http://lod.bco-dmo.org/id/dataset/991400
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
2026-01-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Phytoplankton cell count data from laboratory cultures of Crocosphaera watsonii, Micromonas commoda, Prochlorococcus marinus, Synechococcus, Gephyrocapsa huxleyi, and Thalassiosira pseudonana collected from September to December 2022
2026-02-18
publication
2026-02-18
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2026-03-02
publication
https://doi.org/10.26008/1912/bco-dmo.991400.1
Rogier Braakman
Massachusetts Institute of Technology
principalInvestigator
Sonya T. Dyhrman
Lamont-Doherty Earth Observatory
principalInvestigator
Elizabeth Kujawinski
Woods Hole Oceanographic Institution
principalInvestigator
Yuting Zhu
Woods Hole Oceanographic Institution
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: Zhu, Y., Anderson, H., Gray, L., Kujawinski, E., Dyhrman, S. T., Braakman, R. (2026) Phytoplankton cell count data from laboratory cultures of Crocosphaera watsonii, Micromonas commoda, Prochlorococcus marinus, Synechococcus, Gephyrocapsa huxleyi, and Thalassiosira pseudonana collected from September to December 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-02-18 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.991400.1 [access date]
PXMI - Phytoplankton cell count data Dataset Description: Methods and Sampling: <p>Axenic cultures included <em>G. huxleyi</em> CCMP371, <em>M. commoda</em> RCC299, <em>T. pseudonana</em> CCMP1335, <em>Synechococcus</em> sp. WH8102, <em>C. watsonii</em> WH8501, <em>Prochlorococcus</em> MIT 9301. <em>G. huxleyi</em>, <em>M. commoda, </em>and <em>T. pseudonana </em>were grown in<em> </em>L1 growth media prepared according to Guillard and Hargraves (1993), and <em>Synechococcus </em>was grown in SN media prepared according to Waterbury et al. (1986), all with a base of 0.2-micrometer (µm) filtered coastal seawater collected from Vineyard Sound, MA, United States. <em>G. huxleyi </em>media excluded Si. <em>C. watsonii </em>was grown in SO media, which followed the SN media recipe but omitted NaNO<sub>3</sub>, with a base of 75% Sargasso seawater (diluted to 75% with MilliQ). <em>Prochlorococcus</em> was grown in Pro99 in a Sargasso seawater base prepared according to Moore et al. (2007). Axenic strains of <em>C. watsonii</em>, <em>G. huxleyi</em>, <em>M. commoda</em>, <em>Synechococcus</em>, and <em>T. pseudonana</em> were inoculated into 25-millimeter (mm) borosilicate glass culture tubes containing 25 milliliters (mL) of sterile media. Axenic <em>Prochlorococcus</em> was inoculated into borosilicate culture tubes containing 35 mL of sterile media. Nine biological replicates were monitored for all strains on a 14:10 hour light-dark cycle, with the exception of <em>Prochlorococcus</em>, which was grown on a 13:11 hour light-dark cycle. Isolates were cultured with light intensities ranging from 45-130 µmol photons m<sup>-2</sup> s<sup>-1</sup> depending on taxonomy.</p>
<p>Growth was monitored daily by <em>in vivo</em> chlorophyll fluorescence on a Turner Designs 10-AU fluorometer. Measurements for all genera except <em>Prochlorococcus </em>were made at the same time each day, 3-4 hours after the beginning of the light cycle, to avoid diel changes in cell physiology. Daily sampling times for <em>Prochlorococcus</em> varied as<em> </em>cells divide only at night when acclimated to diel conditions, and thus sampling time throughout the day is less likely to influence cell counts. Six (6) replicates of each isolate were harvested by gentle vacuum filtration during exponential growth to maximize metabolite generation. The remaining three cultures were monitored as described above until they reached stationary phase, which occurred between 3-7 days after harvesting, depending on the strain. For all six phytoplankton strains, cells were filtered onto filters (47 mm, 0.2 µm Omnipore filters, Whatman) and the filtrates were collected into combusted (450 degrees Celsius (°C) for at least 4 hours) glass side-arm flasks. The vacuum pump pressure did not exceed ~5" Hg to minimize cell lysis and endometabolite contamination in filtrate samples. Filtrates were transferred into pre-combusted 40 mL amber vials. Culture media blanks (with no algal biomass) for all media types were also filtered using the same method. All filtrate samples were stored upright at -20°C until analysis. Growth rates during the exponential phase were calculated using relative fluorescent