http://lod.bco-dmo.org/id/dataset/864826
eng; USA
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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.
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2021-11-15
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Nitrogen isotope fractionation for ammonium assimilation by marine phytoplankton (Biological Nitrogen Isotope Fractionation project)
2021-11-15
publication
2021-11-15
revision
BCO-DMO Linked Data URI
2021-11-15
creation
http://lod.bco-dmo.org/id/dataset/864826
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., Mathuri, M. (2021) Nitrogen isotope fractionation for ammonium assimilation by marine phytoplankton (Biological Nitrogen Isotope Fractionation project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-11-15 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/864826 [access date]
Dataset Description: <p><strong>Model code description</strong></p>
<p>To query the physiological mechanism of nitrogen (N) isotope fractionation during ammonium (NH<sub>4</sub><sup>+</sup>) assimilation, we constructed a time-dependent finite-differencing box model that tracks discrete <sup>14</sup>N and <sup>15</sup>N in the different N pools during the growth of marine algae with NH<sub>4</sub><sup>+</sup> as the sole N source. The model entails three N reservoirs: external N (medium), intracellular reservoir, and the phytoplankton nitrogen (biomass). We prescribe a non-fractionating active NH<sub>4</sub><sup>+</sup> uptake by the cells via specialized NH<sub>4</sub><sup>+</sup> transport proteins (AMTs), that follows Michaelis-Menten kinetics with half-saturation constant of 50 nM. Inside the cell, NH<sub>4</sub><sup>+</sup> is condensed with glutamate by glutamine synthetase (GS) to biomass – the rate-determining and isotope-fractionating step for NH<sub>4</sub><sup>+</sup> assimilation. The isotope fractionation imparted internally is then communicated to the external medium largely by passive diffusion of ammonia (NH<sub>3</sub>). A full description of the physiological model and the different scenarios tested can be found in the article. Below is an outline of the various constants and variables used in the model.</p>
<p><strong>Constants</strong></p>
<p>0.00367 – initial ratio of <sup>15</sup>N/<sup>14</sup>N for all the N pools other than external NH<sub>4</sub><sup>+</sup></p>
<p>0.003695 – initial ratio of <sup>15</sup>N/<sup>14</sup>N for external NH<sub>4</sub><sup>+</sup></p>
<p>1.76 x 10<sup>-5</sup> – equilibrium constant for protonation of NH<sub>3</sub></p>
<p>1.58 x 10<sup>-6</sup> – concentration of OH<sup>-</sup> in the external medium at pH 8.2 (mol L<sup>-1</sup>)</p>
<p>1.0 x 10<sup>-7</sup> – concentration of OH<sup>-</sup> in the cytoplasm at pH 7.0 (mol L<sup>-1</sup>)</p>
<p>1.0 x 10<sup>-9</sup> – concentration of OH<sup>-</sup> in the vacuole at pH 5.0 (mol L<sup>-1</sup>)</p>
<p>µmax – maximum specific growth rate (hr<sup>-1</sup>)</p>
<p>VGSmax – maximum GS rate for NH<sub>4</sub><sup>+</sup> condensation with glutamate (hr<sup>-1</sup>)</p>
<p>alphaGS – N isotope fractionation factor for GS</p>
<p>alphaCat – N isotope fractionation factor for catabolic NH<sub>4</sub><sup>+</sup> production</p>
<p>MultLA – multiplier of the maximum specific growth rate for the low-affinity uptake</p>
<p>MultHA – multiplier of the maximum specific growth rate for the high-affinity uptake</p>
<p>PC_NH3 – permeability coefficient for NH<sub>3</sub> (cm hr<sup>-1</sup>)</p>
<p>PC_NH4 – permeability coefficient for NH<sub>4</sub><sup>+</sup> (cm hr<sup>-1</sup>)</p>
<p>BetaNH4 – a term in the constant field equation for NH<sub>4</sub><sup>+</sup> diffusion across the cellular membrane</p>
<p>expBetaNH4 – exponent of BetaNH4</p>
<p>BetaVac – a term in the constant field equation for NH<sub>4</sub><sup>+</sup> diffusion across the vacuolar membrane</p>
<p>expBetaVac – exponent of BetaVac</p>
<p>SA – surface area of the phytoplankton cell (cm<sup>-2</sup>)</p>
<p>SAVac – surface area of the cell vacuole (cm<sup>-2</sup>)</p>
<p>Cellular N quota – 1.66 x 10<sup>-6</sup> µmol N cell<sup>-1</sup></p>
<p>Phytoplankton cell volume – 1.15 x 10<sup>-12</sup> L</p>
