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| Dataset Title: | [HPLC Photopigment Data for Bioassays] - Results of HPLC derived photopigment concentrations for bioassays done in the North Inlet Estuary - Georgetown, South Carolina during 2014 (Photomixotrophy project) (Assimilation rates of dissolved organic carbon by photomixotrophic estuarine phytoplankton) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_710144) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
Year {
Int16 _FillValue 32767;
Int16 actual_range 2014, 2014;
String bcodmo_name "year";
String description "Year sample was taken; YYYY";
String long_name "Year";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
String units "unitless";
}
Month {
String bcodmo_name "month";
String description "Month sample was taken";
String long_name "Month";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/MNTHXXXX/";
String units "unitless";
}
Number {
String bcodmo_name "sample";
String description "Sample number";
String long_name "Number";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
Sample_Volume {
Float32 _FillValue NaN;
Float32 actual_range 0.1, 0.4;
String bcodmo_name "sample_volume";
String description "Volume of water filtered";
String long_name "Sample Volume";
String units "liters";
}
Chl {
Float32 _FillValue NaN;
Float32 actual_range 0.46, 40.58;
String bcodmo_name "chl_c1_c2";
String description "Chlorophyll c1+c2 concentration";
String long_name "CHL";
String units "micrograms per liter";
}
Perid {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.51;
String bcodmo_name "peridinin";
String description "Peridinin concentration";
String long_name "Perid";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PERIHPP1/";
String units "micrograms per liter";
}
ButFuc_19 {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.43;
String bcodmo_name "fucox_but";
String description "19' Butanoyloxyfucoxanthin concentration";
String long_name "But Fuc 19";
String units "micrograms per liter";
}
Fuco {
Float32 _FillValue NaN;
Float32 actual_range 0.19, 13.88;
String bcodmo_name "fucox";
String description "Fucoxanthin concentration";
String long_name "Fuco";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/FUCXHPP1/";
String units "micrograms per liter";
}
HexFuc_19 {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.6;
String bcodmo_name "fucox_hex";
String description "19' Hexanoyloxyfucoxathin concentration";
String long_name "Hex Fuc 19";
String units "micrograms per liter";
}
Neo {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.29;
String bcodmo_name "neox";
String description "Neoxanthin concentration";
String long_name "Neo";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/NEOXHPP1/";
String units "micrograms per liter";
}
Prasino {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.14;
String bcodmo_name "prasinox";
String description "Prasionxanthin concentration";
String long_name "Prasino";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PRSXHPP1/";
String units "micrograms per liter";
}
Viola {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.29;
String bcodmo_name "violax";
String description "Violaxanthin concentration";
String long_name "Viola";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/VILXHPP1/";
String units "micrograms per liter";
}
Diad {
Float32 _FillValue NaN;
Float32 actual_range 0.01, 1.8;
String bcodmo_name "diatox";
String description "Diatoxanthin concentration";
String long_name "Diad";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DIATHPP1/";
String units "micrograms per liter";
}
Anther {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.0;
String bcodmo_name "antherax";
String description "Antheraxanthin concentration";
String long_name "Anther";
String units "micrograms per liter";
}
Allox {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.24;
String bcodmo_name "allox";
String description "Alloxanthin concentration";
String long_name "Allox";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ALLOHPP1/";
String units "micrograms per liter";
}
Monado {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.0;
String bcodmo_name "monadoxanthin";
String description "Monadoxanthin concentration";
String long_name "Monado";
String units "micrograms per liter";
}
Diat {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.71;
String bcodmo_name "diatox";
String description "Diatoxanthin concentration";
String long_name "Diat";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DIATHPP1/";
String units "micrograms per liter";
}
Lutein {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.06;
String bcodmo_name "lutein";
String description "Lutein concentration";
