http://lod.bco-dmo.org/id/dataset/998934
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)
Laboratory-based growth studies with multiple G. huxleyi strains for genome sequencing
2026-05-19
publication
2026-05-19
revision
BCO-DMO Linked Data URI
2026-05-19
creation
http://lod.bco-dmo.org/id/dataset/998934
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) Laboratory-based growth studies with multiple G. huxleyi strains for genome sequencing. 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/998934 [access date]
Methods and Sampling: <p>All <em>G. huxleyi</em> isolates were obtained from either the National Center for Marine Algae and Microbiota (East Boothbay, ME) or the Roscoff Culture Collection (Roscoff, France) and maintained in incubators with ~100 µE m-2 s-1 light on a 14:10 light:dark cycle in autoclaved L1 media with a 0.2-µm filtered Vineyard Sound (MA) seawater base. Isolates were grown at different temperatures, as determined by their collection location (reported in strain metadata from NCMA and/or Roscoff; e.g., CCMP371 was collected in June 1987 in the Sargasso Sea at 32°N, 62°W with a culture collection maintenance temperature of 20 °C). To generate enough biomass needed for downstream genome sequencing (details reported elsewhere), large (1 L) batch cultures of each isolate were grown. For each separate isolate, a 25 mL nutrient-replete (L1) culture was used to inoculate 1 L nutrient-replete (L1) media in a Fernbach flask. No replicate cultures were grown for this experiment, as replicates were not necessary given the goal of obtaining DNA for genome sequencing.</p>
<p>Growth was monitored daily at the same time of day by in vivo chlorophyll fluorescence (relative fluorescence units, RFUs) on a Turner Designs Aquafluor handheld fluorometer (in vivo chlorophyll <em>a</em> channel). Briefly, each culture was mixed by swirling 3 times clockwise and then 3 times counterclockwise before aseptically removing a 2 mL subsample with a serological pipette. The subsample was transferred to a 10 mm × 10 mm methacrylate cuvette and placed in the Aquafluor for RFU measurement. A blank measurement was also taken daily using deionized water in place of a culture sample in the same type of cuvette. The RFU value obtained from the blank was subtracted from the RFU value of the culture for a “blank-corrected” RFU. Negative values for the blank were a result of instrument drift and were subtracted as described above. No RFUs in the dataset were missing or anomalous.</p>
<p>The exponential population growth rate for each <em>G. huxleyi</em> strain was calculated by measuring changes in blank-corrected RFUs (in vivo chlorophyll <em>a</em>) as a proxy for biomass over time during the exponential growth phase (minimally 4 days), using the formula µ = (ln(N2) - ln(N1))/t2-t1, where N1 is the in vivo chlorophyll <em>a</em> (RFU) at the start, N2 is the in vivo chlorophyll <em>a</em> (RFU) at the end, t1 is the first timepoint (day), and t2 is the final timepoint (day). RFUs were ln-transformed and fitted with a linear regression of ln(RFU) versus time (days). The regression slope over the most linear portion (where R2 &gt; 98%) of the growth curve was taken as the best estimate of mean daily population growth rate.</p>
<p>The resulting datasets from applying this method included <em>G. huxleyi</em> strain growth conditions, <em>G. huxleyi</em> growth (biomass proxied by relative fluorescence units from in vivo chlorophyll <em>a</em>), and <em>G. huxleyi</em> exponential growth rates.</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
Turner Designs Aquafluor
theme
None, User defined
Turner Designs Aquafluor 8000
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
2026-05-19
0
BCO-DMO catalogue of parameters from Laboratory-based growth studies with multiple G. huxleyi strains for genome sequencing
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/998934/data/download
download
onLine
dataset