units (RFUs) for all strains with the exception of <em>Prochlorococcus</em>, where daily cell count data were used, and then averaged across replicates. For all species except <em>Prochlorococcus</em>, the final cell yields were evaluated via microscopy. Briefly, 1 to 2 mL of well-mixed cultures were removed immediately prior to harvesting and preserved in paraformaldehyde (for <em>Synechococcus</em>; 0.24% final concentration) or neutral Lugol's iodine solution (for all others; 2% final concentration). <em>Synechococcus</em> samples were diluted and collected on a filter (black 0.2 µm, 25 mm polycarbonate filters, Whatman) for cell counts using an epifluorescence microscope (63x, oil immersion), while Lugol's-preserved samples were counted using a hemocytometer and light microscope (10x). <em>Prochlorococcus</em> cell counts were obtained using flow cytometry. Briefly, flow cytometry samples were run live on a Guava EasyCyte flow cytometer (Cytek Biosciences) for 10,000 counts or 5 minutes each. Cells were excited with a blue 488 nanometer (nm) laser and cell counts, cell size, and chlorophyll content were analyzed using FlowJo.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2019589 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2019589
completed
Rogier Braakman
Massachusetts Institute of Technology
MA
USA
braakman@mit.edu
pointOfContact
Sonya T. Dyhrman
Lamont-Doherty Earth Observatory
845-365-8465
102E Geoscience 61 Route 9W, PO Box 1000
Palisades
NY
10964
USA
dyhrman@ldeo.columbia.edu
pointOfContact
Elizabeth Kujawinski
Woods Hole Oceanographic Institution
508-289-3493
266 Woods Hole Rd. MS #4
Woods Hole
MA
02543
USA
ekujawinski@whoi.edu
pointOfContact
Yuting Zhu
Woods Hole Oceanographic Institution
y2zhu@odu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
species
strain
day
replicate
RFUs
cells_per_mL
Guava EasyCyte flow cytometer (Cytek Biosciences)
epifluorescence microscope
light microscope
Turner Designs 10-AU fluorometer
theme
None, User defined
species scientific name (binomial)
strain identifier
time_point
replicate
fluorescence
abundance
featureType
BCO-DMO Standard Parameters
Flow Cytometer
Fluorescence Microscope
Microscope - Optical
Turner Designs Fluorometer 10-AU
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.
Center for Chemical Currencies of a Microbial Planet
https://ccomp-stc.org/
Center for Chemical Currencies of a Microbial Planet
Functions carried out by microscopic inhabitants of the surface ocean affect every aspect of life on our planet, regardless of distance from the coast. Ocean phytoplankton are responsible for half of the photosynthesis on Earth, the first step in a complex system that annually withdraws 50 billion metric tons of carbon from the atmosphere to sustain their growth. Of this, 25 billion metric tons participate in a rapid cycle in which biologically reactive material is released into seawater and converted back into carbon dioxide by marine bacteria within hours to days. The chemical-microbe network at the heart of this fast cycle remains poorly constrained; consequently, its primary currencies and controls remain elusive; its sensitivities to changing ocean conditions are unknown; and its responses to future climate scenarios are not predictable. The Center for Chemical Currencies of a Microbial Planet (C-CoMP) integrates research, education and knowledge transfer activities to develop a mechanistic understanding of surface ocean carbon flux within the context of a changing ocean and through increased participation in ocean sciences. C-CoMP supports science teams that merge biology, chemistry, modeling, and informatics to close long-standing knowledge gaps in the identities and dynamics of organic molecules that serve as the currencies of elemental transfer between the ocean and atmosphere. C-CoMP fosters education, outreach, and knowledge transfer activities that engage students of all ages, broaden participation in the next generation of ocean scientists, and extend novel open-science approaches into complementary academic and industrial communities. The Center framework is critical to this mission, uniquely facilitating an open exchange of experimental and computational science, methodological and conceptual challenges, and collaborations that establish integrated science and education partnerships. With expanded participation in ocean science research and ocean literacy across the US society, the next generation of ocean scientists will better reflect the diverse US population.