String long_name "Lutein";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/LUTNHPP1/";
String units "micrograms per liter";
}
Zeax {
Float32 _FillValue NaN;
Float32 actual_range 0.01, 0.38;
String bcodmo_name "pigment_concentration";
String description "Zeaxanthin concentration";
String long_name "Zeax";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/OPWC/";
String units "micrograms per liter";
}
Gyro {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.04;
String bcodmo_name "Gyroxanthin-Diester";
String description "Gyroxanthin concentration";
String long_name "Gyro";
String units "micrograms per liter";
}
Chl_b {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.36;
String bcodmo_name "chl_b";
String description "Chlorophyll b concentration";
String long_name "CHL B";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CHLBHPP1/";
String units "micrograms per liter";
}
Croco {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.0;
String bcodmo_name "crocoxanthin";
String description "Crocoxanthin concentration";
String long_name "Croco";
String units "micrograms per liter";
}
Chla_Allomer {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.29;
String bcodmo_name "chl_a_allo";
Float64 colorBarMaximum 30.0;
Float64 colorBarMinimum 0.03;
String colorBarScale "Log";
String description "Chlorophyll a allomer concentration";
String long_name "Concentration Of Chlorophyll In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CLAAHPP1/";
String units "micrograms per liter";
}
Chl_a {
Float32 _FillValue NaN;
Float32 actual_range 0.33, 21.76;
String bcodmo_name "chlorophyll a";
Float64 colorBarMaximum 30.0;
Float64 colorBarMinimum 0.03;
String colorBarScale "Log";
String description "Chlorophyll a concentration";
String long_name "Concentration Of Chlorophyll In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CPHLHPP1/";
String units "micrograms per liter";
}
Chla_prime {
Float32 _FillValue NaN;
Float32 actual_range 0.01, 1.59;
String bcodmo_name "chl_a_prime";
Float64 colorBarMaximum 30.0;
Float64 colorBarMinimum 0.03;
String colorBarScale "Log";
String description "Chlorophyll a prime concentration";
String long_name "Concentration Of Chlorophyll In Sea Water";
String units "micrograms per liter";
}
alpha_Carotene {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.68;
String bcodmo_name "carotene_a";
String description "alpha Carotene concentration";
String long_name "Alpha Carotene";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ACARHPP1/";
String units "micrograms per liter";
}
beta_Carotene {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.16;
String bcodmo_name "carotene_b";
String description "beta Carotene concentration";
String long_name "Beta Carotene";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/BCARHPP1/";
String units "micrograms per liter";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Bioassays
Bioassays consisted of 4 treatments incubated at 3 irradiance exposure levels
(Table 2). \\u00a0Treatments were composed of 1) addition of 1 umol 14C-glucose
(specific activity 200 mCi/mmol) for a final activity of 0.26 uCi \\u00a0ml-1,
2) addition of 1 umol 14C-glucose and 20 uM DCMU, 3) addition of H14CO3-, and
4) Control (no additions). \\u00a0Each treatment has 5 replicates.
\\u00a0Bottles with the 4 treatments will be incubated at 3 irradiance levels,
75% of the surface irradiance, 25% of the surface irradiance, and complete
darkness. \\u00a0Thus the bioassay used 60 (12 treatments x 5 replicates) clear
polycarbonate flasks (Nalgene, 2.0 l), filled with ambient estuary water at
high tide. \\u00a0Flasks will be placed in a floating corrals covered with
neutral density screen to simulate 75% and 25% of the water surface solar
irradiance. \\u00a0The dark samples were incubated in opaque flasks.
\\u00a0Samples were incubated for 24 h (sunrise to sunrise) to allow turnover
of pigment pools and measure \\u201cdaily\\u201d net primary productivity.
\\u00a0After the incubation, aliquots (250 - 500 ml) of the incubation water
were filtered under a gentle vacuum (<50 KPa) through glass fiber filters (25
mm dia. Whatman GF/F), immediately frozen, and stored at -80deg C.
Analytical Methods
Phytoplankton community composition, based on biomarker photopigment
concentrations, were determined for all bioassay incubations (Millie et al.
1993, Jeffrey et al. 1997, Wright & Jeffrey 2006). \\u00a0Pigment
concentrations were analyzed using ChemTax to determine the relative abundance
of major phytoplankton groups (Mackey et al. 1996, Pinckney et al. 2001,
Lewitus et al. 2005). \\u00a0The initial pigment ratio matrix used for this
analysis was derived from Lewitus et al. (2005), which was based on
empirically measured pigment ratios for North Inlet estuarine phytoplankton.
\\u00a0The convergence procedure outlined by Latasa (2007) was used to minimize
errors in algal group biomass due to inaccurate pigment ratio seed values.
\\u00a0In addition, 20 ml of the incubation water was preserved with 5%
Lugol\\u2019s solution and archived for later qualitative microscopy for
comparison with the ChemTax results.
Filters were lyophilized for 18-24 hours at -50 deg C. \\u00a0Photopigments
were extracted by adding 750 ul of 90% aqueous acetone solvent followed by
storage for 12-20 hours at -20deg C. \\u00a0Filtered extracts (250 ul) were
injected into a Shimadzu HPLC with a single monomeric column (Rainin
Microsorb, 0.46 \\u00d7 1.5 cm, 3 um packing) and a polymeric (Vydac 201TP54,
0.46\\u00d7 25 cm, 5 um packing) reverse-phase C18 column in series. \\u00a0A
non-linear binary gradient consisting of solvent A (80% methanol : 20% 0.5 M
ammonium acetate) and solvent B (80% methanol : 20% acetone) was used for the
mobile phase (Pinckney et al. 1996, Hooker et al. 2010). \\u00a0Absorption
spectra and chromatograms (440 +/- 4 nm) was obtained using a Shimadzu SPD-
M10av photodiode array detector and pigment peaks were identified by comparing
retention times and absorption spectra with pure standards (DHI, Denmark).
\\u00a0The synthetic carotenoid \\u03b2-apo-8'-carotenal (Sigma) was used as an
internal standard. \\u00a0The 14C-specific activity of chl a was measured using
an in-line flow scintillation counter (Packard Radiomatic 525a, 500 ul
counting cell) placed downstream from the photodiode array detector.
\\u00a0Radioactivity was quantified after automatic in-line mixing of a low-
viscosity scintillation cocktail (Packard Ultima-Flo M) with HPLC eluant (3:1
mixing ratio). \\u00a0Radiograms were converted to disintegrations per minute
(dpm) after accounting for variable flow rates, counting cell volume, mixing
rates, and counting efficiency (quench) (Pinckney et al. 1996).";
String awards_0_award_nid "553533";
String awards_0_award_number "OCE-1260134";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1260134";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "David L. Garrison";
String awards_0_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"HPLC Photopigment Data for Bioassays
J. Pinckney, PI
Version 28 July 2017";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2017-07-28T17:55:25Z";
String date_modified "2019-03-20T20:03:11Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.710144.1";
String history
"2024-11-23T17:30:14Z (local files)
2024-11-23T17:30:14Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_710144.html";
String infoUrl "https://www.bco-dmo.org/dataset/710144";
String institution "BCO-DMO";
String instruments_0_acronym "HPLC";
String instruments_0_dataset_instrument_description "Used in HPLC analysis";
String instruments_0_dataset_instrument_nid "710154";
String instruments_0_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.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB11/";
String instruments_0_instrument_name "High Performance Liquid Chromatograph";
String instruments_0_instrument_nid "506";
String instruments_0_supplied_name "Photodiode array detector (PDA, Shimadzu SPD-M10A vp; 200 to 800 nm range)";
String instruments_1_acronym "HPLC";
String instruments_1_dataset_instrument_description "Used in HPLC Analysis";
String instruments_1_dataset_instrument_nid "710153";
String instruments_1_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.";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB11/";
String instruments_1_instrument_name "High Performance Liquid Chromatograph";
String instruments_1_instrument_nid "506";
String instruments_1_supplied_name "Temperature-controlled autosampler (Shimadzu SIL10-A vp) with a 500 µl injection loop";
String instruments_2_acronym "LSC";
String instruments_2_dataset_instrument_description "Used to measure chl a";
String instruments_2_dataset_instrument_nid "710155";
String instruments_2_description "Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used the quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.";
String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB21/";
String instruments_2_instrument_name "Liquid Scintillation Counter";
String instruments_2_instrument_nid "624";
String instruments_2_supplied_name "Flow Scintillation Counter (Packard Radiomatic 525a, 500 ul counting cell)";
String instruments_3_dataset_instrument_description "Used in HPLC analysis";
String instruments_3_dataset_instrument_nid "710152";
String instruments_3_description "A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps";
String instruments_3_instrument_name "Pump";
