http://lod.bco-dmo.org/id/dataset/3789
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
2012-11-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
CTD data, bottle nutrients, and chlorophyll-a from phytoplankton taxa from R/V Pelican PE08-54, PE09-12, PE10-01 in the Northwest Florida shelf off Panama City FL. from 2008-2009 (BenDiM project)
2012-11-21
publication
2012-11-21
revision
BCO-DMO Linked Data URI
2012-11-21
creation
http://lod.bco-dmo.org/id/dataset/3789
Daniel Kamykowski
North Carolina State University - Marine, Earth and Atmospheric Sciences
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: Kamykowski, D. (2012) CTD data, bottle nutrients, and chlorophyll-a from phytoplankton taxa from R/V Pelican PE08-54, PE09-12, PE10-01 in the Northwest Florida shelf off Panama City FL. from 2008-2009 (BenDiM project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2012-11-21 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3789 [access date]
CTD data, bottle nutrients, and the contribution to total Chlorophyl-a by phytoplankton taxa Dataset Description: <p>CTD data, bottle nutrients, and the contribution to total Chlorophyl-a by phytoplankton taxa.</p> Methods and Sampling: <p>At each hydrographic station, The R/V Pelican&rsquo;s SeaBird CTD provided profiles for light attenuation, pressure, temperature, salinity, dissolved oxygen, chlorophyll fluorescence and turbidity during the first downcast. Beam-t measurements obtained from the CTD transmissometer were used to approximate potential PAR attenuation based on the sequential application of the percent transmission through successive 1 m layers of the water column. A Secchi disc was attached to the top of the CTD (2009).&nbsp;</p>
<p>A SeaBird Rosette on the CTD was configured with eleven 5 L Niskin bottles that were triggered during the first upcast near the sediment interface and then at 2 m intervals (~9 bottles) as well as mid-depth in the remaining water column to the surface (1 bottle) and at the surface (1 bottle).</p>
<p>The seawater collected by the Rosette was used for nitrate-nitrite (NO3- + NO2-) analyses and HPLC pigment determinations. In May 2008, phosphate (PO4) and silicate (SiO4) were also measured.&nbsp; For nutrient samples, 10 ml of the filtered seawater were frozen immediately after collection and returned to NCSU for laboratory analyses. In the laboratory, these samples were thawed and analyzed against a standard of natural seawater with low nitrate concentrations. NO3- + NO2-&nbsp; were determined colorimetrically at NCSU using an automated QuAAtro Continuous-Flow Analysis system. Precision of the NO3- + NO2- analysis was 0.1 &micro;M with a detection limit of 1.4 &micro;M.</p>
<p>For High-Performance Liquid Chromatography (HPLC) analysis, approximately 1000 ml of water from selected sample depths were filtered through a 2.5 cm diameter GF-F filters under a low pressure vacuum (&lt; 200 mmHg). The filters were frozen with liquid nitrogen and stored for 6-9 months. In the laboratory of Dr. J. L. Pinckney (USC), excess water was removed and the filters for HPLC analysis were analyzed in the dark on a Shimadzu dual LC10-AT vp and Controller SCL-10A vs binary gradient pump. Pigments on the filters were extracted after they were allowed to incubate for 18-24 hours in an acetone solution. The supernatant separated from the filter was extracted and inserted into smaller amber vials. The HPLC analysis was run with solvent A of 80% methanol and 20% ammonium acetate and a solvent B of 80% methanol and 20% acetone. Spectra measurements between 380-700 nm were taken every 2 seconds and peaks were identified based on retention time. CHEMTAX, a matrix factorization program, was used to optimize the contribution of the selected groups to total Chl a. The taxonomic groups, dinoflagellates (both gyroxanthin and peridinin types), and diatoms in May 2008, plus chlorophytes, cyanobacteria, cryptophytes, chrysophytes, and prymnesiophytes in Oct. 2008 and 2009, were selected according to the 'hierarchical guide to interpreting pigment data'.&nbsp; Initial pigment ratios were selected from the literature and regional studies. The initial pigment ratio was optimized using multiple randomly generated starting points as seed values.&nbsp; Output ratios from the previous runs were used as input values for successive runs. Values are reported here as absolute chlorophyll units.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0726271 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0726271
completed
Daniel Kamykowski
North Carolina State University - Marine, Earth and Atmospheric Sciences
919-515-7894
1125 Jordan Hall
Raleigh
NC
27695-8208
dkamyko@ncsu.edu
pointOfContact
asNeeded
Unknown
cruise_id
taxon
station
date
time
lat
lon
pres
depth
temp
sal
sigma_0
spar
dpar
O2_sat_pcent
O2
fluor
beamt
secchi
NO3_NO2
PO4
SiO4
chl_a
chla_taxon
cruise_name
CTD Sea-Bird
High Performance Liquid Chromatograph
Niskin bottle
Photosynthetically Available Radiation Sensor
Secchi Disc
theme
None, User defined
Cruise identfier
taxon
station
date
time of day
latitude
longitude
water pressure
depth
water temperature at measurement depth
salinity
sigma-theta
SPAR
PAR
Dissolved oxygen (percent)
dissolved Oxygen
fluorescence
beam attenuation
turbidity
nitrate plus nitrite
reactive phosphorus (PO4)
Silicate (reactive silica)
chlorophyll a
cruise name
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird
High-Performance Liquid Chromatograph
Niskin bottle
Photosynthetically Available Radiation Sensor
Secchi Disc
instrument
BCO-DMO Standard Instruments
PE08-54
PE09-12
PE10-01
service
Deployment Activity
Northwest Florida shelf off Panama City FL.
