http://lod.bco-dmo.org/id/dataset/820902
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
2020-08-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Cell abundance, growth rate, cellular P quotas, and alkaline phosphatase activity from a laboratory experiment examining the response of three species of marine phytoplankton grown under different phosphorus (P) conditions
2020-08-14
publication
2020-08-14
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-09-02
publication
https://doi.org/10.26008/1912/bco-dmo.820902.1
LeAnn P. Whitney
Bigelow Laboratory for Ocean Sciences
principalInvestigator
Michael W. Lomas
Bigelow Laboratory for Ocean Sciences
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: Whitney, L., Lomas, M. (2020) Cell abundance, growth rate, cellular P quotas, and alkaline phosphatase activity from a laboratory experiment examining the response of three species of marine phytoplankton grown under different phosphorus (P) conditions. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-08-14 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.820902.1 [access date]
Dataset Description: <p>Three species of marine phytoplankton – <em>Micromonas commoda</em>, <em>Emiliania huxleyi</em>, and <em>Phaeodactylum tricornutum</em> – were grown under four phosphorus (P) conditions. These include phosphate (Pi) replete and deplete conditions and the phosphonate conditions where cultures received either methylphosphonate (MPN) or 2-aminoethylphosphonate (2-AEPN) as the sole source of phosphorus at replete levels. Samples for cell abundance were collected throughout the experiment to monitor growth. In addition, particulate P, to calculate cellular P quota, as well as alkaline phosphatase activity was measured at a single time point when cells were in exponential growth.</p> Methods and Sampling: <p>Axenic cultures of the pico-prasinophyte <em>Micromonas commoda</em> (CCMP 2709), the coccolithophore <em>Emiliania huxleyi</em> (CCMP 2090), and the diatom <em>Phaeodactylum tricornutum</em> (CCMP 2561) were obtained from the National Center for Marine Algae and Microbiota (Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine). The cultures remained axenic throughout the experiments as determined by SYTO-staining and flow cytometric counting on a BD FACSJazz cell sorter; all cultures were free of bacteria during these experiments. Phytoplankton were grown in artificial sea water amended with L1 media with (<em>P. tricornutum</em>) or without (<em>M. commoda and E. huxleyi</em>) silica. The P source was added separately to achieve the desired growth conditions; Pi-replete media contained 36 µM PO₄³⁻, the Pi-deficient condition received 0.1 µM PO₄³⁻, and the phosphonate treatments received either 36 µM MPN or 2-AEPN. The Pi-deficient treatment (0.1 µM) represents a control for the low level of contaminating Pi measured in the phosphonate media; thus, an increase in growth in the MPN and 2-AEPN conditions above that measured in the Pi-deficient condition is due to phosphonate utilization. The potential for abiotic breakdown of phosphonate to Pi was investigated in media-only tubes exposed to the experimental temperature and light conditions for 10 days. Pi levels did not change throughout the experimental period (MPN average Pi = 0.11 µM ± 0.02; 2-AEPN average Pi = 0.10 µM ± 0.02), strongly supporting the notion of active enzymatic breakdown of phosphonates for growth. Natural P concentrations are much lower than those used in this study; the replete nutrient concentrations were used to support high cell yields necessary for analytical measurements. Cultures were acclimated to the four growth conditions described above as they had been maintained in each P treatment for a minimum of two transfers (20 days). Cultures were grown at 20°C in a 14h light/10h dark cycle at ~100 µE m⁻² s⁻¹ with a starting concentration of ~1x10⁴ cells mL⁻¹ in 25 mL culture volumes. Phytoplankton growth was monitored by fluorescence measurements using a Turner TD-700 fluorometer and cell counts analyzed by flow cytometry. Specific growth rates (μ) were calculated from the linear regression of the natural log of cell counts during the exponential growth phase of cultures. Quadruplicate cultures were setup for each treatment; three replicates were harvested in the late exponential phase of growth for physiological measurements, while the fourth was used to monitor cell abundances later in the growth cycle.</p>
<p>Physiological measurements:<br />
