http://lod.bco-dmo.org/id/dataset/906927
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
2023-08-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Single-factor temperature experiment physiology and carbonate chemistry from laboratory experiments with Pseudo-nitzschia australis conducted from 2021 to 2022
2023-08-28
publication
2023-08-28
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-11-15
publication
https://doi.org/10.26008/1912/bco-dmo.906927.1
Feixue Fu
University of Southern California
principalInvestigator
Matthew Bertin
University of Rhode Island
principalInvestigator
Liang Chen
University of Southern California
principalInvestigator
David A. Hutchins
University of Southern California
principalInvestigator
Bethany D. Jenkins
University of Rhode Island
principalInvestigator
Kyla Jean Kelly
University of Southern California
principalInvestigator
Andrew Kim
University of Rhode Island
principalInvestigator
Lily A Mancini
University of Southern California
principalInvestigator
Amjad Mansour
University of Southern California
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: Kelly, K. J., Fu, F., Hutchins, D. A., Bertin, M., Mansour, A., Mancini, L. A., Jenkins, B. D., Chen, L., Kim, A. (2023) Single-factor temperature experiment physiology and carbonate chemistry from laboratory experiments with Pseudo-nitzschia australis conducted from 2021 to 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-08-28 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.906927.1 [access date]
Methods and Sampling: <p>These experiments were conducted with a strain of (strain NWFSC 731)&nbsp;isolated from Long Beach, Washington State, USA on November 3, 2020. The temperature and salinity were 14°C and 27 ppt, respectively at the time of collection. The data was collected in laboratory experiments at the University of Southern California.&nbsp;The experiments began in September 2021 and finished in July of 2022.<br />
<br />
The following section provides a methodology summary for this dataset&nbsp;and references related datasets collected as part of the same experiment&nbsp;(see&nbsp;"Related Datasets" section for data access). A full methodology was published in "Simulated upwelling and marine heatwave events promote similar growth rates but differential domoic acid toxicity in Pseudo-nitzschia australis" in Harmful Algae (Kelly et al., 2023).<br />
<br />
Pseudo-nitzschia australis was grown under upwelling heatwave, and extreme heatwave conditions (e.g., combined temperature, nutrient, and carbon dioxide levels specific to each condition) and in single-factor response curves for carbon dioxide, temperature, and varying nitrogen:phosphorus (N:P) ratios/total nutrient concentrations.</p>
<p>Samples for chlorophyll a (used to calculate growth rates) were filtered on GF/F filters, extracted in 6 mL of 90 % acetone at -20°C for 24 h, then analyzed using a Turner 10AU field fluorometer (Welschmeyer 1994; Fu et al. 2007).</p>
<p>For elemental analysis (particulate organic carbon and nitrogen, POC and PON), cells were filtered onto pre-combusted GF/F filters, dried, and analyzed on a Costech 4010 Elemental Analyzer (Fu et al. 2007).&nbsp;</p>
<p>Samples for particulate domoic acid were filtered onto Supor 0.2 µm 47 mm PES filters. Samples were analyzed using LC-MS/MS on a Prominence UFLC system (Shimadzu, Kyoto, Japan) coupled to a SCIEX 4500 QTRAP mass spectrometer (AB Sciex, Framingham, MA, USA). Methods described in Wang et al. 2012.</p>
<p>Primary production was determined by measuring the uptake of radiolabeled bicarbonate (Fu et al. 2008). 14C-bicarbonate was added to 45 mL sub-cultures at T24 h and incubated for 24 h (approximating net carbon fixation) under the respective experimental conditions. After the incubation period, cells were collected on GF/F filters and placed in a scintillation vial containing scintillation cocktail. Samples were stored for 24 h before being read on a Wallac System 1400 liquid scintillation counter.</p>
<p>pH measurements were made on a Mettler Toledo SevenCompact pH meter using a three-point calibration curve and total pH scale (Cooley and Yager 2006). Samples for total DIC analysis were collected at Tfinal. Seawater from undisturbed culture bottles was removed with a sterile syringe, ejected into pre-evacuated borosilicate Exetainers, and poisoned with 5% MgCl2. Total DIC was then measured using a Picarro cavity ring-down spectrophotometer according to Subhas et al. (2015).</p>
