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Dataset Title:  Experimental results: Exopolymer production by phytoplankton under oxidative
stress; conducted at the Thornton lab, TAMU from 2007-2012 (Diatom EPS
Production project)
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_511217)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Files | Make a graph
 
Variable ?   Optional
Constraint #1 ?
Optional
Constraint #2 ?
   Minimum ?
 
   Maximum ?
 
 species (dimensionless) ?          "Synechococcus_elon..."    "Thalassiosira_weis..."
 day (dimensionless) ?          0    3
 H2O2 (micromolar (uM)) ?          0    100
 turbidity (NTU) ?          0.0302    0.1368
 cell_conc (cells per milliliter (cells mL-1)) ?          68800    7510000
 chla (micrograms per liter (ug L-1)) ?          144.0    491.67
 PSII (quantum yield of photosystem II) ?          0.2    0.7
 caspase_like_activity (relative fluorescence units per milligrams protein per hour (RFU mg protein-1 h-1)) ?          79.445    1787.544
 stained_cells_pcnt (percent (%)) ?          1.0    80.25
 TEP_conc (micrometers TEP per milliliter (um2 mL-1)) ?          124295402    769625835
 TEP_abund (TEP per milliliter (mL-1)) ?          485361    1827594
 TEP_per_chla (square millimeters of TEP per nanogram of chla (mm2 (ng chl. a)-1)) ?          4.85361E-7    2.39
 CSP_conc (micrometers CSP per milliliter (um2 mL-1)) ?          3717141.325    3.728874422E8
 CSP_abund (CSP per milliliter (mL-1)) ?          44941    826912
 CSP_per_chla (square millimeters of CSP per nanogram of chlorophyll a (mm2 (ng chl. a)-1)) ?          0.0156    1.045
 
