http://lod.bco-dmo.org/id/dataset/778158
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
2019-09-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Trial B test of the dissolution method for estimates of the 15N2 atom% of incubations
2019-10-02
publication
2019-10-02
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-01-06
publication
https://doi.org/10.1575/1912/bco-dmo.778158.1
Julie Granger
University of Connecticut
principalInvestigator
Annie Bourbonnais
University of Massachusetts Dartmouth
principalInvestigator
Samuel Wilson
University of Hawaii
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., Bourbonnais, A., Wilson, S. (2019) Trial B test of the dissolution method for estimates of the 15N2 atom% of incubations. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-10-02 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.778158.1 [access date]
Trial b test of the dissolution method Dataset Description: <p>Trial b test of the dissolution method</p> Methods and Sampling: <p>Inocula of 15N2-enriched water were prepared according to either of two protocols outlined by Klawonn et al. (2015).&nbsp;<br />
In a first Trial A, respective 1.9 mL of 15N2 gas aliquots (Cambridge Isotope Laboratories, Lot #I-21065) were injected into crimped-sealed 120 mL glass serum vials filled with deionized water. To dissolve the 15N2 bubble, each of the two serum vials was vortexed for 5 minutes. Two subsamples of each inoculum were dispensed into Exetainers™ with a peristaltic pump for analysis on the MIMS. An aliquot of each inoculum (5 % vol/vol) was then dispensed in replicate 160 mL serum incubation bottles containing air-equilibrated deionized water (Trials A1-A4), which were then crimped-sealed. Following homogenization, triplicate subsamples of each incubation were collected in Exetainers™ for MIMS analysis. The 15N atom % of the inocula and of the corresponding incubations were measured by MIMS at the University of Connecticut (Bay Instruments) and computed as follows:&nbsp;<br />
<br />
Equation 4:&nbsp;<img alt="equation 4" src="https://datadocs.bco-dmo.org/docs/302/EAGER_NitFix/data_docs/equation_4.jpg" style="height:97px; width:975px" /></p>
<div>In Trial B, duplicate 6 mL, 12 mL, and 24 mL aliquots of enriched seawater, prepared as per Wilson et al. (2012; Cambridge Isotope Laboratories 15N2 gas aliquots, Lot #I-19168A), were added to 100 mL glass serum vials, filled with air equilibrated seawater, and crimp-sealed with no headspace using Teflon-lined septa. Triplicate subsamples of this dilution series and the enriched seawater were analyzed at the University of Hawaii on a MIMS (Bay Instruments; Eq. 4).<br />
&nbsp;</div>
<div>In both trials, the concentration of N2 isotopologues (m/z 28, 29, and 30) in each of the 15N2-enriched inocula was then extrapolated from the ionization efficiency of N isotopologues in air-equilibrated seawater. We define the ionization efficiency as the ratio of the isotopologue ion current measured by MIMS relative to its concentration in air-equilibrated seawater (ASW):&nbsp;<br />
&nbsp;</div>
<div>Equation S2:&nbsp;<img alt="equation S2" src="https://datadocs.bco-dmo.org/docs/302/EAGER_NitFix/data_docs/equation_s2.jpg" style="height:91px; width:975px" /></div>
<div><br />
For instance, at a temperature of 25ºC and salinity of 35 psu, the solubility coefficients of Hamme and Emerson (2004) predict a N2 concentration of 388.9 μmol kg-1. The fraction of 15N in N2 (i.e., 15N/(14N+15N)) for air-equilibrated seawater is 0.003663 (Mariotti, 1983), such that the expected fractions of 28N2, 29N2, and 30N2 derived from their binomial probability distributions are as follows:<br />
&nbsp;</div>
<div><img alt="equation s3a" src="https://datadocs.bco-dmo.org/docs/302/EAGER_NitFix/data_docs/equation_s3a.jpg" style="height:102px; width:975px" /></div>
