http://lod.bco-dmo.org/id/dataset/870832
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
2022-03-09
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Dissolved inorganic carbon (DIC) fixation and dissolved organic carbon (DOC) release measurements of marine nitrifier cultures grown under different culture conditions
2022-03-09
publication
2022-03-09
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-03-17
publication
https://doi.org/10.26008/1912/bco-dmo.870832.1
Alyson E. Santoro
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: Bayer, B., Santoro, A. E. (2022) Dissolved inorganic carbon (DIC) fixation and dissolved organic carbon (DOC) release measurements of marine nitrifier cultures grown under different culture conditions. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-03-09 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.870832.1 [access date]
Nitrifier C fixation release Dataset Description: Methods and Sampling: <p>DIC fixation was measured via the incorporation of [<sup>14</sup>C]-bicarbonate as previously described (Herndl et al. 2005) with modifications. [<sup>14</sup>C]-bicarbonate (specific activity 56 mCi mmol<sup>-1</sup>/2.072 x 10<sup>9</sup> Bq mmol<sup>-1</sup>, Perkin Elmer) was added to 5 mL of culture (between 6 and 65 µCi were added depending on the activity of the culture). For every culture condition, at least three replicate live samples and one formaldehyde-fixed blank (3% v/v) were incubated in temperature-controlled incubators in the dark. Parallel incubations without [<sup>14</sup>C]-tracer additions were used to determine cell abundance and nitrite concentration. Incubations were terminated by adding formaldehyde (3% v/v) to 5 mL of sample. After 30-60 min, every sample was individually filtered onto 25 mm, 0.2 µm pore size polycarbonate filters (Millipore) and rinsed with 0.5 mL of artificial seawater using a glass filtration set (Millipore). The individual filtrates (5.5 mL per sample) were collected and transferred to scintillation vials to determine the fraction of [<sup>14</sup>C]-dissolved organic carbon ([<sup>14</sup>C]-DOC). Excess [<sup>14</sup>C]-bicarbonate from the filters was removed by exposing them to fumes of concentrated HCl (37 %) for 24 h. The filters were transferred to scintillation vials and 10 mL of scintillation cocktail (Ultima Gold, Perkin Elmer) was added. The filtrates were acidified to pH ∼2 with HCl (25 %) as previously described (Marañón et al. 2004), and filtrates were kept for 24 h in open scintillation vials placed on an orbital shaker before 10 mL scintillation cocktail was added to each vial. Samples were shaken for ca. 30 sec and incubated in the dark for at least 24 hours prior to counting the disintegrations per minute (DPM) in a scintillation counter (Beckman Coulter LS6500) for 15 min. Total radioactivity measurements were performed to verify added [<sup>14</sup>C]-bicarbonate concentrations by pipetting 100µl of sample into scintillation vials containing 400µl beta-phenylethylamine (to prevent outgassing of <sup>14</sup>CO<sub>2</sub>). Scintillation cocktail was added, vials were shaken for ca. 30 sec and immediately measured in the scintillation counter.&nbsp;&nbsp;</p>
<p>A detailed description of materials and methods can be found in 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
asNeeded
Dataset Version: 1
Unknown
Nitrifier_strain
Substrate_conc
Temp
Culture_medium
Treatment
Growth_phase
DPM_POC_Blank_corrected
DPM_DOC_Blank_corrected
DOC_release_percent
Incubation_time
Activity_tracer
DPM_tracer
DIC_conc
Fixed_DIC
Fixed_DIC_DOC
Cell_abundance
DIC_fixation_rate
Produced_cells
C_content
N_oxidized
DIC_fixation_yield
DOC_corrected_DIC_fixation_yield
Beckman Coulter LS6500 Scintillation counter
theme
None, User defined
taxon
treatment
water temperature at measurement depth
growth
particulate organic Carbon (POC)
dissolved organic Carbon
incubation time or duration
14C
dissolved inorganic Carbon
No BCO-DMO term
abundance
number