<p>For cell count samples (for normalizing cellular domoic acid), 1 mL of the final experimental culture was preserved with 40 ul glutaraldehyde and stored at 4°C in the dark. Cells were counted on a Olympus BX51 microscope using a Sedgewick Rafter Chamber.<br />
<br />
Organism:<br />
Pseudo-nitzschia australis, LSID (urn:lsid:marinespecies.org:taxname:246604)</p>
Funding provided by National Oceanic and Atmospheric Administration (NOAA) Award Number: NA18OAR4170094
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2120619 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2120619
Funding provided by National Institutes of Health (NIH) Award Number: NIH-P20GM103430 Award URL: https://taggs.hhs.gov/Detail/AwardDetail?arg_AwardNum=P20GM103430&arg_ProgOfficeCode=127
completed
Feixue Fu
University of Southern California
2137403188
Department of Biology, MC 0371, University of Southern California 3616 Trousdale Pkwy
Los Angeles
CA
90089
USA
ffu@usc.edu
pointOfContact
Matthew Bertin
University of Rhode Island
401 874 5016
mbertin@uri.edu
pointOfContact
Liang Chen
University of Southern California
cliang27@usc.edu
pointOfContact
David A. Hutchins
University of Southern California
213-740-5616
Department of Biological Sciences 3616 Trousdale Parkway, AHF 20
Los Angeles
CA
90089
USA
dahutch@usc.edu
pointOfContact
Bethany D. Jenkins
University of Rhode Island
401-874-7551
Department of Cell and Molecular Biology and Graduate School of Oceanography 279 CBLS, 120 Flagg Road
Kingston
RI
02881
USA
bdjenkins@uri.edu
pointOfContact
Kyla Jean Kelly
University of Southern California
kylakell@usc.edu
pointOfContact
Andrew Kim
University of Rhode Island
kim2267@uri.edu
pointOfContact
Lily A Mancini
University of Southern California
lamancini01@gmail.com
pointOfContact
Amjad Mansour
University of Southern California
aamansou@usc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Treatment
Replicate
Growth_rate
Particulate_DA
DA_production_rate
Costech 4010 Elemental Analyzer
Turner 10AU field fluorometer
Prominence UFLC system (Shimadzu, Kyoto, Japan)
SCIEX 4500 QTRAP mass spectrometer (AB Sciex, Framingham, MA, USA)
Olympus BX51 microscope
theme
None, User defined
water temperature at measurement depth
replicate
growth
domoic acid
featureType
BCO-DMO Standard Parameters
Elemental Analyzer
Fluorometer
High-Performance Liquid Chromatograph
Mass Spectrometer
Microscope - Optical
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.
MCA: Developing transcriptomics as a tool to investigate toxic diatom responses to ocean heatwave and upwelling events
https://osprey.bco-dmo.org/project/855438
MCA: Developing transcriptomics as a tool to investigate toxic diatom responses to ocean heatwave and upwelling events
<p><em>NSF Award Abstract:</em><br />
The diatom Pseudo-nitzschia forms large, toxic harmful algal blooms along the U.S. West Coast, killing wildlife and harming valuable ocean fisheries. Understanding the causes of these blooms and predicting their occurrence, both now and under future changing climate conditions, is critical to coastal environmental and economic health. Puzzlingly, these blooms seem to happen during periods when coastal seawater upwelling results in cold, nutrient-rich, low pH sea surface conditions, and also during times when heat wave events cause warm, nutrient-poor, high pH conditions. These two extremes are forecast to get even more intense with climate change. This project is experimentally testing how Pseudo-nitzschia responds to upwelling and heat wave events using measurements of cell growth, toxin production, and gene expression. Broader impacts of this project include training the principal investigator in new gene expression methods, graduate and undergraduate research training, high school research mentoring experiences, and outreach and communications activities aimed at the commercial fishing industry. Societal benefits include obtaining a better understanding of the causes of damaging toxic algal blooms, and how they may change in the future coastal ocean.</p>
