http://lod.bco-dmo.org/id/dataset/940093
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
2024-10-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Dissolved Fe and Sc concentrations, chlorophyll, nutrients from a scandium incubation experiment during the PUPCYCLE I R/V Oceanus cruise 1905B in the California Current System in 2019
2024-10-10
publication
2024-10-10
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-10-24
publication
https://doi.org/10.26008/1912/bco-dmo.940093.1
Adrian Marchetti
University of North Carolina at Chapel Hill
principalInvestigator
Claire P. Till
Cal Poly Humboldt (formerly Humboldt State University)
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: Till, C. P., Freiberger, R. B., Pierce, E., Lin, Y., Marchetti, A. (2024) Dissolved Fe and Sc concentrations, chlorophyll, nutrients from a scandium incubation experiment during the PUPCYCLE I R/V Oceanus cruise 1905B in the California Current System in 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-10-10 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.940093.1 [access date]
Dataset Description: <p>See the "Related Datasets" section for other datasets from this experiment.</p> Methods and Sampling: <p>Sampling:&nbsp;</p>
<p>Seawater for the incubation was collected from ~15m at&nbsp;35°55.4’N, 121°32.4’W&nbsp;using acid-cleaned HDPE tubing taped directly to the amsteel blue line.&nbsp;&nbsp;A lead weight coated with&nbsp;fiberglass and epoxy paint was at the bottom of the line.&nbsp;&nbsp;The pump was a teflon Wilden air-operated double-diaphragm pump.&nbsp;The tubing was run into a trace metal clean positive pressure bubble, where it was homogenized in acid-cleaned 50 gallon plastic barrels. From there,&nbsp;4L cubitainers for the different treatments were rinsed and filled with the homogenized seawater, and then spiked appropriately based on treatment. These cubitainers had been pre-cleaned using the methods of&nbsp;Crawford et al. 2003.</p>
<p>The incubation setup:&nbsp;</p>
<p>We had five different treatments, with three replicates each:&nbsp;&nbsp;<br />
control: no addition<br />
+Fe: 5 nmol/kg added dissolved Fe<br />
+Sc: 5 nmol/kg added dissolved Sc<br />
+Fe and +Sc: 5 nmol/kg each of dissolved Sc and Fe added<br />
filtered +Fe and + Sc: the seawater was filtered with 0.2 micrometer pre-cleaned supor Acropak filter before rinsing and filling the cubitainer, and then spiking with 5 nmol/kg each of dissolved Sc and Fe.</p>
<p>The cubitainers were incubated in an on-deck&nbsp;plexiglass incubator that was surface-seawater chilled and covered with a screening to achieve 30% of the incident irradiance. After 24 hours, the incubation was ended and each treatment was&nbsp;harvested.</p>
<p>Sample analysis:&nbsp;</p>
<p>Dissolved metals:&nbsp;Samples were filtered in a trace metal clean bubble to 0.2 micrometers with a pre-cleaned supor Acropak filter, and acidified to pH 1.8 at sea with optima HCl.&nbsp;Samples were analyzed post-cruise using the methods of Biller and Bruland (2012) with modifications as described in Parker et al. (2016). Briefly this method involves preconcentrating the metals of interest on a PA1 chelating resin at pH 6.0 +/- 0.2 and analyzing the extracts on an Element 2 Extended Range ICP-MS. Standard addition curves are made in low-metal seawater for calibration, and blanks are quantified by loading less than 0.5 mL of low-metal seawater on the columns and extracting as usual. Rhodium is used as an internal standard. Samples were analyzed in the Till lab by PI Till and undergraduate Freiberger.&nbsp;</p>
<p>Nutrients samples were filtered to 0.2 micrometers using the same Acropak filters and frozen at sea. They were analyzed by the&nbsp;Wetland Biogeochemistry Analytical Services at&nbsp;Louisiana State University using&nbsp;OI Analytical Flow Solutions IV segmented flow auto analyzer methologies.</p>
<p>Chlorophyll concentrations were measured by Emily Pierce and&nbsp;YuanYu Lin in the Marchetti lab, with two different filter sizes: 0.7 and 5 micrometers.&nbsp;Chlorophyll a (Chl a) measurements were obtained by gravity filtering seawater through a 5 μm polycarbonate filter followed by vacuum filtration through a GF/F filter using a series filter cascade for size fractionation. Filters were frozen at −80degC until analysis. Extractions were performed ship-board using 90% acetone kept at −20decC for 24 h followed by fluorometric quantification with a Turner Designs 10-AU fluorometer using the acidification method (Parsons et al. 1984).&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1751805 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1751805
Funding provided by Research Corporation for Science Advancement (RCSA) Award Number: RCSA-26844 Award URL: https://rescorp.org/news/2020/02/rcsa-names-25-new-cottrell-scholars-for-2020
