http://lod.bco-dmo.org/id/dataset/929471 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 2024-06-06 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) In vivo fluorescence and flow cytometry cell counts from dissolved organic phosphorus (DOP) hydrolysis experiments with marine cyanobacterium Synechococcus laboratory cultures (WH8102 and WH5701) from 2018-2023 2024-06-06 publication 2024-06-06 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2024-07-15 publication https://doi.org/10.26008/1912/bco-dmo.929471.1 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) In vivo fluorescence and flow cytometry cell counts from dissolved organic phosphorus (DOP) hydrolysis experiments with marine cyanobacterium Synechococcus laboratory cultures (WH8102 and WH5701) from 2018-2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-06-06 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.929471.1 [access date] Dataset Description: &lt;p&gt;This dataset was utilized for&amp;nbsp;Waggoner et al. (2024).&amp;nbsp;See &quot;Related Datasets&quot; section on this page for other closely-related data from this study published in Waggoner et al. (2024).&amp;nbsp; They are also listed under the&amp;nbsp;BCO-DMO Project Page: https://www.bco-dmo.org/project/747715.&lt;/p&gt; Methods and Sampling: &lt;p&gt;This data is part of the DOP Hydrolysis Experiments:&lt;/p&gt; &lt;p&gt;&lt;em&gt;Synechococcus Growth&lt;/em&gt;–&amp;nbsp;Axenic&amp;nbsp;&lt;em&gt;Synechococcus&lt;/em&gt;&amp;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&amp;nbsp;&lt;em&gt;et al.&lt;/em&gt;&amp;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). At the late-exponential phase, cultures were transferred in triplicate to one of two SN media: (1) +P&lt;em&gt;i&lt;/em&gt;&amp;nbsp;(45 µmol L&lt;sup&gt;-1&lt;/sup&gt;&amp;nbsp;KH&lt;sub&gt;2&lt;/sub&gt;PO&lt;sub&gt;4&lt;/sub&gt;, following Waterbury&amp;nbsp;&lt;em&gt;et al.&lt;/em&gt;&amp;nbsp;(1986)) and (2) -P&lt;em&gt;i&lt;/em&gt;&amp;nbsp;(no KH&lt;sub&gt;2&lt;/sub&gt;PO&lt;sub&gt;4&lt;/sub&gt;&amp;nbsp;added; P&lt;em&gt;i&lt;/em&gt;&amp;nbsp;below detection limit). All cultures were incubated at 25°C on a 12h:12h light cycle at 130 µmol m&lt;sup&gt;-1&lt;/sup&gt;&amp;nbsp;s&lt;sup&gt;-1&lt;/sup&gt;&amp;nbsp;in sterile culture flasks with a vent cap (0.22 µm hydrophobic membrane).&lt;/p&gt; &lt;p&gt;&lt;em&gt;IVF and Flow Cytometry Cell Counts&lt;/em&gt;–&amp;nbsp;For each triplicate culture flask and media type (+P and -P),&amp;nbsp;&lt;em&gt;in vivo&amp;nbsp;&lt;/em&gt;fluorescence (IVF) was measured (AquaFluor®, Turner Designs) as a proxy for&amp;nbsp;&lt;em&gt;Synechococcus&lt;/em&gt;&amp;nbsp;biomass. In parallel, over the growth curve, 2-mL&amp;nbsp;&lt;em&gt;Synechococcus&lt;/em&gt;&amp;nbsp;culture aliquots were collected, fixed (final concentration of 0.2% paraformaldehyde), and stored at -80°C until cell abundance analysis using the Guava® EasyCyte flow cytometer (Millipore). Briefly,&amp;nbsp;&lt;em&gt;Synechococcus&lt;/em&gt;&amp;nbsp;was enumerated in unstained samples based on red fluorescence (&lt;em&gt;i.e.&lt;/em&gt;, chlorophyll) and forward scatter signals using a low flow rate of 0.24 µL s&lt;sup&gt;-1&lt;/sup&gt;&amp;nbsp;for 1 minute. Instrument-specific beads (Guava® Check Kit, Luminex) were used to calibrate the instrument.&amp;nbsp;&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Organism identifiers (Life Science Identifier, LSID):&lt;/strong&gt;&lt;br /&gt; Synechococcus, urn:lsid:marinespecies.org:taxname:160572&lt;/p&gt; 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 time_day media_and_phosphate_level in_vivo_fluor_trip1 in_vivo_fluor_trip2 in_vivo_fluor_trip3 cell_counts_trip1 cell_counts_trip2 cell_counts_trip3 Molecular Devices M2 multimode plate reader (Spectra Max) theme None, User defined sample description time_elapsed treatment fluorescence cell_concentration featureType BCO-DMO Standard Parameters plate reader 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 In vivo fluorescence and flow cytometry cell counts from dissolved organic phosphorus (DOP) hydrolysis experiments with marine cyanobacterium Synechococcus laboratory cultures (WH8102 and WH5701) from 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/929495.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/929496.rdf Name: time_day Units: days Description: <p>The day a culture aliquot was taken. 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/929497.rdf Name: media_and_phosphate_level Units: unitless Description: <p>culture was grown in SN media either with phosphate (+P) or without (-P). See methods.