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Dataset Title:  Experimental results: Exopolymer and carbohydrate production by diatoms with
growth; conducted at the Thornton lab, TAMU from 2007-2012 (Diatom EPS
Production project)
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_511526)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
 
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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";
  }
  growth_phase {
    String bcodmo_name "unknown";
    String description "Growth phase of the diatom (exponential, stationary, declining, death).";
    String long_name "Growth Phase";
    String units "dimensionless";
  }
  day {
    Byte _FillValue 127;
    Byte actual_range 6, 43;
    String bcodmo_name "unknown";
    String description "Day of the experiment.";
    String long_name "Day";
    String units "dimensionless";
  }
  culture {
    Byte _FillValue 127;
    Byte actual_range 1, 3;
    String bcodmo_name "replicate";
    String description "Identifier of the culture replicate.";
    String long_name "Culture";
    String units "dimensionless";
  }
  cell_abundance {
    Float32 _FillValue NaN;
    Float32 actual_range 22700.0, 560970.0;
    String bcodmo_name "diatom";
    String description "Cell count. 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 Abundance";
    String units "cells per milliliter (mL-1)";
  }
  cell_vol_mean {
    Float32 _FillValue NaN;
    Float32 actual_range 21.73, 567.15;
    String bcodmo_name "unknown";
    String description "Mean cell volume calculated assuming that both T. wessiflogii and S. marinoi were cylinders. The volume of Cylindrotheca closterium was estimated assuming that its shape was equivalent to two cones.";
    String long_name "Cell Vol Mean";
    String units "cubic micrometers (um^3)";
  }
  chla {
    Float32 _FillValue NaN;
    Float32 actual_range 0.02, 366.79;
    String bcodmo_name "chlorophyll a";
    Float64 colorBarMaximum 30.0;
    Float64 colorBarMinimum 0.03;
    String colorBarScale "Log";
    String description "Concentration of 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)";
  }
  chla_per_cell {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 5.14;
    String bcodmo_name "unknown";
    Float64 colorBarMaximum 30.0;
    Float64 colorBarMinimum 0.03;
    String colorBarScale "Log";
    String description "Concentration of chlorophyll a per cell.";
    String long_name "Concentration Of Chlorophyll In Sea Water";
    String units "picograms per cell (pg cell-1)";
  }
  chla_per_cell_vol {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 94.0;
    String bcodmo_name "unknown";
    Float64 colorBarMaximum 30.0;
    Float64 colorBarMinimum 0.03;
    String colorBarScale "Log";
    String description "Concentration of chlorophyll a per cell volume.";
    String long_name "Concentration Of Chlorophyll In Sea Water";
    String units "femtograms per cubic micrometer (fg um-3)";
  }
  tot_carb {
    Float32 _FillValue NaN;
    Float32 actual_range 1.95, 52.48;
    String bcodmo_name "unknown";
    String description "Total carbohydrate concentration measured using the PSA method (Dubois et al. 1956).";
    String long_name "Tot Carb";
    String units "micrograms per milliliter (ug mL-1)";
  }
  tot_carb_per_cell {
    Float32 _FillValue NaN;
    Float32 actual_range 8.52, 496.09;
    String bcodmo_name "unknown";
    String description "Total carbohydrate concentration per cell.";
    String long_name "Tot Carb Per Cell";
    String units "picograms per cell (pg cell-1)";
  }
  tot_carb_per_cell_vol {
    Float32 _FillValue NaN;
    Float32 actual_range 62.44, 16122.66;