<p>The toxic diatom Pseudo-nitzschia causes annual harmful blooms along the US West Coast, a region where wind-driven upwelling brings rich nutrient supplies into the euphotic zone. However, this region is also experiencing unprecedented episodic ocean heatwave events linked to global warming. Thus, future climate trends in this region suggest an exaggeration of current physio-chemical extremes between colder, more nutrient-rich, low pH upwelling, and warmer, more nutrient-depleted, higher pH heatwaves. Surprisingly, toxic Pseudo-nitzschia spp. can bloom under both upwelling and heatwave conditions, despite opposite trends in key environmental controls like nutrients, temperature, and carbonate chemistry. This project is testing how this happens by first obtaining full response curves for each of the individual factors, temperature, pCO2, phosphorus, nitrogen, and silicon for two Pseudo-nitzschia isolates. Then, these variables are combined in holistic upwelling and heatwave scenario incubation experiments, to compare how growth and toxicity is affected in both cultures and natural blooms of Pseudo-nitzschia. The PI is assessing toxic diatom responses in these experiments using her existing expertise in algal physiology, as well as by expanding her professional horizons to develop new skills in transcriptome bioinformatics in partnership with Dr. Bethany Jenkins from the University of Rhode Island. Experiments are conducted to test the physiological responses of Pseudo-nitzschia to changes in nutrient concentrations, temperature and pCO2 during simulated upwelling or heatwave occurrences, and measure expression of key metabolic pathway genes such as toxin synthesis pathways. This project is helping to understand and interpret the surprising niche flexibility of toxic Pseudo-nitzschia in a changing ocean, and at the same time offers the PI a new avenue forward for her future career development.</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>
Toxic diatoms and heatwaves
largerWorkCitation
project
eng; USA
oceans
-124.060591
-124.060591
46.495103
46.495103
2020-11-01
2022-07-01
University of Southern California
0
BCO-DMO catalogue of parameters from Single-factor temperature experiment physiology and carbonate chemistry from laboratory experiments with Pseudo-nitzschia australis conducted from 2021 to 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/906994.rdf
Name: Treatment
Units: degrees Celsius (deg C)
Description: <p>Treatment temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/906995.rdf
Name: Replicate
Units: unitless
Description: <p>replicate number (1..3)</p>
http://lod.bco-dmo.org/id/dataset-parameter/906996.rdf
Name: Growth_rate
Units: per day (d-1)
Description: <p>Growth rate per day. Chlorophyll a samples were collected at T-initial and T-final and used for determination of growth rates. The following equation was used to calculate specific growth rates: growth rate = ln(Tfinal-Tinitial)/2 (where Tfinal and Tinitial are the chlorophyll a samples collected at their respective times, and 2 is the number of days between sampling).</p>
http://lod.bco-dmo.org/id/dataset-parameter/906997.rdf
Name: Particulate_DA
Units: nanograms of domoic acid per micromole of carbon (ng DA/umol C)
Description: <p>Particulate domoic acid. The amount of intracellular domoic acid normalized to particulate organic carbon.</p>
http://lod.bco-dmo.org/id/dataset-parameter/906998.rdf
Name: DA_production_rate
Units: nanograms of domoic acid per micromole of carbon per day (ng DA/umol C/day)
Description: <p>Domoic acid production rate. Domoic acid production rates were calculated by multiplying specific growth rates by DA quotas. This value provides an estimate of how toxic a bloom might be, based on the ability of Pseudo-nitzschia to increase cell abundances and produce high DA quotas (per mol POC).</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
1133
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/1c76ec02-1cb5-473d-81f9-f08fe7767e86/content
download
https://doi.org/10.26008/1912/bco-dmo.906927.1
download
onLine
dataset
<p>These experiments were conducted with a strain of (strain NWFSC 731)&nbsp;isolated from Long Beach, Washington State, USA on November 3, 2020. The temperature and salinity were 14°C and 27 ppt, respectively at the time of collection. The data was collected in laboratory experiments at the University of Southern California.&nbsp;The experiments began in September 2021 and finished in July of 2022.<br />
<br />
The following section provides a methodology summary for this dataset&nbsp;and references related datasets collected as part of the same experiment&nbsp;(see&nbsp;"Related Datasets" section for data access). A full methodology was published in "Simulated upwelling and marine heatwave events promote similar growth rates but differential domoic acid toxicity in Pseudo-nitzschia australis" in Harmful Algae (Kelly et al., 2023).<br />