completed
Adrian Marchetti
University of North Carolina at Chapel Hill
919-843-3473
123 South Rd.
Chapel Hill
NC
27514
USA
amarchet@email.unc.edu
pointOfContact
Claire P. Till
Cal Poly Humboldt (formerly Humboldt State University)
707-826-3266
Chemistry Department 1 Harpst Street
Arcata
CA
95521
USA
claire.till@humboldt.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Label
Timepoint
Treatment
Replicate
Chl_gt_5um
Chl_gt_0pt7um
NO3
PO4
SiO2
dissolved_Fe
dissolved_Sc
dissolved_Sc_flag
Thermo Element XR
theme
None, User defined
sample identification
time_elapsed
treatment
replicate
chlorophyll a
Nitrate
reactive phosphorus (PO4)
silicate, silicon dioxide SiO2
Iron
Scandium
flag
featureType
BCO-DMO Standard Parameters
Inductively Coupled Plasma Mass Spectrometer
Turner Designs Fluorometer 10-AU
instrument
BCO-DMO Standard Instruments
OC1905B
service
Deployment Activity
California Current System
place
Locations
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.
CAREER: An integrated molecular and physiological approach to examining the dynamics of upwelled phytoplankton in current and changing oceans
https://osprey.bco-dmo.org/project/768006
CAREER: An integrated molecular and physiological approach to examining the dynamics of upwelled phytoplankton in current and changing oceans
<p><em>NSF Award Abstract:</em><br />
Upwelling zones are hotspots of photosynthesis that are very dynamic in space and time. Microsocopic algae, known as phytoplankton, bloom when deep, nutrient-rich waters are upwelled into sunlit surface layers of the ocean, providing nourishment that supports productive food webs and draws down carbon dioxide (CO2) from the atmosphere to the deep ocean. Photosynthetic microbes in these regions must constantly adapt to changes in their chemical and physical environments. For example, subsurface populations respond to changes in light as they approach the surface. When upwelled waters move offshore, cells sink out of the illuminated zone, establishing seed populations that remain inactive until the next upwelling event. This process is called the upwelling conveyor belt cycle (UCBC). How phytoplankton respond to these changes in environmental conditions and how they may influence their nutrient requirements remains unknown. With future ocean changes predicted to alter seawater chemistry, including ocean acidification and decreased iron availability, some phytoplankton groups may be more vulnerable than others. Accompanying educational activities provide learning experiences to enhance understanding and awareness of marine microbes. The development of a research hub at UNC aims to provide infrastructure and support for scientists and students conducting research on environmental genomics. A laboratory component for an upper-level undergraduate course focused on marine phytoplankton is being developed. Educational outreach activities to broader communities include creation of a lesson plan on phytoplankton in upwelling zones and a virtual research cruise experience for middle-school students, as well as a hands-on lab activity for a local museum focused on marine phytoplankton and the important roles they play in shaping our planet.</p>
<p>The project examines how phytoplankton respond at the molecular and physiological level to the different UCBC stages, which seed populations (i.e., surface versus subsurface) contribute most to phytoplankton blooms during upwelling events of varying intensity, how phytoplankton elemental compositions are altered throughout UCBC stages, and how future predicted ocean conditions will affect the phytoplankton responses to UCBC conditions. This project contains both laboratory and fieldwork. In the laboratory, phytoplankton isolates recently obtained from upwelling regions are exposed to simulated UCBC conditions to examine changes in gene expression, growth and photosynthetic characteristics and elemental composition. Cultures are subjected to both current and future ocean conditions, including reduced iron availability and higher CO2. In the field, research cruises within upwelling regions study the dynamics of natural phytoplankton communities (both surface and subsurface) experiencing upwelling and relaxation and within simulated upwelling incubation experiments. Knowledge of how phytoplankton are affected by UCBC conditions at an integrated molecular, physiological and elemental level under both current and future scenarios is imperative for the proper conservation and management of these critically important ecosystems.</p>