    String bcodmo_name "unknown";
    String description "Total carbohydrate concentration per cell volume.";
    String long_name "Tot Carb Per Cell Vol";
    String units "femtograms per cubic micrometer (fg um-3)";
  }
  colloidal_carb {
    Float64 _FillValue NaN;
    Float64 actual_range 0.01, 26.31;
    String bcodmo_name "unknown";
    String description "Colloidal carbohydrate concentration. Different fractions of carbohydrate were extracted from the cultures using methods described in Underwood et al. (1995) and Underwood et al. (2004). The colloidal carbohydrate fractions were measured using the PSA method (Dubois et al. 1956).";
    String long_name "Colloidal Carb";
    String units "micrograms per milliliter (ug mL-1)";
  }
  collodial_per_cell {
    Float32 _FillValue NaN;
    Float32 actual_range 0.05, 684.56;
    String bcodmo_name "unknown";
    String description "Colloidal carbohydrate concentration per cell.";
    String long_name "Collodial Per Cell";
    String units "picograms per cell (pg cell-1)";
  }
  colloidal_per_cell_vol {
    Float32 _FillValue NaN;
    Float32 actual_range 0.2, 18219.25;
    String bcodmo_name "unknown";
    String description "Colloidal carbohydrate concentration per cell volume.";
    String long_name "Colloidal Per Cell Vol";
    String units "femtograms per cubic micrometer (fg um-3)";
  }
  EPS_carb {
    Float32 _FillValue NaN;
    Float32 actual_range 0.17, 4.14;
    String bcodmo_name "unknown";
    String description "Exopolymer (EPS) carbohydrate concentration. Different fractions of carbohydrate were extracted from the cultures using methods described in Underwood et al. (1995) and Underwood et al. (2004). The EPS carbohydrate fractions were measured using the PSA method (Dubois et al. 1956).";
    String long_name "EPS Carb";
    String units "micrograms per milliliter (ug mL-1)";
  }
  EPS_carb_per_cell {
    Float32 _FillValue NaN;
    Float32 actual_range 0.61, 49.57;
    String bcodmo_name "unknown";
    String description "Exopolymer (EPS) carbohydrate concentration per cell.";
    String long_name "EPS Carb Per Cell";
    String units "picograms per cell (pg cell-1)";
  }
  EPS_carb_per_cell_vol {
    Float32 _FillValue NaN;
    Float32 actual_range 2.07, 1043.18;
    String bcodmo_name "unknown";
    String description "Exopolymer (EPS) carbohydrate concentration per cell volume.";
    String long_name "EPS Carb Per Cell Vol";
    String units "femtograms per cubic micrometer (fg um-3)";
  }
  HW_carb {
    Float32 _FillValue NaN;
    Float32 actual_range 0.12, 29.05;
    String bcodmo_name "unknown";
    String description "Intracellular carbohydrate (hot water (HW) extraction) concentration. Different fractions of carbohydrate were extracted from the cultures using methods described in Underwood et al. (1995) and Underwood et al. (2004). The HW carbohydrate fractions were measured using the PSA method (Dubois et al. 1956).";
    String long_name "HW Carb";
    String units "micrograms per milliliter (ug mL-1)";
  }
  HW_carb_per_cell {
    Float32 _FillValue NaN;
    Float32 actual_range 1.88, 170.88;
    String bcodmo_name "unknown";
    String description "Intracellular carbohydrate (hot water (HW) extraction) concentration per cell.";
    String long_name "HW Carb Per Cell";
    String units "picograms per cell (pg cell-1)";
  }
  HW_carb_per_cell_vol {
    Float32 _FillValue NaN;
    Float32 actual_range 7.93, 1752.36;
    String bcodmo_name "unknown";
    String description "Intracellular carbohydrate (hot water (HW) extraction) concentration per cell volume.";
    String long_name "HW Carb Per Cell Vol";
    String units "femtograms per cubic micrometer (fg um-3)";