<p>Vacuole volume – 3.45 x 10<sup>-13</sup> L</p>
<p>NH<sub>4</sub><sup>+</sup>-NH<sub>3</sub> equilibrium isotope effect – 15‰</p>
<p><strong>Variables</strong></p>
<p>CellN14 – <sup>14</sup>N in the phytoplankton nitrogen in the culture (µmol L<sup>-1</sup>)</p>
<p>CellN15 – <sup>15</sup>N in the phytoplankton nitrogen in the culture (µmol L<sup>-1</sup>)</p>
<p>Gln14 – <sup>14</sup>N in the glutamine pool in the culture (µmol L<sup>-1</sup>)</p>
<p>Gln15 – <sup>15</sup>N in the glutamine pool in the culture (µmol L<sup>-1</sup>)</p>
<p>NH4cyt14 – <sup>14</sup>N in the cytoplasmic NH<sub>4</sub><sup>+</sup> in the culture (µmol L<sup>-1</sup>)</p>
<p>NH4cyt15 – <sup>15</sup>N in the cytoplasmic NH<sub>4</sub><sup>+</sup> in the culture (µmol L<sup>-1</sup>)</p>
<p>NH4out14 – <sup>14</sup>N in the external NH<sub>4</sub><sup>+</sup> pool (µmol L<sup>-1</sup>)</p>
<p>NH4out15 – <sup>15</sup>N in the external NH<sub>4</sub><sup>+</sup> pool (µmol L<sup>-1</sup>)</p>
<p>Vacuole14 – <sup>14</sup>N in the vacuolar NH<sub>4</sub><sup>+</sup> in the culture (µmol L<sup>-1</sup>)</p>
<p>Vacuole15 – <sup>15</sup>N in the vacuolar NH<sub>4</sub><sup>+</sup> in the culture (µmol L<sup>-1</sup>)</p>
<p>MMLAU – Michaelis-Menten term for low-affinity NH<sub>4</sub><sup>+</sup> uptake with half-saturation constant of 30 µmol L<sup>-1</sup></p>
<p>MMHAU – Michaelis-Menten term for high-affinity NH<sub>4</sub><sup>+</sup> uptake with half-saturation constant of 50 nmol L<sup>-1</sup></p>
<p>Cell_N_total – phytoplankton nitrogen in the culture (µmol L<sup>-1</sup>)</p>
<p>"Cells_L-1" – cell density per liter of the culture medium (cells L<sup>-1</sup>)</p>
<p>CytoplasmNH4conc – cellular concentration of NH<sub>4</sub><sup>+</sup> in the cytoplasm (µmol L<sup>-1</sup>)</p>
<p>CytoplasmNH3conc – cellular concentration of NH<sub>3</sub> in the cytoplasm (µmol L<sup>-1</sup>)</p>
<p>NH4concOut – external NH<sub>4</sub><sup>+</sup> pool (µmol L<sup>-1</sup>)</p>
<p>F15NH4out – fraction of <sup>15</sup>N in the external NH<sub>4</sub><sup>+</sup></p>
<p>NH3concOut – external NH<sub>3</sub> pool (µmol L<sup>-1</sup>)</p>
<p>Delta_NH3in – difference in NH<sub>3</sub> concentration between the cytoplasm and external medium (µmol L<sup>-1</sup>)</p>
<p>EffluxNH3 – rate of cellular NH<sub>3</sub> efflux from the cytoplasm to the external medium (µmol cell<sup>-1</sup> hr<sup>-1</sup>)</p>
<p>d15NH4cyt – N isotope composition of NH<sub>4</sub><sup>+</sup> in the cytoplasm (‰ vs. air)</p>
<p>d15NH3cyt – N isotope composition of NH<sub>3</sub> in the cytoplasm (‰ vs. air)</p>
<p>R15NH3cyt – ratio of <sup>15</sup>N in the cytoplasmic NH<sub>3</sub></p>
<p>F15NH3cyt – fraction of <sup>15</sup>N in the cytoplasmic NH<sub>3</sub></p>
<p>VENH314 – rate of <sup>14</sup>N NH<sub>3</sub> efflux from the cytoplasm to the external medium in the culture (µmol hr<sup>-1</sup>)</p>
<p>Delta_NH4in – difference in NH<sub>4</sub><sup>+</sup> concentration between the cytoplasm and external medium (µmol L<sup>-1</sup>)</p>
<p>EffluxNH4 – rate of cellular NH<sub>4</sub><sup>+</sup> efflux from the cytoplasm to the external medium (µmol cell<sup>-1</sup> hr<sup>-1</sup>)</p>
<p>F15NH4cyt – fraction of <sup>15</sup>N in the cytoplasmic NH<sub>4</sub><sup>+</sup></p>
<p>VENH414 – rate of <sup>14</sup>N NH<sub>4</sub><sup>+</sup> efflux from the cytoplasm to the external medium in the culture (µmol hr<sup>-1</sup>)</p>
<p>VINH3Vac14 – rate of <sup>14</sup>N NH<sub>3</sub> influx from the cytoplasm to the vacuole in the culture (µmol hr<sup>-1</sup>)</p>
<p>MMGS – Michaelis-Menten term for GS with half-saturation constant of 10 µmol L<sup>-1</sup></p>
<p>GS14 – rate of <sup>14</sup>N NH<sub>4</sub><sup>+</sup> condensation with glutamate by GS in the culture (µmol hr<sup>-1</sup>)</p>
<p>GlnConc – cellular concentration of glutamine (µmol L<sup>-1</sup>)</p>
<p>MMGln – Michaelis-Menten term for glutamate synthase (GOGAT) with half-saturation constant of 700 µmol L<sup>-1</sup></p>
<p>F15Gln – fraction of <sup>15</sup>N in the glutamine pool</p>
<p>GOGAT14 – rate of assimilation of <sup>14</sup>N glutamine into phytoplankton nitrogen by GOGAT in the culture (µmol hr<sup>-1</sup>)</p>
