http://lod.bco-dmo.org/id/dataset/1005573 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) Iron use efficiency (IUE) of the model marine ammonia-oxidizing archaea (AOA), Nitrosopumilus maritimus, under controlled laboratory conditions across a range of temperatures and iron concentrations 2026-08-19 publication 2026-08-19 revision BCO-DMO Linked Data URI 2026-08-19 creation http://lod.bco-dmo.org/id/dataset/1005573 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) Iron use efficiency (IUE) of the model marine ammonia-oxidizing archaea (AOA), Nitrosopumilus maritimus, under controlled laboratory conditions across a range of temperatures and iron concentrations. 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/1005573 [access date] IUE of marine AOA under different temp and FE Dataset Description: Methods and Sampling: &lt;p&gt;Trace metal clean culturing experiments were conducted using the marine ammonia-oxidizing archaeon &lt;em&gt;Nitrosopumilus maritimus&amp;nbsp;&lt;/em&gt;(urn:lsid:marinespecies.org:taxname:559434) grown in 2.7 L trace metal clean polycarbonate bottles containing 2 L artificial seawater medium supplemented with 1 mM ammonium. All bottles and media were acid-cleaned and treated with Chelex resin to remove trace metal contaminants, and all manipulations were performed under HEPA-filtered conditions to minimize contamination. Cultures were acclimated to experimental conditions (23, 27, and 32 °C; low Fe: 250 nM; high Fe: 1250 nM) for at least six growth cycles prior to measurements. Three biological replicates were established for each treatment.&lt;/p&gt; &lt;p&gt;Carbon fixation rates were determined using 14C-labeled bicarbonate incorporation. Briefly, 45 mL culture subsamples were amended with 14C-NaHCO3 and incubated for 4 hours in the dark. Incubations were terminated by filtration onto 0.1 μm polyethersulfone filters (25 mm), and radioactivity was quantified using liquid scintillation counting.&lt;/p&gt; &lt;p&gt;Particulate organic carbon (POC) was measured by filtering 100–200 mL of culture onto precombusted glass fiber filters (GF75, 0.3 μm), followed by drying (~60 °C) and analysis using an elemental analyzer calibrated with organic standards.&lt;/p&gt; &lt;p&gt;Cellular iron quotas were determined under trace metal clean conditions. Culture samples (200–400 mL) were filtered onto acid-cleaned 0.1 μm polyethersulfone filters and rinsed with EDTA-oxalate to remove extracellular metals. Filters were stored at −20 °C prior to digestion. Samples were digested in 50% nitric acid at 90 °C for 2–3 days, dried, and re-dissolved in 0.1 M HNO3 with indium as an internal standard. Iron concentrations were measured using inductively coupled plasma mass spectrometry (ICP-MS).&lt;/p&gt; &lt;p&gt;Iron use efficiency (IUE) was calculated as the ratio of carbon fixation rate to cellular iron quota.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2336533 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2336533 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 Condition total_iron_concentration Temperature POC POC_std Fe Fe_std Fe_C_ratio Fe_C_ratio_std Carbon_fixation Carbon_fixation_std iron_use_efficiency iron_use_efficiency_std Replicates Costech elemental analyzer (Costech Analytical Technologies Inc.) Wallac 1400 liquid scintillation counter (PerkinElmer) Thermo Scientific Element2 inductively coupled plasma mass spectrometer (ICP-MS) theme None, User defined treatment Iron water temperature at measurement depth particulate organic Carbon (POC) standard deviation ratio No BCO-DMO term replicate featureType BCO-DMO Standard Parameters Elemental Analyzer Liquid Scintillation Counter Thermo Fisher Scientific ELEMENT 2 inductively coupled plasma mass spectrometer instrument BCO-DMO Standard Instruments 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 2026-08-19 Eastern North Pacific: HNLC and subtropical gyre; SPOT time-series station; HOT time-series station. 0 BCO-DMO catalogue of parameters from Iron use efficiency (IUE) of the model marine ammonia-oxidizing archaea (AOA), Nitrosopumilus maritimus, under controlled laboratory conditions across a range of temperatures and iron concentrations 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/1005665.rdf Name: Condition Units: unitless Description: <p>Iron treatment condition (e.g., iron-replete or iron-limited) applied to the culture</p> http://lod.bco-dmo.org/id/dataset-parameter/1005666.rdf Name: total_iron_concentration Units: nanomole per liter (nM) Description: <p>Total dissolved iron concentration added to the culture medium under the specified treatment</p> http://lod.bco-dmo.org/id/dataset-parameter/1005667.rdf Name: Temperature Units: degrees Celsius (°C) Description: <p>Incubation temperature</p> http://lod.bco-dmo.org/id/dataset-parameter/1005668.rdf Name: POC Units: micromole carbon per liter (μmol C L⁻¹) Description: <p>Mean