featureType
BCO-DMO Standard Parameters
Liquid Scintillation Counter
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: 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
-119.84912
-119.84912
34.413962
34.413962
2020-12-14
2021-08-13
Eastern Tropical Pacific
0
BCO-DMO catalogue of parameters from Dissolved inorganic carbon (DIC) fixation and dissolved organic carbon (DOC) release measurements of marine nitrifier cultures grown under different culture conditions
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/870932.rdf
Name: Nitrifier_strain
Units: unitless
Description: <p>Name of cultured nitrifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/870933.rdf
Name: Substrate_conc
Units: micromoles per liter (umol/L)
Description: <p>Concentration of substrate (NH4+ or NO2-)</p>
http://lod.bco-dmo.org/id/dataset-parameter/870934.rdf
Name: Temp
Units: degrees Celsius
Description: <p>Incubation temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/870935.rdf
Name: Culture_medium
Units: unitless
Description: <p>Type of culture medium (ASW, artificial seawater; NSW, natural seawater; ASW_HEPES, artificial seawater buffered with HEPES)</p>
http://lod.bco-dmo.org/id/dataset-parameter/870936.rdf
Name: Treatment
Units: unitless
Description: <p>Additional amendments to culture medium (none; NH4+ addition; tryptone addition)</p>
http://lod.bco-dmo.org/id/dataset-parameter/870937.rdf
Name: Growth_phase
Units: unitless
Description: <p>Growth phase of the culture when the measurement was taken (EEXP, early exponential growth; LEXP, late exponential growth; STAT, stationary phase)</p>
http://lod.bco-dmo.org/id/dataset-parameter/870938.rdf
Name: DPM_POC_Blank_corrected
Units: disintegrations per minute (DPM)
Description: <p>Activity measured on filters (particulate fraction) following incubation with 14C-bicarbonate. Blank value was subtracted</p>
http://lod.bco-dmo.org/id/dataset-parameter/870939.rdf
Name: DPM_DOC_Blank_corrected
Units: disintegrations per minute (DPM)
Description: <p>Activity measured in filtrates (dissolved fraction) following incubation with 14C-bicarbonate. Blank value was subtracted</p>
http://lod.bco-dmo.org/id/dataset-parameter/870940.rdf
Name: DOC_release_percent
Units: percent (%)
Description: <p>Released DOC as a fraction of fixed DIC</p>
http://lod.bco-dmo.org/id/dataset-parameter/870941.rdf
Name: Incubation_time
Units: hours (h)
Description: <p>Length of incubation with 14C-bicarbonate</p>
http://lod.bco-dmo.org/id/dataset-parameter/870942.rdf
Name: Activity_tracer
Units: microcurie (uCi)
Description: <p>Activity of added 14C-bicarbonate</p>
http://lod.bco-dmo.org/id/dataset-parameter/870943.rdf
Name: DPM_tracer
Units: disintegrations per minute (DPM)
Description: <p>Activity of added 14C-bicarbonate</p>
http://lod.bco-dmo.org/id/dataset-parameter/870944.rdf
Name: DIC_conc
Units: micromoles per liter (umol/L)
Description: <p>Concentration of dissolved inorganic carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/870945.rdf
Name: Fixed_DIC
Units: micromoles per liter (umol/L)
Description: <p>Total fixed DIC (excluding the fraction released as DOC)</p>
http://lod.bco-dmo.org/id/dataset-parameter/870946.rdf
Name: Fixed_DIC_DOC
Units: micromoles per liter (umol/L)
Description: <p>Total fixed DIC (including the fraction released as DOC)</p>
http://lod.bco-dmo.org/id/dataset-parameter/870947.rdf
Name: Cell_abundance
Units: cells per liter (cells/L)
Description: <p>Cell numbers of cultured nitrifiers</p>
http://lod.bco-dmo.org/id/dataset-parameter/870948.rdf
Name: DIC_fixation_rate
Units: femtomoles per cell per day (fmol/cell/d)
Description: <p>Cell-normalized DIC fixation rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/870949.rdf
Name: Produced_cells
Units: cells per liter (cells/L)
Description: <p>Number of cells newly produced during the incubation period</p>
http://lod.bco-dmo.org/id/dataset-parameter/870950.rdf
Name: C_content
Units: femtogram per cell (fg/cell)
Description: <p>Cellular carbon content</p>