<p>VENH315 – rate of <sup>15</sup>N NH<sub>3</sub> efflux from the cytoplasm to the external medium in the culture (µmol hr<sup>-1</sup>)</p>
<p>VENH415 – rate of <sup>15</sup>N NH<sub>4</sub><sup>+</sup> efflux from the cytoplasm to the external medium in the culture (µmol hr<sup>-1</sup>)</p>
<p>VINH3Vac15 – rate of <sup>15</sup>N NH<sub>3</sub> influx from the cytoplasm to the vacuole in the culture (µmol hr<sup>-1</sup>)</p>
<p>GS15 – rate of <sup>15</sup>N NH<sub>4</sub><sup>+</sup> condensation with glutamate by GS in the culture (µmol hr<sup>-1</sup>)</p>
<p>GOGAT15 – rate of assimilation of <sup>15</sup>N glutamine into phytoplankton nitrogen by GOGAT in the culture (µmol hr<sup>-1</sup>)</p>
<p>VENH4Vac14 – rate of <sup>14</sup>N NH<sub>4</sub><sup>+</sup> efflux from the vacuole to the cytoplasm in the culture (µmol hr<sup>-1</sup>)</p>
<p>VENH4Vac15 – rate of <sup>15</sup>N NH<sub>4</sub><sup>+</sup> efflux from the vacuole to the cytoplasm in the culture (µmol hr<sup>-1</sup>)</p>
<p>VU14 – rate of <sup>14</sup>N NH<sub>4</sub><sup>+</sup> uptake into the cytoplasm via AMTs in the culture (µmol hr<sup>-1</sup>)</p>
<p>alphaTR – sigmoidal parametrization of N isotope fractionation factor for NH<sub>4</sub><sup>+</sup> transport via AMTs</p>
<p>VU15 – rate of <sup>15</sup>N NH<sub>4</sub><sup>+</sup> uptake into the cytoplasm via AMTs in the culture (µmol hr<sup>-1</sup>)</p>
<p>d15NCell – N isotope composition of cellular N (‰ vs. air)</p>
<p>d15NH4Vac – N isotope composition of NH<sub>4</sub><sup>+</sup> in the vacuole (‰ vs. air)</p>
<p>d15NH3Vac – N isotope composition of NH<sub>3</sub> in the vacuole (‰ vs. air)</p>
<p>d15NH4out – N isotope composition of NH<sub>4</sub><sup>+</sup> in the external pool (‰ vs. air)</p>
<p>NH4concVac – vacuolar concentration of NH<sub>4</sub><sup>+</sup> (µmol L<sup>-1</sup>)</p>
<p>NH3concVac – vacuolar concentration of NH<sub>3</sub> (µmol L<sup>-1</sup>)</p>
<p>Delta_NH3Vac – difference in NH<sub>3</sub> concentration between the cytoplasm and vacuole (µmol L<sup>-1</sup>)</p>
<p>Delta_NH4Vac – difference in NH<sub>4</sub><sup>+</sup> concentration between the cytoplasm and vacuole (µmol L<sup>-1</sup>)</p>
<p>EffluxNH4Vac – rate of cellular NH<sub>4</sub><sup>+</sup> efflux from the vacuole to the cytoplasm (µmol cell<sup>-1</sup> hr<sup>-1</sup>)</p>
<p>F15NH4Vac – fraction of <sup>15</sup>N in the vacuolar NH<sub>4</sub><sup>+</sup></p>
<p>InfluxNH3Vac – rate of cellular NH<sub>3</sub> influx from the cytoplasm to the vacuole (µmol cell<sup>-1</sup> hr<sup>-1</sup>)</p> Methods and Sampling: <p><strong>Phytoplankton cultures</strong></p>
<p>Two strains of marine algae, the diatom <em>Thalassiosira weissflogii</em> (actin) and the prasinophyte <em>Tetraselmis</em> sp. were grown in batch cultures in sterile, acid-washed borosilicate glass or polycarbonate bottles using artificial seawater medium in an environmental chamber at 18<sup>0</sup>C, illuminated with fluorescent light (40 <em>μ</em>mol photons m<sup>-2</sup> s<sup>-1</sup> photosynthetically available radiation) on a 12-hour light and 12-hour dark cycle. The artificial seawater medium was prepared from low nutrient Instant Ocean™ salt dissolved in Milli-Q water and filtered through a 47 mm Whatman GF/F glass microfiber filter (0.7 μm nominal pore-size) and sterilized by autoclaving at 100<sup>0</sup>C via Pasteurization cycle in PRIMUS steam sterilizer, then supplemented with filter-sterilized 100 – 250 <em>μ</em>M NH<sub>4</sub><sup>+</sup>, 10 <em>μ</em>M phosphate, 100 <em>μ</em>M silicic acid (only for <em>T. weissflogii</em> cultures), and f/2 trace metals and vitamins (Guillard and Ryther 1962). The batch cultures were initiated from inocula of approximately 1,000 cells mL<sup>-1</sup>, and cell densities monitored daily using Multisizer 4 Beckman Coulter counter. Media subsamples were collected during exponential growth for analyses of NH<sub>4</sub><sup>+</sup> concentration and N isotope ratios. Subsamples were filtered through a 0.45 μm pore-size polyether-sulfone (PES) syringe filters and collected into acid-washed High Density Poly-Ethylene (HDPE) bottles, solution pH adjusted to