http://lod.bco-dmo.org/id/dataset/858440
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
2021-08-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
ATP and cell numbers in laboratory experiments with Thalassiosira weissflogii conducted in 2019
2021-08-13
publication
2021-08-13
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-10-29
publication
https://doi.org/10.26008/1912/bco-dmo.858440.1
Alexander Boris Bochdansky
Old Dominion University
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: Bochdansky, A. B. (2021) ATP and cell numbers in laboratory experiments with Thalassiosira weissflogii conducted in 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-08-13 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.858440.1 [access date]
ATP and cell numbers T. weissflogii 2019 Dataset Description: Methods and Sampling: <p>Complete methodology published in Bochdansky et al. (2021). Data are in Figure 3 of&nbsp;Bochdansky et al. (2021). The experiments were conducted from&nbsp;June 19 to July 10, 2019 at&nbsp;Old Dominion University.</p>
<p><strong>Growth rate experiments with <em>Thalassiosira weissflogii</em></strong><br />
Experiments were performed at room temperature (~ 22° Celsius). In all experiments, sampling occurred daily, beginning at the day of inoculation of the f/2<sup>+</sup> medium. After agitating the flasks to resuspend and evenly mix settled cells, 25 ml were withdrawn from each flask using a sterile disposable pipette. Then, 5 ml were immediately filtered through a 25 mm diameter, 0.2 um polycarbonate filter (Isopore type GTTP) at a vacuum of 200 mbar in a filter station preloaded with six filters. The filtrate was captured in 15 ml polypropylene centrifuge tubes (Falcon) placed below the filter funnel inside the vacuum flasks. The filters were quickly transferred into 15 ml polypropylene centrifuge tubes, and ~ 4.5 ml boiling-hot ultrapure water (18.2 MΩ) was added. The centrifuge tubes were vortexed for a few seconds and then immersed in a beaker containing hot water (&gt; 90 °C). The hot ultrapure water breaks up cells and inactivates ATPases. For unfiltered whole water, triplicate samples of 0.5 ml were added to 15 ml centrifuge tubes chased by ~ 4 ml boiling-hot water and vortexed. Of the filtrate, 0.5 ml was transferred to the centrifuge tubes and treated in the same fashion as the whole water samples. All tubes were kept in hot-water baths for approximately 15 minutes. The samples were subsequently cooled to room temperature and analyzed the same day. Using a muffled Pasteur pipette, ultrapure water was added dropwise to exactly the 5 ml mark (markings on the 15 ml Falcon centrifuge tubes are sufficiently accurate). For analysis, 50 ul of sample, 3 ml of ultrapure water, and 50 ul of the ATP working stock (for the internal standard only, see below), and 50 ul of firefly extract (CellTiter-Glo 2.0, Promega Corp.) were combined in 6 ml plastic scintillation vials (Pico Prias, Perkin Elmer) and briefly vortexed.</p>
<p>The scintillation counter was programmed to run samples in sequence repeatedly up to 10 times.&nbsp;Data of the second cycle only were used in the analysis. Samples and corresponding internal standards were run alternately.</p>
<p><strong>Standards</strong><br />
Adenosine-5’-triphosphate disodium salt hydrate (Millipore Sigma) was dissolved ultrapure water (Barnstaed Nanopure, 18.2 MΩ) and serially diluted to a stock concentration of ~10 uM using ultrapure water. The stock solution was then divided into individual 15-ml polypropylene centrifuge vials and stored frozen at -20 °C. The exact concentration of the ~10 uM standard was determined using a spectrophotometer (Shimadzu UV-2401PC) at a wavelength of 259 nm, a 1 cm cuvette and a molar absorptivity coefficient of 15.4 x 10<sup>3</sup> M<sup>-1</sup> cm<sup>-1</sup> (Karl 1993) in the equation:</p>
<p><em>C</em> = A/(l*e)<br />
<br />
where <em>C</em> is the molar concentration of ATP (<em>M</em>), A the absorption, <em>l</em> the pathlength of the cuvette (cm), and <em>e</em> the molar absorptivity coefficient (<em>M</em><sup>-1</sup> cm<sup>-1</sup>). The concentration of the stock solution was 16.4 uM throughout the experiment. A working stock solution was prepared daily by diluting 250 ul of the stock solution to 250 ml with ultrapure water in a volumetric flask (1000x dilution to 10 nM). This working stock was added as the internal standard (see above).</p>
<p><strong>Calculations</strong><br />
ATP concentrations in the samples were calculated as displayed in Equation 2:</p>