Cell samples (5 mL culture volume) for particulate P were collected onto precombusted 25 mm Whatman glass fiber filters, rinsed with 0.17 M Na₂SO₄, and stored frozen at -20°C until analysis. Determinations were made as previously described (Lomas et al. 2010). Briefly, filters were rinsed with 0.017 M MgSO₄, dried at 90°C, and combusted at 500°C for 2 h. Upon cooling, 0.2 M HCl was added and hydrolyzed at 80°C for 30 min. After cooling, mixed reagent was added, the samples were centrifuged, and absorbance was read at 885 nm using a Genesys 10 spectrophotometer.</p>
<p>Alkaline phosphatase content (APA) measurements were made by quantifying the hydrolysis of 6,8-difluoro-4-methylumbelliferyl phosphate using a Molecular Devices FilterMax F5 microplate reader. Abiotic substrate hydrolysis was accounted for in killed controls that were boiled and cooled prior to substrate addition, as well as in media-only controls. The fluorescent reference standard, 6,8-difluoro-4-methylcoumarin was used to calculate the rate of hydrolysis, which was then normalized to cell abundance to determine APA per cell.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756271 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756271
completed
LeAnn P. Whitney
Bigelow Laboratory for Ocean Sciences
207-326-2396
1 Pleasant Street
Castine
ME
04420
USA
leann.whitney@mma.edu
pointOfContact
Michael W. Lomas
Bigelow Laboratory for Ocean Sciences
207-315-2567 ext 311
60 Bigelow Drive PO Box 380
East Boothbay
ME
04544
United States
mlomas@bigelow.org
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Strain_No
Taxonomic_ID
Phosphorus_source
Phosphorus_condition
Time
Average_Cell_abundance
SD_of_Cell_abundance
Average_Growth_rate
SD_of_growth_rate
Average_QP
SD_of_QP
Average_APA
SD_of_APA
BD FACSJazz cell sorter
Molecular Devices FilterMax F5 microplate reader
Genesys 10 spectrophotometer
Turner TD-700 fluorometer
theme
None, User defined
taxon
treatment
time_elapsed
abundance
growth
Phosphorus
alkaline phosphatase
featureType
BCO-DMO Standard Parameters
Flow Cytometer
plate reader
Spectrophotometer
Turner Designs 700 Laboratory 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.
Phosphonate Utilization by Eukaryotic Phytoplankton: Who, How, and Where?
https://osprey.bco-dmo.org/project/720969
Phosphonate Utilization by Eukaryotic Phytoplankton: Who, How, and Where?
<p><em>NSF Award Abstract:</em><br />
Phosphorus (P) is an essential nutrient for all living cells. It is a central component of genetic material and cellular membranes and is integral to energy production and regulating enzyme activity. In the marine environment, P occurs as inorganic (Pi) and dissolved organic (DOP) forms; the availability and concentration of these different forms of P is an important control on marine phytoplankton growth. Marine phytoplankton are single-celled photosynthetic organisms and can be both prokaryotic bacteria and eukaryotic plants. While Pi is the preferred form of P for marine phytoplankton, in large regions of the oceans it is at such low levels that it restricts phytoplankton growth. In these regions, DOP is the most important P source. The composition of the DOP pool can generally be divided into two major groups: P esters and phosphonates. All marine phytoplankton are capable of using P esters to support growth; in contrast, phosphonates have only been shown to be an important source of P in the nutrition of bacteria to date. This project will determine the ability of marine eukaryotic phytoplankton to use phosphonates as a source of P for growth. Genomic analyses will determine the metabolic response of eukaryotic phytoplankton species to growth on phosphonates as well as the relevance of phosphonate use by natural populations. It is critical to understand the metabolic capabilities of phytoplankton which control marine nutrient cycling. In addition, the project is of great value in understanding the potential impacts of a changing ocean on phytoplankton growth. The project supports reseach opportunities for undergraduates from a local community college as well as hands-on enrichment programs for an afterschool program that serves a diverse student population.</p>
<p>Comprising up to 10% of the marine DOP pool, phosphonates have been shown to be a dynamic P pool both being assimilated and produced by marine photosynthetic bacteria. The ability of eukaryotic phytoplankton to supplement their growth with phosphonates remains vastly unexplored. Several eukaryotic phytoplankton species have been shown to use glyphosate, a chemically synthesized herbicidal phosphonate, as a P source; it remains unknown if open ocean eukaryotic phytoplankton can utilize phosphonates found naturally in the marine environment. Preliminary experiments suggest at least some eukaryotic phytoplankton are able to directly utilize extracellular phosphonates. This project characterizes the pervasiveness