<div>&nbsp; = 99.2687 % Equation S3a</div>
<div><img alt="equation s3b" src="https://datadocs.bco-dmo.org/docs/302/EAGER_NitFix/data_docs/equation_s3b.jpg" style="height:97px; width:975px" />= 0.7299 % Equation S3b</div>
<div><img alt="equation s3c" src="https://datadocs.bco-dmo.org/docs/302/EAGER_NitFix/data_docs/equation_s3c.jpg" style="height:102px; width:975px" />= 0.0013 % Equation S3c<br />
&nbsp;</div>
<div>Accordingly, air-equilibrated concentrations of 28N2, 29N2, and 30N2 at this temperature and salinity are 386.0, 2.8, and 0.005 μmol kg-1, respectively. The ionization efficiency of the isotopologues is then equal to the ion current of m/z 28 recorded for ASW divided by the corresponding 28N2 concentration (Eq. S2). We used the ionization efficiency of m/z 28 in ASW to derive the N2 isotopologue concentrations in the inocula from their respective MIMS ion currents. We did not derive distinct ionization efficiencies from the ion current-to-concentration of m/z 29 and 30 in ASW, as these isotopologues are poorly resolved by the MIMS at natural abundance. Thus, we are assuming that the ionization efficiency of m/z 29 and 30 isotopologues is roughly similar to that of m/z 28 (i.e., that ionization isotope effects are negligible for our purposes). The initial expected AN2 of the “incubations” was then calculated using a linear mixing model with N2 isotopologue concentrations in ambient and enriched seawater</div>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1732246 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1732246
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
Annie Bourbonnais
University of Massachusetts Dartmouth
abourbonnais@seoe.sc.edu
pointOfContact
Samuel Wilson
University of Hawaii
808-956-0573
1950 East-West Road C-MORE Hale
Honlulu
HI
96822
USA
stwilson@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_ID
Time
Mass_z_28
Mass_z_29
Mass_z_30
Mass_z_32
Mass_z_40
O2_Ar
ratio_30_28
atom_pcnt_15N
Isotope Ratio Mass Spectrometer
Membrane Inlet Mass Spectrometer
theme
None, User defined
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Isotope-ratio Mass Spectrometer
Membrane Inlet 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.
EAGER: Collaborative Research: Detection limit in marine nitrogen fixation measurements - Constraints of rates from the mesopelagic ocean
https://www.bco-dmo.org/project/772534
EAGER: Collaborative Research: Detection limit in marine nitrogen fixation measurements - Constraints of rates from the mesopelagic ocean
<p>NSF Award Abstract:<br />
The availability of nitrogen is required to support the growth and production of organisms living in the surface of our global ocean. This element can be scarce. To alleviate this scarcity, a special class of bacteria and archaea, called nitrogen fixers, can derive the nitrogen needed for growth from nitrogen gas. This project would carefully examine one specific method for measuring nitrogen fixation that has been used recently to suggest the occurrence of small amounts of nitrogen fixation in subsurface ocean waters. If these reports are verified, then a revision of our understanding of the marine nitrogen cycle may be needed. The Ocean Carbon and Biogeochemistry program will be used as a platform to develop community consensus for best practices in nitrogen fixation measurements and detection of diversity, activity, and abundances of the organisms responsible. In addition, a session will be organized in a future national/international conference to communicate with the broader scientific community while developing these best practices.</p>