http://lod.bco-dmo.org/id/dataset-parameter/870951.rdf
Name: N_oxidized
Units: micromoles per liter (umol/L)
Description: <p>Amount of NH4+ or NO2- oxidized by cultured nitrifiers during the incubation period</p>
http://lod.bco-dmo.org/id/dataset-parameter/870952.rdf
Name: DIC_fixation_yield
Units: moles of carbon per mole of nitrogen (mol C/mol N)
Description: <p>Moles of C fixed per mole of N oxidized</p>
http://lod.bco-dmo.org/id/dataset-parameter/870953.rdf
Name: DOC_corrected_DIC_fixation_yield
Units: moles of carbon per mole of nitrogen (mol C/mol N)
Description: <p>Moles of C fixed per mole of N oxidized including the fraction of C released as DOC</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
29232
https://darchive.mblwhoilibrary.org/bitstream/1912/28206/1/dataset-870832_nitrifier-c-fixation-release__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.870832.1
download
onLine
dataset
<p>DIC fixation was measured via the incorporation of [<sup>14</sup>C]-bicarbonate as previously described (Herndl et al. 2005) with modifications. [<sup>14</sup>C]-bicarbonate (specific activity 56 mCi mmol<sup>-1</sup>/2.072 x 10<sup>9</sup> Bq mmol<sup>-1</sup>, Perkin Elmer) was added to 5 mL of culture (between 6 and 65 µCi were added depending on the activity of the culture). For every culture condition, at least three replicate live samples and one formaldehyde-fixed blank (3% v/v) were incubated in temperature-controlled incubators in the dark. Parallel incubations without [<sup>14</sup>C]-tracer additions were used to determine cell abundance and nitrite concentration. Incubations were terminated by adding formaldehyde (3% v/v) to 5 mL of sample. After 30-60 min, every sample was individually filtered onto 25 mm, 0.2 µm pore size polycarbonate filters (Millipore) and rinsed with 0.5 mL of artificial seawater using a glass filtration set (Millipore). The individual filtrates (5.5 mL per sample) were collected and transferred to scintillation vials to determine the fraction of [<sup>14</sup>C]-dissolved organic carbon ([<sup>14</sup>C]-DOC). Excess [<sup>14</sup>C]-bicarbonate from the filters was removed by exposing them to fumes of concentrated HCl (37 %) for 24 h. The filters were transferred to scintillation vials and 10 mL of scintillation cocktail (Ultima Gold, Perkin Elmer) was added. The filtrates were acidified to pH ∼2 with HCl (25 %) as previously described (Marañón et al. 2004), and filtrates were kept for 24 h in open scintillation vials placed on an orbital shaker before 10 mL scintillation cocktail was added to each vial. Samples were shaken for ca. 30 sec and incubated in the dark for at least 24 hours prior to counting the disintegrations per minute (DPM) in a scintillation counter (Beckman Coulter LS6500) for 15 min. Total radioactivity measurements were performed to verify added [<sup>14</sup>C]-bicarbonate concentrations by pipetting 100µl of sample into scintillation vials containing 400µl beta-phenylethylamine (to prevent outgassing of <sup>14</sup>CO<sub>2</sub>). Scintillation cocktail was added, vials were shaken for ca. 30 sec and immediately measured in the scintillation counter.&nbsp;&nbsp;</p>
<p>A detailed description of materials and methods can be found in Bayer et al. 2022.</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:</strong><br />
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 DIC concentration in the culture media. A detailed description of data processing can be found in Bayer et al. 2022.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- renamed fields to conform with BCO-DMO naming conventions;<br />
- replaced "NA" with "nd" (no data).</p>
Specified by the Principal Investigator(s)
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
Beckman Coulter LS6500 Scintillation counter
Beckman Coulter LS6500 Scintillation counter
PI Supplied Instrument Name: Beckman Coulter LS6500 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 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/