve future reuse and interoperability.
CURATION ACTIONS PERFORMED ON DATA
- Loaded XLSX file "SPOT_nutrients and dark carbon fixation_20250219.xlsx" (sheet 1), naming the table spot_nutrients_dark_carbon_fixation, header row set to row 1, with preserve_formatting and adjust_floating_point_error enabled; set empty string and "nd" as missing values via schema override
- Renamed columns to fix a naming convention violation caused by a "/" character and to remove units from parameter names: DCF_nM_C/day to DCF, Depth_m to Depth, Ammonia_nM to Ammonia, Nitrite_nM to Nitrite, Nitrate_uM to Nitrate
- Output as 1005611_v1_spot_nutrients_dark_carbon_fixation.csv
CURATION ACTIONS PERFORMED ON METADATA
- Adjusted title to conform with BCO-DMO conventions
ISSUES POTENTIALLY IMPACTING REUSE
- The source or calculation of the ambient dissolved inorganic carbon (DIC) values used to calculate dark carbon fixation rates was not provided
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
Wallac System 1400 liquid scintillation counter
Wallac System 1400 liquid scintillation counter
PI Supplied Instrument Name: Wallac System 1400 liquid scintillation counter PI Supplied Instrument Description:Dark carbon fixation rates were determined using 14C-bicarbonate incorporation and quantified by liquid scintillation counting (Wallac System 1400 liquid scintillation counter). 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/
Niskin bottles
Niskin bottles
PI Supplied Instrument Name: Niskin bottles PI Supplied Instrument Description:Water samples for nutrient analyses were collected from CTD Niskin bottles at discrete depths (15–100 m) from a single CTD cast. 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/
Sea-Bird Electronics SBE 9plus
Sea-Bird Electronics SBE 9plus
PI Supplied Instrument Name: Sea-Bird Electronics SBE 9plus PI Supplied Instrument Description:CTD rosette systems (Sea-Bird Electronics SBE 9plus or equivalent) were used for seawater collection. Instrument Name: Sea-Bird SBE 9plus CTD Instrument Short Name:Seabird SBE 9plus Instrument Description: High precision and accuracy CTD comprising an SBE 9plus underwater unit (SBE 3plus temperature, SBE 4C conductivity, and Paroscientific Digiquartz pressure sensors, and an SBE 5T submersible pump). Can be used for either real-time data acquisition or for autonomous operations at a sampling speed of up to 24 Hz. The instrument package also includes a TC duct, to reduce salinity spiking caused by ship heave for improved resolution of water column features, and to ensure that temperature and conductivity measurements are made on the same parcel of water. Supplied with both an aluminium and titanium main housing, allowing for use up to 6800 and 10,500 metre depths respectively. Also capable of measuring from eight auxiliary sensors.
Shimadzu UV-1800 UV–Vis spectrophotometer
Shimadzu UV-1800 UV–Vis spectrophotometer
PI Supplied Instrument Name: Shimadzu UV-1800 UV–Vis spectrophotometer PI Supplied Instrument Description:Nutrient concentrations were measured using standard fluorescence and spectrophotometric methods with calibrated instruments (Turner Designs Trilogy fluorometer and Shimadzu UV-1800 UV–Vis spectrophotometer) and external standards. 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 Trilogy fluorometer
Turner Designs Trilogy fluorometer
PI Supplied Instrument Name: Turner Designs Trilogy fluorometer PI Supplied Instrument Description:Nutrient concentrations were measured using standard fluorescence and spectrophotometric methods with calibrated instruments (Turner Designs Trilogy fluorometer and Shimadzu UV-1800 UV–Vis spectrophotometer) and external standards. 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: SPOT_20250219
SPOT_20250219
R/V Yellowfin
R/V Yellowfin
vessel
R/V Yellowfin
R/V Yellowfin
vessel