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.
Benthic Dinoflagellate Migration: Occurrence and Processes
https://osprey.bco-dmo.org/project/2243
Benthic Dinoflagellate Migration: Occurrence and Processes
<p>Most applications of the standardized dinoflagellate diel vertical migration (DVM) hypothesis consider a surface goal in daylight and a subsurface nutrient goal at night because of the visibility of surface blooms. The sub-surface nutrient source, however, can be so deep that dinoflagellates are unable to reach the surface during a 12 h ascent. At least three literature reports document a sediment-oriented expression of an alternative DVM pattern characteristic of continental boundaries with wider, more gently sloping shelves that can yield high biomass, near-bottom dinoflagellate accumulations. The targeted dinoflagellate niche, here termed 'Benthic Dinoflagellate Migration' or 'BenDiM', is influenced by light and nutrient gradients but is unique in that a DVM exists between a nutrient source near or at the sediment-sea interface and a light intensity in the lower euphotic zone that supports a net increase in population size. The project specifically deals with: 1) the different dinoflagellate species that occupy the BenDiM niche on the continental shelf off Panama City, FL between the 60 m and 20 m contours between May and Nov; 2) the light acclimation, the nutrient uptake capabilities, and the behavioral patterns required of different dinoflagellate species that occupy the BenDiM niche; and, 3) the effect of representative physical water motion on the formation, transport and fate of the different BenDiM dinoflagellate species populations. The study includes: 1) a pelagic/benthic field program with three 7-day cruises during different months between May and Oct in 2008 and Jul 2009; 2) laboratory studies on the light, nutrient, and behavioral characteristics of BenDiM dinoflagellates that allow successful competition with near-bottom pelagic diatoms and the microphytobenthos; and 3) a physical-biological modeling study to plan, integrate and extend the field and laboratory results. The cruise program applies standard UNOLS ship capabilities extended with instrumentation that includes: 1) an Acrobat undulating system instrumented with SeaBird CTD-O2 system, Biospherical PAR, SeaPoint Chlorophyll and CDOM Fluorometers, Seapoint Turbidity, Satlantic ISUS Nitrate Sensor, Brooke-Oceans Laser Optical Plankton Counter, and General Oceanics Flow Meter with integrated GPS and echo sounding location system and a real-time graphical display of the collected data, 2) the FlowCAM, and 3) the autonomous vertical profiler (AVP). The laboratory effort applies a proven motion analysis system for studying dinoflagellate behavior and a well-developed mesocosm capability for studying dinoflagellate physiology, biochemistry, and behavior. The modeling effort builds on an existing, biologically intense modeling approach that incorporates parameterization of dinoflagellate physiology, biochemistry and behavior in a representative physical field.</p>
BenDiM
largerWorkCitation
project
eng; USA
oceans
Northwest Florida shelf off Panama City FL.
2012-11-21
Northwest Florida shelf off Panama City, FL
0
BCO-DMO catalogue of parameters from CTD data, bottle nutrients, and chlorophyll-a from phytoplankton taxa from R/V Pelican PE08-54, PE09-12, PE10-01 in the Northwest Florida shelf off Panama City FL. from 2008-2009 (BenDiM 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
http://lod.bco-dmo.org/id/dataset-parameter/30901.rdf
Name: cruise_id
Units: text
Description: <p>cruise identification, official name in R2R catalog (<a href="http://www.rvdata.us/">http://www.rvdata.us/</a>)</p>
http://lod.bco-dmo.org/id/dataset-parameter/30902.rdf
Name: taxon
Units: text
Description: <p>plankton taxonomic name</p>
http://lod.bco-dmo.org/id/dataset-parameter/30903.rdf
Name: station
Units: integer
Description: <p>station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/30904.rdf
Name: date
Units: mm/dd/yyyy
Description: <p>date of transect, gmt</p>
http://lod.bco-dmo.org/id/dataset-parameter/30905.rdf
Name: time
Units: HHMM
Description: <p>time of transect, gmt</p>
http://lod.bco-dmo.org/id/dataset-parameter/30906.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; North is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/30907.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; East is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/30908.rdf
Name: pres
Units: decibars
Description: <p>pressure</p>
http://lod.bco-dmo.org/id/dataset-parameter/30909.rdf
Name: depth
Units: meters
Description: <p>depth </p>
http://lod.bco-dmo.org/id/dataset-parameter/30910.rdf
Name: temp
Units: degrees Celsius
Description: <p>seawater temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/30911.rdf
Name: sal
Units: dimensionless; salinity units
Description: <p>salinity on Practical Salinity Scale</p>
http://lod.bco-dmo.org/id/dataset-parameter/30912.rdf
Name: sigma_0
Units: kg/m^3
Description: <p>Potential density, Sigma-theta is denoted 'sigma_0', where the last digit, a zero, is used to represent the Greek letter theta. This altered density which takes into account adiabatic heating/cooling with changes in pressure is called the 'potential density'.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30913.rdf
Name: spar
Units: micro-Einsteins/m2.s
Description: <p>Surface Photosynthetically Available [Active] Radiation; surface irradiance</p>
http://lod.bco-dmo.org/id/dataset-parameter/30914.rdf
Name: dpar
Units: microEinsteins/m2.s
Description: <p>PAR at depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/30915.rdf
Name: O2_sat_pcent
Units: %
Description: <p>percent oxygen saturation</p>
http://lod.bco-dmo.org/id/dataset-parameter/30916.rdf
Name: O2
Units: milliliters/liter
Description: <p>dissolved oxygen</p>
http://lod.bco-dmo.org/id/dataset-parameter/30917.rdf
Name: fluor
Units: milligrams/meter^3
Description: <p>fluorescence</p>
http://lod.bco-dmo.org/id/dataset-parameter/30918.rdf
Name: beamt
Units: 1/m^2
Description: <p>attenuation (loss of light) of a narrow well collimated beam of light; beam attenuation due to particles</p>
http://lod.bco-dmo.org/id/dataset-parameter/30919.rdf
Name: secchi
Units: Formazin Turbidity Units (FTU)
Description: <p>Turbidity as measured by a Secchi disk</p>
http://lod.bco-dmo.org/id/dataset-parameter/30920.rdf
Name: NO3_NO2
Units: micromoles/liter
Description: <p>nitrates plus nitrites in phytoplankton sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/30921.rdf
Name: PO4
Units: micromoles/liter
Description: <p>phosphates</p>
http://lod.bco-dmo.org/id/dataset-parameter/30922.rdf
Name: SiO4
Units: micromoles/liter
Description: <p>silicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/30923.rdf
Name: chl_a
Units: micrograms chl a /liter
Description: <p>total chlorophyll-a of the bottle sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/30924.rdf
Name: chla_taxon
Units: micrograms chl a /liter
Description: <p>chlorophyll-a contribution by the specific taxon</p>
http://lod.bco-dmo.org/id/dataset-parameter/34062.rdf
Name: cruise_name
Units: text
Description: <p>Local name chosen by project investigators for the research expedition on a vessel, as opposed to the formal/official cruise ID asserted by the vessel operator.</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
4039764
https://datadocs.bco-dmo.org/file/yppz4YKTyY6wPD/phytoplankton_chl.csv
phytoplankton_chl.csv
Primary data file for dataset ID 3789
download
https://osprey.bco-dmo.org/dataset/3789/data/download
download
onLine
dataset
<p>At each hydrographic station, The R/V Pelican&rsquo;s SeaBird CTD provided profiles for light attenuation, pressure, temperature, salinity, dissolved oxygen, chlorophyll fluorescence and turbidity during the first downcast. Beam-t measurements obtained from the CTD transmissometer were used to approximate potential PAR attenuation based on the sequential application of the percent transmission through successive 1 m layers of the water column. A Secchi disc was attached to the top of the CTD (2009).&nbsp;</p>
<p>A SeaBird Rosette on the CTD was configured with eleven 5 L Niskin bottles that were triggered during the first upcast near the sediment interface and then at 2 m intervals (~9 bottles) as well as mid-depth in the remaining water column to the surface (1 bottle) and at the surface (1 bottle).</p>
<p>The seawater collected by the Rosette was used for nitrate-nitrite (NO3- + NO2-) analyses and HPLC pigment determinations. In May 2008, phosphate (PO4) and silicate (SiO4) were also measured.&nbsp; For nutrient samples, 10 ml of the filtered seawater were frozen immediately after collection and returned to NCSU for laboratory analyses. In the laboratory, these samples were thawed and analyzed against a standard of natural seawater with low nitrate concentrations. NO3- + NO2-&nbsp; were determined colorimetrically at NCSU using an automated QuAAtro Continuous-Flow Analysis system. Precision of the NO3- + NO2- analysis was 0.1 &micro;M with a detection limit of 1.4 &micro;M.</p>
<p>For High-Performance Liquid Chromatography (HPLC) analysis, approximately 1000 ml of water from selected sample depths were filtered through a 2.5 cm diameter GF-F filters under a low pressure vacuum (&lt; 200 mmHg). The filters were frozen with liquid nitrogen and stored for 6-9 months. In the laboratory of Dr. J. L. Pinckney (USC), excess water was removed and the filters for HPLC analysis were analyzed in the dark on a Shimadzu dual LC10-AT vp and Controller SCL-10A vs binary gradient pump. Pigments on the filters were extracted after they were allowed to incubate for 18-24 hours in an acetone solution. The supernatant separated from the filter was extracted and inserted into smaller amber vials. The HPLC analysis was run with solvent A of 80% methanol and 20% ammonium acetate and a solvent B of 80% methanol and 20% acetone. Spectra measurements between 380-700 nm were taken every 2 seconds and peaks were identified based on retention time. CHEMTAX, a matrix factorization program, was used to optimize the contribution of the selected groups to total Chl a. The taxonomic groups, dinoflagellates (both gyroxanthin and peridinin types), and diatoms in May 2008, plus chlorophytes, cyanobacteria, cryptophytes, chrysophytes, and prymnesiophytes in Oct. 2008 and 2009, were selected according to the 'hierarchical guide to interpreting pigment data'.&nbsp; Initial pigment ratios were selected from the literature and regional studies. The initial pigment ratio was optimized using multiple randomly generated starting points as seed values.&nbsp; Output ratios from the previous runs were used as input values for successive runs. Values are reported here as absolute chlorophyll units.</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
CTD Sea-Bird
CTD Sea-Bird
PI Supplied Instrument Name: CTD Sea-Bird Instrument Name: CTD Sea-Bird Instrument Short Name:CTD Sea-Bird Instrument Description: A Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics. This instrument designation is used when specific make and model are not known or when a more specific term is not available in the BCO-DMO vocabulary. Refer to the dataset-specific metadata for more information about the specific CTD used. More information from: http://www.seabird.com/ Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
High Performance Liquid Chromatograph
High Performance Liquid Chromatograph
PI Supplied Instrument Name: High Performance Liquid Chromatograph 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/
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle PI Supplied Instrument Description:The CTD was configured with eleven 5 L Niskin bottles that were triggered during the first upcast near the sediment interface and then at 2 m intervals (~9 bottles) as well as mid-depth in the remaining water column to the surface (1 bottle) and at the surface (1 bottle). The seawater collected by the Rosette was used for nitrate-nitrite (NO3- + NO2-) analyses and HPLC pigment determinations. Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Photosynthetically Available Radiation Sensor
Photosynthetically Available Radiation Sensor
PI Supplied Instrument Name: Photosynthetically Available Radiation Sensor Instrument Name: Photosynthetically Available Radiation Sensor Instrument Short Name:PAR sensor Instrument Description: A PAR sensor measures photosynthetically available (or active) radiation. The sensor measures photon flux density (photons per second per square meter) within the visible wavelength range (typically 400 to 700 nanometers). PAR gives an indication of the total energy available to plants for photosynthesis. This instrument name is used when specific type, make and model are not known. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/122/
Secchi Disc
Secchi Disc
PI Supplied Instrument Name: Secchi Disc Instrument Name: Secchi Disc Instrument Short Name:Secchi Disc Instrument Description: Typically, a 16 inch diameter white/black quadrant disc used to measure water optical clarity Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0430/
Cruise: PE08-54
PE08-54
R/V Pelican
Community Standard Description
International Council for the Exploration of the Sea
R/V Pelican
vessel
PE08-54
Daniel Kamykowski
North Carolina State University - Marine, Earth and Atmospheric Sciences
Cruise: PE09-12
PE09-12
R/V Pelican
Community Standard Description
International Council for the Exploration of the Sea
R/V Pelican
vessel
PE09-12
Daniel Kamykowski
North Carolina State University - Marine, Earth and Atmospheric Sciences
Cruise: PE10-01
PE10-01
R/V Pelican
Community Standard Description
International Council for the Exploration of the Sea
R/V Pelican
vessel
PE10-01
Daniel Kamykowski
North Carolina State University - Marine, Earth and Atmospheric Sciences
R/V Pelican
Community Standard Description
International Council for the Exploration of the Sea
R/V Pelican
vessel