<p>ATP (nM) = ([ATP] * (CPM_sample - CPM_blank)) / (CPM_standards - CPM_samples) * (<em>V<sub>std </sub></em>* <em>R</em>) / <em>V<sub>extr</sub></em></p>
<p>where [ATP] is the concentration of the internal standard (i.e., 16.4 nM), CPM_sample the photon counts per minute for the sample, CPM_blank the average value of 4 to 6 blanks (50 ul of firefly reagent added to 3 ml ultrapure water only), CPM_standards the average counts per minute for the standard vials, CPM_samples the average value of the samples, <em>V<sub>std</sub></em> the volume of the standard added to the scintillation vial in ul, <em>R</em> the ratio between volume of the extract (numerator) and volume of sample filtered (denominator), and <em>V<sub>extr</sub></em> the volume of the extract added to the scintillation vial (ul). Internal standard values were regressed against time. This regression was applied to every sample based on its time stamp in the counting protocol. This procedure, rather than using the values from the adjacent vials, reduces variance caused by standard-to-standard variability. To arrive at the final ATP values in the results, the values were further multiplied by two to correct for the extraction efficiency difference between material collected on filters and whole water samples.</p>
<p><strong>Cell counts</strong><br />
<em>Thalassiosira weissflogii</em> was enumerated in a Z2 Coulter Counter Multisizer with a 100 um orifice tube. Seven measurements each were made for particle sizes larger than 10 um, the first values discarded, and the next six measurements recorded (the first measurement may still contain air bubbles).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851368 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851368
completed
Alexander Boris Bochdansky
Old Dominion University
757-683-4933
Ocean, Earth and Atmospheric Sciences 4600 Elkhorn Ave.
Norfolk
VA
23529
USA
abochdan@odu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Elapsed_days
Elapsed_hours
Temperature
Temperature_group
Flask
Cell_concentration
Corrected_ATP
ATP_filtrate
Z2 Coulter Counter Multisizer
Shimadzu UV-2401PC
theme
None, User defined
time_elapsed
water temperature at measurement depth
treatment
bottle
count
Adenosinetriphosphate
featureType
BCO-DMO Standard Parameters
Centrifuge
Coulter Counter
Spectrophotometer
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: Transforming Carbon in the Deep Sea
https://osprey.bco-dmo.org/project/817462
Collaborative Research: Transforming Carbon in the Deep Sea
<p><em>NSF Award Abstract:</em><br />
Through understanding the biological pump (the ocean's biologically driven sequestration of carbon from the atmosphere to the ocean interior and seafloor sediments), scientists know that the world's oceans absorb more carbon dioxide than it returns to the atmosphere. While much is known about the biological processes largely responsible for the transfer of carbon into the deep sea, very little is known about the microbial decay and subsequent remineralization processes that occur when the carbon reaches the deep sea. Using newly-designed deep-sea incubators deployed off the east coast of the United States, researchers will explore the microbial communities and remineralization processes that transform carbon in the deep sea. The incubators will be filled with tracer-labeled algae or fecal material mimicking the diet and waste products of animal plankton. The tracers allow the researchers to follow the material through the microbial food web, and simultaneously determine the net release of carbon dioxide during the incubations. Using a combination of genetic analysis and novel analytical techniques, the researchers will be able to identify the organisms involved in the decay processes and rates at which changes occur at the single-cell level. Results will shed light on these understudied biological phenomena and contribute to an improved understanding of the global carbon cycle. In addition to novel advancements in oceanographic technology, the research supports graduate and undergraduate student education, and public outreach through partnerships with the Virginia Aquarium and National Ocean Sciences Bowl to increase ocean science literacy.</p>