particulate organic carbon concentration in the culture, measured by elemental analyzer</p> http://lod.bco-dmo.org/id/dataset-parameter/1005669.rdf Name: POC_std Units: micromole carbon per liter (μmol C L⁻¹) Description: <p>Standard deviation of particulate organic carbon across three biological replicates</p> http://lod.bco-dmo.org/id/dataset-parameter/1005670.rdf Name: Fe Units: nanomole per liter (nM) Description: <p>Mean cellular iron concentration in the culture, measured by ICP-MS</p> http://lod.bco-dmo.org/id/dataset-parameter/1005671.rdf Name: Fe_std Units: nanomole per liter (nM) Description: <p>Standard deviation of cellular iron concentration across three biological replicates</p> http://lod.bco-dmo.org/id/dataset-parameter/1005672.rdf Name: Fe_C_ratio Units: micromole per mole (μmol mol⁻¹) Description: <p>Mean cellular iron-to-carbon ratio (Fe:C), calculated by normalizing cellular iron quota to particulate organic carbon</p> http://lod.bco-dmo.org/id/dataset-parameter/1005673.rdf Name: Fe_C_ratio_std Units: micromole per mole (μmol mol⁻¹) Description: <p>Standard deviation of Fe:C ratio calculated across three biological replicates</p> http://lod.bco-dmo.org/id/dataset-parameter/1005674.rdf Name: Carbon_fixation Units: micromole carbon per liter per day (μmol C L⁻¹ d⁻¹) Description: <p>Mean rate of carbon fixation by the culture, determined from ¹⁴C-bicarbonate incorporation assays</p> http://lod.bco-dmo.org/id/dataset-parameter/1005675.rdf Name: Carbon_fixation_std Units: micromole carbon per liter per day (μmol C L⁻¹ d⁻¹) Description: <p>Standard deviation of the carbon fixation rate calculated across three biological replicates</p> http://lod.bco-dmo.org/id/dataset-parameter/1005676.rdf Name: iron_use_efficiency Units: micromole carbon per hour per micromole iron (μmol C h⁻¹ μmol Fe⁻¹) Description: <p>Mean iron use efficiency (IUE), calculated as the carbon fixation rate normalized to the cellular iron quota, representing carbon fixed per unit of cellular iron per hour</p> http://lod.bco-dmo.org/id/dataset-parameter/1005677.rdf Name: iron_use_efficiency_std Units: micromole carbon per hour per micromole iron (μmol C h⁻¹ μmol Fe⁻¹) Description: <p>Standard deviation of iron use efficiency calculated across three biological replicates</p> http://lod.bco-dmo.org/id/dataset-parameter/1005678.rdf Name: Replicates Units: count Description: <p>Number of biological replicate cultures used to calculate the mean and standard deviation for each treatment (temperature × iron concentration combination)</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/1005573/data/download download onLine dataset &lt;p&gt;Trace metal clean culturing experiments were conducted using the marine ammonia-oxidizing archaeon &lt;em&gt;Nitrosopumilus maritimus&amp;nbsp;&lt;/em&gt;(urn:lsid:marinespecies.org:taxname:559434) grown in 2.7 L trace metal clean polycarbonate bottles containing 2 L artificial seawater medium supplemented with 1 mM ammonium. All bottles and media were acid-cleaned and treated with Chelex resin to remove trace metal contaminants, and all manipulations were performed under HEPA-filtered conditions to minimize contamination. Cultures were acclimated to experimental conditions (23, 27, and 32 °C; low Fe: 250 nM; high Fe: 1250 nM) for at least six growth cycles prior to measurements. Three biological replicates were established for each treatment.&lt;/p&gt; &lt;p&gt;Carbon fixation rates were determined using 14C-labeled bicarbonate incorporation. Briefly, 45 mL culture subsamples were amended with 14C-NaHCO3 and incubated for 4 hours in the dark. Incubations were terminated by filtration onto 0.1 μm polyethersulfone filters (25 mm), and radioactivity was quantified using liquid scintillation counting.&lt;/p&gt; &lt;p&gt;Particulate organic carbon (POC) was measured by filtering 100–200 mL of culture onto precombusted glass fiber filters (GF75, 0.3 μm), followed by drying (~60 °C) and analysis using an elemental analyzer calibrated with organic standards.&lt;/p&gt; &lt;p&gt;Cellular iron quotas were determined under trace metal clean conditions. Culture samples (200–400 mL) were filtered onto acid-cleaned 0.1 μm polyethersulfone filters and rinsed with EDTA-oxalate to remove extracellular metals. Filters were stored at −20 °C prior to digestion. Samples were digested in 50% nitric acid at 90 °C for 2–3 days, dried, and re-dissolved in 0.1 M HNO3 with indium as an internal standard. Iron concentrations were measured using inductively coupled plasma mass spectrometry (ICP-MS).&lt;/p&gt; &lt;p&gt;Iron use efficiency (IUE) was calculated as the ratio of carbon fixation rate to cellular iron quota.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;Carbon fixation rates were calculated from 14C incorporation measurements by converting scintillation counts to rates using the specific activity of added 14C-bicarbonate, with background correction applied where appropriate.