http://lod.bco-dmo.org/id/dataset/864157
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
2021-11-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bioavailability factor of polyphosphate, nucleotides, and methyl phosphonate in bioassay experiments with seawater from R/V Savannah cruise SAV-19-02 in the NW Atlantic Ocean in Spring of 2019
2021-11-02
publication
2021-11-02
revision
BCO-DMO Linked Data URI
2021-11-02
creation
http://lod.bco-dmo.org/id/dataset/864157
Solange Duhamel
Columbia University
principalInvestigator
Julia Diaz
University of Georgia
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: Duhamel, S., Diaz, J. (2021) Bioavailability factor of polyphosphate, nucleotides, and methyl phosphonate in bioassay experiments with seawater from R/V Savannah cruise SAV-19-02 in the NW Atlantic Ocean in Spring of 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-11-02 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/864157 [access date]
Methods and Sampling: <p><strong>Sampling and analytical procedures: </strong></p>
<p>Bioassay experiments were conducted at station 1 and stations 3. At each station, inorganic and organic phosphate amendments were performed on seawater with and without nitrogen enrichment&nbsp; (NH<sub>4</sub>Cl, NaNO<sub>3</sub>). Bioassay Experiments consisted in incubating, over an incubation period of 48h, surface seawater (5m) with inorganic or organic phosphate compounds (20 µM; final concentration of P) including, polyphosphate (polyp), inorganic phosphate (Pi), nucleotides (ATP or AMP) and methylphosphonate (Mepn). In each incubation experiment, a control treatment (surface seawater without amendment) was included.</p>
<p>In bioassay experiments, the bioavailability factor (BF) was determined at T0 for polyphosphate, nucleotides (ATP or AMP) and methylphosphonate (Mepn). BF is calculated as follows:&nbsp;BF=TE-TN/ TP-TN (Björkman and Karl, 1994), where T<sub>E</sub> reflects PO<sub>4</sub><sup>3-</sup> turnover time in the DOP amended treatment, T<sub>N</sub> is the PO<sub>4</sub><sup>3- </sup>turnover time in the control (no additions) and T<sub>P</sub> is the PO<sub>4</sub><sup>3- </sup>turnover time in the treatment amended with Pi. BF ranges from 0 for an unavailable substrate, to a value of 1 for a DOP model substrate having a bioavailability equal to that of +Pi.</p>
<p><strong>Instrument:</strong> Radioactivity was assayed on a Packard Tri-Carb liquid scintillation counter.&nbsp;<br />
<strong>Location:&nbsp; </strong>Northwestern Atlantic surface waters. Depth: surface-50 m.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1736967 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1736967
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1737083 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1737083
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2001212 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2001212
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1948042 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1948042
onGoing
Solange Duhamel
Columbia University
520-621-6047
1007 E Lowell Street Life Sciences South 315
Tucson
AZ
85721
USA
duhamel@arizona.edu
pointOfContact
Julia Diaz
University of Georgia
j2diaz@ucsd.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
data_subset_name
Id_treatments
station
incubation_hours
BF
Packard Tri-Carb liquid scintillation counter
theme
None, User defined
brief description
treatment
station
time_elapsed
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Liquid Scintillation Counter
instrument
BCO-DMO Standard Instruments
SAV-19-02
service
Deployment Activity
Northwestern Atlantic
place
Locations
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: Assessing the role of compound-specific phosphorus hydrolase transformations in the marine phosphorus cycle
https://osprey.bco-dmo.org/project/747715
Collaborative Research: Assessing the role of compound-specific phosphorus hydrolase transformations in the marine phosphorus cycle
<p><em>NSF Award Abstract:</em><br />