Upwelled Phytoplankton Dynamics
largerWorkCitation
project
eng; USA
oceans
California Current System
-121.54
-121.54
35.92333
35.92333
2019-06-02
2019-06-02
California Upwelling Zone
0
BCO-DMO catalogue of parameters from Dissolved Fe and Sc concentrations, chlorophyll, nutrients from a scandium incubation experiment during the PUPCYCLE I R/V Oceanus cruise 1905B in the California Current System in 2019
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/940138.rdf
Name: Label
Units: unitless
Description: <p>The name of each sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940139.rdf
Name: Timepoint
Units: hours
Description: <p>Timepoint (hours). how long the particular sample incubated for (24 hours in most cases; 0 hours for measurements of the initial conditions before the incubation)</p>
http://lod.bco-dmo.org/id/dataset-parameter/940140.rdf
Name: Treatment
Units: unitless
Description: <p>Description of the treatment for the particular sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940141.rdf
Name: Replicate
Units: unitless
Description: <p>There were three replicates for each treatment. This parameter serves to disambiguate them. </p>
http://lod.bco-dmo.org/id/dataset-parameter/940142.rdf
Name: Chl_gt_5um
Units: micrograms per liter (ug/L)
Description: <p>Chlorophyll concentration for the greater than 5 micrometers size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/940143.rdf
Name: Chl_gt_0pt7um
Units: micrograms per liter (ug/L)
Description: <p>Chlorophyll concentration for the greater than 0.7 micrometers size fraction </p>
http://lod.bco-dmo.org/id/dataset-parameter/940144.rdf
Name: NO3
Units: micromolar (uM)
Description: <p>Nitrate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/940145.rdf
Name: PO4
Units: micromolar (uM)
Description: <p>Phosphate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/940146.rdf
Name: SiO2
Units: micromolar (uM)
Description: <p>Silicate concentration (silicon dioxide)</p>
http://lod.bco-dmo.org/id/dataset-parameter/940147.rdf
Name: dissolved_Fe
Units: nanomoles per kilogram (nmol/kg)
Description: <p>Dissolved (less than 0.2 micrometers) iron concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/940148.rdf
Name: dissolved_Sc
Units: picomoles per kilogram (pmol/kg)
Description: <p>dissolved (less than 0.2 micrometers) scandium concentration. Detection limits, defined as 3x the standard deviation of the blank, were 0.1 nmol/kg for Fe and 1.4 pmol/kg for Sc. See column "dissolved_Sc_flag" for information about where measurements were below detection limit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/940149.rdf
Name: dissolved_Sc_flag
Units: unitless
Description: <p>Flag for the dissolved_Sc column. The value "<LOD" is indicated where dissolved_Sc was below detection limit and came out negative. The one datapoint that was below detection limit but came out positive is left in the dataset as an indication of magnitude. Detection limits, defined as 3x the standard deviation of the blank, were 0.1 nmol/kg for Fe and 1.4 pmol/kg for Sc.</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
1677
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/150b8281-6df5-4757-b9cd-d4a24ec30c0e/content
download
https://doi.org/10.26008/1912/bco-dmo.940093.1
download
onLine
dataset
<p>Sampling:&nbsp;</p>
<p>Seawater for the incubation was collected from ~15m at&nbsp;35°55.4’N, 121°32.4’W&nbsp;using acid-cleaned HDPE tubing taped directly to the amsteel blue line.&nbsp;&nbsp;A lead weight coated with&nbsp;fiberglass and epoxy paint was at the bottom of the line.&nbsp;&nbsp;The pump was a teflon Wilden air-operated double-diaphragm pump.&nbsp;The tubing was run into a trace metal clean positive pressure bubble, where it was homogenized in acid-cleaned 50 gallon plastic barrels. From there,&nbsp;4L cubitainers for the different treatments were rinsed and filled with the homogenized seawater, and then spiked appropriately based on treatment. These cubitainers had been pre-cleaned using the methods of&nbsp;Crawford et al. 2003.</p>
<p>The incubation setup:&nbsp;</p>
<p>We had five different treatments, with three replicates each:&nbsp;&nbsp;<br />
control: no addition<br />
+Fe: 5 nmol/kg added dissolved Fe<br />
+Sc: 5 nmol/kg added dissolved Sc<br />
+Fe and +Sc: 5 nmol/kg each of dissolved Sc and Fe added<br />