</p> http://lod.bco-dmo.org/id/dataset-parameter/929498.rdf Name: in_vivo_fluor_trip1 Units: relative fluorescence units (RFU) Description: <p>in vivo fluorescence for triplicate flask #1</p> http://lod.bco-dmo.org/id/dataset-parameter/929499.rdf Name: in_vivo_fluor_trip2 Units: relative fluorescence units (RFU) Description: <p>in vivo fluorescence for triplicate flask #2</p> http://lod.bco-dmo.org/id/dataset-parameter/929500.rdf Name: in_vivo_fluor_trip3 Units: relative fluorescence units (RFU) Description: <p>in vivo fluorescence for triplicate flask #3</p> http://lod.bco-dmo.org/id/dataset-parameter/929501.rdf Name: cell_counts_trip1 Units: cells per milliliter (cells mL-1) Description: <p>Flow cytometry cell counts for triplicate flask #1</p> http://lod.bco-dmo.org/id/dataset-parameter/929502.rdf Name: cell_counts_trip2 Units: cells per milliliter (cells mL-1) Description: <p>Flow cytometry cell counts for triplicate flask #2</p> http://lod.bco-dmo.org/id/dataset-parameter/929503.rdf Name: cell_counts_trip3 Units: cells per milliliter (cells mL-1) Description: <p>Flow cytometry cell counts for triplicate 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 3118 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/aee15383-0c46-4fd9-8f33-90c84454fcd1/content download https://doi.org/10.26008/1912/bco-dmo.929471.1 download onLine dataset &lt;p&gt;This data is part of the DOP Hydrolysis Experiments:&lt;/p&gt; &lt;p&gt;&lt;em&gt;Synechococcus Growth&lt;/em&gt;–&amp;nbsp;Axenic&amp;nbsp;&lt;em&gt;Synechococcus&lt;/em&gt;&amp;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&amp;nbsp;&lt;em&gt;et al.&lt;/em&gt;&amp;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). At the late-exponential phase, cultures were transferred in triplicate to one of two SN media: (1) +P&lt;em&gt;i&lt;/em&gt;&amp;nbsp;(45 µmol L&lt;sup&gt;-1&lt;/sup&gt;&amp;nbsp;KH&lt;sub&gt;2&lt;/sub&gt;PO&lt;sub&gt;4&lt;/sub&gt;, following Waterbury&amp;nbsp;&lt;em&gt;et al.&lt;/em&gt;&amp;nbsp;(1986)) and (2) -P&lt;em&gt;i&lt;/em&gt;&amp;nbsp;(no KH&lt;sub&gt;2&lt;/sub&gt;PO&lt;sub&gt;4&lt;/sub&gt;&amp;nbsp;added; P&lt;em&gt;i&lt;/em&gt;&amp;nbsp;below detection limit). All cultures were incubated at 25°C on a 12h:12h light cycle at 130 µmol m&lt;sup&gt;-1&lt;/sup&gt;&amp;nbsp;s&lt;sup&gt;-1&lt;/sup&gt;&amp;nbsp;in sterile culture flasks with a vent cap (0.22 µm hydrophobic membrane).&lt;/p&gt; &lt;p&gt;&lt;em&gt;IVF and Flow Cytometry Cell Counts&lt;/em&gt;–&amp;nbsp;For each triplicate culture flask and media type (+P and -P),&amp;nbsp;&lt;em&gt;in vivo&amp;nbsp;&lt;/em&gt;fluorescence (IVF) was measured (AquaFluor®, Turner Designs) as a proxy for&amp;nbsp;&lt;em&gt;Synechococcus&lt;/em&gt;&amp;nbsp;biomass. In parallel, over the growth curve, 2-mL&amp;nbsp;&lt;em&gt;Synechococcus&lt;/em&gt;&amp;nbsp;culture aliquots were collected, fixed (final concentration of 0.2% paraformaldehyde), and stored at -80°C until cell abundance analysis using the Guava® EasyCyte flow cytometer (Millipore). Briefly,&amp;nbsp;&lt;em&gt;Synechococcus&lt;/em&gt;&amp;nbsp;was enumerated in unstained samples based on red fluorescence (&lt;em&gt;i.e.&lt;/em&gt;, chlorophyll) and forward scatter signals using a low flow rate of 0.24 µL s&lt;sup&gt;-1&lt;/sup&gt;&amp;nbsp;for 1 minute. Instrument-specific beads (Guava® Check Kit, Luminex) were used to calibrate the instrument.&amp;nbsp;&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Organism identifiers (Life Science Identifier, LSID):&lt;/strong&gt;&lt;br /&gt; Synechococcus, urn:lsid:marinespecies.org:taxname:160572&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;DOP hydrolysis rates were normalized to flow cytometry cell counts to account for biomass differences between strains and treatments. The DOP hydrolysis rates can be found in the 'Synechococcus DOP Hydrolysis Experiment - hydrolysis rates' dataset (see &quot;Related Datasets&quot; section).&lt;/p&gt; Specified by the Principal Investigator(s) * Sheet 1 of submitted file &quot;Synechococcus_DOPHydrolysisExperiment_IVF_CellCounts.xlsx&quot; was imported into the BCO-DMO data system for this dataset. Values &quot;NaN&quot; imported as missing data values.  ** Missing data values are displayed differently based on the file format you download.  They are blank in csv files, &quot;NaN&quot; in MatLab files, etc. * 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 Molecular Devices M2 multimode plate reader (Spectra Max) Molecular Devices M2 multimode plate reader (Spectra Max) PI Supplied Instrument Name: Molecular Devices M2 multimode plate reader (Spectra Max) Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.