<br />
Pseudo-nitzschia australis was grown under upwelling heatwave, and extreme heatwave conditions (e.g., combined temperature, nutrient, and carbon dioxide levels specific to each condition) and in single-factor response curves for carbon dioxide, temperature, and varying nitrogen:phosphorus (N:P) ratios/total nutrient concentrations.</p>
<p>Samples for chlorophyll a (used to calculate growth rates) were filtered on GF/F filters, extracted in 6 mL of 90 % acetone at -20°C for 24 h, then analyzed using a Turner 10AU field fluorometer (Welschmeyer 1994; Fu et al. 2007).</p>
<p>For elemental analysis (particulate organic carbon and nitrogen, POC and PON), cells were filtered onto pre-combusted GF/F filters, dried, and analyzed on a Costech 4010 Elemental Analyzer (Fu et al. 2007).&nbsp;</p>
<p>Samples for particulate domoic acid were filtered onto Supor 0.2 µm 47 mm PES filters. Samples were analyzed using LC-MS/MS on a Prominence UFLC system (Shimadzu, Kyoto, Japan) coupled to a SCIEX 4500 QTRAP mass spectrometer (AB Sciex, Framingham, MA, USA). Methods described in Wang et al. 2012.</p>
<p>Primary production was determined by measuring the uptake of radiolabeled bicarbonate (Fu et al. 2008). 14C-bicarbonate was added to 45 mL sub-cultures at T24 h and incubated for 24 h (approximating net carbon fixation) under the respective experimental conditions. After the incubation period, cells were collected on GF/F filters and placed in a scintillation vial containing scintillation cocktail. Samples were stored for 24 h before being read on a Wallac System 1400 liquid scintillation counter.</p>
<p>pH measurements were made on a Mettler Toledo SevenCompact pH meter using a three-point calibration curve and total pH scale (Cooley and Yager 2006). Samples for total DIC analysis were collected at Tfinal. Seawater from undisturbed culture bottles was removed with a sterile syringe, ejected into pre-evacuated borosilicate Exetainers, and poisoned with 5% MgCl2. Total DIC was then measured using a Picarro cavity ring-down spectrophotometer according to Subhas et al. (2015).</p>
<p>For cell count samples (for normalizing cellular domoic acid), 1 mL of the final experimental culture was preserved with 40 ul glutaraldehyde and stored at 4°C in the dark. Cells were counted on a Olympus BX51 microscope using a Sedgewick Rafter Chamber.<br />
<br />
Organism:<br />
Pseudo-nitzschia australis, LSID (urn:lsid:marinespecies.org:taxname:246604)</p>
Specified by the Principal Investigator(s)
<p>Data were processed in using excel, which was used to calculate rates, averages, and standard deviations.&nbsp;</p>
Specified by the Principal Investigator(s)
* File Temperature_experiment.csv was loaded into the BCO-DMO data system.
* The "Treatment" column temperature was filled in for each row. It was only entered in the source csv file for the first row of each temperature/treatement and implied for blank rows below each entry.
* degree symbol and "C" was removed from values in the Treatment column and added to units description.
* 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
Costech 4010 Elemental Analyzer
Costech 4010 Elemental Analyzer
PI Supplied Instrument Name: Costech 4010 Elemental Analyzer Instrument Name: Elemental Analyzer Instrument Short Name: Instrument Description: Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB01/
Turner 10AU field fluorometer
Turner 10AU field fluorometer
PI Supplied Instrument Name: Turner 10AU field fluorometer Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
Prominence UFLC system (Shimadzu, Kyoto, Japan)
Prominence UFLC system (Shimadzu, Kyoto, Japan)
PI Supplied Instrument Name: Prominence UFLC system (Shimadzu, Kyoto, Japan) PI Supplied Instrument Description:Prominence UFLC system (Shimadzu, Kyoto, Japan) coupled to a SCIEX 4500 QTRAP mass spectrometer (AB Sciex, Framingham, MA, USA) Instrument Name: High-Performance Liquid Chromatograph Instrument Short Name:HPLC Instrument Description: A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/
SCIEX 4500 QTRAP mass spectrometer (AB Sciex, Framingham, MA, USA)
SCIEX 4500 QTRAP mass spectrometer (AB Sciex, Framingham, MA, USA)
PI Supplied Instrument Name: SCIEX 4500 QTRAP mass spectrometer (AB Sciex, Framingham, MA, USA) Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Olympus BX51 microscope
Olympus BX51 microscope
PI Supplied Instrument Name: Olympus BX51 microscope 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/