<p>The goal of this study is to conduct a thorough examination of potential experimental and analytical errors inherent to the 15N2-tracer nitrogen fixation method, in tandem with comprehensive molecular measurements, in mesopelagic ocean waters. Samples will be collected and experimental work conducted on a cruise transect in the North Atlantic Ocean, followed by analytical work in the laboratory. The specific aims of this study are to (1) determine the minimum quantifiable rates of 15N2 fixation based on incubations of mesopelagic waters via characterization of sources of experimental and analytical error, and (2) seek evidence of presence and expression of nitrogen fixation genes via comprehensive molecular approaches on corresponding samples. The range of detectable rates and diazotroph activity from the measurements made in this study will be informative for the understanding of the importance of nitrogen fixation in the oceanic nitrogen budget.</p>
EAGER NitFix
largerWorkCitation
project
eng; USA
oceans
2019-10-02
North Atlantic Ocean, Pacific Ocean
0
BCO-DMO catalogue of parameters from Trial B test of the dissolution method for estimates of the 15N2 atom% of incubations
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/778189.rdf
Name: Sample_ID
Units: unitless
Description: sample
http://lod.bco-dmo.org/id/dataset-parameter/778190.rdf
Name: Time
Units: unitless
Description: time
http://lod.bco-dmo.org/id/dataset-parameter/778191.rdf
Name: Mass_z_28
Units: unitless
Description: mass-to-charge
http://lod.bco-dmo.org/id/dataset-parameter/778192.rdf
Name: Mass_z_29
Units: unitless
Description: mass-to-charge
http://lod.bco-dmo.org/id/dataset-parameter/778193.rdf
Name: Mass_z_30
Units: unitless
Description: mass-to-charge
http://lod.bco-dmo.org/id/dataset-parameter/778194.rdf
Name: Mass_z_32
Units: unitless
Description: mass-to-charge
http://lod.bco-dmo.org/id/dataset-parameter/778195.rdf
Name: Mass_z_40
Units: unitless
Description: mass-to-charge
http://lod.bco-dmo.org/id/dataset-parameter/778196.rdf
Name: O2_Ar
Units: unitless
Description: O2 to Ar ratio
http://lod.bco-dmo.org/id/dataset-parameter/778197.rdf
Name: ratio_30_28
Units: unitless
Description: ratio 30/28
http://lod.bco-dmo.org/id/dataset-parameter/778198.rdf
Name: atom_pcnt_15N
Units: unitless
Description: 15N atom %
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
3759
https://darchive.mblwhoilibrary.org/bitstream/1912/25121/1/dataset-778158_trialb__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.778158.1
download
onLine
dataset
<p>Inocula of 15N2-enriched water were prepared according to either of two protocols outlined by Klawonn et al. (2015).&nbsp;<br />
In a first Trial A, respective 1.9 mL of 15N2 gas aliquots (Cambridge Isotope Laboratories, Lot #I-21065) were injected into crimped-sealed 120 mL glass serum vials filled with deionized water. To dissolve the 15N2 bubble, each of the two serum vials was vortexed for 5 minutes. Two subsamples of each inoculum were dispensed into Exetainers™ with a peristaltic pump for analysis on the MIMS. An aliquot of each inoculum (5 % vol/vol) was then dispensed in replicate 160 mL serum incubation bottles containing air-equilibrated deionized water (Trials A1-A4), which were then crimped-sealed. Following homogenization, triplicate subsamples of each incubation were collected in Exetainers™ for MIMS analysis. The 15N atom % of the inocula and of the corresponding incubations were measured by MIMS at the University of Connecticut (Bay Instruments) and computed as follows:&nbsp;<br />
<br />
Equation 4:&nbsp;<img alt="equation 4" src="https://datadocs.bco-dmo.org/docs/302/EAGER_NitFix/data_docs/equation_4.jpg" style="height:97px; width:975px" /></p>
<div>In Trial B, duplicate 6 mL, 12 mL, and 24 mL aliquots of enriched seawater, prepared as per Wilson et al. (2012; Cambridge Isotope Laboratories 15N2 gas aliquots, Lot #I-19168A), were added to 100 mL glass serum vials, filled with air equilibrated seawater, and crimp-sealed with no headspace using Teflon-lined septa. Triplicate subsamples of this dilution series and the enriched seawater were analyzed at the University of Hawaii on a MIMS (Bay Instruments; Eq. 4).<br />