ca. 4.5 with dilute hydrochloric acid in order to minimize ammonia volatilization during storage, and samples stored at –20<sup>0</sup>C pending analysis. Particulate organic nitrogen (PON) was also sampled during the exponential growth phase by filtering aqueous subsamples onto a pre-combusted 25 mm Whatman GF/F glass microfiber filters (0.7 μm pore-size) and stored in pre-combusted aluminum foils at –20<sup>0</sup>C pending analysis of N isotope ratio analysis. To capture lower NH<sub>4</sub><sup>+</sup> concentrations, short-term NH<sub>4</sub><sup>+</sup> uptake experiments with <em>T. weissflogii</em> and <em>Tetraselmis</em> sp. were conducted. A first set of experiments was conducted with <em>T. weissflogii</em> and <em>Tetraselmis</em> sp. cells in early stationary phase, wherein NH<sub>4</sub><sup>+</sup> was exhausted from the medium. The cells were collected by gentle filtration onto a 5 μm pore-size 47 mm Isopore<sup>TM</sup> polycarbonate membrane filter and resuspended into fresh medium containing ~60 <em>μ</em>M NH<sub>4</sub><sup>+</sup> for <em>T. weissflogii</em> and 20 <em>μ</em>M NH<sub>4</sub><sup>+</sup> for <em>Tetraselmis</em> sp. Aqueous subsamples were collected at regular time intervals until NH<sub>4</sub><sup>+</sup> in the medium was exhausted. A second set of experiments was conducted with N-replete (cells in exponential growth phase) and N-starved cells (cells two days into stationary phase) of <em>T. weissflogii</em> and <em>Tetraselmis</em> sp. Cell cultures were either diluted into fresh medium containing ~20 µM NH<sub>4</sub><sup>+</sup>, or gently filtered onto a polycarbonate membrane filter and resuspended into said medium. Short-term incubations occurred largely under constant illumination, although some <em>Tetraselmis</em> sp. uptake experiments were inadvertently subject to light-dark conditions.</p>
<p><strong>Determination of NH<sub>4</sub><sup>+</sup> concentration</strong></p>
<p>Ammonium concentrations at or above 50 <em>μ</em>M were measured fluorometrically following derivatization with o-phthalaldehyde (OPA; Holmes et al. 1999) while concentrations &lt; 50 μM were analyzed with the indophenol method (Solórzano 1969).</p>
<p><strong>Analyses of N isotopes of NH<sub>4</sub><sup>+</sup> and PON</strong></p>
<p>Ammonium samples were diluted to 5 µM or 1 µM with deep Atlantic seawater and N isotope ratios determined using the hypobromite-azide method (Zhang et al. 2007), wherein NH<sub>4</sub><sup>+</sup> is first oxidized to nitrite by hypobromite, after which nitrite is converted to a nitrous oxide gas analyte by reacting with azide. The N isotopic composition of the nitrous oxide product was analyzed using a continuous flow purge and dual cryogenic trap system coupled to a custom-modified Gas Bench II device interfaced with a Thermo Delta V gas chromatograph isotope ratio mass spectrometer (GC-IRMS; see Casciotti et al. 2002; McIlvin and Casciotti 2011). Calibration to reference (dinitrogen gas in air) was achieved from parallel reactions of NH<sub>4</sub><sup>+</sup> reference materials IAEA-N1 and IAEA-N2 diluted in deep Atlantic seawater (5 µM or 1 µM solutions), with respective assigned δ<sup>15</sup>N values of 0.43‰ and 20.3‰ vs. air (Böhlke et al. 1993). To analyze N isotopes of PON, frozen glass microfiber filters were lyophilized for 24 hours using an Edwards Super Modulyo freeze-dryer. The filters were packed into tin capsules and analyzed by combustion to dinitrogen gas on a Costech ECS 4010 Elemental Analyzer followed by N isotope ratio analysis of the resulting dinitrogen gas on a Thermo Delta V isotope ratio mass spectrometer. Samples were calibrated with corresponding aliquots of L-glutamic acid reference materials USGS-40 and USGS-41, with δ<sup>15</sup>N values of –4.52 and 47.57‰ vs. air, respectively (Qi et al. 2003).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1554474 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1554474
onGoing
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: 1
Unknown
Strain
Experiment_type
Experiment_number
Date_and_time_EST
Date_and_time_UTC
Incubation_time_in_days
Cell_density
Initial_cell_density
NH4_plus