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  species {
    String bcodmo_name "species";
    String description "Species name.";
    String long_name "Species";
    String units "dimensionless";
  }
  day {
    Byte _FillValue 127;
    Byte actual_range 0, 3;
    String bcodmo_name "day";
    String description "Day of the experiment.";
    String long_name "Day";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DAYXXXXX/";
    String units "dimensionless";
  }
  H2O2 {
    Byte _FillValue 127;
    Byte actual_range 0, 100;
    String bcodmo_name "Hydrogen Peroxide";
    String description "Hydrogen peroxide concentration.";
    String long_name "H2 O2";
    String units "micromolar (uM)";
  }
  turbidity {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0302, 0.1368;
    String bcodmo_name "turbidity";
    String description "Turbidity of the cultures measured by absorbance at 750 nm in a 1 cm path cuvette using a spectrophotometer.";
    String long_name "Turbidity";
    String units "NTU";
  }
  cell_conc {
    Int32 _FillValue 2147483647;
    Int32 actual_range 68800, 7510000;
    String bcodmo_name "unknown";
    String description "Cell concentration. Counts of 400 cells were made by transmitted light microscopy using a hemacytometer (Fuchs-Rosenthal ruling Hauser Scientific) (Guillard & Sieracki 2005).";
    String long_name "Cell Conc";
    String units "cells per milliliter (cells mL-1)";
  }
  chla {
    Float32 _FillValue NaN;
    Float32 actual_range 144.0, 491.67;
    String bcodmo_name "chlorophyll a";
    Float64 colorBarMaximum 30.0;
    Float64 colorBarMinimum 0.03;
    String colorBarScale "Log";
    String description "Chlorophyll a measured by fluorescence (Arar & Collins 1997; Method 445.0. EPA).";
    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 (ug L-1)";
  }
  PSII {
    Float32 _FillValue NaN;
    Float32 actual_range 0.2, 0.7;
    String bcodmo_name "unknown";
    String description "Quantum yield of photosystem II measured after Marwood et al. (1999) using pulse amplitude modulated chlorophyll fluorometer.";
    String long_name "PSII";
    String units "quantum yield of photosystem II";
  }
  caspase_like_activity {
    Float32 _FillValue NaN;
    Float32 actual_range 79.445, 1787.544;
    String bcodmo_name "unknown";
    String description "Caspase-like activity was measured after Bouchard & Purdie (2011).";
    String long_name "Caspase Like Activity";
    String units "relative fluorescence units per milligrams protein per hour (RFU mg protein-1 h-1)";
  }
  stained_cells_pcnt {
    Float32 _FillValue NaN;
    Float32 actual_range 1.0, 80.25;
    String bcodmo_name "unknown";
    String description "% of SYTOX Green stained cells. Uptake and staining with the membrane-impermeable SYTOX Green (Invitrogen) was used to determine what proportion of the diatom population had permeable cell membranes (Veldhuis et al. 2001; Franklin et al. 2012). Four hundred cells were examined using an epifluorescence microscope and the number of cells that stained with SYTOX Green was enumerated.";
    String long_name "Stained Cells Pcnt";
    String units "percent (%)";
  }
  TEP_conc {
    Int32 _FillValue 2147483647;
    Int32 actual_range 124295402, 769625835;
    String bcodmo_name "unknown";
    String description "Transparent exopolymer particles (TEP) concentration. TEP retained on 0.4 polycarbonate filters and stained with Alcian blue (Alldredge et al. 1993).";
    String long_name "TEP Conc";
    String units "micrometers TEP per milliliter (um2 mL-1)";
  }
  TEP_abund {
    Int32 _FillValue 2147483647;
    Int32 actual_range 485361, 1827594;
    String bcodmo_name "unknown";
    String description "Transparent exopolymer particles (TEP) abundance. TEP retained on 0.4 polycarbonate filters and stained with Alcian blue (Alldredge et al. 1993).";
    String long_name "TEP Abund";
    String units "TEP per milliliter (mL-1)";
  }
  TEP_per_chla {
    Float32 _FillValue NaN;
    Float32 actual_range 4.85361e-7, 2.39;
    String bcodmo_name "unknown";
    Float64 colorBarMaximum 30.0;
    Float64 colorBarMinimum 0.03;
    String colorBarScale "Log";
    String description "Transparent exopolymer particles (TEP) per chlorophyll a.";
    String long_name "Concentration Of Chlorophyll In Sea Water";
    String units "square millimeters of TEP per nanogram of chla (mm2 (ng chl. a)-1)";
  }
  CSP_conc {
    Float64 _FillValue NaN;
    Float64 actual_range 3717141.325, 3.728874422e+8;
    String bcodmo_name "unknown";
    String description "Coomassie staining particles (CSP) concentration. CSP retained on 0.4 polycarbonate filters and stained with Coomassie briliant blue blue (Long & Azam 1996).";
    String long_name "CSP Conc";
    String units "micrometers CSP per milliliter (um2 mL-1)";
  }
  CSP_abund {
    Int32 _FillValue 2147483647;
    Int32 actual_range 44941, 826912;
    String bcodmo_name "unknown";
    String description "Coomassie staining particles (CSP) abundance. CSP retained on 0.4 polycarbonate filters and stained with Coomassie briliant blue blue (Long & Azam 1996).";
    String long_name "CSP Abund";
    String units "CSP per milliliter (mL-1)";
  }
  CSP_per_chla {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0156, 1.045;
    String bcodmo_name "unknown";
    Float64 colorBarMaximum 30.0;
    Float64 colorBarMinimum 0.03;
    String colorBarScale "Log";
    String description "Coomassie staining particles (CSP) per chlorophyll a.";
    String long_name "Concentration Of Chlorophyll In Sea Water";
    String units "square millimeters of CSP per nanogram of chlorophyll a (mm2 (ng chl. a)-1)";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Growth of the phytoplankton  
 The diatom Thalassiosira wessiflogii (CCMP 1051) and the cyanobacterium
Synechococcus elongates_cf (CCMP 1379) were obtained from the National Center
for Culture of Marine Algae and Microbiota (NCMA). Replicated (n = 3) Batch
cultures were grown in artificial seawater (Berges et al. 2001) containing
nitrogen, phosphorus and silicon at 400 \\u00b5M (as NaNO3), 25 \\u00b5M
(NaH2PO4), and 400 \\u00b5M (Na2SiO3), respectively. Culture temperatures were
maintained at 20 \\u00b1 1 \\u00b0C. Photon flux density on the surface of the
culture bottles was 40 to 45 \\u00b5mol m-2 s-1 on a 14 hour light: 10 hour
dark cycle. During exponential growth, each culture was split into three
treatments in which oxidative stress was induced by the addition of hydrogen
peroxide at final concentrations of 0 (control), 10 and 100 \\u00b5M H2O2. The
treatments were sampled once a day over the next three days.
 