Climate-carbon feedbacks on the marine carbon reservoir are major uncertainties for future climate projections, and the trajectory and rate of ocean changes depend directly on microbial responses to temperature increases, ocean acidification, and other perturbations driven by climate change. C-CoMP research closes an urgent knowledge gap in the mechanisms driving carbon flow between ocean and atmosphere, with global implications for predictive climate models. The Center supports interdisciplinary science teams following open and reproducible science practices to address: (1) the chemical currencies of surface ocean carbon flux; (2) the structure and regulation of the chemical-microbe network that mediates this flux; and (3) sensitivity of the network and its feedbacks on climate. C-CoMP leverages emerging tools and technologies to tackle critical challenges in these themes, in synergy with existing ocean programs and consistent with NSF’s Big Ideas. C-CoMP education and outreach activities seek to overcome barriers to ocean literacy and diversify participation in ocean research. The Center is developing (1) initiatives to expand ocean literacy in K-12 and the broader public, (2) ocean sciences undergraduate curricula and research opportunities that provide multiple entry points into research experiences, (3) post-baccalaureate programs to transition undergraduates into graduate education and careers in ocean science, and (4) interdisciplinary graduate student and postdoctoral programs that prepare the next generation of ocean scientists. The C-CoMP team includes education faculty who evaluate the impacts of education and outreach activities and export successful STEM initiatives to the education community. C-CoMP is revolutionizing the technologies for studying chemical transformations in microbial systems to build understanding of the outsized impact of microbes on elemental cycles. Open science, cross-disciplinary collaborations, community engagement, and inclusive practices foster strategic advances in critical science problems and STEM initiatives. C-CoMP science, education, and knowledge-transfer themes are efficiently addressed through a sustained network of scientists addressing critical research challenges while broadening the workforce that will tackle multi-disciplinary problems with academic, industrial and policy partners.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
The Program's Data Management Plan (DMP) is available as a PDF document.
C-CoMP
largerWorkCitation
program
Phytoplankton Exometabolites
https://ccomp-stc.org/
Phytoplankton Exometabolites
<p>The Center for Chemical Currencies of a Microbial Planet (C-CoMP) is focused on understanding marine chemical currencies. This project examines exometabolites released from representative taxa of marine phytoplankton to better characterize the composition of labile marine dissolved organic matter and understand the biological sources of these metabolites to the marine environment. Specifically, this project integrates novel metabolomics, genomics, transcriptomics, and proteomics methods to identify extracellular metabolites and link them with their production pathways under environmentally relevant conditions.</p>
C-CoMP Phytoplankton Exometabolites
largerWorkCitation
project
eng; USA
oceans
2022-09-17
2022-12-05
Lab study
0
BCO-DMO catalogue of parameters from Phytoplankton cell count data from laboratory cultures of Crocosphaera watsonii, Micromonas commoda, Prochlorococcus marinus, Synechococcus, Gephyrocapsa huxleyi, and Thalassiosira pseudonana collected from September to December 2022
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/991438.rdf
Name: species
Units: unitless
Description: <p>phytoplankton strain grown in the experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/991439.rdf
Name: strain
Units: unitless
Description: <p>strain identifier of the phytoplankton species</p>
http://lod.bco-dmo.org/id/dataset-parameter/991440.rdf
Name: day
Units: unitless
Description: <p>The day of the experiment the measurement was taken</p>
http://lod.bco-dmo.org/id/dataset-parameter/991441.rdf
Name: replicate
Units: unitless
Description: <p>9 biological replicates of each culture, this denotes which replicate the measurement refers to</p>
http://lod.bco-dmo.org/id/dataset-parameter/991442.rdf
Name: RFUs
Units: unitless
Description: <p>Relative fluorescence units</p>
http://lod.bco-dmo.org/id/dataset-parameter/991443.rdf
Name: cells_per_mL
Units: cells per milliliter
Description: <p>Number of cells per mL, determined via flow cytometer for Prochlorococcus and via microscopy for all other isolates</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://doi.org/10.26008/1912/bco-dmo.991400.1
download
onLine
dataset