stdev_sigma_NH4_plus
negative_natural_logarithm_of_NH4_plus
delta_15NNH4_plus
stdev_sigma_delta_15NNH4_plus
f_lnf_1_f
delta_15NPON
Light_conditions
Growth_stage
Notes
Multisizer 4 Beckman Coulter Counter
Costech ECS 4010 Elemental Analyzer coupled with Thermo Delta V isotope ratio mass spectrometer
Thermo Delta V gas chromatograph isotope ratio mass spectrometer (GC-IRMS)
U-3010 VIS Spectrophotometer
Turner Trilogy Fluorometer
theme
None, User defined
species scientific name (binomial)
experiment type
experiment id
ISO_DateTime_Local
ISO_DateTime_UTC
incubation time or duration
cell_concentration
Ammonium
percent composition
treatment
stage
comments
featureType
BCO-DMO Standard Parameters
Coulter Counter
Elemental Analyzer
Gas Chromatograph Mass Spectrometer
Spectrophotometer
Turner Designs Trilogy fluorometer
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.
CAREER: The biological nitrogen isotope systematics of ammonium consumption and production
https://osprey.bco-dmo.org/project/856532
CAREER: The biological nitrogen isotope systematics of ammonium consumption and production
<p><strong>NSF Award Abstract:</strong><br />
The nitrogen (N) cycle in the marine environment is controlled by biological processes. Unfortunately, quantifying these processes and assessing their effect on the N cycle is difficult by direct measurements because of large spatial and temporal differences. Isotopic composition measurements of N provide a means to constrain these processes indirectly; however, there is still a great deal to be understood about isotope fractionation of recycled nitrogen through biological processes, which has made interpretation of novel nitrogen isotope data difficult. A researcher from the University of Connecticut plans to determine the influence of biological consumption and production on the isotope fractionation in ammonium. By helping to understand the processes surrounding fractionation of recycled ammonium at the organism level, this research will create a basis for which future researchers can better interpret isotope composition data to infer nitrogen cycle dynamics. A graduate student, a postdoctoral fellow, and two or more undergraduate students will be involved in the research. The researcher plans to integrate science with community-engaged learning by developing an undergraduate field and laboratory course that will require the students to present their research to stakeholders in the community. There will be a manual created for this course that will be disseminated in open-access forums for teachers hoping to develop similar courses.</p>
<p>Biological nitrogen isotope fractionation associated with nitrogen recycling remains poorly constrained despite the advent of a variety of new techniques to analyze nitrogen isotopes in recent years. The use of isotopic composition data can be incredibly useful to interpreting nitrogen cycle processes in the ocean that are difficult to measure directly, which makes it crucial to further understand the processes behind fractionation to catch up with the advancement of the datasets available to researchers. This research will characterize the isotope fractionation dynamics of ammonium during biological consumption and production. The researchers will investigate whether the characteristic low concentrations of ammonium in the surface ocean affect isotope fractionation when the ammonium is recycled and whether there is a trophic isotope effect associated with ammonium recycling by protozoan grazers. With this research, there will be a baseline from which researchers can interpret recycled nitrogen dynamics from ammonium isotope datasets. The methods of comparing nitrogen cycling studies will become significantly clearer with such a standard making interpretation uniform by removing significant uncertainties.</p>
Biological Nitrogen Isotope Fractionation
largerWorkCitation
project
eng; USA
oceans
2018-09-09
2020-01-03
0
BCO-DMO catalogue of parameters from Nitrogen isotope fractionation for ammonium assimilation by marine phytoplankton (Biological Nitrogen Isotope Fractionation 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/865280.rdf
Name: Strain
Units: unitless
