http://lod.bco-dmo.org/id/dataset/808280
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
2020-04-06
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Organic polymer formation and domoic acid adsorption from experiments conducted using water samples collected in northern Gulf of Mexico in 2018 and 2019
2020-06-24
publication
2020-06-24
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-07-14
publication
https://doi.org/10.26008/1912/bco-dmo.808280.1
Jeffrey W. Krause
Dauphin Island Sea Lab
principalInvestigator
Kanchan Maiti
Louisiana 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: Marquez Jr., I., Maiti, K., Krause, J. (2020) Organic polymer formation and domoic acid adsorption from experiments conducted using water samples collected in northern Gulf of Mexico in 2018 and 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-06-24 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.808280.1 [access date]
Dataset Description: Organic polymer formation and domoic acid adsorption. Results from lab experiments designed to investigate organic polymer formation and domoic acid adsorption. Water samples were collected in the northern Gulf of Mexico in 2018 and 2019.
Related datasets:
Domoic acid assimilation in copepods https://www.bco-dmo.org/dataset/808402
Field domoic acid and copepods https://www.bco-dmo.org/dataset/808413 Methods and Sampling: Location
Water collection sites in the northern Gulf of Mexico, particularly at the mouth of Mobile Bay and Little Lagoon, AL.
Water Collection
Briefly, water was collected from the field using a 5-gallon bucket, pre-screened with a 200 µm nitex mesh, and gently poured into 10-20 L carboys and kept in the dark until returning to the laboratory for same-day processing.
Terminology
dDA – dissolved Domoic Acid
pDAa – particulate Domoic Acid (algal fraction)
pDAOP – particulate Domoic Acid (bound to organic polymers)
cDA – Domoic Acid in copepods
POC – Particulate Organic Carbon
Organic polymer formation and sorption of DA
Seawater organic polymers were formed in controlled laboratory conditions to verify whether they could scavenge dDA. Surface seawater was collected from Dauphin Island (AL, USA) and filtered through a new 0.2 µm polycap filter (Pall Brand, USA). The freshly filtered seawater was partitioned into 1-L polycarbonate bottles and the initial measurements of dDA, pDA, cDA, pDAOP, and POC were made. POC was used as a proxy for organic polymer formation. The same filtration techniques were used for dDA and pDA as described above. Laboratory-reared adult Acartia tonsa were collected on a 200 µm screen and gently rinsed with freshly filtered artificial seawater, then transferred into 2 mL cryovials and stored in -20°C until analyzed for cDA. Twenty-five mm glass fiber filters were pre-combusted at 500°C for four hours and used to collect organic polymers. The organic polymer collection method was modified from Passow et al. (1995); loss of organic polymers via filtration was minimized by maintaining low-vacuum (<200 mbar) and filtering samples for a maximum of 15 minutes. Lastly, the treatment bottles were spiked with a DA standard to bring the final concentration to 10 µg DA L-1 and, for specific treatment bottles, 30 copepods were added to each bottle (for copepod data see dataset https://www.bco-dmo.org/dataset/808402). Bottles were then placed on orbital shaker tables and gently shaken for 24 hours. Controls were not shaken. Samples for dDA, pDA, cDA, pDAOP, and POC were collected after the 24-hour time period.
Liquid chromatography-mass spectrometry method for domoic acid quantification
LC-MS sample preparation followed was modified from Wang et al. (2012) for the determination of dDA, pDA, pDAOP and cDA. The samples for DA determination were cleaned and concentrated using Bond Elut LRC - C18, 200 mg, solid-phase extraction (SPE) columns from Agilent Technologies. For dDA, 30 mL seawater samples were filtered using a 47 mm glass fiber filter; the filtrate was collected and acidified with formic acid to yield a 0.2% final solution. SPE columns were conditioned with one column volume of HPLC-grade methanol followed by one column volume of HPLC-grade water. Samples were then loaded on the SPE column and filtered at ~1 mL min-1 using a vacuum manifold, followed by 10 mL of 0.2% formic acid as a rinse for the sample tube and SPE column. The SPE column was then allowed to go dry and was eluted with 1.5 mL of 20 mM ammonium acetate in 50% methanol (pH 8) and collected in a glass tube. The tubes were centrifuged for 5 minutes at ~1300 x g, supernatant was transferred into an LC vial with a Pasteur pipette, and stored at 4°C until further analysis. For pDAa 100 mL of seawater were filtered through a 5 µm polycarbonate filter and stored in a 50 mL polypropylene tube at -20°C. Similarly, for pDAOP 150 mL of seawater was filtered through a pre-combusted 25 mm glass-fiber filter and stored at -20°C. Prior to concentration and clean-up for pDA, pDAOP, and cDA, the filters were submerged in 2 mL of 80% methanol and sonicated to ensure cells and copepods were lysed. Sonication pulses were done for a total of 45 seconds (5 seconds on/off) on a Sonics Materials Ultrasonic Processor (model - VCX 130) at 75% power. Subsequent clean-up using the SPE column is the same as for the dDA samples.