<p>In this project, researchers will study the organisms, mechanisms, and physical and ecological factors that modulate the remineralization of organic material in the deep sea. The methods include using in situ incubations of well-defined and stable isotope-labeled sources of organic carbon (live and dead phytoplankton and fecal pellets of zooplankton) with natural microbial communities. The incubations will take place northeast of Cape Hatteras, a region characterized by strong offshore transport of phytoplankton carbon. Net carbon dioxide release rates will be measured over time by conversion of Carbon-13 labeled organic carbon to 13CO2 . The dependence of degradation rates on the source material, seasonality, oxygen concentration, and the type of microbial colonizers will be assessed. Parallel laboratory experiments will elucidate the exact shape of the time course of carbon release by phytoplankton into dissolved organic and inorganic fractions as well as determine how representative laboratory and ship-board generated values are relative to those obtained in situ. Target eukaryotic and prokaryotic taxa are identified by fluorescence in-situ hybridization (FISH) after the incubations and individually interrogated using Raman microspectrometry to investigate the relative Carbon-13-enrichment rates in organisms assimilating labeled detrital carbon. This multi-faceted approach will provide better constrained parameters for ecosystem and biological pump models and shed light on carbon balances of the deep sea. The research contributes to the development of new oceanographic technology, including new deep-sea incubators and application of single-cell Raman microspectrometry to natural microbial communities.</p>
Carbon in the Deep Sea
largerWorkCitation
project
eng; USA
oceans
-76.30765
-76.30765
36.88493
36.88493
2019-06-19
2019-07-10
Mesopelagic North Atlantic
0
BCO-DMO catalogue of parameters from ATP and cell numbers in laboratory experiments with Thalassiosira weissflogii conducted in 2019
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/858450.rdf
Name: Elapsed_days
Units: number of days
Description: <p>Elapsed time since the beginning of the experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/858451.rdf
Name: Elapsed_hours
Units: number of hours
Description: <p>Elapsed time since the beginning of the experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/858452.rdf
Name: Temperature
Units: degrees Celsius
Description: <p>Incubation temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/858453.rdf
Name: Temperature_group
Units: unitless
Description: <p>One of three temperature groups (15, 20, 25 C)</p>
http://lod.bco-dmo.org/id/dataset-parameter/858454.rdf
Name: Flask
Units: unitless
Description: <p>Bottle number</p>
http://lod.bco-dmo.org/id/dataset-parameter/858455.rdf
Name: Cell_concentration
Units: cells per milliliter
Description: <p>Coulter Counter cell counts > 10 micrometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/858456.rdf
Name: Corrected_ATP
Units: nanomolar (nM)
Description: <p>Particulate ATP corrected for filtration losses</p>
http://lod.bco-dmo.org/id/dataset-parameter/858457.rdf
Name: ATP_filtrate
Units: nanomolar (nM)
Description: <p>ATP in the 0.2 micrometer filtrate; bd = below detection</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
5129
https://darchive.mblwhoilibrary.org/bitstream/1912/27679/1/dataset-858440_atp-and-cell-numbers-t-weissflogii-2019__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.858440.1
download
onLine
dataset
<p>Complete methodology published in Bochdansky et al. (2021). Data are in Figure 3 of&nbsp;Bochdansky et al. (2021). The experiments were conducted from&nbsp;June 19 to July 10, 2019 at&nbsp;Old Dominion University.</p>
<p><strong>Growth rate experiments with <em>Thalassiosira weissflogii</em></strong><br />
Experiments were performed at room temperature (~ 22° Celsius). In all experiments, sampling occurred daily, beginning at the day of inoculation of the f/2<sup>+</sup> medium. After agitating the flasks to resuspend and evenly mix settled cells, 25 ml were withdrawn from each flask using a sterile disposable pipette. Then, 5 ml were immediately filtered through a 25 mm diameter, 0.2 um polycarbonate filter (Isopore type GTTP) at a vacuum of 200 mbar in a filter station preloaded with six filters. The filtrate was captured in 15 ml polypropylene centrifuge tubes (Falcon) placed below the filter funnel inside the vacuum flasks. The filters were quickly transferred into 15 ml polypropylene centrifuge tubes, and ~ 4.5 ml boiling-hot ultrapure water (18.2 MΩ) was added. The centrifuge tubes were vortexed for a few seconds and then immersed in a beaker containing hot water (&gt; 90 °C). The hot ultrapure water breaks up cells and inactivates ATPases. For unfiltered whole water, triplicate samples of 0.5 ml were added to 15 ml centrifuge tubes chased by ~ 4 ml boiling-hot water and vortexed. Of the