http://lod.bco-dmo.org/id/dataset/998992
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
2026-05-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
G. huxleyi cell count data from RCC874 and RCC914 N amendment laboratory experiment
2026-05-19
publication
2026-05-19
revision
BCO-DMO Linked Data URI
2026-05-19
creation
http://lod.bco-dmo.org/id/dataset/998992
Harriet Alexander
Woods Hole Oceanographic Institution
principalInvestigator
Sonya T. Dyhrman
Lamont-Doherty Earth Observatory
principalInvestigator
Sheean Haley
Lamont-Doherty Earth Observatory
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: Dyhrman, S. T., Alexander, H., Haley, S. (2026) G. huxleyi cell count data from RCC874 and RCC914 N amendment laboratory experiment. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-05-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/998992 [access date]
Methods and Sampling: <p><em>G. huxleyi</em> strains RCC874 and RCC914 were obtained from the Roscoff Culture Collection (RCC). The cultures were transferred from the maintenance stock into artificial seawater (40 g Instant Ocean® Sea Salt per L Milli-Q® water) amended with nutrients, trace metals, and vitamins according to the L1 recipe (<a class="decorated-link" href="https://ncma.bigelow.org/algae-media-recipes" rel="noopener" target="_new">https://ncma.bigelow.org/algae-media-recipes</a>) without silica (herein reported as L1-Si). The temperatures were selected to simulate no heat stress (18°C), moderate heat stress (22°C), and high heat stress conditions (25°C and 28°C for RCC874 and RCC914, respectively). The cultures were acclimated to the temperature conditions under a 14:10 light/dark cycle for approximately 10 days prior to the start of the experiment.</p>
<p>Following acclimation, cultures were transferred in triplicate into 2.8 L Fernbach flasks at an initial concentration of 1.0 ✕ 10⁵ cells mL⁻¹. The cultures were divided into two conditions: nitrogen-replete (N replete; L1-Si with standard 8.82 ✕ 10⁻⁴ M NaNO₃) and nitrogen-limited (N limited; L1-Si with 8.82 ✕ 10⁻⁵ M NaNO₃). Cell abundances and optical properties were measured daily using flow cytometry with a BD Accuri C6 Plus equipped with a C-Sampler (BD, USA).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1948025 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1948025
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1948409 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1948409
onGoing
Harriet Alexander
Woods Hole Oceanographic Institution
508 289 3565
266 Woods Hole Rd. MS#51
Woods Hole
MA
02540
USA
halexander@whoi.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
Sheean Haley
Lamont-Doherty Earth Observatory
shaley@ldeo.columbia.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
BD Accuri C6 Plus equipped with a C-Sampler (BD, USA)
theme
None, User defined
BD Biosciences Accuri C6 Plus flow cytometer
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: Defining the role of the pan genome in Emiliania huxleyi ecology and biogeography
https://osprey.bco-dmo.org/project/789439
Collaborative Research: Defining the role of the pan genome in Emiliania huxleyi ecology and biogeography
<p><em>NSF Award Abstract:</em><br />
Emiliania huxleyi is a numerically and ecologically important phytoplankton species in the ocean known for its cosmopolitan distribution and ability to form large blooms in coastal and open ocean regions. Studies of E. huxleyi variants in culture have found differences in growth, function and activity potential among them. The E. huxleyi variants also differ in some of the genes they carry. It has been hypothesized that this genomic variability may underlie the global success of this phytoplankton species by allowing adaptation of variants to diverse environments. Yet, the direct connection between genomic content and ecological success remains unclear. This project investigates how the conserved and variable portions of E. huxleyi genome may be connected to its success and its dynamics under varied environmental conditions. This work is critical to our understanding of how this important phytoplankton species may shift and respond to future changes. This project also supports the development of a series of hands-on activities designed to teach middle school students advance computational data analysis in ocean science. These activities are in collaboration with the Girls Who Code Club at the Our Sisters School, a tuition-free, non-sectarian, independent school for girls from low-income families, located in New Bedford, MA.</p>