An ultra-performance liquid chromatography (UPLC) – tandem mass spectrometry (MS) system was used for the quantification of DA.The LC-MS system consisted of Acquity UPLC system (Waters, Milford, MA) coupled to a 5500 QTRAP triple quadrupole / linear ion trap mass spectrometer equipped with a TurboIonSpray interface (Sciex, Foster City, CA, USA). The analytes were separated on a Luna C18 (2), 2.0 x 100 mm column (Phenomenex, Torrance, CA, USA) with column temperature held at 40ºC. The mobile phase was water (A) and 95% aqueous acetonitrile (B) with 0.1% formic acid additive and the flow rate was 0.4 ml/min. Gradient program was: 5% B for 3 min, linear gradient to 60% B at 10 min, 95% B at 10.1 min, hold at 95% B for 2 min. MS was operated in positive ion mode. Ion spray voltage was 5 kV and declustering potential was 80 V. Gas parameter settings were: nebulizer gas, 50 psi; turbo gas, 50 psi at 500ºC; curtain gas, 20 psi; and collision gas, medium setting. The collision energy applied was 25eV. The transitions used for selected reaction monitoring were m/z 312→266, 193, 220. The transition m/z 312→266 was used for quantitation.
For field-simulation experiment results and methodology see dataset https://www.bco-dmo.org/dataset/808413
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1558957 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1558957
Funding provided by U.S. Food and Drug Administration (FDA) Award Number: 5U19FD005923-04 Award URL: https://federalreporter.nih.gov/Projects/Details/?projectId=1156385
completed
Jeffrey W. Krause
Dauphin Island Sea Lab
251-861-2141 x2289
101 Bienville Blvd
Dauphin Island
AL
36528
USA
jkrause@disl.org
pointOfContact
Kanchan Maiti
Louisiana State University
225-578-4531
1143 Energy Coast Env Bldg
Baton Rouge
LA
70803
USA
kmaiti@lsu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
ISO_DateTime_UTC
Latitude_N
Longitude_W
Date
Time
Experiment
Treatment
Replicate_bottle
Replicate_subsample
POC_mass
pDA_OP_mass
POC_tox
DA_to_C
POC_conc
pDA_conc
Acquity UPLC system coupled to a 5500 QTRAP
Sonics Materials Ultrasonic Processor (model - VCX 130)
theme
None, User defined
ISO_DateTime_UTC
latitude
longitude
date_local
time_local
experiment id
treatment
replicate
particulate organic Carbon (POC)
domoic acid
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Mass Spectrometer
Homogenizer
Costech International Elemental Combustion System (ECS) 4010
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.