  }
  HB_carb {
    Float32 _FillValue NaN;
    Float32 actual_range 0.24, 9.08;
    String bcodmo_name "unknown";
    String description "Cell-wall associated carbohydrate (hot bicarbonate (HB) extraction) concentration. Different fractions of carbohydrate were extracted from the cultures using methods described in Underwood et al. (1995) and Underwood et al. (2004). The HB carbohydrate fractions were measured using the PSA method (Dubois et al. 1956).";
    String long_name "HB Carb";
    String units "micrograms per milliliter (ug mL-1)";
  }
  HB_carb_per_cell {
    Float32 _FillValue NaN;
    Float32 actual_range 0.93, 135.08;
    String bcodmo_name "unknown";
    String description "Cell-wall associated carbohydrate (hot bicarbonate (HB) extraction) concentration per cell.";
    String long_name "HB Carb Per Cell";
    String units "picograms per cell (pg cell-1)";
  }
  HB_carb_per_cell_vol {
    Float32 _FillValue NaN;
    Float32 actual_range 10.0, 3951.35;
    String bcodmo_name "unknown";
    String description "Cell-wall associated carbohydrate (hot bicarbonate (HB) extraction) concentration per cell volume.";
    String long_name "HB Carb Per Cell Vol";
    String units "femtograms per cubic micrometer (fg um-3)";
  }
  residual_carb {
    Float32 _FillValue NaN;
    Float32 actual_range 0.11, 5.07;
    String bcodmo_name "unknown";
    String description "Residual carbohydrate concentration. Different fractions of carbohydrate were extracted from the cultures using methods described in Underwood et al. (1995) and Underwood et al. (2004). The residual carbohydrate fractions were measured using the PSA method (Dubois et al. 1956).";
    String long_name "Residual Carb";
    String units "micrograms per milliliter (ug mL-1)";
  }
  residual_carb_per_cell {
    Float32 _FillValue NaN;
    Float32 actual_range 0.33, 50.91;
    String bcodmo_name "unknown";
    String description "Residual carbohydrate concentration per cell.";
    String long_name "Residual Carb Per Cell";
    String units "picograms per cell (pg cell-1)";
  }
  residual_carb_per_cell_vol {
    Float32 _FillValue NaN;
    Float32 actual_range 1.36, 738.83;
    String bcodmo_name "unknown";
    String description "Residual carbohydrate concentration per cell volume.";
    String long_name "Residual Carb Per Cell Vol";
    String units "femtograms per cubic micrometer (fg um-3)";
  }
  TPTZ_intracell_mono {
    Float32 _FillValue NaN;
    Float32 actual_range 0.02, 1.82;
    String bcodmo_name "unknown";
    String description "Intracellular monosaccharide concentration determined using the TPTZ method (Myklestad et al. 1997).";
    String long_name "TPTZ Intracell Mono";
    String units "micrograms per milliliter (ug mL-1)";
  }
  TPTZ_extracell_mono {
    Float32 _FillValue NaN;
    Float32 actual_range 0.09, 0.97;
    String bcodmo_name "unknown";
    String description "Extracellular monosaccharide concentration determined using the TPTZ method (Myklestad et al. 1997).";
    String long_name "TPTZ Extracell Mono";
    String units "micrograms per milliliter (ug mL-1)";
  }
  TPTZ_intracell_polysacc {
    Float32 _FillValue NaN;
    Float32 actual_range 0.2, 7.75;
    String bcodmo_name "unknown";
    String description "Intracellular polysaccharide concentration determined using the TPTZ method (Myklestad et al. 1997).";
    String long_name "TPTZ Intracell Polysacc";
    String units "micrograms per milliliter (ug mL-1)";
  }
  TPTZ_extracell_polysacc {
    Float32 _FillValue NaN;
    Float32 actual_range 0.04, 2.31;
    String bcodmo_name "unknown";
    String description "Extracellular polysaccharide concentration  determined using the TPTZ method (Myklestad et al. 1997).";
