http://lod.bco-dmo.org/id/dataset/929212
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
2024-06-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Laboratory-cultured Synechococcus (WH8102 and WH5701) growth (vivo fluorescence) on dissolved organic phosphorus (DOP) from experiments between 2018-2023
2024-06-03
publication
2024-06-03
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-07-15
publication
https://doi.org/10.26008/1912/bco-dmo.929212.1
Solange Duhamel
University of Arizona
principalInvestigator
Julia Diaz
University of California-San Diego Scripps
principalInvestigator
Kahina Djaoudi
University of Arizona
principalInvestigator
Emily Waggoner
University of Arizona
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., Djaoudi, K., Waggoner, E. (2024) Laboratory-cultured Synechococcus (WH8102 and WH5701) growth (vivo fluorescence) on dissolved organic phosphorus (DOP) from experiments between 2018-2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-06-03 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.929212.1 [access date]
Dataset Description: <p>This dataset was utilized for Waggoner et al. (2024) Figure 1. See "Related Datasets" section on this page for other closely-related data from this study published in Waggoner et al. (2024).&nbsp; They are also listed under the BCO-DMO Project Page: https://www.bco-dmo.org/project/747715.</p> Methods and Sampling: <p><em><span style="font-family:arial,sans-serif; font-size:11pt">Synechococcus Growth&nbsp;</span></em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">–&nbsp;Axenic&nbsp;<em>Synechococcus</em>&nbsp;WH8102 (open ocean strain) and WH5701 (coastal strain) were obtained from the National Center for Marine Algae and Microbiota (NCMA, Bigelow Laboratories, East Boothbay, Maine). Both strains were grown in batch culture using SN media (Waterbury&nbsp;<em>et al.</em>&nbsp;1986) made with aged, filtered (0.2 µm), and autoclaved (120°C, 30 minutes) seawater from station ALOHA (A Long-term Oligotrophic Habitat Assessment). All cultures were incubated at 25°C on a 12h:12h light cycle at 130 µmol m<sup>-1</sup>&nbsp;s<sup>-1</sup>&nbsp;in sterile culture flasks with a vent cap (0.22 µm hydrophobic membrane).</span></p>
<p><em><span style="font-family:arial,sans-serif; font-size:11pt">Growth on DOP Substrates –</span></em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">&nbsp;The capacity of <em>Synechococcus</em> WH8102 and WH5701 to grow on DOP as a sole phosphorus source was tested in -Pi SN media amended with a single DOP substrate (45 µmol L-1 P, final concentration, Waterbury et al. (1986)). Representative DOP compounds included the P-monoesters glucose-6-phosphate (Glc-6-P) and adenosine 5’-monophosphate (AMP); the P-diester Bis(4-methylumbelliferyl) phosphate (BisMUF-P); the short and long chain polyphosphates: 3-polyphosphate (3-PolyP) and 45-polyphosphate (45-PolyP); the P-monoester and P-anhydride containing adenosine 5’-triphosphate (ATP); and the phosphonates: 4-nitrophenyl phenylphosphonate (4-NpPn), 2-aminomethylphosphonic acid (2-AEPn), methylphosphonic acid (MPn), and ethylphosphonic acid (EPn). Two separate experiments were carried out in triplicate to test growth on 1) P-monoester and PolyP substrates and 2) a P-diester and phosphonates. Two control treatments (culture grown in +Pi and -Pi media) were carried out in triplicate for each experiment. IVF was measured daily in each treatment over ~20 days, and cell axenicity was tested every ~5 days.&nbsp;</span><br />
<br />
<strong>Organism identifiers </strong>(Life Science Identifier, LSID):<br />
<em>Synechococcus</em>, urn:lsid:marinespecies.org:taxname:160572</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
completed
Solange Duhamel
University of Arizona
520-621-6047
1007 E Lowell Street Life Sciences South 315
Tucson
AZ
85721
USA
duhamel@arizona.edu
pointOfContact
Julia Diaz
University of California-San Diego Scripps
j2diaz@ucsd.edu
pointOfContact
Kahina Djaoudi
University of Arizona
+33605626480
djaoudikahina@gmail.com
pointOfContact
Emily Waggoner
University of Arizona
ewaggoner@arizona.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
synechococcus_strain
experiment_number
time_day
DOP_substrate
in_vivo_fluorescence_trip1
in_vivo_fluorescence_trip2
in_vivo_fluorescence_trip3
AquaFluor® Handheld Fluorometer and Turbidimeter (Turner Designs)
AquaFluor® Handheld Fluorometer and Turbidimeter (Turner Designs)
theme
None, User defined
sample description
experiment id
time_elapsed
fluorescence
featureType
BCO-DMO Standard Parameters
Fluorometer
Turbidity Meter
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: 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
2018-01-01
2023-01-01
0
BCO-DMO catalogue of parameters from Laboratory-cultured Synechococcus (WH8102 and WH5701) growth (vivo fluorescence) on dissolved organic phosphorus (DOP) from experiments between 2018-2023
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/929228.rdf
Name: synechococcus_strain
Units: unitless
Description: <p>Synechococcus strain. Two were tested, WH8102 and WH5701</p>
http://lod.bco-dmo.org/id/dataset-parameter/929229.rdf
Name: experiment_number
Units: unitless
Description: <p>Experiment number (1 or 2). Two experiments were carried out, 1. growth on P-monoesters and PolyP; and 2. growth on P-diester and phosphonates</p>
http://lod.bco-dmo.org/id/dataset-parameter/929230.rdf