filtrate, 0.5 ml was transferred to the centrifuge tubes and treated in the same fashion as the whole water samples. All tubes were kept in hot-water baths for approximately 15 minutes. The samples were subsequently cooled to room temperature and analyzed the same day. Using a muffled Pasteur pipette, ultrapure water was added dropwise to exactly the 5 ml mark (markings on the 15 ml Falcon centrifuge tubes are sufficiently accurate). For analysis, 50 ul of sample, 3 ml of ultrapure water, and 50 ul of the ATP working stock (for the internal standard only, see below), and 50 ul of firefly extract (CellTiter-Glo 2.0, Promega Corp.) were combined in 6 ml plastic scintillation vials (Pico Prias, Perkin Elmer) and briefly vortexed.</p>
<p>The scintillation counter was programmed to run samples in sequence repeatedly up to 10 times.&nbsp;Data of the second cycle only were used in the analysis. Samples and corresponding internal standards were run alternately.</p>
<p><strong>Standards</strong><br />
Adenosine-5’-triphosphate disodium salt hydrate (Millipore Sigma) was dissolved ultrapure water (Barnstaed Nanopure, 18.2 MΩ) and serially diluted to a stock concentration of ~10 uM using ultrapure water. The stock solution was then divided into individual 15-ml polypropylene centrifuge vials and stored frozen at -20 °C. The exact concentration of the ~10 uM standard was determined using a spectrophotometer (Shimadzu UV-2401PC) at a wavelength of 259 nm, a 1 cm cuvette and a molar absorptivity coefficient of 15.4 x 10<sup>3</sup> M<sup>-1</sup> cm<sup>-1</sup> (Karl 1993) in the equation:</p>
<p><em>C</em> = A/(l*e)<br />
<br />
where <em>C</em> is the molar concentration of ATP (<em>M</em>), A the absorption, <em>l</em> the pathlength of the cuvette (cm), and <em>e</em> the molar absorptivity coefficient (<em>M</em><sup>-1</sup> cm<sup>-1</sup>). The concentration of the stock solution was 16.4 uM throughout the experiment. A working stock solution was prepared daily by diluting 250 ul of the stock solution to 250 ml with ultrapure water in a volumetric flask (1000x dilution to 10 nM). This working stock was added as the internal standard (see above).</p>
<p><strong>Calculations</strong><br />
ATP concentrations in the samples were calculated as displayed in Equation 2:</p>
<p>ATP (nM) = ([ATP] * (CPM_sample - CPM_blank)) / (CPM_standards - CPM_samples) * (<em>V<sub>std </sub></em>* <em>R</em>) / <em>V<sub>extr</sub></em></p>
<p>where [ATP] is the concentration of the internal standard (i.e., 16.4 nM), CPM_sample the photon counts per minute for the sample, CPM_blank the average value of 4 to 6 blanks (50 ul of firefly reagent added to 3 ml ultrapure water only), CPM_standards the average counts per minute for the standard vials, CPM_samples the average value of the samples, <em>V<sub>std</sub></em> the volume of the standard added to the scintillation vial in ul, <em>R</em> the ratio between volume of the extract (numerator) and volume of sample filtered (denominator), and <em>V<sub>extr</sub></em> the volume of the extract added to the scintillation vial (ul). Internal standard values were regressed against time. This regression was applied to every sample based on its time stamp in the counting protocol. This procedure, rather than using the values from the adjacent vials, reduces variance caused by standard-to-standard variability. To arrive at the final ATP values in the results, the values were further multiplied by two to correct for the extraction efficiency difference between material collected on filters and whole water samples.</p>
<p><strong>Cell counts</strong><br />
<em>Thalassiosira weissflogii</em> was enumerated in a Z2 Coulter Counter Multisizer with a 100 um orifice tube. Seven measurements each were made for particle sizes larger than 10 um, the first values discarded, and the next six measurements recorded (the first measurement may still contain air bubbles).</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing:<br />
- renamed fields to conform with BCO-DMO naming conventions.</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
PI Supplied Instrument Name: Instrument Name: Centrifuge Instrument Short Name: Instrument Description: A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.
Z2 Coulter Counter Multisizer
Z2 Coulter Counter Multisizer
PI Supplied Instrument Name: Z2 Coulter Counter Multisizer 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
Shimadzu UV-2401PC
Shimadzu UV-2401PC
PI Supplied Instrument Name: Shimadzu UV-2401PC 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/