Measures of phytoplankton abundance and biomass  
 Counts of 400 cells from each culture were made using hemocytometers
(Guillard and Sieracki 2005) from samples preserved in Lugol\\u2019s iodine
(Parsons et al. 1984) using a light microscope (Axioplan 2, Carl Zeiss
MicroImaging). Turbidity of the cultures, used as an indicator of growth, was
measured by absorbance at 750 nm in a 1 cm path cuvette using a UV-Mini 1240
spectrophotometer (Shimadzu Corporation).
 
Chlorophyll a concentration 90% acetone extractions from biomass retained on
GF/C (Whatman) were measured using a Turner Designs 700 fluorometer, which was
calibrated using chlorophyll a standards (Sigma) (Arar and Collins 1997). The
extract was diluted with 90% acetone if the chl a concentration were too high.
 
Cell permeability  
 Uptake and staining with the membrane-impermeable SYTOX Green (Invitrogen)
was used to determine what proportion of the diatom population had permeable
cell membranes (Veldhuis et al. 2001, Franklin et al. 2012). Four hundred
cells were examined using an epifluorescence microscope (Axioplan 2, Carl
Zeiss MicroImaging) and the number of cells that stained with SYTOX Green was
enumerated.
 
TEP staining and analysis  
 Transparent exopolymer particles (TEP) were sampled according to Alldredge
et al. (1993) and TEP abundance was enumerated by image analysis (Logan et al.
1994, Engel 2009). Ten photomicrographs were taken of each slide using a light
microscope (Axioplan 2, Carl Zeiss MicroImaging). Images were analyzed using
ImageJ software (National Institutes of Health) based on the method of Engel
(2009). Thresholding during image processing was done using the triangle
method (Zack et al. 1977).
 
CSP staining and analysis  
 Coomassie staining particles (CSP) were sampled according to Long and Azam
et al. (1996) and CSP abundance was enumerated by image analysis (Logan et al.
1994, Engel 2009). Ten photomicrographs were taken of each slide using a light
microscope (Axioplan 2, Carl Zeiss MicroImaging). Images were analyzed using
ImageJ software (National Institutes of Health) based on the method of Engel
(2009). Thresholding during image processing was done using the triangle
method (Zack et al. 1977).
 
Quantum yield of photosystem II  
 The quantum yield of photosystem II was used as an indicator of
phytoplankton health and measured using the saturating pulse method (Genty et
al. 1989) using a pulse amplitude modulated fluorometer (PAM-210, Heinz Walz
GmbH) folowing a protocol based on Marwood et al. (1999).
 
Caspase-like activity  
 Caspase-like activity was measured based on the method of Bouchard & Purdie
(2011). Phytoplankton were collected by centrifugation, then lysed in a
buffer, and the caspase-3 like activity was measured in the extracted proteins
using a Enzcheck Caspase-3 Assay Kit #1 (Invitrogen inc.). The fluorescent
product was measured by fluorescence using a microplate reader (SPECTRAmax
GeminiEM, Molecular Devices).
 