Description: <p>The two marine algal strains used in the laboratory experiments; a diatom Thalassiosira weissflogii and a prasinophyte Tetraselmis sp.</p>
http://lod.bco-dmo.org/id/dataset-parameter/865281.rdf
Name: Experiment_type
Units: unitless
Description: <p>The algal strains were incubated either under batch cultures or short-term ammonium uptake experiments</p>
http://lod.bco-dmo.org/id/dataset-parameter/865282.rdf
Name: Experiment_number
Units: unitless
Description: <p>Experiment identifier; a and b represent replicate trials for batch cultures</p>
http://lod.bco-dmo.org/id/dataset-parameter/865283.rdf
Name: Date_and_time_EST
Units: unitless
Description: <p>Date and time of sampling in EST; %Y-%m-%d %H:%M</p>
http://lod.bco-dmo.org/id/dataset-parameter/865284.rdf
Name: Date_and_time_UTC
Units: unitless
Description: <p>Date and time of sampling in UTC; %Y-%m-%dT%H:%MZ</p>
http://lod.bco-dmo.org/id/dataset-parameter/865285.rdf
Name: Incubation_time_in_days
Units: days
Description: <p>Number of days from the start of the experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/865286.rdf
Name: Cell_density
Units: cells mL-1
Description: <p>Number of cells per one milliliter of the culture media at different times during the incubation period as determined using Beckman Coulter counter</p>
http://lod.bco-dmo.org/id/dataset-parameter/865287.rdf
Name: Initial_cell_density
Units: cells mL-1
Description: <p>Number of cells per one milliliter of the culture media at start of short-term uptake experiments</p>
http://lod.bco-dmo.org/id/dataset-parameter/865288.rdf
Name: NH4_plus
Units: umol L-1
Description: <p>Ammonium concentration. Concentrations ≥ 50 µM measured fluorometrically on Turner Trilogy Fluorometer with the o-phthalaldehyde (OPA) method (Holmes et al. 1999). Concentrations < 50 _M analyzed on U-3010 VIS Specrophotometer with the indophenol method (Solorzano 1969)</p>
http://lod.bco-dmo.org/id/dataset-parameter/865289.rdf
Name: stdev_sigma_NH4_plus
Units: unitless
Description: <p>Standard deviation for [NH4+] derived from analytical replicates</p>
http://lod.bco-dmo.org/id/dataset-parameter/865290.rdf
Name: negative_natural_logarithm_of_NH4_plus
Units: unitless
Description: <p>Negative natural logarithm of ammonium concentration as used in the Rayleigh substrate (NH4+) equation (Mariotti et al. 1981)</p>
http://lod.bco-dmo.org/id/dataset-parameter/865291.rdf
Name: delta_15NNH4_plus
Units: ‰ vs. air
Description: <p>N isotope composition of NH4+ measured using hypobronite-azide method (Zhang et al. 2007) on Thermo Delta V GC-IRMS with modified Gas Bench II and a PAL autosampler</p>
http://lod.bco-dmo.org/id/dataset-parameter/865292.rdf
Name: stdev_sigma_delta_15NNH4_plus
Units: units
Description: <p>Standard deviation for _15NNH4+ derived from analytical replicates using monte carlo error propagation</p>
http://lod.bco-dmo.org/id/dataset-parameter/865293.rdf
Name: f_lnf_1_f
Units: units
Description: <p>Used in the Rayleigh product (PON) equation (Mariotti et al. 1981), where f represents the fraction of ammonium in the media at every sampling time relative to the initial concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/865294.rdf
Name: delta_15NPON
Units: ‰ vs. air
Description: <p>N isotope composition of PON measured by combustion on a Thermo Delta V IRMS linked through a Costech ECS 4010 Elementral Analyzer</p>
http://lod.bco-dmo.org/id/dataset-parameter/865295.rdf
Name: Light_conditions
Units: unitless
Description: <p>Experiments conducted under 12-hour light and 12-hour dark conditions. Most of the short-term experiments were conducted in light but a few with Tetraselmis sp. extended into the dark period</p>
http://lod.bco-dmo.org/id/dataset-parameter/865296.rdf
Name: Growth_stage
Units: unitless
Description: <p>Short-term uptake experiments were conducted with cells harvested in their exponential growth phase (N-replete), early stationary phase (stationary), and in late stationary phase (N-starved).</p>
http://lod.bco-dmo.org/id/dataset-parameter/865297.rdf
Name: Notes
Units: unitless
Description: <p>Notes</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/864826/data/download
download