<p>Axenic cultures included <em>G. huxleyi</em> CCMP371, <em>M. commoda</em> RCC299, <em>T. pseudonana</em> CCMP1335, <em>Synechococcus</em> sp. WH8102, <em>C. watsonii</em> WH8501, <em>Prochlorococcus</em> MIT 9301. <em>G. huxleyi</em>, <em>M. commoda, </em>and <em>T. pseudonana </em>were grown in<em> </em>L1 growth media prepared according to Guillard and Hargraves (1993), and <em>Synechococcus </em>was grown in SN media prepared according to Waterbury et al. (1986), all with a base of 0.2-micrometer (µm) filtered coastal seawater collected from Vineyard Sound, MA, United States. <em>G. huxleyi </em>media excluded Si. <em>C. watsonii </em>was grown in SO media, which followed the SN media recipe but omitted NaNO<sub>3</sub>, with a base of 75% Sargasso seawater (diluted to 75% with MilliQ). <em>Prochlorococcus</em> was grown in Pro99 in a Sargasso seawater base prepared according to Moore et al. (2007). Axenic strains of <em>C. watsonii</em>, <em>G. huxleyi</em>, <em>M. commoda</em>, <em>Synechococcus</em>, and <em>T. pseudonana</em> were inoculated into 25-millimeter (mm) borosilicate glass culture tubes containing 25 milliliters (mL) of sterile media. Axenic <em>Prochlorococcus</em> was inoculated into borosilicate culture tubes containing 35 mL of sterile media. Nine biological replicates were monitored for all strains on a 14:10 hour light-dark cycle, with the exception of <em>Prochlorococcus</em>, which was grown on a 13:11 hour light-dark cycle. Isolates were cultured with light intensities ranging from 45-130 µmol photons m<sup>-2</sup> s<sup>-1</sup> depending on taxonomy.</p>
<p>Growth was monitored daily by <em>in vivo</em> chlorophyll fluorescence on a Turner Designs 10-AU fluorometer. Measurements for all genera except <em>Prochlorococcus </em>were made at the same time each day, 3-4 hours after the beginning of the light cycle, to avoid diel changes in cell physiology. Daily sampling times for <em>Prochlorococcus</em> varied as<em> </em>cells divide only at night when acclimated to diel conditions, and thus sampling time throughout the day is less likely to influence cell counts. Six (6) replicates of each isolate were harvested by gentle vacuum filtration during exponential growth to maximize metabolite generation. The remaining three cultures were monitored as described above until they reached stationary phase, which occurred between 3-7 days after harvesting, depending on the strain. For all six phytoplankton strains, cells were filtered onto filters (47 mm, 0.2 µm Omnipore filters, Whatman) and the filtrates were collected into combusted (450 degrees Celsius (°C) for at least 4 hours) glass side-arm flasks. The vacuum pump pressure did not exceed ~5" Hg to minimize cell lysis and endometabolite contamination in filtrate samples. Filtrates were transferred into pre-combusted 40 mL amber vials. Culture media blanks (with no algal biomass) for all media types were also filtered using the same method. All filtrate samples were stored upright at -20°C until analysis. Growth rates during the exponential phase were calculated using relative fluorescent units (RFUs) for all strains with the exception of <em>Prochlorococcus</em>, where daily cell count data were used, and then averaged across replicates. For all species except <em>Prochlorococcus</em>, the final cell yields were evaluated via microscopy. Briefly, 1 to 2 mL of well-mixed cultures were removed immediately prior to harvesting and preserved in paraformaldehyde (for <em>Synechococcus</em>; 0.24% final concentration) or neutral Lugol's iodine solution (for all others; 2% final concentration). <em>Synechococcus</em> samples were diluted and collected on a filter (black 0.2 µm, 25 mm polycarbonate filters, Whatman) for cell counts using an epifluorescence microscope (63x, oil immersion), while Lugol's-preserved samples were counted using a hemocytometer and light microscope (10x). <em>Prochlorococcus</em> cell counts were obtained using flow cytometry. Briefly, flow cytometry samples were run live on a Guava EasyCyte flow cytometer (Cytek Biosciences) for 10,000 counts or 5 minutes each. Cells were excited with a blue 488 nanometer (nm) laser and cell counts, cell size, and chlorophyll content were analyzed using FlowJo.</p>
Specified by the Principal Investigator(s)
- Imported original file "rfu_cell_counts_1-15-26.csv" into the BCO-DMO system.
- Saved the final file as "991400_v1_phytoplankton_cell_counts.csv".
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
Guava EasyCyte flow cytometer (Cytek Biosciences)
Guava EasyCyte flow cytometer (Cytek Biosciences)
PI Supplied Instrument Name: Guava EasyCyte flow cytometer (Cytek Biosciences) PI Supplied Instrument Description:flow cytometry samples were run live on a Guava EasyCyte flow cytometer (Cytek Biosciences) for 10,000 counts or 5 minutes each 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/
epifluorescence microscope
epifluorescence microscope
PI Supplied Instrument Name: epifluorescence microscope PI Supplied Instrument Description:Synechococcus samples were diluted and collected on a filter for cell counts using an epifluorescence microscope (63x, oil immersion) Instrument Name: Fluorescence Microscope Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/
light microscope
light microscope
PI Supplied Instrument Name: light microscope PI Supplied Instrument Description:Samples were counted using a hemocytometer and light microscope (10x) Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Turner Designs 10-AU fluorometer
Turner Designs 10-AU fluorometer
PI Supplied Instrument Name: Turner Designs 10-AU fluorometer PI Supplied Instrument Description:Growth was monitored daily by in vivo chlorophyll fluorescence on a Turner Designs 10-AU fluorometer. Instrument Name: Turner Designs Fluorometer 10-AU Instrument Short Name:Turner Fluorometer 10-AU Instrument Description: The Turner Designs 10-AU Field Fluorometer is used to measure Chlorophyll fluorescence. The 10AU Fluorometer can be set up for continuous-flow monitoring or discrete sample analyses. A variety of compounds can be measured using application-specific optical filters available from the manufacturer (read more from Turner Designs, turnerdesigns.com, Sunnyvale, CA, USA). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0393/