String instruments_3_instrument_nid "726";
String instruments_3_supplied_name "Binary Gradient Pump (Shimadzu dual LC10-AT vp and Controller SCL-10A vp)";
String keywords "allox, alpha, alpha_Carotene, anther, bco, bco-dmo, beta, beta_Carotene, biological, but, ButFuc_19, carotene, chemical, chemistry, chl, Chl_a, Chl_b, Chla_Allomer, Chla_prime, chlorophyll, concentration, concentration_of_chlorophyll_in_sea_water, croco, data, dataset, diad, diat, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Chlorophyll, erddap, fuc, fuco, gyro, hex, HexFuc_19, lutein, management, monado, month, neo, number, ocean, oceanography, oceans, office, perid, prasino, preliminary, sample, Sample_Volume, science, sea, seawater, viola, volume, water, year, zeax";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/710144/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/710144";
String param_mapping "{'710144': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/710144/parameters";
String people_0_affiliation "University of South Carolina at Columbia";
String people_0_person_name "James Pinckney";
String people_0_person_nid "553536";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Woods Hole Oceanographic Institution";
String people_1_affiliation_acronym "WHOI BCO-DMO";
String people_1_person_name "Hannah Ake";
String people_1_person_nid "650173";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "Photomixotrophy";
String projects_0_acronym "Photomixotrophy";
String projects_0_description "Phytoplankton, traditionally viewed as primary producers at the base of aquatic food webs, provide an energy source for higher trophic levels. However, some phytoplankton species function as both primary producers and heterotrophic secondary consumers. Phytoplankton that are photosynthetically competent but also take up and assimilate organic compounds are classified as facultative mixotrophs or, more simply, photomixotrophs. Unfortunately, we currently have few estimates of the proportion of the phytoplankton community that function as photomixotrophs, their rate of secondary production, or their temporal variation in abundance. Current paradigms about trophodynamics in marine systems do not consider this potentially important alternative pathway for energy flow for phytoplankton. The implication is that we may be missing a significant, fundamental process that affects carbon cycling and trophodynamics in estuarine systems. Furthermore, changes in the DOC composition due to anthropogenic alterations may result in changes in phytoplankton community structure and possibly promote the proliferation of harmful algal bloom species. In terms of ecosystem function, even moderate rates of photomixotrophy could potentially alter our current understanding of phytoplankton productivity, overall C turnover, competitive interactions, and energy transfer in estuarine environments. This project will use a novel approach to provide quantitative measures of the in situ rates and magnitudes of facultative heterotrophy in natural, estuarine phytoplankton communities over seasonal time scales in a representative estuarine ecosystem. The project will utilize a unique 14C radiolabeling technique to quantify the in situ assimilation rates of DOC by estuarine photomixotrophs and estimate the amount of DOC converted to phytoplankton biomass by photomixotrophy over seasonal time scales. This information will provide new insights into carbon dynamics in estuaries, the contribution of DOC to estuarine food webs, and the importance of photomixotrophy in determining the structural and functional characteristics of estuarine phytoplankton communities.";
String projects_0_end_date "2016-04";
String projects_0_geolocation "North Inlet, SC: 33 19.5 N, 79 11W";
String projects_0_name "Assimilation rates of dissolved organic carbon by photomixotrophic estuarine phytoplankton";
String projects_0_project_nid "553534";
String projects_0_project_website "https://sites.google.com/site/jaypinckney/";
String projects_0_start_date "2013-05";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "Year,Anther";
String summary "Results of HPLC derived photopigment concentrations for bioassays done in the North Inlet Estuary - Georgetown, South Carolina during 2014 (Photomixotrophy project)";
String title "[HPLC Photopigment Data for Bioassays] - Results of HPLC derived photopigment concentrations for bioassays done in the North Inlet Estuary - Georgetown, South Carolina during 2014 (Photomixotrophy project) (Assimilation rates of dissolved organic carbon by photomixotrophic estuarine phytoplankton)";
String version "1";
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.