The biotic and abiotic controls on the Silicon cycle in the northern Gulf of Mexico
https://www.bco-dmo.org/project/712667
The biotic and abiotic controls on the Silicon cycle in the northern Gulf of Mexico
<p><em>NSF Award Abstract:</em><br />
The Louisiana Shelf system in the northern Gulf of Mexico is fed by the Mississippi River and its many tributaries which contribute large quantities of nutrients from agricultural fertilizer to the region. Input of these nutrients, especially nitrogen, has led to eutrophication. Eutrophication is the process wherein a body of water such as the Louisiana Shelf becomes enriched in dissolved nutrients that increase phytoplankton growth which eventually leads to decreased oxygen levels in bottom waters. This has certainly been observed in this area, and diatoms, a phytoplankton which represents the base of the food chain, have shown variable silicon/nitrogen (Si/N) ratios. Because diatoms create their shells from silicon, their growth is controlled not only by nitrogen inputs but the availability of silicon. Lower Si/N ratios are showing that silicon may be playing an increasingly important role in regulating diatom production in the system. For this reason, a scientist from the University of South Alabama will determine the biogeochemical processes controlling changes in Si/N ratios in the Louisiana Shelf system. One graduate student on their way to a doctorate degree and three undergraduate students will be supported and trained as part of this project. Also, four scholarships for low-income, high school students from Title 1 schools will get to participate in a month-long summer Marine Science course at the Dauphin Island Sea Laboratory and be included in the research project. The study has significant societal benefits given this is an area where $2.4 trillion gross domestic product revenue is tied up in coastal resources. Since diatoms are at the base of the food chain that is the biotic control on said coastal resources, the growth of diatoms in response to eutrophication is important to study.</p>
<p>Eutrophication of the Mississippi River and its tributaries has the potential to alter the biological landscape of the Louisiana Shelf system in the northern Gulf of Mexico by influencing the Si/N ratios below those that are optimal for diatom growth. A scientist from the University of South Alabama believes the observed changes in the Si/N ratio may indicate silicon now plays an important role in regulating diatom production in the system. As such, understanding the biotic and abiotic processes controlling the silicon cycle is crucial because diatoms dominate at the base of the food chain in this highly productive region. The study will focus on following issues: (1) the importance of recycled silicon sources on diatom production; (2) can heavily-silicified diatoms adapt to changing Si/N ratios more effectively than lightly-silicified diatoms; and (3) the role of reverse weathering in sequestering silicon thereby reducing diffusive pore-water transport. To attain these goals, a new analytical approach, the PDMPO method (compound 2-(4-pyridyl)-5-((4-(2-dimethylaminoethylamino-carbamoyl)methoxy)phenyl)oxazole) that quantitatively measures taxa-specific silica production would be used.</p>
CLASiC
largerWorkCitation
project
eng; USA
oceans
-88.075097
-87.554261
30.250473
30.278166
2018-11-13
2019-02-07
Northern Gulf of Mexico, specifically the Louisiana Shelf region dominated by the discharge of the Mississippi River on the western side of the delta
0
BCO-DMO catalogue of parameters from Organic polymer formation and domoic acid adsorption from experiments conducted using water samples collected in northern Gulf of Mexico in 2018 and 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/816726.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: Date/Time (UTC) in ISO 8601 format yyyy-mm-ddTHH:MMZ
http://lod.bco-dmo.org/id/dataset-parameter/816727.rdf
Name: Latitude_N
Units: decimal degrees
Description: Latitude in decimal degrees
http://lod.bco-dmo.org/id/dataset-parameter/816728.rdf
Name: Longitude_W
Units: decimal degrees
Description: Longitude in decimal degrees
http://lod.bco-dmo.org/id/dataset-parameter/816729.rdf
Name: Date
Units: unitless
