http://lod.bco-dmo.org/id/dataset/564509
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
2015-08-12
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
N and O isotope effects of nitrate reduction by 3 forms of nitrate reductase (15N2 Contamination project)
2015-08-12
publication
2015-08-12
revision
BCO-DMO Linked Data URI
2015-08-12
creation
http://lod.bco-dmo.org/id/dataset/564509
Julie Granger
University of Connecticut
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: Granger, J. (2015) N and O isotope effects of nitrate reduction by 3 forms of nitrate reductase (15N2 Contamination project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 12 Aug 2015) Version Date 2015-08-12 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/564509 [access date]
N and O isotope effects of nitrate reduction by 3 forms of nitrate reductase. Dataset Description: <p>Enzyme assays were conducted to determine the N and O isotope effects of nitrate reduction by 3 forms of nitrate reductase: respiratory nitrate reductase (Nar), periplasmic nitrate reductase (Nap), and eukaryotic assimilatory nitrate reductase (EukNR).</p> Methods and Sampling: <p>Sources of Nitrate Reductase:<br />
Enzymatic assays were conducted on (a) cell homogenates from the denitrifying bacterial strain Paracoccus denitrificans (American Type Culture Collection [ATCC] 19367) cultured under anaerobic vs. aerobic conditions, on (b) cell homogenates from the photo-heterotrophic bacterial strain Rhodobacter sphaeroides (Deutsche Sammlung von Mikroorganismen [DSM] 158) cultured aerobically, and on (c) purified extracts of recombinant eukaryotic assimilatory nitrate reductases (EukNR) from the flowering plant Arabidopsis thaliana (AtNaR: &nbsp;E.C. 1.7.1.1) and from the yeast Pichia angusta (YNaR1: E.C. 1.7.1.2), both purchased from NECi (nitrate.com).</p>
<p>Enzymatic assay preparations:<br />
Assays contained 0.5 or 1 mL of cell suspension or of commercially purified EukNR buffered solution, 1 mL of 200 umol L-1 reducing agent – either membrane-permeant benzyl viologen dichloride [Sigma-Aldrich, CAS: 1102-19-8], methyl viologen dichloride hydrate [Sigma-Aldrich, CAS: 75365-73-0], or hydroquinone (for dissimilatory reductases only; [MP Organics]) –&nbsp; 0.2 or 1 mL 10 mmol L-1 KNO3 to a final concentration of 200 or 1000 umol L-1, and the remaining volume of 100 mmol L-1 phosphate buffer [pH 7.9] containing 100 umol L-1 to a final assay volume of 10 mL. After drawing an initial 1 mL sample for quantitation of [NO3-] and [NO2-], the denitrification reaction was commenced by the addition of 1 mL of 57 mmol L-1 sodium dithionite in 29 mmol L-1&nbsp; sodium bicarbonate, which reduces the electron donor. Initial [NO3-] and [NO2-] values are corrected for this dilution. Serial 1 mL samples were drawn approximately every 90 seconds during room temperature assays and every 3 minutes during assays conducted at 4 degrees C. Samples were mixed vigorously on a vortex mixer for 30 s immediately upon collection to halt the reaction through oxidation of the methyl or benzyl viologen or hydroquinone.&nbsp; In selected assays, additional ~ 50 uL samples were also drawn throughout the assay reactions for determination of [NO2-] and were measured immediately. In order to ensure complete cessation of enzyme activity, samples placed in an 80 degrees C water bath for 2 to 10 minutes. NO2- was then removed from the samples via the addition of 55 uL 4% (wt/vol) sulfamic acid in 10% vol/vol HCl.</p>
<p>Determination of [NO3-]:<br />
[NO3-] was measured in samples by chemiluminescence detection on a NOx analyzer (model T200 Teledyne Advanced Pollution Instrumentation) following reduction to NO in a heated vanadium solution (Braman and Hendrix 1989). Nitrite had been previously removed from these samples, as vanadium reduces both nitrate and nitrite to NO.</p>
<p>Nitrate N and O isotope ratio analyses:<br />
NO3- δ15N and δ18O were determined with the denitrifier method (Sigman et al. 2001; Casciotti et al. 2002), wherein denitrifying bacteria lacking terminal nitrous oxide reductase (P. chlororaphis f. sp. aureofaciens ATCC 1398) quantitatively convert sample NO3- to N2O gas, which is then extracted, purified and analyzed through a modified Thermo-Scientific Gas Bench II and Delta V Advantage gas chromatograph isotope ratio mass spectrometer.&nbsp; Samples were standardized through comparison to reference standards IAEA-N3, USGS-34, and USGS-32, which have δ15N (vs air N2) and δ18O (vs V-SMOW) of 4.7‰ and 25.6‰, -1.8‰ and -27.9‰, and 180‰ and 25.6‰ respectively after individually being referenced to pure N2O injections from a common reference gas cylinder.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1233897 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1233897
completed
Julie Granger
University of Connecticut
860-405-9094
Department of Marine Sciences 1080 Shenecossett Road
Groton
CT
06340
USA
julie.granger@uconn.edu
pointOfContact
asNeeded
Dataset Version: 12 Aug 2015
Unknown
assay
sample
date
reductant
enzyme_form
bacteria
cells_lysed
growth_conditions
temp
NO3_corr
d15N
d15N_sd
d18O
d18O_sd
gas chromatograph
isotope ratio mass spectrometer
theme
None, User defined
No BCO-DMO term
sample identification
date
d15N_NO3
standard deviation
d18O_NO3
featureType
BCO-DMO Standard Parameters
Gas Chromatograph
Isotope-ratio 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.
The Ocean Nitrogen Imbalance Paradox: Environmental Controls on the Denitrification Isotope Effect
https://osprey.bco-dmo.org/project/528935
The Ocean Nitrogen Imbalance Paradox: Environmental Controls on the Denitrification Isotope Effect
<p><em>Description from NSF award abstract:</em><br />
This study will test the sensitivity of the amplitude of the denitrification isotope effect to culture conditions pertinent to the ocean environment. The isotope effect amplitude will be explored with respect to electron donor, trace oxygenation, and temperature, in both batch and continuous culture experiments of denitrifiers. The proposed work will also involve measurements of the enzymatic isotope effect of the respiratory nitrate reductase of denitrifiers, measurements of its enzymatic activity among cultures, and examination of cellular nitrate transport kinetics of denitrifying strains. The experiments are designed to reveal the physiological basis of the modulation of the isotope effect amplitude, which will further resolve this manifestation in the environment.</p>
<p>In regards to the broader significance and importance of this study, these new experimental data will provide a basis for integration of nitrogen isotope dynamics in ocean models to test how key environmental parameters can affect the global ocean distribution of nitrogen isotopes.</p>
15N2 Contamination
largerWorkCitation
project
eng; USA
oceans
2015-08-12
0
BCO-DMO catalogue of parameters from N and O isotope effects of nitrate reduction by 3 forms of nitrate reductase (15N2 Contamination 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/564517.rdf
Name: assay
Units: dimensionless
Description: <p>Assay identification number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/564518.rdf
Name: sample
Units: dimensionless
Description: <p>Sample identification number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/564519.rdf
Name: date
Units: mmddyyyy
Description: <p>Month, day, and year.</p>
http://lod.bco-dmo.org/id/dataset-parameter/564520.rdf
Name: reductant
Units: dimensionless
Description: <p>Chemical used to donate electrons for assay reductions (methyl viologen OR benzyl viologen OR hydroquinone).</p>
http://lod.bco-dmo.org/id/dataset-parameter/564521.rdf
Name: enzyme_form
Units: dimensionless
Description: <p>Whether cell suspensions or pure enzyme extracts were used in experimental assays (cell suspensions OR pure extract).</p>
http://lod.bco-dmo.org/id/dataset-parameter/564522.rdf
Name: bacteria
Units: dimensionless
Description: <p>Bacteria from which nitrate reductase enzymes used in assays were procured.</p>
http://lod.bco-dmo.org/id/dataset-parameter/564523.rdf
Name: cells_lysed
Units: dimensionless
Description: <p>Whether cells were lysed before incorporation in experimental assays (nd for pure extracts).</p>
http://lod.bco-dmo.org/id/dataset-parameter/564524.rdf
Name: growth_conditions
Units: dimensionless
Description: <p>Whether cells were grown aerobically or anaerobically before preparation for experimental assays (nd for pure extracts).</p>
http://lod.bco-dmo.org/id/dataset-parameter/564525.rdf
Name: temp
Units: degrees Celsius ( C)
Description: <p>Temperature at which assay was conducted.</p>
http://lod.bco-dmo.org/id/dataset-parameter/564526.rdf
Name: NO3_corr
Units: micromolar (uM NO3-)
Description: <p>Concentration of nitrate remaining in samples.</p>
http://lod.bco-dmo.org/id/dataset-parameter/564527.rdf
Name: d15N
Units: permille (‰)
Description: <p>delta-N15 of nitrate, reported as an average of replicate measurements.</p>
http://lod.bco-dmo.org/id/dataset-parameter/564528.rdf
Name: d15N_sd
Units: permille (‰)
Description: <p>Standard deviation of replicate delta-N15 measurements.</p>
http://lod.bco-dmo.org/id/dataset-parameter/564529.rdf
Name: d18O
Units: permille (‰)
Description: <p>delta-O18 of nitrate, reported as an average of replicate measurements.</p>
http://lod.bco-dmo.org/id/dataset-parameter/564530.rdf
Name: d18O_sd
Units: permille (‰)
Description: <p>Standard deviation of replicate delta-O18 measurements.</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
23234
https://datadocs.bco-dmo.org/file/N77GrNzSZ5Z7gW/nitrate_reductases.csv
nitrate_reductases.csv
Primary data file for dataset ID 564509
download
https://osprey.bco-dmo.org/dataset/564509/data/download
download
onLine
dataset
<p>Sources of Nitrate Reductase:<br />
Enzymatic assays were conducted on (a) cell homogenates from the denitrifying bacterial strain Paracoccus denitrificans (American Type Culture Collection [ATCC] 19367) cultured under anaerobic vs. aerobic conditions, on (b) cell homogenates from the photo-heterotrophic bacterial strain Rhodobacter sphaeroides (Deutsche Sammlung von Mikroorganismen [DSM] 158) cultured aerobically, and on (c) purified extracts of recombinant eukaryotic assimilatory nitrate reductases (EukNR) from the flowering plant Arabidopsis thaliana (AtNaR: &nbsp;E.C. 1.7.1.1) and from the yeast Pichia angusta (YNaR1: E.C. 1.7.1.2), both purchased from NECi (nitrate.com).</p>
<p>Enzymatic assay preparations:<br />
Assays contained 0.5 or 1 mL of cell suspension or of commercially purified EukNR buffered solution, 1 mL of 200 umol L-1 reducing agent – either membrane-permeant benzyl viologen dichloride [Sigma-Aldrich, CAS: 1102-19-8], methyl viologen dichloride hydrate [Sigma-Aldrich, CAS: 75365-73-0], or hydroquinone (for dissimilatory reductases only; [MP Organics]) –&nbsp; 0.2 or 1 mL 10 mmol L-1 KNO3 to a final concentration of 200 or 1000 umol L-1, and the remaining volume of 100 mmol L-1 phosphate buffer [pH 7.9] containing 100 umol L-1 to a final assay volume of 10 mL. After drawing an initial 1 mL sample for quantitation of [NO3-] and [NO2-], the denitrification reaction was commenced by the addition of 1 mL of 57 mmol L-1 sodium dithionite in 29 mmol L-1&nbsp; sodium bicarbonate, which reduces the electron donor. Initial [NO3-] and [NO2-] values are corrected for this dilution. Serial 1 mL samples were drawn approximately every 90 seconds during room temperature assays and every 3 minutes during assays conducted at 4 degrees C. Samples were mixed vigorously on a vortex mixer for 30 s immediately upon collection to halt the reaction through oxidation of the methyl or benzyl viologen or hydroquinone.&nbsp; In selected assays, additional ~ 50 uL samples were also drawn throughout the assay reactions for determination of [NO2-] and were measured immediately. In order to ensure complete cessation of enzyme activity, samples placed in an 80 degrees C water bath for 2 to 10 minutes. NO2- was then removed from the samples via the addition of 55 uL 4% (wt/vol) sulfamic acid in 10% vol/vol HCl.</p>
<p>Determination of [NO3-]:<br />
[NO3-] was measured in samples by chemiluminescence detection on a NOx analyzer (model T200 Teledyne Advanced Pollution Instrumentation) following reduction to NO in a heated vanadium solution (Braman and Hendrix 1989). Nitrite had been previously removed from these samples, as vanadium reduces both nitrate and nitrite to NO.</p>
<p>Nitrate N and O isotope ratio analyses:<br />
NO3- δ15N and δ18O were determined with the denitrifier method (Sigman et al. 2001; Casciotti et al. 2002), wherein denitrifying bacteria lacking terminal nitrous oxide reductase (P. chlororaphis f. sp. aureofaciens ATCC 1398) quantitatively convert sample NO3- to N2O gas, which is then extracted, purified and analyzed through a modified Thermo-Scientific Gas Bench II and Delta V Advantage gas chromatograph isotope ratio mass spectrometer.&nbsp; Samples were standardized through comparison to reference standards IAEA-N3, USGS-34, and USGS-32, which have δ15N (vs air N2) and δ18O (vs V-SMOW) of 4.7‰ and 25.6‰, -1.8‰ and -27.9‰, and 180‰ and 25.6‰ respectively after individually being referenced to pure N2O injections from a common reference gas cylinder.</p>
Specified by the Principal Investigator(s)
<p>Nitrate Calculations: delta 15N and delta 18O NO3 were calculated from uncorr_d45_44 and uncorr_d46_44 using equations outlined in the <a href="http://dmoserv3.whoi.edu/data_docs/15N2_Contamination/Nitrate_isotope_corrections.PDF">"Nitrate isotope corrections" supplementary file</a> (PDF), followed by reference to IAEA N-3, US34, US32 standards.</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
gas chromatograph
gas chromatograph
PI Supplied Instrument Name: gas chromatograph PI Supplied Instrument Description:NO3- δ15N and δ18O were determined with the denitrifier method (Sigman et al. 2001; Casciotti et al. 2002), wherein denitrifying bacteria lacking terminal nitrous oxide reductase (P. chlororaphis f. sp. aureofaciens ATCC 1398) quantitatively convert sample NO3- to N2O gas, which is then extracted, purified and analyzed through a modified Thermo-Scientific Gas Bench II and Delta V Advantage gas chromatograph isotope ratio mass spectrometer. Instrument Name: Gas Chromatograph Instrument Short Name:Gas Chromatograph Instrument Description: Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB02/
isotope ratio mass spectrometer
isotope ratio mass spectrometer
PI Supplied Instrument Name: isotope ratio mass spectrometer PI Supplied Instrument Description:NO3- δ15N and δ18O were determined with the denitrifier method (Sigman et al. 2001; Casciotti et al. 2002), wherein denitrifying bacteria lacking terminal nitrous oxide reductase (P. chlororaphis f. sp. aureofaciens ATCC 1398) quantitatively convert sample NO3- to N2O gas, which is then extracted, purified and analyzed through a modified Thermo-Scientific Gas Bench II and Delta V Advantage gas chromatograph isotope ratio mass spectrometer. Instrument Name: Isotope-ratio Mass Spectrometer Instrument Short Name:IR Mass Spec; IRMS Instrument Description: The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/