    String long_name "TPTZ Extracell Polysacc";
    String units "micrograms per milliliter (ug mL-1)";
  }
  TEP_conc_mean {
    Float64 _FillValue NaN;
    Float64 actual_range 754623.41, 5.429096222e+7;
    String bcodmo_name "unknown";
    String description "Mean transparent exopolymer particle (TEP) concentration. TEP retained on 0.4 polycarbonate filters and stained with Alcian blue (Alldredge et al. 1993).";
    String long_name "TEP Conc Mean";
    String units "TEP per milliliter (TEP mL-1)";
  }
  TEP_mean_size {
    Float32 _FillValue NaN;
    Float32 actual_range 62.13, 1059.08;
    String bcodmo_name "unknown";
    String description "Mean size of Transparent exopolymer particles (TEP).";
    String long_name "TEP Mean Size";
    String units "square micrometers (um^2)";
  }
  tot_TEP_area {
    Float32 _FillValue NaN;
    Float32 actual_range 89.68, 8358.71;
    String bcodmo_name "unknown";
    String description "Total TEP area.";
    String long_name "Tot TEP Area";
    String units "square millimeters per milliliter (mm^2 mL-1)";
  }
  CSP_conc_mean {
    Float64 _FillValue NaN;
    Float64 actual_range 227584.84, 1.766777039e+7;
    String bcodmo_name "unknown";
    String description "Mean coomassie staining particle (CSP) concentration. CSP retained on 0.4 polycarbonate filters and stained with Coomassie briliant blue blue (Long & Azam 1996).";
    String long_name "CSP Conc Mean";
    String units "CSP per milliliter (mL-1)";
  }
  CSP_mean_size {
    Float32 _FillValue NaN;
    Float32 actual_range 30.41, 411.4;
    String bcodmo_name "unknown";
    String description "Mean size of coomassie staining particle (CSP).";
    String long_name "CSP Mean Size";
    String units "square micrometers (um^2)";
  }
  tot_CSP_area {
    Float32 _FillValue NaN;
    Float32 actual_range 12.69, 5529.74;
    String bcodmo_name "unknown";
    String description "Total CSP area.";
    String long_name "Tot CSP Area";
    String units "square millimeters per milliliter (mm^2 mL-1)";
  }
  stained_cells_pcnt {
    Float32 _FillValue NaN;
    Float32 actual_range 2.5, 95.5;
    String bcodmo_name "unknown";
    String description "% of SYTOX Green stained cells. Cell permeability was determined by SYTOX Green staining (Veldhuis et al. 1997). 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 (%)";
  }
  bacteria {
    Float64 _FillValue NaN;
    Float64 actual_range 5356.54, 648811.25;
    String bcodmo_name "bact_abundance";
    String description "Bacteria abundance determined by DAPI staining and counts using an epifluorescence microscope (Porter & Feig 1980).";
    String long_name "Bacteria";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/BNTX";
    String units "cells per milliliter (mL-1)";
  }
  bact_per_diatom {
    Float32 _FillValue NaN;
    Float32 actual_range 0.03, 25.04;
    String bcodmo_name "unknown";
    String description "Bacteria abundance per diatom.";
    String long_name "Bact Per Diatom";
    String units "dimensionless";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Growth of the diatoms  
 The diatoms Thalassiosira weissflogii (CCMP 1051), Skeletonema marinoi (CCMP
1332), and Cylindrotheca closterium (CCMP 339) were grown in artificial
seawater (Berges et al. 2001) in batch culture at 20 \\u00b0C with 100
\\u00b5M\\u00a0 NaNO3, 200 \\u00b5M of NaH2PO4\\u00b7H2O, and 200 \\u00b5M of
Na2SiO3\\u00b79H2O. Illumination was on a 14 h:10 h light:dark cycle at a
photon flux density of 160 \\u00b5mol m-2 s-1. There were three replicate
cultures. Cultures were sampled during both the growth and death of the
cultures over several weeks.
 