Description: Local date water was collected in format yyyymmdd
http://lod.bco-dmo.org/id/dataset-parameter/816730.rdf
Name: Time
Units: unitless
Description: Local time water was collected in format hhmm (24 hr)
http://lod.bco-dmo.org/id/dataset-parameter/816731.rdf
Name: Experiment
Units: unitless
Description: Experiment name
http://lod.bco-dmo.org/id/dataset-parameter/816732.rdf
Name: Treatment
Units: unitless
Description: Treatment name
http://lod.bco-dmo.org/id/dataset-parameter/816733.rdf
Name: Replicate_bottle
Units: unitless
Description: Letters denote a unique bottle that was sampled for each measurement
http://lod.bco-dmo.org/id/dataset-parameter/816734.rdf
Name: Replicate_subsample
Units: unitless
Description: Numbers denote a subsample from a unique bottle
http://lod.bco-dmo.org/id/dataset-parameter/816735.rdf
Name: POC_mass
Units: micrograms (µg)
Description: Particulate Organic Carbon captured on a 25 mm glass-fiber filter
http://lod.bco-dmo.org/id/dataset-parameter/816736.rdf
Name: pDA_OP_mass
Units: nanograms (ng)
Description: Domoic Acid associated with organic polymers and captured on a 25 mm glass-fiber filter
http://lod.bco-dmo.org/id/dataset-parameter/816737.rdf
Name: POC_tox
Units: parts per million (ppm)
Description: Toxicity of Particulate Organic Carbon containing Domoic Acid
http://lod.bco-dmo.org/id/dataset-parameter/816738.rdf
Name: DA_to_C
Units: dimensionless
Description: Ratio of Domoic Acid to Carbon in the organic polymers (nanomoles Domoic Acid : micromoles of Carbon)
http://lod.bco-dmo.org/id/dataset-parameter/816739.rdf
Name: POC_conc
Units: micrograms (µg) per liter (L)
Description: Particulate Organic Carbon concentration in one liter of seawater
http://lod.bco-dmo.org/id/dataset-parameter/816740.rdf
Name: pDA_conc
Units: nanograms (ng) per liter (L)
Description: particulate Domoic Acid concentrations in one liter of seawater
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
3064
https://darchive.mblwhoilibrary.org/bitstream/1912/25967/1/dataset-808280_organic-polymers-and-domoic-acid__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.808280.1
download
onLine
dataset
Location
Water collection sites in the northern Gulf of Mexico, particularly at the mouth of Mobile Bay and Little Lagoon, AL.
Water Collection
Briefly, water was collected from the field using a 5-gallon bucket, pre-screened with a 200 µm nitex mesh, and gently poured into 10-20 L carboys and kept in the dark until returning to the laboratory for same-day processing.
Terminology
dDA – dissolved Domoic Acid
pDAa – particulate Domoic Acid (algal fraction)
pDAOP – particulate Domoic Acid (bound to organic polymers)
cDA – Domoic Acid in copepods
POC – Particulate Organic Carbon
Organic polymer formation and sorption of DA
Seawater organic polymers were formed in controlled laboratory conditions to verify whether they could scavenge dDA. Surface seawater was collected from Dauphin Island (AL, USA) and filtered through a new 0.2 µm polycap filter (Pall Brand, USA). The freshly filtered seawater was partitioned into 1-L polycarbonate bottles and the initial measurements of dDA, pDA, cDA, pDAOP, and POC were made. POC was used as a proxy for organic polymer formation. The same filtration techniques were used for dDA and pDA as described above. Laboratory-reared adult Acartia tonsa were collected on a 200 µm screen and gently rinsed with freshly filtered artificial seawater, then transferred into 2 mL cryovials and stored in -20°C until analyzed for cDA. Twenty-five mm glass fiber filters were pre-combusted at 500°C for four hours and used to collect organic polymers. The organic polymer collection method was modified from Passow et al. (1995); loss of organic polymers via filtration was minimized by maintaining low-vacuum (<200 mbar) and filtering samples for a maximum of 15 minutes. Lastly, the treatment bottles were spiked with a DA standard to bring the final concentration to 10 µg DA L-1 and, for specific treatment bottles, 30 copepods were added to each bottle (for copepod data see dataset https://www.bco-dmo.org/dataset/808402). Bottles were then placed on orbital shaker tables and gently shaken for 24 hours. Controls were not shaken. Samples for dDA, pDA, cDA, pDAOP, and POC were collected after the 24-hour time period.