onLine
dataset
<p><strong>Phytoplankton cultures</strong></p>
<p>Two strains of marine algae, the diatom <em>Thalassiosira weissflogii</em> (actin) and the prasinophyte <em>Tetraselmis</em> sp. were grown in batch cultures in sterile, acid-washed borosilicate glass or polycarbonate bottles using artificial seawater medium in an environmental chamber at 18<sup>0</sup>C, illuminated with fluorescent light (40 <em>μ</em>mol photons m<sup>-2</sup> s<sup>-1</sup> photosynthetically available radiation) on a 12-hour light and 12-hour dark cycle. The artificial seawater medium was prepared from low nutrient Instant Ocean™ salt dissolved in Milli-Q water and filtered through a 47 mm Whatman GF/F glass microfiber filter (0.7 μm nominal pore-size) and sterilized by autoclaving at 100<sup>0</sup>C via Pasteurization cycle in PRIMUS steam sterilizer, then supplemented with filter-sterilized 100 – 250 <em>μ</em>M NH<sub>4</sub><sup>+</sup>, 10 <em>μ</em>M phosphate, 100 <em>μ</em>M silicic acid (only for <em>T. weissflogii</em> cultures), and f/2 trace metals and vitamins (Guillard and Ryther 1962). The batch cultures were initiated from inocula of approximately 1,000 cells mL<sup>-1</sup>, and cell densities monitored daily using Multisizer 4 Beckman Coulter counter. Media subsamples were collected during exponential growth for analyses of NH<sub>4</sub><sup>+</sup> concentration and N isotope ratios. Subsamples were filtered through a 0.45 μm pore-size polyether-sulfone (PES) syringe filters and collected into acid-washed High Density Poly-Ethylene (HDPE) bottles, solution pH adjusted to ca. 4.5 with dilute hydrochloric acid in order to minimize ammonia volatilization during storage, and samples stored at –20<sup>0</sup>C pending analysis. Particulate organic nitrogen (PON) was also sampled during the exponential growth phase by filtering aqueous subsamples onto a pre-combusted 25 mm Whatman GF/F glass microfiber filters (0.7 μm pore-size) and stored in pre-combusted aluminum foils at –20<sup>0</sup>C pending analysis of N isotope ratio analysis. To capture lower NH<sub>4</sub><sup>+</sup> concentrations, short-term NH<sub>4</sub><sup>+</sup> uptake experiments with <em>T. weissflogii</em> and <em>Tetraselmis</em> sp. were conducted. A first set of experiments was conducted with <em>T. weissflogii</em> and <em>Tetraselmis</em> sp. cells in early stationary phase, wherein NH<sub>4</sub><sup>+</sup> was exhausted from the medium. The cells were collected by gentle filtration onto a 5 μm pore-size 47 mm Isopore<sup>TM</sup> polycarbonate membrane filter and resuspended into fresh medium containing ~60 <em>μ</em>M NH<sub>4</sub><sup>+</sup> for <em>T. weissflogii</em> and 20 <em>μ</em>M NH<sub>4</sub><sup>+</sup> for <em>Tetraselmis</em> sp. Aqueous subsamples were collected at regular time intervals until NH<sub>4</sub><sup>+</sup> in the medium was exhausted. A second set of experiments was conducted with N-replete (cells in exponential growth phase) and N-starved cells (cells two days into stationary phase) of <em>T. weissflogii</em> and <em>Tetraselmis</em> sp. Cell cultures were either diluted into fresh medium containing ~20 µM NH<sub>4</sub><sup>+</sup>, or gently filtered onto a polycarbonate membrane filter and resuspended into said medium. Short-term incubations occurred largely under constant illumination, although some <em>Tetraselmis</em> sp. uptake experiments were inadvertently subject to light-dark conditions.</p>
<p><strong>Determination of NH<sub>4</sub><sup>+</sup> concentration</strong></p>
<p>Ammonium concentrations at or above 50 <em>μ</em>M were measured fluorometrically following derivatization with o-phthalaldehyde (OPA; Holmes et al. 1999) while concentrations &lt; 50 μM were analyzed with the indophenol method (Solórzano 1969).</p>
<p><strong>Analyses of N isotopes of NH<sub>4</sub><sup>+</sup> and PON</strong></p>