References cited  
 Alldredge, A. L., Passow, U. & Logan B. E. 1993. The abundance and
significance of a class of large, transparent organic particles in the ocean.
Deep-Sea Res. Oceanogr., I. 40: 1131-1140.
doi:[10.1016/0967-0637(93)90129-Q](\\\\\"https://dx.doi.org/10.1016/0967-0637%2893%2990129-Q\\\\\")
 
Arar, E. J. & Collins, G. B. 1997. Method 445.0. In Vitro Determination of
Chlorophyll a and Pheophytin a in Marine and Freshwater Algae by Fluorescence
U.S. Environmental Protection Agency, Cincinnati, Ohio.
 
Berges, J. A., Franklin D. J. & Harrison, P. J. 2001. Evolution of an
artificial seawater medium: Improvements in enriched seawater, artificial
water over the last two decades. J. Phycol. 37:1138-1145.
doi:[10.1046/j.1529-8817.2001.01052.x](\\\\\"https://dx.doi.org/10.1046/j.1529-8817.2001.01052.x\\\\\")
 
Bouchard, J. N., Purdie, D. A. 2011. Effect of elevated temperature, darkness,
and hydrogen peroxide treatment on oxidative stress and cell death in the
bloom-forming toxic cyanobacterium Microcystis aeruginosa. J. Phycol., 47(6),
1316-1325.
doi:[10.1111/j.1529-8817.2011.01074.x](\\\\\"https://dx.doi.org/10.1111/j.1529-8817.2011.01074.x\\\\\")
 
Engel, A. 2009. Determination of Marine Gel Particles. In Wurl, O. [Ed.]
Practical Guidelines for the Analysis of Seawater. CRC Press, Taylor & Francis
Group, Boca Raton, Florida, pp.125-142.
 
Franklin, D. J., Airs, R. L., Fernandes, M., Bell, T. G., Bongaerts, R. J.,
Berges, J. A. & Malin, G. 2012. Identification of senescence and death in
Emiliania huxleyi and Thalassiosira pseudonana: Cell staining, chlorophyll
alterations, and dimethylsulfoniopropionate (DMSP) metabolism. Limnol.
Oceanogr. 57: 305\\u2013317. doi:10.4319/lo.2012.57.1.0305
 
Genty, B., Briantais, J. M., Baker N. R. 1989. The relationship between the
quantum yield of photosynthetic electron-transport and quenching of
chlorophyll fluorescence, Biochimica et Biophysica Acta, 990(1), 87-92.
doi:[10.1016/S0304-4165(89)80016-9](\\\\\"https://dx.doi.org/10.1016/S0304-4165\\(89\\)80016-9\\\\\")
 
Guillard, R. R. L. & Sieracki, M. S. 2005. Counting cells in cultures with the
light microscope. In Andersen R. A. [Ed.] Algal Culturing Techniques. Elsevier
Academic Press, Burlington, MA, pp. 239-252.
 
Logan, B. E., Grossart, H. P. & Simon, M. 1994. Direct observation of
phytoplankton, TEP and aggregates on polycarbonate filters using brightfield
microscopy. J. Plankton Res.16:
1811-1815.doi:[10.1093/plankt/16.12.1811](\\\\\"https://dx.doi.org/10.1093/plankt/16.12.1811\\\\\")
 
Marwood, C. A., Smith, R. E. H., Soloman, K. R., Charlton, M. N., Greenberg,
B. M. 1999. Intact and photomodified polycyclic aromatic hydrocarbons inhibit
photosynthesis in natural assemblages of Lake Erie phytoplankton exposed to
solar radiation. Ecotox Environ Safe 44:322-327.
doi:[10.1006/eesa.1999.1840](\\\\\"https://dx.doi.org/10.1006/eesa.1999.1840\\\\\")
 
Parsons, T. R., Maita, Y. & Lalli, C. M. 1984. A Manual of Chemical and
Biological Methods for Seawater Analysis. Pergamon Press, Oxford, UK.
 