&nbsp;</div>
<div>In both trials, the concentration of N2 isotopologues (m/z 28, 29, and 30) in each of the 15N2-enriched inocula was then extrapolated from the ionization efficiency of N isotopologues in air-equilibrated seawater. We define the ionization efficiency as the ratio of the isotopologue ion current measured by MIMS relative to its concentration in air-equilibrated seawater (ASW):&nbsp;<br />
&nbsp;</div>
<div>Equation S2:&nbsp;<img alt="equation S2" src="https://datadocs.bco-dmo.org/docs/302/EAGER_NitFix/data_docs/equation_s2.jpg" style="height:91px; width:975px" /></div>
<div><br />
For instance, at a temperature of 25ºC and salinity of 35 psu, the solubility coefficients of Hamme and Emerson (2004) predict a N2 concentration of 388.9 μmol kg-1. The fraction of 15N in N2 (i.e., 15N/(14N+15N)) for air-equilibrated seawater is 0.003663 (Mariotti, 1983), such that the expected fractions of 28N2, 29N2, and 30N2 derived from their binomial probability distributions are as follows:<br />
&nbsp;</div>
<div><img alt="equation s3a" src="https://datadocs.bco-dmo.org/docs/302/EAGER_NitFix/data_docs/equation_s3a.jpg" style="height:102px; width:975px" /></div>
<div>&nbsp; = 99.2687 % Equation S3a</div>
<div><img alt="equation s3b" src="https://datadocs.bco-dmo.org/docs/302/EAGER_NitFix/data_docs/equation_s3b.jpg" style="height:97px; width:975px" />= 0.7299 % Equation S3b</div>
<div><img alt="equation s3c" src="https://datadocs.bco-dmo.org/docs/302/EAGER_NitFix/data_docs/equation_s3c.jpg" style="height:102px; width:975px" />= 0.0013 % Equation S3c<br />
&nbsp;</div>
<div>Accordingly, air-equilibrated concentrations of 28N2, 29N2, and 30N2 at this temperature and salinity are 386.0, 2.8, and 0.005 μmol kg-1, respectively. The ionization efficiency of the isotopologues is then equal to the ion current of m/z 28 recorded for ASW divided by the corresponding 28N2 concentration (Eq. S2). We used the ionization efficiency of m/z 28 in ASW to derive the N2 isotopologue concentrations in the inocula from their respective MIMS ion currents. We did not derive distinct ionization efficiencies from the ion current-to-concentration of m/z 29 and 30 in ASW, as these isotopologues are poorly resolved by the MIMS at natural abundance. Thus, we are assuming that the ionization efficiency of m/z 29 and 30 isotopologues is roughly similar to that of m/z 28 (i.e., that ionization isotope effects are negligible for our purposes). The initial expected AN2 of the “incubations” was then calculated using a linear mixing model with N2 isotopologue concentrations in ambient and enriched seawater</div>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing Notes:<br />
- table was extracted from original spreadsheet.<br />
-&nbsp;added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions</p>
<p>&nbsp;</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
Isotope Ratio Mass Spectrometer
Isotope Ratio Mass Spectrometer
PI Supplied Instrument Name: Isotope Ratio Mass Spectrometer PI Supplied Instrument Description:continuous flow Delta V Isotope Ratio Mass Spectrometer (Smith et al. 2015), and continuous flow-GV Isoprime IRMS (Charoenpong et al., 2014) 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/
Membrane Inlet Mass Spectrometer
Membrane Inlet Mass Spectrometer
PI Supplied Instrument Name: Membrane Inlet Mass Spectrometer PI Supplied Instrument Description:Membrane Inlet Mass Spectrometer (Bay Instruments) Instrument Name: Membrane Inlet Mass Spectrometer Instrument Short Name:MIMS Instrument Description: Membrane-introduction mass spectrometry (MIMS) is a method of introducing analytes into the mass spectrometer's vacuum chamber via a semipermeable membrane.