Liquid chromatography-mass spectrometry method for domoic acid quantification
LC-MS sample preparation followed was modified from Wang et al. (2012) for the determination of dDA, pDA, pDAOP and cDA. The samples for DA determination were cleaned and concentrated using Bond Elut LRC - C18, 200 mg, solid-phase extraction (SPE) columns from Agilent Technologies. For dDA, 30 mL seawater samples were filtered using a 47 mm glass fiber filter; the filtrate was collected and acidified with formic acid to yield a 0.2% final solution. SPE columns were conditioned with one column volume of HPLC-grade methanol followed by one column volume of HPLC-grade water. Samples were then loaded on the SPE column and filtered at ~1 mL min-1 using a vacuum manifold, followed by 10 mL of 0.2% formic acid as a rinse for the sample tube and SPE column. The SPE column was then allowed to go dry and was eluted with 1.5 mL of 20 mM ammonium acetate in 50% methanol (pH 8) and collected in a glass tube. The tubes were centrifuged for 5 minutes at ~1300 x g, supernatant was transferred into an LC vial with a Pasteur pipette, and stored at 4°C until further analysis. For pDAa 100 mL of seawater were filtered through a 5 µm polycarbonate filter and stored in a 50 mL polypropylene tube at -20°C. Similarly, for pDAOP 150 mL of seawater was filtered through a pre-combusted 25 mm glass-fiber filter and stored at -20°C. Prior to concentration and clean-up for pDA, pDAOP, and cDA, the filters were submerged in 2 mL of 80% methanol and sonicated to ensure cells and copepods were lysed. Sonication pulses were done for a total of 45 seconds (5 seconds on/off) on a Sonics Materials Ultrasonic Processor (model - VCX 130) at 75% power. Subsequent clean-up using the SPE column is the same as for the dDA samples.
An ultra-performance liquid chromatography (UPLC) – tandem mass spectrometry (MS) system was used for the quantification of DA.The LC-MS system consisted of Acquity UPLC system (Waters, Milford, MA) coupled to a 5500 QTRAP triple quadrupole / linear ion trap mass spectrometer equipped with a TurboIonSpray interface (Sciex, Foster City, CA, USA). The analytes were separated on a Luna C18 (2), 2.0 x 100 mm column (Phenomenex, Torrance, CA, USA) with column temperature held at 40ºC. The mobile phase was water (A) and 95% aqueous acetonitrile (B) with 0.1% formic acid additive and the flow rate was 0.4 ml/min. Gradient program was: 5% B for 3 min, linear gradient to 60% B at 10 min, 95% B at 10.1 min, hold at 95% B for 2 min. MS was operated in positive ion mode. Ion spray voltage was 5 kV and declustering potential was 80 V. Gas parameter settings were: nebulizer gas, 50 psi; turbo gas, 50 psi at 500ºC; curtain gas, 20 psi; and collision gas, medium setting. The collision energy applied was 25eV. The transitions used for selected reaction monitoring were m/z 312→266, 193, 220. The transition m/z 312→266 was used for quantitation.
For field-simulation experiment results and methodology see dataset https://www.bco-dmo.org/dataset/808413
Specified by the Principal Investigator(s)
<p>BCO-DMO Data Manager Processing Notes:<br />
* Data from sheet "Lab_DA-org. polymers"&nbsp;from originally submitted Excel file "DATASET_DA-org polymers-cop grazing_BCO-DMO_params_IAM.xlsx" extracted to csv.<br />
* Column names modified to meet BCO-DMO naming conventions designed for interoperability (only letter, numbers, and underscores, no spaces).<br />
* Data loaded into the bco-dmo data system with -999 as a missing data identifier.</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
Acquity UPLC system coupled to a 5500 QTRAP
Acquity UPLC system coupled to a 5500 QTRAP
PI Supplied Instrument Name: Acquity UPLC system coupled to a 5500 QTRAP PI Supplied Instrument Description:Acquity UPLC system (Waters, Milford, MA) coupled to a 5500 QTRAP triple quadrupole / linear ion trap mass spectrometer equipped with a TurboIonSpray interface (Sciex, Foster City, CA, 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/
Sonics Materials Ultrasonic Processor (model - VCX 130)
Sonics Materials Ultrasonic Processor (model - VCX 130)
PI Supplied Instrument Name: Sonics Materials Ultrasonic Processor (model - VCX 130) Instrument Name: Homogenizer Instrument Short Name:Homogenizer Instrument Description: A homogenizer is a piece of laboratory equipment used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
PI Supplied Instrument Name: Instrument Name: Costech International Elemental Combustion System (ECS) 4010 Instrument Short Name:Costech ECS 4010 Instrument Description: The ECS 4010 Nitrogen / Protein Analyzer is an elemental combustion analyser for CHNSO elemental analysis and Nitrogen / Protein determination. The GC oven and separation column have a temperature range of 30-110 degC, with control of +/- 0.1 degC.