Name: time_day
Units: days
Description: <p>The day a culture aliquot was taken to measure IVF. Days since T0 of the experiment when the culture was transferred to new media and marked the start of the experiment.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929231.rdf
Name: DOP_substrate
Units: unitless
Description: <p>DOP substrate added to -P SN media as the sole phosphorus source for culture (see methodology)</p>
http://lod.bco-dmo.org/id/dataset-parameter/929232.rdf
Name: in_vivo_fluorescence_trip1
Units: relative fluorescence units (RFU)
Description: <p>in vivo fluorescence for triplicate culture flask #1</p>
http://lod.bco-dmo.org/id/dataset-parameter/929233.rdf
Name: in_vivo_fluorescence_trip2
Units: relative fluorescence units (RFU)
Description: <p>in vivo fluorescence for triplicate culture flask #2</p>
http://lod.bco-dmo.org/id/dataset-parameter/929234.rdf
Name: in_vivo_fluorescence_trip3
Units: relative fluorescence units (RFU)
Description: <p>in vivo fluorescence for triplicate culture flask #3</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
7658
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/d98abe8e-d57b-4b6a-b4ee-ec814ab29ecf/content
download
https://doi.org/10.26008/1912/bco-dmo.929212.1
download
onLine
dataset
<p><em><span style="font-family:arial,sans-serif; font-size:11pt">Synechococcus Growth&nbsp;</span></em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">–&nbsp;Axenic&nbsp;<em>Synechococcus</em>&nbsp;WH8102 (open ocean strain) and WH5701 (coastal strain) were obtained from the National Center for Marine Algae and Microbiota (NCMA, Bigelow Laboratories, East Boothbay, Maine). Both strains were grown in batch culture using SN media (Waterbury&nbsp;<em>et al.</em>&nbsp;1986) made with aged, filtered (0.2 µm), and autoclaved (120°C, 30 minutes) seawater from station ALOHA (A Long-term Oligotrophic Habitat Assessment). All cultures were incubated at 25°C on a 12h:12h light cycle at 130 µmol m<sup>-1</sup>&nbsp;s<sup>-1</sup>&nbsp;in sterile culture flasks with a vent cap (0.22 µm hydrophobic membrane).</span></p>
<p><em><span style="font-family:arial,sans-serif; font-size:11pt">Growth on DOP Substrates –</span></em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">&nbsp;The capacity of <em>Synechococcus</em> WH8102 and WH5701 to grow on DOP as a sole phosphorus source was tested in -Pi SN media amended with a single DOP substrate (45 µmol L-1 P, final concentration, Waterbury et al. (1986)). Representative DOP compounds included the P-monoesters glucose-6-phosphate (Glc-6-P) and adenosine 5’-monophosphate (AMP); the P-diester Bis(4-methylumbelliferyl) phosphate (BisMUF-P); the short and long chain polyphosphates: 3-polyphosphate (3-PolyP) and 45-polyphosphate (45-PolyP); the P-monoester and P-anhydride containing adenosine 5’-triphosphate (ATP); and the phosphonates: 4-nitrophenyl phenylphosphonate (4-NpPn), 2-aminomethylphosphonic acid (2-AEPn), methylphosphonic acid (MPn), and ethylphosphonic acid (EPn). Two separate experiments were carried out in triplicate to test growth on 1) P-monoester and PolyP substrates and 2) a P-diester and phosphonates. Two control treatments (culture grown in +Pi and -Pi media) were carried out in triplicate for each experiment. IVF was measured daily in each treatment over ~20 days, and cell axenicity was tested every ~5 days.&nbsp;</span><br />
<br />
<strong>Organism identifiers </strong>(Life Science Identifier, LSID):<br />
<em>Synechococcus</em>, urn:lsid:marinespecies.org:taxname:160572</p>
Specified by the Principal Investigator(s)
<p>DOP hydrolysis rates were normalized to flow cytometry cell counts (can be found in the '<em>Synechococcus</em> DOP Hydrolysis Experiment - Cell Counts and IVF' dataset under this project) to account for biomass differences between strains and treatments.</p>
Specified by the Principal Investigator(s)
* Sheet 1 of submitted file "Synechococcus_DOPHydrolysisExperiment_HydrolysisRates.xlsx" was imported into the BCO-DMO data system for this dataset.
* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]
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
AquaFluor® Handheld Fluorometer and Turbidimeter (Turner Designs)
AquaFluor® Handheld Fluorometer and Turbidimeter (Turner Designs)
PI Supplied Instrument Name: AquaFluor® Handheld Fluorometer and Turbidimeter (Turner Designs) Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
AquaFluor® Handheld Fluorometer and Turbidimeter (Turner Designs)
AquaFluor® Handheld Fluorometer and Turbidimeter (Turner Designs)
PI Supplied Instrument Name: AquaFluor® Handheld Fluorometer and Turbidimeter (Turner Designs) Instrument Name: Turbidity Meter Instrument Short Name:Turbidity Meter Instrument Description: A turbidity meter measures the clarity of a water sample. A beam of light is shown through a water sample. The turbidity, or its converse clarity, is read on a numerical scale. Turbidity determined by this technique is referred to as the nephelometric method from the root meaning "cloudiness". This word is used to form the name of the unit of turbidity, the NTU (Nephelometric Turbidity Unit). The meter reading cannot be used to compare the turbidity of different water samples unless the instrument is calibrated. Description from: http://www.gvsu.edu/wri/education/instructor-s-manual-turbidity-10.htm
(One example is the Orion AQ4500 Turbidimeter)