of phosphonate utilization within eukaryotic phytoplankton lineages and identifies the cellular underpinnings that support the acquisition of and growth on naturally occuring phosphonates. The project uses whole-cell transcriptomics and functional gene complementation assays, in addition to phylogenetic analyses, to understand the bioavailability of phosphonates and relevance of phosphonate utilization by natural eukaryotic phytoplankton populations. It is critical to understand the metabolic capabilities of phytoplankton which control marine biogeochemical cycles. This is especially important given the prediction that future oceans may become more stratified which could increase the importance of DOP, including phosphonates, in supporting phytoplankton growth.</p>
Euk Phn Utilization
largerWorkCitation
project
eng; USA
oceans
2020-08-14
Laboratory culture studies
0
BCO-DMO catalogue of parameters from Cell abundance, growth rate, cellular P quotas, and alkaline phosphatase activity from a laboratory experiment examining the response of three species of marine phytoplankton grown under different phosphorus (P) conditions
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/820911.rdf
Name: Strain_No
Units: unitless
Description: <p>National Center for Marine Algae and Microbiota numerical designation (CCMPxxxx)</p>
http://lod.bco-dmo.org/id/dataset-parameter/820912.rdf
Name: Taxonomic_ID
Units: unitless
Description: <p>Genus species identification of strain</p>
http://lod.bco-dmo.org/id/dataset-parameter/820913.rdf
Name: Phosphorus_source
Units: unitless
Description: <p>Compound containing phosphorus included in the growth media</p>
http://lod.bco-dmo.org/id/dataset-parameter/820914.rdf
Name: Phosphorus_condition
Units: unitless
Description: <p>Status of phosphorus addition at the beginning of the experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/820915.rdf
Name: Time
Units: days
Description: <p>Days since the start of the experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/820916.rdf
Name: Average_Cell_abundance
Units: cells per milliliter (cells/mL)
Description: <p>Direct phytoplankton cell counts</p>
http://lod.bco-dmo.org/id/dataset-parameter/820917.rdf
Name: SD_of_Cell_abundance
Units: cells per milliliter (cells/mL)
Description: <p>Standard deviation of replicate cell counts</p>
http://lod.bco-dmo.org/id/dataset-parameter/820918.rdf
Name: Average_Growth_rate
Units: growth per day
Description: <p>Calculated from the linear regression of the natural log of cell counts during the exponential growth phase</p>
http://lod.bco-dmo.org/id/dataset-parameter/820919.rdf
Name: SD_of_growth_rate
Units: growth per day
Description: <p>Standard deviation of the linear regression of the natural log of cell counts during the exponential growth phase</p>
http://lod.bco-dmo.org/id/dataset-parameter/820920.rdf
Name: Average_QP
Units: femtomoles per cell (fmol/cell)
Description: <p>Cellular P quota</p>
http://lod.bco-dmo.org/id/dataset-parameter/820921.rdf
Name: SD_of_QP
Units: femtomoles per cell (fmol/cell)
Description: <p>Standard Deviation of cellular P quota</p>
http://lod.bco-dmo.org/id/dataset-parameter/820922.rdf
Name: Average_APA
Units: femtomoles P per cell per hour (fmol P cell-1 h-1)
Description: <p>Alkaline phosphatase activity</p>
http://lod.bco-dmo.org/id/dataset-parameter/820923.rdf
Name: SD_of_APA
Units: femtomoles P per cell per hour (fmol P cell-1 h-1)
Description: <p>Standard Deviation of alkaline phosphatase activity</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
5686
https://darchive.mblwhoilibrary.org/bitstream/1912/26156/1/dataset-820902_phytoplankton-phosphonate-utilization__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.820902.1
download
onLine
dataset
<p>Axenic cultures of the pico-prasinophyte <em>Micromonas commoda</em> (CCMP 2709), the coccolithophore <em>Emiliania huxleyi</em> (CCMP 2090), and the diatom <em>Phaeodactylum tricornutum</em> (CCMP 2561) were obtained from the National Center for Marine Algae and Microbiota (Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine). The cultures remained axenic throughout the experiments as determined by SYTO-staining and flow cytometric counting on a BD FACSJazz cell sorter; all cultures were free of bacteria during these experiments. Phytoplankton were grown in artificial sea water amended with L1 media with (<em>P. tricornutum</em>) or without (<em>M. commoda and E. huxleyi</em>) silica. The P source was added separately to achieve the desired growth conditions; Pi-replete media contained 36 µM PO₄³⁻, the Pi-deficient condition received 0.1 µM PO₄³⁻, and the phosphonate treatments received either 36 µM MPN or 2-AEPN. The Pi-deficient