<p>All <em>G. huxleyi</em> isolates were obtained from either the National Center for Marine Algae and Microbiota (East Boothbay, ME) or the Roscoff Culture Collection (Roscoff, France) and maintained in incubators with ~100 µE m-2 s-1 light on a 14:10 light:dark cycle in autoclaved L1 media with a 0.2-µm filtered Vineyard Sound (MA) seawater base. Isolates were grown at different temperatures, as determined by their collection location (reported in strain metadata from NCMA and/or Roscoff; e.g., CCMP371 was collected in June 1987 in the Sargasso Sea at 32°N, 62°W with a culture collection maintenance temperature of 20 °C). To generate enough biomass needed for downstream genome sequencing (details reported elsewhere), large (1 L) batch cultures of each isolate were grown. For each separate isolate, a 25 mL nutrient-replete (L1) culture was used to inoculate 1 L nutrient-replete (L1) media in a Fernbach flask. No replicate cultures were grown for this experiment, as replicates were not necessary given the goal of obtaining DNA for genome sequencing.</p>
<p>Growth was monitored daily at the same time of day by in vivo chlorophyll fluorescence (relative fluorescence units, RFUs) on a Turner Designs Aquafluor handheld fluorometer (in vivo chlorophyll <em>a</em> channel). Briefly, each culture was mixed by swirling 3 times clockwise and then 3 times counterclockwise before aseptically removing a 2 mL subsample with a serological pipette. The subsample was transferred to a 10 mm × 10 mm methacrylate cuvette and placed in the Aquafluor for RFU measurement. A blank measurement was also taken daily using deionized water in place of a culture sample in the same type of cuvette. The RFU value obtained from the blank was subtracted from the RFU value of the culture for a “blank-corrected” RFU. Negative values for the blank were a result of instrument drift and were subtracted as described above. No RFUs in the dataset were missing or anomalous.</p>
<p>The exponential population growth rate for each <em>G. huxleyi</em> strain was calculated by measuring changes in blank-corrected RFUs (in vivo chlorophyll <em>a</em>) as a proxy for biomass over time during the exponential growth phase (minimally 4 days), using the formula µ = (ln(N2) - ln(N1))/t2-t1, where N1 is the in vivo chlorophyll <em>a</em> (RFU) at the start, N2 is the in vivo chlorophyll <em>a</em> (RFU) at the end, t1 is the first timepoint (day), and t2 is the final timepoint (day). RFUs were ln-transformed and fitted with a linear regression of ln(RFU) versus time (days). The regression slope over the most linear portion (where R2 &gt; 98%) of the growth curve was taken as the best estimate of mean daily population growth rate.</p>
<p>The resulting datasets from applying this method included <em>G. huxleyi</em> strain growth conditions, <em>G. huxleyi</em> growth (biomass proxied by relative fluorescence units from in vivo chlorophyll <em>a</em>), and <em>G. huxleyi</em> exponential growth rates.</p>
Specified by the Principal Investigator(s)
<p>Relative fluorescence unit (RFU) values for each day and for each <em>G. huxleyi</em> strain were calculated by subtracting the blank RFU for that day from the RFU of the strain for that day. This yielded a “blank-corrected” RFU. Negative values for the blank were a result of instrument drift. The exponential population growth rate for each <em>G. huxleyi</em> strain was calculated from RFUs from the linear portion of the growth curve (minimally 4 days). RFUs were ln-transformed in Prism 11 (GraphPad) and fitted with a linear regression of ln(RFU) versus time (days). The regression slope over the most linear portion (where R2 &gt; 98%) of the growth curve was taken as the best estimate of mean daily population growth rate.</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
Turner Designs Aquafluor
Turner Designs Aquafluor
PI Supplied Instrument Name: Turner Designs Aquafluor PI Supplied Instrument Description:Turner Designs Aquafluor (Turner Designs 8000-406), in vivo chlorophyll a channel (Ex: 395/130 nm; Em: ≥ 660 nm). 10 mm x 10 mm methacrylate cuvette. Instrument Name: Turner Designs Aquafluor 8000 Instrument Short Name:Turner Designs Aquafluor 8000 Instrument Description: The Turner Designs Aquafluor 8000 is a lightweight, handheld fluorometer/turbidimeter ideal for field use. It can be configured with one or two channels to measure turbidity, chlorophyll, algae, dyes, ammonium, CDOM, and more. Detailed description at https://www.turnerdesigns.com/aquafluor-handheld-fluorometer