<p>Ammonium samples were diluted to 5 µM or 1 µM with deep Atlantic seawater and N isotope ratios determined using the hypobromite-azide method (Zhang et al. 2007), wherein NH<sub>4</sub><sup>+</sup> is first oxidized to nitrite by hypobromite, after which nitrite is converted to a nitrous oxide gas analyte by reacting with azide. The N isotopic composition of the nitrous oxide product was analyzed using a continuous flow purge and dual cryogenic trap system coupled to a custom-modified Gas Bench II device interfaced with a Thermo Delta V gas chromatograph isotope ratio mass spectrometer (GC-IRMS; see Casciotti et al. 2002; McIlvin and Casciotti 2011). Calibration to reference (dinitrogen gas in air) was achieved from parallel reactions of NH<sub>4</sub><sup>+</sup> reference materials IAEA-N1 and IAEA-N2 diluted in deep Atlantic seawater (5 µM or 1 µM solutions), with respective assigned δ<sup>15</sup>N values of 0.43‰ and 20.3‰ vs. air (Böhlke et al. 1993). To analyze N isotopes of PON, frozen glass microfiber filters were lyophilized for 24 hours using an Edwards Super Modulyo freeze-dryer. The filters were packed into tin capsules and analyzed by combustion to dinitrogen gas on a Costech ECS 4010 Elemental Analyzer followed by N isotope ratio analysis of the resulting dinitrogen gas on a Thermo Delta V isotope ratio mass spectrometer. Samples were calibrated with corresponding aliquots of L-glutamic acid reference materials USGS-40 and USGS-41, with δ<sup>15</sup>N values of –4.52 and 47.57‰ vs. air, respectively (Qi et al. 2003).</p>
Specified by the Principal Investigator(s)
<p><strong>Processing notes from data submitter:</strong></p>
<ul>
<li>Data table generated from laboratory experiments were processed using Microsoft Excel</li>
<li>Model code written in MatLab</li>
</ul>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
- Dates converted from mm-dd-yy format to yyyy-mm-dd format
- UTC date time column added
- Column names changed to meet FAIR standards (spaces were replaced with underscores and special characters were removed).
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
Multisizer 4 Beckman Coulter Counter
Multisizer 4 Beckman Coulter Counter
PI Supplied Instrument Name: Multisizer 4 Beckman Coulter Counter PI Supplied Instrument Description:Used to determine phytoplankton cell density. Instrument Name: Coulter Counter Instrument Short Name: Instrument Description: An apparatus for counting and sizing particles suspended in electrolytes. It is used for cells, bacteria, prokaryotic cells and virus particles. A typical Coulter counter has one or more microchannels that separate two chambers containing electrolyte solutions.
from https://en.wikipedia.org/wiki/Coulter_counter
Costech ECS 4010 Elemental Analyzer coupled with Thermo Delta V isotope ratio mass spectrometer
Costech ECS 4010 Elemental Analyzer coupled with Thermo Delta V isotope ratio mass spectrometer
PI Supplied Instrument Name: Costech ECS 4010 Elemental Analyzer coupled with Thermo Delta V isotope ratio mass spectrometer PI Supplied Instrument Description:Combustion of PON samples to produce dinitrogen gas for N isotope analyses, with calibration achieved using L-glutamic acid references USGS-40 and USGS-41. 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/
Thermo Delta V gas chromatograph isotope ratio mass spectrometer (GC-IRMS)
Thermo Delta V gas chromatograph isotope ratio mass spectrometer (GC-IRMS)
PI Supplied Instrument Name: Thermo Delta V gas chromatograph isotope ratio mass spectrometer (GC-IRMS) PI Supplied Instrument Description:Used to analyze N isotopes of nitrous oxide gas derived from chemical oxidation of NH4+ using the hypobromite-azide method (Zhang et al. 2007), with calibrations achieved using NH4+ reference materials IAEA-N1 and IAEA-N2. Instrument Name: Gas Chromatograph Mass Spectrometer Instrument Short Name: Instrument Description: Instruments 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 by a mass spectrometer.
U-3010 VIS Spectrophotometer
U-3010 VIS Spectrophotometer
PI Supplied Instrument Name: U-3010 VIS Spectrophotometer PI Supplied Instrument Description:Used to measure NH4+ concentration < 50 µM. 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 Trilogy Fluorometer
Turner Trilogy Fluorometer
PI Supplied Instrument Name: Turner Trilogy Fluorometer PI Supplied Instrument Description:Used to measure NH4+ concentration ≥ 50 µM. 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.