<p>Understanding how phytoplankton diversity and phenotype are driven by changes in the environment is crucial for better predicting carbon cycle dynamics in the future ocean. While much work has investigated competition among phytoplankton species, intraspecific diversity and dynamics remain largely unknown for many eukaryotic phytoplankton. The overarching goal of this project is to define the role of the pan genome (set of variable genes) in E. huxleyi ecology and biogeography through a series of genomic analyses, computational field surveys, and laboratory-based experiments. This project is sequencing the genomes of several E. huxleyi isolates from across the global ocean and combining them with existing genome sequences to constrain the core and variable portions of the pan genome. Using this new pan genome reference database and leveraging global scale metagenomics and metatranscriptomic surveys, this project is estimating ecotype diversity of E. huxleyi across ocean regions to identify patterns of environmental selection. This project additionally focuses on identifying the physiological and transcriptional responses of a selection of sequenced strains and their responses to shifts in their nutrient environments in controlled laboratory studies. As E. huxleyi plays such a significant role in marine ecosystems and the global carbon cycle it is important that its pan genome and its impact on the biogeography and ecology of E. huxleyi is taken into consideration. It is likely that these dynamics are acutely important to predicting how this genus, and perhaps others, respond to changing environmental conditions in the future ocean.</p>
<p>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.</p>
ECO-PAN-EHUX
largerWorkCitation
project
eng; USA
oceans
2023-10-12
2024-01-30
0
BCO-DMO catalogue of parameters from G. huxleyi cell count data from RCC874 and RCC914 N amendment laboratory experiment
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
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/998992/data/download
download
onLine
dataset
<p><em>G. huxleyi</em> strains RCC874 and RCC914 were obtained from the Roscoff Culture Collection (RCC). The cultures were transferred from the maintenance stock into artificial seawater (40 g Instant Ocean® Sea Salt per L Milli-Q® water) amended with nutrients, trace metals, and vitamins according to the L1 recipe (<a class="decorated-link" href="https://ncma.bigelow.org/algae-media-recipes" rel="noopener" target="_new">https://ncma.bigelow.org/algae-media-recipes</a>) without silica (herein reported as L1-Si). The temperatures were selected to simulate no heat stress (18°C), moderate heat stress (22°C), and high heat stress conditions (25°C and 28°C for RCC874 and RCC914, respectively). The cultures were acclimated to the temperature conditions under a 14:10 light/dark cycle for approximately 10 days prior to the start of the experiment.</p>
<p>Following acclimation, cultures were transferred in triplicate into 2.8 L Fernbach flasks at an initial concentration of 1.0 ✕ 10⁵ cells mL⁻¹. The cultures were divided into two conditions: nitrogen-replete (N replete; L1-Si with standard 8.82 ✕ 10⁻⁴ M NaNO₃) and nitrogen-limited (N limited; L1-Si with 8.82 ✕ 10⁻⁵ M NaNO₃). Cell abundances and optical properties were measured daily using flow cytometry with a BD Accuri C6 Plus equipped with a C-Sampler (BD, USA).</p>
Specified by the Principal Investigator(s)
<p><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,tahoma,verdana,sans-serif; font-size:15px">FCS data was processed using flowCore version 2.18.in R version 4.4.0.</span></p>
Specified by the Principal Investigator(s)
- Loaded sheet 1 from Excel file "CellCounts_GhuxleyiCultures_WHOI_Oct2023-Jan2024.xlsx" with headers in row 1; empty strings and "nd" treated as missing values
- Applied find/replace on the "Date" column, replacing "/" with "-"
- Converted "Date" column from format "%m-%d-%y" to ISO format "%Y-%m-%d" (datetime output type)
- Set column types: "ConcCellmL" as number, "Date" as date ("%Y-%m-%d"), "Well" as string, "day_number" as integer, "n_conc" as string, "rep" as string, "strain" as integer, "temp_c" as integer
- Output written to "998992_v1_G_huxleyi_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
BD Accuri C6 Plus equipped with a C-Sampler (BD, USA)
BD Accuri C6 Plus equipped with a C-Sampler (BD, USA)
PI Supplied Instrument Name: BD Accuri C6 Plus equipped with a C-Sampler (BD, USA) PI Supplied Instrument Description:Cell abundances and optical properties were measured daily using flow cytometry with a BD Accuri C6 Plus equipped with a C-Sampler (BD, USA). Instrument Name: BD Biosciences Accuri C6 Plus flow cytometer Instrument Short Name:Accuri C6 Plus Instrument Description: A flow cytometer designed to detect fluorochromes (including FITC, PE, APC), polymer dyes, and fluorescent proteins (including GFP, YFP, mCherry). The instrument is equipped with a blue and red laser, two light scatter detectors, and four fluorescence detectors with user-interchangeable filters. A non-pressurised peristaltic pump system drives the fluidics. The system monitors the sample volume pulled per run and can calculate absolute counts or sample concentration per microliter (uL). In the standard configuration (3-blue/1-red), three detectors read fluorescence emissions from fluorochromes excited by the blue laser, while a fourth detector reads emissions from fluorochromes excited by the red laser. The optional Selectable Laser Module allows the system to operate in 2-blue/2-red and 4-blue configurations. The minimum detectable particle size and sample volume are 0.5 micrometers (um) and 0.5 uL respectively. The maximum number of events is 1 million with an acquisition rate of up to 10,000 events/second.