Passow, U. & Alldredge, A. L. 1995. A dye-binding assay for the
spectrophotometric measurement of transparent exopolymer particles (TEP).
Limnol. Oceanogr. 40: 1326-1335.
doi:[10.4319/lo.1995.40.7.1326](\\\\\"https://dx.doi.org/10.4319/lo.1995.40.7.1326\\\\\")
 
Veldhuis, M. J. W., Kraay, G. W. & Timmermans, K. R. 2001. Cell death in
phytoplankton: correlation between changes in membrane permeability,
photosynthetic activity, pigmentation and growth. Eur. J. Phycol. 36:
167\\u2013177.
doi:[10.1080/09670260110001735318](\\\\\"https://dx.doi.org/10.1080/09670260110001735318\\\\\")
 
Zack, G. W., Rogers, W.E., Latt S. A. 1977. Automatic-measurement of sister
chromatid exchange frequency, J. Histochem. Cytochem., 25(7), 741-753.
doi:[10.1177/25.7.70454](\\\\\"https://dx.doi.org/10.1177/25.7.70454\\\\\")";
    String awards_0_award_nid "55158";
    String awards_0_award_number "OCE-0726369";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0726369";
    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 
"TEP production under oxidative stress 
 PI: Daniel C.O. Thornton (Texas A&M) 
 Version: 15 April 2014";
    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 "2014-04-15T14:57:24Z";
    String date_modified "2019-11-21T17:52:15Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.511217.1";
    String history 
"2022-10-07T15:38:12Z (local files)
2022-10-07T15:38:12Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_511217.html";
    String infoUrl "https://www.bco-dmo.org/dataset/511217";
    String institution "BCO-DMO";
    String instruments_0_acronym "Fluorometer";
    String instruments_0_dataset_instrument_description "The quantum yield of photosystem II was measured using the saturating pulse method (Genty et al. 1989) using a pulse amplitude modulated fluorometer (PAM-210, Heinz Walz GmbH).";
    String instruments_0_dataset_instrument_nid "511359";
    String instruments_0_description "A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/113/";
    String instruments_0_instrument_name "Fluorometer";
    String instruments_0_instrument_nid "484";
    String instruments_0_supplied_name "Pulse Amplitude Modulated Fluorometer";
    String instruments_1_acronym "UV Spectrophotometer-Shimadzu";
    String instruments_1_dataset_instrument_description "Turbidity of the cultures was measured by absorbance at 750 nm in a 1 cm path cuvette using a UV-Mini 1240 Spectrophotometer (Shimadzu Corporation).";
    String instruments_1_dataset_instrument_nid "511356";
    String instruments_1_description "The Shimadzu UV Spectrophotometer is manufactured by Shimadzu Scientific Instruments (ssi.shimadzu.com). Shimadzu manufacturers several models of spectrophotometer; refer to dataset for make/model information.";
    String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB20/";
    String instruments_1_instrument_name "UV Spectrophotometer-Shimadzu";
    String instruments_1_instrument_nid "595";
    String instruments_1_supplied_name "UV-Mini 1240 Spectrophotometer";
    String instruments_2_acronym "TD-700";
    String instruments_2_dataset_instrument_description "Chlorophyll a concentration 90% acetone extractions from biomass retained on GF/C (Whatman) were measured using a Turner Designs 700 fluorometer, which was calibrated using chlorophyll a standards (Sigma) (Arar and Collins 1997).";
    String instruments_2_dataset_instrument_nid "511357";
    String instruments_2_description "The TD-700 Laboratory Fluorometer is a benchtop fluorometer designed to detect fluorescence over the UV to red range. The instrument can measure concentrations of a variety of compounds, including chlorophyll-a and fluorescent dyes, and is thus suitable for a range of applications, including chlorophyll, water quality monitoring and fluorescent tracer studies. Data can be output as concentrations or raw fluorescence measurements.";
    String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0510/";
    String instruments_2_instrument_name "Turner Designs 700 Laboratory Fluorometer";
    String instruments_2_instrument_nid "694";
    String instruments_2_supplied_name "Turner Designs 700 Fluorometer";
    String instruments_3_dataset_instrument_description "Cell permeability was determined using an epifluorescence microscope (Axioplan 2, Carl Zeiss MicroImaging).";
    String instruments_3_dataset_instrument_nid "511358";
    String instruments_3_description "Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.";
    String instruments_3_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB06/";
    String instruments_3_instrument_name "Microscope-Fluorescence";
    String instruments_3_instrument_nid "695";
    String instruments_3_supplied_name "Epifluorescence Microscope";
    String instruments_4_acronym "Hemocytometer";
    String instruments_4_dataset_instrument_description "Counts of 400 cells from each culture were made using hemocytometers (Guillard and Sieracki 2005) from samples preserved in Lugol’s iodine (Parsons et al. 1984) using a light microscope.";
    String instruments_4_dataset_instrument_nid "511354";
    String instruments_4_description 
"A hemocytometer is a small glass chamber, resembling a thick microscope slide, used for determining the number of cells per unit volume of a suspension. Originally used for performing blood cell counts, a hemocytometer can be used to count a variety of cell types in the laboratory. Also spelled as \"haemocytometer\". Description from:
http://hlsweb.dmu.ac.uk/ahs/elearning/RITA/Haem1/Haem1.html.";
    String instruments_4_instrument_name "Hemocytometer";
    String instruments_4_instrument_nid "704";
    String instruments_4_supplied_name "Hemocytometer";
    String instruments_5_dataset_instrument_description "Counts of 400 cells from each culture were made using hemocytometers (Guillard and Sieracki 2005) from samples preserved in Lugol’s iodine (Parsons et al. 1984) using a light microscope (Axioplan 2, Carl Zeiss MicroImaging). A light microscope (Axioplan 2, Carl Zeiss MicroImaging) was also used to enumerate TEP and CSP by image analysis.";
    String instruments_5_dataset_instrument_nid "511355";
    String instruments_5_description "Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a \"light microscope\".";
    String instruments_5_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB05/";
    String instruments_5_instrument_name "Microscope-Optical";
    String instruments_5_instrument_nid "708";
    String instruments_5_supplied_name "Light Microscope";
    String keywords "abund, activity, bco, bco-dmo, biological, caspase, caspase_like_activity, cell, cell_conc, cells, chemical, chemistry, chla, chlorophyll, chlorophyll-a, conc, concentration, concentration_of_chlorophyll_in_sea_water, csp, CSP_abund, CSP_conc, CSP_per_chla, data, dataset, day, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Chlorophyll, erddap, H2O2, like, management, O2, ocean, oceanography, oceans, office, oxygen, pcnt, preliminary, psii, science, sea, seawater, species, stained, stained_cells_pcnt, tep, TEP_abund, TEP_conc, TEP_per_chla, turbidity, water";
    String keywords_vocabulary "GCMD Science Keywords";
    String license "https://www.bco-dmo.org/dataset/511217/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/511217";
    String param_mapping "{'511217': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/511217/parameters";
    String people_0_affiliation "Texas A&M University";
    String people_0_affiliation_acronym "TAMU";
    String people_0_person_name "Daniel C.O. Thornton";
    String people_0_person_nid "51644";
    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 "Shannon Rauch";
    String people_1_person_nid "51498";
    String people_1_role "BCO-DMO Data Manager";
    String people_1_role_type "related";
    String project "Diatom EPS Production";
    String projects_0_acronym "Diatom EPS Production";
    String projects_0_description 
"Description from NSF Propsoal:
It is necessary to determine the fate of organic matter in the ocean to understand marine food webs, biogeochemical cycles, and climate change. Diatoms fix approximately a quarter of the net global primary production each year, and a significant proportion of this production is excreted as extracellular polymeric substances (EPS). EPS have a profound impact on pelagic ecosystems by affecting the formation of aggregates. Diatoms and other particulate organic carbon (POC) sink rapidly as aggregates, affecting the biological carbon pump, which plays a pivotal role in the sequestration of carbon in the ocean. The proposed research will test the central hypothesis: Temperature increase affects diatom release of EPS, which act as a glue, increasing aggregation. Previous work by the investigator showed that increased temperatures affected the aggregation of Skeletonema costatum. Four specific hypotheses will be tested:
H1: Diatoms produce more EPS with increasing temperature.
H2: Diatoms produce more transparent exopolymer particles (TEP) with increasing temperature.
H3: The quantity or composition of cell-surface carbohydrates in diatoms changes with temperature.
H4: Aggregation of diatom cultures and natural plankton increases with temperature.
Laboratory experiments (years 1 - 2) will be conducted with three model diatom species grown at controlled growth rates and defined limitation (nitrogen or light) in continuous culture. Culture temperature will be stepped up or down in small increments to determine the effect of the temperature change on EPS production, aggregation, and partitioning of carbon in intra- and extracellular pools. Similar experiments in year 3 will be carried out using natural plankton populations from a coastal site where diatoms contribute a significant proportion to the biomass.
The proposed research will increase our understanding of the ecology and physiology of one of the dominant groups of primary producers on Earth. EPS are a central aspect of diatom biology, though the physiology, function and broader ecosystem impacts of EPS production remain unknown. This research will determine how temperature, light limitation, and nutrient limitation affect the partitioning of production between dissolved, gel, and particulate phases in the ocean. Measurements of plankton stickiness (alpha) under different conditions will be important to model aggregation processes in the ocean as alpha is an important (and variable) term in coagulation models. Determining how carbon is cycled between the ocean, atmosphere and lithosphere is key to understanding climate change on both geological and human time scales. This is a major societal issue as atmospheric CO2 concentrations are steadily increasing, correlating with a 0.6 C rise in global average temperature during the last century. This research will address potential feedbacks between warming of the surface ocean, diatom ecophysiology and the biological carbon pump.
Related Publications:
Rzadkowolski, Charles E. and Thornton, Daniel C. O. (2012) Using laser scattering to identify diatoms and conduct aggregation experiments. Eur. J. Phycol., 47(1): 30-41. DOI: 10.1080/09670262.2011.646314
Thornton, Daniel C. O. (2009) Effect of Low pH on Carbohydrate Production by a Marine Planktonic Diatom (Chaetoceros muelleri). Research Letters in Ecology, vol. 2009, Article ID 105901, 4 pages. DOI: 10.1155/2009/105901
Thornton, D.C.O. (2014) Dissolved organic matter (DOM) release by phytoplankton in the contemporary and future ocean. European Journal of Phycology 49: 20-46. DOI: 10.1080/09670262.2013.875596
Thornton, D.C.O., Visser, L.A. (2009) Measurement of acid polysaccharides (APS) associated with microphytobenthos in salt marsh sediments. Aquat Microb Ecol 54:185-198. DOI: 10.3354/ame01265";
    String projects_0_end_date "2012-08";
    String projects_0_geolocation "O&M Building, Texas A&M University, College Station, TX 77840";
    String projects_0_name "Effect of Temperature on Extracellular Polymeric Substance Production (EPS) by Diatoms";
    String projects_0_project_nid "2255";
    String projects_0_start_date "2007-09";
    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 summary "Data from laboratory experiment on exopolymer production by the diatom Thalassiosira wessiflogii (CCMP 1051) and the cyanobacterium Synechococcus elongates_cf (CCMP 1379) under conditions of oxidative stress.";
    String title "Experimental results: Exopolymer production by phytoplankton under oxidative stress; conducted at the Thornton lab, TAMU from 2007-2012 (Diatom EPS Production project)";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

 

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

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.


 
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