Measures of diatom abundance and biomass  
 Counts of 400 cells from each culture were made using a hemacytometer
(Fuchs-Rosenthal ruling, Hauser Scientific) (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).
 
Cell volume was determined using live cells (Menden-Deuer and Lessard 2000).
The volume of 25 diatoms from each replicate culture was determined by
measuring cell length (pervalver length) and width (valver length) at 400x
magnification using a light microscope (Axioplan 2, Carl Zeiss MicroImaging).
Cell volume was calculated based on the assumption that both T. wessiflogii
and S. marinoi were cylinders. The volume of Cylindrotheca closterium was
estimated assuming that its shape was equivalent to two cones.
 
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.
 
Bacteria abundance  
 Bacteria (400 cells) were counted using an epifluorescence microscope
(Axioplan 2, Carl Zeiss MicroImaging) after staining with
4'6-diamidino-2-phenylindole dihydrochloride (DAPI) (Porter and Feig 1980) at
a final concentration of 0.25 \\u00b5g ml-1.
 
Carbohydrate analysis  
 Two spectrophotometric methods were used to measure carbohydrates, the
phenol sulfuric acid (PSA) method (Dubois et al. 1956) and the 2, 4,
6-tripyridyl-s-triazine (TPTZ) method (Myklestad et al. 1997). The color
produced by both methods was measured in 1 cm path length cuvette using UV-
Mini 1240 spectrophotometer (Shimadzu Corporation). Both methods were
calibrated using D-glucose and the results are expressed as D-glucose
equivalents. Different fractions of carbohydrate were extracted from the
cultures using methods described in Underwood et al. (1995) and Underwood et
al. (2004): total, colloidal, exopolymers (EPS), intracellular carbohydrate
(hot water (HW) extraction), cell-wall associated carbohydrates (hot
bicarbonate (HB) extraction), and residual. These carbohydrate fractions were
measured using the PSA method. The TPTZ method was used to measure the
intracellular and extracellular monosaccharide pools and the intracellular and
extracellular polysaccharide pools after acid hydrolysis of the sample.
 
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).
 
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\\\\\")
 
Dubois, M., Gilles, K. A., Hamilton, J. K., Rebers, P. A. & Smith, F. 1956.
Colorimetric method for determination of sugars and related substances. Anal.
Chem. 28: 350\\u2013356.
doi:[10.1021/ac60111a017](\\\\\"https://dx.doi.org/10.1021/ac60111a017\\\\\")
 
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
 
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\\\\\")
 
Menden-Deuer S. & Lessard, E. J. 2000. Carbon to volume relationships for
dinoflagellates, diatoms, and other protists plankton. Limnol. Oceanogr. 45:
569- 579.
doi:[10.4319/lo.2000.45.3.0569](\\\\\"https://dx.doi.org/10.4319/lo.2000.45.3.0569\\\\\")
 
Myklestad, S. M., Skanoy, E., Hestmann S. 1997. A sensitive and rapid method
for analysis of dissolved mono- and polysaccharides in seawater. Marine
Chemistry 56: 279-286.
doi:[10.1016/S0304-4203(96)00074-6](\\\\\"https://dx.doi.org/10.1016/S0304-4203\\(96\\)00074-6\\\\\")
 
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\\\\\")
 
Porter, K. G. & Feig, Y. S. 1980. The use of DAPI for identifying and counting
aquatic microflora. Limnol. Oceanogr. 25:943\\u2013948.
doi:[10.4319/lo.1980.25.5.0943](\\\\\"https://dx.doi.org/10.4319/lo.1980.25.5.0943\\\\\")
 
Underwood, G. J. C., Paterson D. M., Parkes R. J. 1995. The measurement of
microbial carbohydrate exopolymers from intertidal sediments. Limnol.
Oceanogr. 40: 1243-1253.
doi:[10.4319/lo.1995.40.7.1243](\\\\\"https://dx.doi.org/10.4319/lo.1995.40.7.1243\\\\\")
 
Underwood, G. J. C., Boulcott, M., Raines, C. A., Waldron K. 2004.
Environmental effects on exopolymer production by marine benthic diatoms:
Dynamics, changes in composition, and pathways of production. J. Phycol. 40:
293-304.
doi:[10.1111/j.1529-8817.2004.03076.x](\\\\\"https://dx.doi.org/10.1111/j.1529-8817.2004.03076.x\\\\\")
 