&lt;/p&gt; &lt;p&gt;Particulate organic carbon (POC) was obtained directly from elemental analyzer measurements.&lt;/p&gt; &lt;p&gt;Cellular iron quotas were derived from ICP-MS measurements following calibration with external standards and correction using an internal indium standard.&lt;/p&gt; &lt;p&gt;Fe:C ratios were calculated by normalizing iron quotas to POC, and iron use efficiency (IUE) was calculated as the ratio of carbon fixation rate to cellular iron quota.&lt;/p&gt; 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 data from an Excel file (Sheet1) titled &quot;Iron use efficiency (IUE) of the model marine ammonia-oxidizing archaea (AOA), Nitrosopumilus maritimus, under controlled laboratory conditions across a range of temperatures and iron concentrations.xlsx&quot;, assigning it the table name iron_use_efficiency_nitrosopumilus; used header row 1, limited rows loaded to 1000, preserved cell display formatting, and set missing value markers to empty string and &quot;nd&quot; - Renamed columns to comply with BCO-DMO parameter naming conventions: &quot;Total iron concentration (nM)&quot; to total_iron_concentration, &quot;Standard deviation of POC (umol C/L)&quot; to POC_std, &quot;Fe (nmol/L)&quot; to Fe, &quot;Standard deviation of Fe (nmol/L)&quot; to Fe_std, &quot;Fe/C (umol/mol)&quot; to Fe_C_ratio, &quot;Standard deviation of Fe/C (umol/mol)&quot; to Fe_C_ratio_std, &quot;Standard deviation of Carbon fixation (umolC L-1 d-1)&quot; to Carbon_fixation_std, &quot;Iron use efficiency (umol C/hr/ umol Fe)&quot; to iron_use_efficiency, &quot;Standard deviation of Iron use efficiency (umol C/hr/ umol Fe)&quot; to iron_use_efficiency_std, &quot;POC (umol C/L)&quot; to POC, and &quot;Carbon fixation (umolC L-1 d-1)&quot; to Carbon_fixation - Output as 1005573_v1_iron_use_efficiency_nitrosopumilus.csv CURATION ACTIONS PERFORMED ON METADATA - Used context from methods section to provide more detail for parameter descriptions - Added WORMS URI: All scientific names in the data are valid and accepted names as of 2026-08-21 ISSUES POTENTIALLY IMPACTING REUSE - The dataset contains only treatment-level means and standard deviations, along with replicate counts. Raw values were 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 Costech elemental analyzer (Costech Analytical Technologies Inc.) Costech elemental analyzer (Costech Analytical Technologies Inc.) PI Supplied Instrument Name: Costech elemental analyzer (Costech Analytical Technologies Inc.) PI Supplied Instrument Description:Particulate organic carbon (POC) was analyzed using a Costech elemental analyzer (Costech Analytical Technologies Inc.) calibrated with methionine and acetanilide standards. Instrument Name: Elemental Analyzer Instrument Short Name: Instrument Description: Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB01/ Wallac 1400 liquid scintillation counter (PerkinElmer) Wallac 1400 liquid scintillation counter (PerkinElmer) PI Supplied Instrument Name: Wallac 1400 liquid scintillation counter (PerkinElmer) PI Supplied Instrument Description:Liquid scintillation counting was performed using a Wallac 1400 liquid scintillation counter (PerkinElmer) to quantify 14C incorporation for carbon fixation rate measurements. 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/ Thermo Scientific Element2 inductively coupled plasma mass spectrometer (ICP-MS) Thermo Scientific Element2 inductively coupled plasma mass spectrometer (ICP-MS) PI Supplied Instrument Name: Thermo Scientific Element2 inductively coupled plasma mass spectrometer (ICP-MS) PI Supplied Instrument Description:Cellular iron concentrations were measured using a Thermo Scientific Element2 inductively coupled plasma mass spectrometer (ICP-MS) at the University of Southern California. Instrument calibration was performed using external iron standards (10 ppb and 90 ppb), and indium was used as an internal standard to correct for signal drift and matrix effects. Instrument Name: Thermo Fisher Scientific ELEMENT 2 inductively coupled plasma mass spectrometer Instrument Short Name:Thermo Scientific Element 2 ICP-MS Instrument Description: The Thermo Scientific Element 2 ICP-MS is a double-focussing magnetic-sector-field Inductively Coupled Plasma Mass Spectrometer equipped with a discrete dynode detector system, linear over nine orders of magnitude - from ppq to ppm concentrations. Other features include: Sensitivity (Concentric Nebuliser) greater than 1 x 10^9 counts per second (cps)/ppm ln; Dark noise less than 0.2 cps; Mass resolution 300, 4,000, 10,000 (10 percent valley, equivalent to 5 percent height), 600, 8,000, 2,000 (FWHM); Signal stability better than 1 percent RSD over 10 minutes or 2 percent RSD over 1 hour; Mass stability: 25 ppm / 8 hours; Magnetic scan speed: m/z 7 to 240 to 7 in less than 150 ms, Electronic scan speed: 1 ms/jump, independent of mass range.