treatment (0.1 µM) represents a control for the low level of contaminating Pi measured in the phosphonate media; thus, an increase in growth in the MPN and 2-AEPN conditions above that measured in the Pi-deficient condition is due to phosphonate utilization. The potential for abiotic breakdown of phosphonate to Pi was investigated in media-only tubes exposed to the experimental temperature and light conditions for 10 days. Pi levels did not change throughout the experimental period (MPN average Pi = 0.11 µM ± 0.02; 2-AEPN average Pi = 0.10 µM ± 0.02), strongly supporting the notion of active enzymatic breakdown of phosphonates for growth. Natural P concentrations are much lower than those used in this study; the replete nutrient concentrations were used to support high cell yields necessary for analytical measurements. Cultures were acclimated to the four growth conditions described above as they had been maintained in each P treatment for a minimum of two transfers (20 days). Cultures were grown at 20°C in a 14h light/10h dark cycle at ~100 µE m⁻² s⁻¹ with a starting concentration of ~1x10⁴ cells mL⁻¹ in 25 mL culture volumes. Phytoplankton growth was monitored by fluorescence measurements using a Turner TD-700 fluorometer and cell counts analyzed by flow cytometry. Specific growth rates (μ) were calculated from the linear regression of the natural log of cell counts during the exponential growth phase of cultures. Quadruplicate cultures were setup for each treatment; three replicates were harvested in the late exponential phase of growth for physiological measurements, while the fourth was used to monitor cell abundances later in the growth cycle.</p>
<p>Physiological measurements:<br />
Cell samples (5 mL culture volume) for particulate P were collected onto precombusted 25 mm Whatman glass fiber filters, rinsed with 0.17 M Na₂SO₄, and stored frozen at -20°C until analysis. Determinations were made as previously described (Lomas et al. 2010). Briefly, filters were rinsed with 0.017 M MgSO₄, dried at 90°C, and combusted at 500°C for 2 h. Upon cooling, 0.2 M HCl was added and hydrolyzed at 80°C for 30 min. After cooling, mixed reagent was added, the samples were centrifuged, and absorbance was read at 885 nm using a Genesys 10 spectrophotometer.</p>
<p>Alkaline phosphatase content (APA) measurements were made by quantifying the hydrolysis of 6,8-difluoro-4-methylumbelliferyl phosphate using a Molecular Devices FilterMax F5 microplate reader. Abiotic substrate hydrolysis was accounted for in killed controls that were boiled and cooled prior to substrate addition, as well as in media-only controls. The fluorescent reference standard, 6,8-difluoro-4-methylcoumarin was used to calculate the rate of hydrolysis, which was then normalized to cell abundance to determine APA per cell.</p>
Specified by the Principal Investigator(s)
<p>Cell abundance data were processed from flow cytometry files by gating logic using Sortware software. Nutrient concentrations, both dissolved and particulate, were calculated based upon the instrument absorbance response to known concentration standards. Alkaline phosphatase activity was calculated based on fluorescence response of a known standard.</p>
<p>Any samples that were not collected are represented by 'nd' in the dataset.</p>
<p>BCO-DMO Processing:<br />
- renamed fields;<br />
- replaced 'NaN' with 'nd' (no data).</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
BD FACSJazz cell sorter
BD FACSJazz cell sorter
PI Supplied Instrument Name: BD FACSJazz cell sorter Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
Molecular Devices FilterMax F5 microplate reader
Molecular Devices FilterMax F5 microplate reader
PI Supplied Instrument Name: Molecular Devices FilterMax F5 microplate reader 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.
Genesys 10 spectrophotometer
Genesys 10 spectrophotometer
PI Supplied Instrument Name: Genesys 10 spectrophotometer 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 TD-700 fluorometer
Turner TD-700 fluorometer
PI Supplied Instrument Name: Turner TD-700 fluorometer Instrument Name: Turner Designs 700 Laboratory Fluorometer Instrument Short Name:TD-700 Instrument Description: The TD-700 Laboratory Fluorometer is a benchtop fluorometer designed to detect fluorescence over the UV to red range. The instrument can measure concentrations of a variety of compounds, including chlorophyll-a and fluorescent dyes, and is thus suitable for a range of applications, including chlorophyll, water quality monitoring and fluorescent tracer studies. Data can be output as concentrations or raw fluorescence measurements. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0510/