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 
"Growth phase exopolymer and carbohydrate production by diatoms 
 PI: Daniel C.O. Thornton (Texas A&M) 
 Version: 16 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 "2014-04-16T15:19:09Z";
    String date_modified "2019-11-21T18:09:10Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.511526.1";
    String history 
"2022-08-09T11:13:03Z (local files)
2022-08-09T11:13:03Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_511526.das";
    String infoUrl "https://www.bco-dmo.org/dataset/511526";
    String institution "BCO-DMO";
    String instruments_0_acronym "UV Spectrophotometer-Shimadzu";
    String instruments_0_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). Two spectrophotometric methods were used to measure carbohydrates, the phenol sulfuric acid (PSA) method (Dubois et al. 1956) and the 2, 4, 6-tripyridyl-s-triazine (TPTZ) method (Myklestad et al. 1997). The color produced by both methods was measured in 1 cm path length cuvette using UV-Mini 1240 spectrophotometer (Shimadzu Corporation).";
    String instruments_0_dataset_instrument_nid "511581";
    String instruments_0_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_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB20/";
    String instruments_0_instrument_name "UV Spectrophotometer-Shimadzu";
    String instruments_0_instrument_nid "595";
    String instruments_0_supplied_name "UV-Mini 1240 Spectrophotometer";
    String instruments_1_acronym "TD-700";
    String instruments_1_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_1_dataset_instrument_nid "511582";
    String instruments_1_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_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0510/";
    String instruments_1_instrument_name "Turner Designs 700 Laboratory Fluorometer";
    String instruments_1_instrument_nid "694";
    String instruments_1_supplied_name "Turner Designs 700 Fluorometer";
    String instruments_2_dataset_instrument_description "Bacteria were counted and cell permeability was determined using an epifluorescence microscope (Axioplan 2, Carl Zeiss MicroImaging).";
    String instruments_2_dataset_instrument_nid "511583";
    String instruments_2_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_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB06/";
    String instruments_2_instrument_name "Microscope-Fluorescence";
    String instruments_2_instrument_nid "695";
    String instruments_2_supplied_name "Epifluorescence Microscope";
    String instruments_3_acronym "Hemocytometer";
    String instruments_3_dataset_instrument_description "Counts of 400 cells from each culture were made using a hemocytometer (Fuchs-Rosenthal ruling, Hauser Scientific) (Guillard and Sieracki 2005) from samples preserved in Lugol’s iodine (Parsons et al. 1984) using a light microscope.";
    String instruments_3_dataset_instrument_nid "511579";
    String instruments_3_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_3_instrument_name "Hemocytometer";
    String instruments_3_instrument_nid "704";
    String instruments_3_supplied_name "Hemocytometer";
    String instruments_4_dataset_instrument_description "Counts of 400 cells from each culture were made using a hemacytometer (Fuchs-Rosenthal ruling, Hauser Scientific) (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 was also used to determine cell volume and to enumerate TEP and CSP by image analysis.";
    String instruments_4_dataset_instrument_nid "511580";
    String instruments_4_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_4_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB05/";
    String instruments_4_instrument_name "Microscope-Optical";
    String instruments_4_instrument_nid "708";
    String instruments_4_supplied_name "Light Microscope";
    String keywords "abundance, area, bact, bact_per_diatom, bacteria, bco, bco-dmo, biological, carb, cell, cell_abundance, cell_vol_mean, cells, chemical, chemistry, chla, chla_per_cell, chla_per_cell_vol, chlorophyll, chlorophyll-a, collodial, collodial_per_cell, colloidal, colloidal_carb, colloidal_per_cell_vol, conc, concentration, concentration_of_chlorophyll_in_sea_water, csp, CSP_conc_mean, CSP_mean_size, culture, data, dataset, day, diatom, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Chlorophyll, eps, EPS_carb, EPS_carb_per_cell, EPS_carb_per_cell_vol, erddap, extracell, growth, growth_phase, HB_carb, HB_carb_per_cell, HB_carb_per_cell_vol, HW_carb, HW_carb_per_cell, HW_carb_per_cell_vol, intracell, management, mean, mono, ocean, oceanography, oceans, office, pcnt, per, phase, polysacc, preliminary, residual, residual_carb, residual_carb_per_cell, residual_carb_per_cell_vol, science, sea, seawater, size, species, stained, stained_cells_pcnt, tep, TEP_conc_mean, TEP_mean_size, tot, tot_carb, tot_carb_per_cell, tot_carb_per_cell_vol, tot_CSP_area, tot_TEP_area, tptz, TPTZ_extracell_mono, TPTZ_extracell_polysacc, TPTZ_intracell_mono, TPTZ_intracell_polysacc, vol, water";
    String keywords_vocabulary "GCMD Science Keywords";
    String license "https://www.bco-dmo.org/dataset/511526/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/511526";
    String param_mapping "{'511526': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/511526/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 and carbohydrate production by
the diatoms Thalassiosira weissflogii (CCMP 1051), Skeletonema marinoi (CCMP
1332), and Cylindrotheca closterium (CCMP 339) during the growth to death
phases of the cultures.
 
Related references:  
 Chen, J. 2014. Factors affecting carbohydrate production and the formation
of transparent exopolymer particles (TEP) by diatoms. Ph.D. dissertation,
Texas A&M University, College Station, TX.";
    String title "Experimental results: Exopolymer and carbohydrate production by diatoms with growth; 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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