filtered +Fe and + Sc: the seawater was filtered with 0.2 micrometer pre-cleaned supor Acropak filter before rinsing and filling the cubitainer, and then spiking with 5 nmol/kg each of dissolved Sc and Fe.</p>
<p>The cubitainers were incubated in an on-deck&nbsp;plexiglass incubator that was surface-seawater chilled and covered with a screening to achieve 30% of the incident irradiance. After 24 hours, the incubation was ended and each treatment was&nbsp;harvested.</p>
<p>Sample analysis:&nbsp;</p>
<p>Dissolved metals:&nbsp;Samples were filtered in a trace metal clean bubble to 0.2 micrometers with a pre-cleaned supor Acropak filter, and acidified to pH 1.8 at sea with optima HCl.&nbsp;Samples were analyzed post-cruise using the methods of Biller and Bruland (2012) with modifications as described in Parker et al. (2016). Briefly this method involves preconcentrating the metals of interest on a PA1 chelating resin at pH 6.0 +/- 0.2 and analyzing the extracts on an Element 2 Extended Range ICP-MS. Standard addition curves are made in low-metal seawater for calibration, and blanks are quantified by loading less than 0.5 mL of low-metal seawater on the columns and extracting as usual. Rhodium is used as an internal standard. Samples were analyzed in the Till lab by PI Till and undergraduate Freiberger.&nbsp;</p>
<p>Nutrients samples were filtered to 0.2 micrometers using the same Acropak filters and frozen at sea. They were analyzed by the&nbsp;Wetland Biogeochemistry Analytical Services at&nbsp;Louisiana State University using&nbsp;OI Analytical Flow Solutions IV segmented flow auto analyzer methologies.</p>
<p>Chlorophyll concentrations were measured by Emily Pierce and&nbsp;YuanYu Lin in the Marchetti lab, with two different filter sizes: 0.7 and 5 micrometers.&nbsp;Chlorophyll a (Chl a) measurements were obtained by gravity filtering seawater through a 5 μm polycarbonate filter followed by vacuum filtration through a GF/F filter using a series filter cascade for size fractionation. Filters were frozen at −80degC until analysis. Extractions were performed ship-board using 90% acetone kept at −20decC for 24 h followed by fluorometric quantification with a Turner Designs 10-AU fluorometer using the acidification method (Parsons et al. 1984).&nbsp;</p>
Specified by the Principal Investigator(s)
<p>Negative dissolved_Sc values below the detection limit were omitted from this data table. The one datapoint that was below detection limit but came out positive was left in the dataset as an indication of magnitude (labeled as "&lt;LOD" in&nbsp;dissolved_Sc_flag column).&nbsp; Detection limits, defined as 3x the standard deviation of the blank, were 0.1 nmol/kg for Fe and 1.4 pmol/kg for Sc.</p>
Specified by the Principal Investigator(s)
* Sheet 1 of submitted file "May 2019 Sc incubation for BCO-DMO.xlsx" was imported into the BCO-DMO data system for this dataset.
** In the BCO-DMO data system missing data identifiers are displayed according to the format of data you access. For example, in csv files it will be blank (null) values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as blank (null) values.
* 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]
* an additional column was added "dissolved_Sc_flag" to contain the "<LOD" values indicating below detection limit for the dissolved_Sc column.
* Additional "<LOD" added to "dissolved_Sc_flag" where dissovled_Sc = 0.15 as data submitter chose to include since small but positive dissovled_Sc value "0.15" and advised the labeling as <LOD over omitting.
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
Thermo Element XR
Thermo Element XR
PI Supplied Instrument Name: Thermo Element XR PI Supplied Instrument Description:Trace metal extracts were analyzed with a Thermo Element XR magnetic sector inductively coupled plasma mass spectrometer (ICP-MS) Instrument Name: Inductively Coupled Plasma Mass Spectrometer Instrument Short Name:ICP Mass Spec Instrument Description: An ICP Mass Spec is an instrument that passes nebulized samples into an inductively-coupled gas plasma (8-10000 K) where they are atomized and ionized. Ions of specific mass-to-charge ratios are quantified in a quadrupole mass spectrometer. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB15/
PI Supplied Instrument Name: PI Supplied Instrument Description:Chlorophyll measurements were made with 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/
Cruise: OC1905B
OC1905B
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
OC1905B
Adrian Marchetti
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel