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)

Website: https://www.bco-dmo.org/dataset/3789
Version:
Version Date: 2012-11-21

Project
» Benthic Dinoflagellate Migration: Occurrence and Processes (BenDiM)
ContributorsAffiliationRole
Kamykowski, DanielNorth Carolina State University (NCSU MEAS)Principal Investigator
Copley, NancyWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager


Dataset Description

CTD data, bottle nutrients, and the contribution to total Chlorophyl-a by phytoplankton taxa.


Acquisition Description

At each hydrographic station, The R/V Pelican’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). 

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).

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.  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-  were determined colorimetrically at NCSU using an automated QuAAtro Continuous-Flow Analysis system. Precision of the NO3- + NO2- analysis was 0.1 µM with a detection limit of 1.4 µM.

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 (< 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'.  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.  Output ratios from the previous runs were used as input values for successive runs. Values are reported here as absolute chlorophyll units.


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Parameters

ParameterDescriptionUnits
cruise_idcruise identification, official name in R2R catalog (http://www.rvdata.us/) text
taxonplankton taxonomic name text
stationstation number integer
datedate of transect, gmt mm/dd/yyyy
timetime of transect, gmt HHMM
latlatitude; North is positive decimal degrees
lonlongitude; East is positive decimal degrees
prespressure decibars
depthdepth meters
tempseawater temperature degrees Celsius
salsalinity on Practical Salinity Scale dimensionless; salinity units
sigma_0Potential 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'. kg/m^3
sparSurface Photosynthetically Available [Active] Radiation; surface irradiance micro-Einsteins/m2.s
dparPAR at depth microEinsteins/m2.s
O2_sat_pcentpercent oxygen saturation %
O2dissolved oxygen milliliters/liter
fluorfluorescence milligrams/meter^3
beamtattenuation (loss of light) of a narrow well collimated beam of light; beam attenuation due to particles 1/m^2
secchiTurbidity as measured by a Secchi disk Formazin Turbidity Units (FTU)
NO3_NO2nitrates plus nitrites in phytoplankton sample micromoles/liter
PO4phosphates micromoles/liter
SiO4silicate micromoles/liter
chl_atotal chlorophyll-a of the bottle sample micrograms chl a /liter
chla_taxonchlorophyll-a contribution by the specific taxon micrograms chl a /liter
cruise_nameLocal 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. text


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Instruments

Dataset-specific Instrument Name
Niskin bottle
Generic Instrument Name
Niskin bottle
Dataset-specific 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.
Generic 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.

Dataset-specific Instrument Name
Photosynthetically Available Radiation Sensor
Generic Instrument Name
Photosynthetically Available Radiation Sensor
Generic 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.

Dataset-specific Instrument Name
CTD Sea-Bird
Generic Instrument Name
CTD Sea-Bird
Generic Instrument Description
Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics, no specific unit identified. This instrument designation is used when specific make and model are not known. See also other SeaBird instruments listed under CTD. More information from Sea-Bird Electronics.

Dataset-specific Instrument Name
High Performance Liquid Chromatograph
Generic Instrument Name
High Performance Liquid Chromatograph
Generic 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.

Dataset-specific Instrument Name
Secchi Disc
Generic Instrument Name
Secchi Disc
Generic Instrument Description
Typically, a 16 inch diameter white/black quadrant disc used to measure water optical clarity


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Deployments

PE08-54

Website
Platform
R/V Pelican
Start Date
2008-05-15
End Date
2008-05-21
Description
Acrobat surveys and CTD/rosettes transects Cruise information and original data are available from the NSF R2R data catalog.

PE09-12

Website
Platform
R/V Pelican
Start Date
2008-10-15
End Date
2008-10-20
Description
Acrobat surveys and CTD/rosettes transects Cruise information and original data are available from the NSF R2R data catalog.

PE10-01

Website
Platform
R/V Pelican
Start Date
2009-07-08
End Date
2009-07-15
Description
Acrobat surveys and CTD/rosettes transects Cruise information and original data are available from the NSF R2R data catalog.


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Project Information

Benthic Dinoflagellate Migration: Occurrence and Processes (BenDiM)

Coverage: Northwest Florida shelf off Panama City, FL


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.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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