Phosphorus (P) is an essential building block for life. Because P is in short supply over vast areas of the ocean, P availability may control biological productivity, such as photosynthesis and carbon fixation, which has implications for uptake of the greenhouse gas carbon dioxide and thus climate regulation. Marine microorganisms must satisfy their nutritional requirement for P by obtaining it from seawater, where P is present in a variety of chemical forms, from simple phosphate ions (Pi) to complex dissolved organic phosphorus (DOP) molecules. The concentration of DOP vastly exceeds Pi over most ocean areas, therefore DOP is a critically important source of P for marine microbial nutrition and productivity. However, much remains unknown about the contribution of specific DOP compounds to the P nutrition, productivity, and structure of marine microbial communities. In this project, the investigators will conduct field experiments in the Atlantic Ocean and perform a series of controlled laboratory studies with pure enzymes and microbial cultures to determine how and to what extent different DOP compounds are degraded to Pi in the marine environment. Furthermore, the contribution of these compound-specific DOP molecules to microbial P nutrition, carbon fixation, and community structure will be determined, thus advancing the current state of knowledge regarding the factors that control the activity and distribution of microbial species in the ocean, and the ocean?s role in the climate system. This project will support two female junior investigators, a postdoctoral researcher, and graduate and undergraduate students. The undergraduate students will be recruited from the Marine Sciences program at Savannah State University, an Historically Black Colleges and Universities. In addition, results will be incorporated into new hands-on K-12 educational tools to teach students about microbial P biogeochemistry, including a digital game and formal lesson plans with hands-on demos. These tools will be validated with K-12 educators and will be widely accessible to the public through various well-known online platforms. These activities will thus reach a broad audience including a significant fraction of underrepresented groups.</p>
<p>P is a vital nutrient for life. Marine microorganisms utilize P-hydrolases, such as alkaline phosphatase (AP), to release and acquire phosphate (Pi) from a wide diversity of dissolved organic P (DOP) compounds, including P-esters (P-O-C bonds), phosphonates (P-C), and polyphosphates (P-O-P). Compound-specific DOP transformations have the potential to exert critical and wide-ranging impacts on marine microbial ecology (e.g. variable DOP bioavailability among species), biogeochemistry (e.g. P geologic sequestration via formation of calcium Pi), and global climate (e.g. aerobic production of the greenhouse gas methane by dephosphorylation of methylphosphonate). However, the mechanisms and comparative magnitude of specific DOP transformations, in addition to their relative contributions to microbial community-level P demand, productivity, and structure, are not completely understood. This study will fill these knowledge gaps by tracking the fate of specific DOP pools in the marine environment. Specifically, this project will test four hypotheses in the laboratory using recombinant enzymes and axenic cultures representative of marine eukaryotic and prokaryotic plankton from high and low nutrient environments, and in the field using observational and experimental approaches along natural Pi gradients in the Atlantic Ocean. In particular, the investigators will reveal potential differences in the hydrolysis and utilization of specific DOP compounds at the community- (bulk enzymatic assays), taxon- (cell sorting of radiolabeled cells in natural samples), species- (axenic cultures) and molecular-levels (pure enzyme kinetic studies and cell-associated proteomes and exoproteomes). Results from our proposed work will provide a robust understanding of the enzymatic basis involved in the transformation of specific forms of DOP and create new knowledge on the relative contribution of these specific P sources to Pi production, marine microbial nutrition, community structure, primary productivity, and thus global carbon cycling and climate. In particular, our refined measurements of the concentration of bioavailable DOP and our unique estimates of DOP remineralization fluxes will provide critical new information to improve models of marine primary production and P cycling.</p>
P-hydrolase
largerWorkCitation
project
eng; USA
oceans
Northwestern Atlantic
-80.7965
-79.8421
31.0175
31.7635
2019-03-30
2019-04-10
0
BCO-DMO catalogue of parameters from Bioavailability factor of polyphosphate, nucleotides, and methyl phosphonate in bioassay experiments with seawater from R/V Savannah cruise SAV-19-02 in the NW Atlantic Ocean in Spring of 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/864597.rdf
Name: data_subset_name
Units: unitless
Description: <p>Data subset name</p>
http://lod.bco-dmo.org/id/dataset-parameter/864598.rdf
Name: Id_treatments
Units: unitless
Description: <p>Labels of dissolved inorganic/organic phosphate amended treatments. Treatments that were amended with Nitrogen (NH4Cl, NaNO3) to avoid nitrogen limitation contain "+NN" in the treatment ID. Acronyms (e.g. Mepn, AMD) are explained in the "Sampling and analytical procedures" section.</p>
http://lod.bco-dmo.org/id/dataset-parameter/864599.rdf
Name: station
Units: unitless
Description: <p>Station at which the treatments were conducted</p>
http://lod.bco-dmo.org/id/dataset-parameter/864600.rdf
Name: incubation_hours
Units: hours
Description: <p>Incubation hours. (T=0 is the start of the treatment).</p>
http://lod.bco-dmo.org/id/dataset-parameter/864601.rdf
Name: BF
Units: unitless
Description: <p>Bioavailability factor (0-1). See methodology for calculations.</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/864157/data/download
download
onLine
dataset
<p><strong>Sampling and analytical procedures: </strong></p>
<p>Bioassay experiments were conducted at station 1 and stations 3. At each station, inorganic and organic phosphate amendments were performed on seawater with and without nitrogen enrichment&nbsp; (NH<sub>4</sub>Cl, NaNO<sub>3</sub>). Bioassay Experiments consisted in incubating, over an incubation period of 48h, surface seawater (5m) with inorganic or organic phosphate compounds (20 µM; final concentration of P) including, polyphosphate (polyp), inorganic phosphate (Pi), nucleotides (ATP or AMP) and methylphosphonate (Mepn). In each incubation experiment, a control treatment (surface seawater without amendment) was included.</p>
<p>In bioassay experiments, the bioavailability factor (BF) was determined at T0 for polyphosphate, nucleotides (ATP or AMP) and methylphosphonate (Mepn). BF is calculated as follows:&nbsp;BF=TE-TN/ TP-TN (Björkman and Karl, 1994), where T<sub>E</sub> reflects PO<sub>4</sub><sup>3-</sup> turnover time in the DOP amended treatment, T<sub>N</sub> is the PO<sub>4</sub><sup>3- </sup>turnover time in the control (no additions) and T<sub>P</sub> is the PO<sub>4</sub><sup>3- </sup>turnover time in the treatment amended with Pi. BF ranges from 0 for an unavailable substrate, to a value of 1 for a DOP model substrate having a bioavailability equal to that of +Pi.</p>
<p><strong>Instrument:</strong> Radioactivity was assayed on a Packard Tri-Carb liquid scintillation counter.&nbsp;<br />
<strong>Location:&nbsp; </strong>Northwestern Atlantic surface waters. Depth: surface-50 m.</p>
Specified by the Principal Investigator(s)
<p>Data were organized using MATLAB and output as .mat files.&nbsp;&nbsp;Gaps in data were filled with NaN in the .mat files.&nbsp;<br />
<br />
<strong>BCO-DMO Data Manager Processing Notes:</strong></p>
<div>* Data from source files BioassayExperiments_Datasets.xslx. Sheets: BF_T0_St1, BF_T0_St1_NN, BF_T0_St3 were imported into the BCO-DMO data system and combined into one data table.&nbsp;&nbsp;<br />
* Data columns were added to contain information that was in the Excel sheet names.&nbsp; The original excel sheet name was added as column&nbsp;data_subset_name.&nbsp; Information extracted to additional columns&nbsp;(incubation_hours, station)<br />
* Parameters (column names) renamed to comply with BCO-DMO naming conventions. See https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions<br />
*&nbsp; Missing data values (Blank/Null)&nbsp;values in this dataset are displayed according to the format of data you access.&nbsp; For example, in csv files it will be blank values. In Matlab .mat&nbsp;files it will be NaN values.&nbsp; When viewing data online at BCO-DMO, the missing value will be shown as "nd" meaning "no data."</div>
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
Packard Tri-Carb liquid scintillation counter
Packard Tri-Carb liquid scintillation counter
PI Supplied Instrument Name: Packard Tri-Carb liquid scintillation counter PI Supplied Instrument Description:Radioactivity was assayed on a Packard Tri-Carb liquid scintillation counter. Instrument Name: Liquid Scintillation Counter Instrument Short Name:LSC Instrument Description: Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used to quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.
Liquid scintillation counters are instruments assaying alpha and beta radiation by quantitative detection of visible light produced by the passage of rays or particles through a suitable scintillant incorporated into the sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB21/
Cruise: SAV-19-02
SAV-19-02
R/V Savannah
Community Standard Description
R/V Savannah
vessel
SAV-19-02
Julia Diaz
University of Georgia
R/V Savannah
Community Standard Description
R/V Savannah
vessel