Accessing BCO-DMO data
Brought to you by BCO-DMO
|
|
BCO-DMO ERDDAP
Accessing BCO-DMO data |
log in
Brought to you by BCO-DMO |
| Dataset Title: | [Thalassiosira wessiflogii growth rate and TEP] - Results from growth rate experiment with the diatom Thalassiosira wessiflogii in semi-continuous culture; conducted at the Thornton lab, TAMU from 2007-2012 (Diatom EPS Production project) (Effect of Temperature on Extracellular Polymeric Substance Production (EPS) by Diatoms) 
|
| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_506135) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Subset
| Files
| Make a graph
|
Attributes {
s {
day {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 15, 123;
String bcodmo_name "unknown";
String description "Day of the experiment.";
String long_name "Day";
String units "dimensionless";
}
dilution_rate {
String bcodmo_name "unknown";
String description "Dilution rate.";
String long_name "Dilution Rate";
String units "per day (day-1)";
}
culture {
String bcodmo_name "replicate";
String description "Identifier of the culture replicate.";
String long_name "Culture";
String units "dimensionless";
}
cell_abundance {
Int32 _FillValue 2147483647;
Int32 actual_range 20100, 146000;
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";
}
cell_vol_mean {
Int16 _FillValue 32767;
Int16 actual_range 388, 1348;
String bcodmo_name "unknown";
String description "Mean cell volume estimated assuming T. weissflogii (CCMP 1051) was a cyclinder using the method of Menden-Deuer & Lessard (2000).";
String long_name "Cell Vol Mean";
String units "cubic micrometers (um^3)";
}
cell_vol_sd {
Int16 _FillValue 32767;
Int16 actual_range 81, 1176;
String bcodmo_name "standard deviation";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Standard deviation of cell_vol_mean.";
String long_name "Cell Vol Sd";
String units "cubic micrometers (um^3)";
}
cell_vol_n {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 25, 25;
String bcodmo_name "number";
String description "n (number of cells) used in determination of cell_vol_mean.";
String long_name "Cell Vol N";
String units "dimensionless";
}
chla {
Float32 _FillValue NaN;
Float32 actual_range 12.0, 126.6;
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 0.51, 1.89;
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 0.5, 2.65;
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 2.47, 13.83;
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 {
Int16 _FillValue 32767;
Int16 actual_range 49, 197;
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 {
Int16 _FillValue 32767;
Int16 actual_range 57, 237;
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)";
}
TEP {
Int32 _FillValue 2147483647;
Int32 actual_range 152800, 504800;
String bcodmo_name "unknown";
String description "Transparent exopolymer particles (TEP) retained on 0.4 polycarbonate filters and stained with Alcian blue (Alldredge et al. 1993).";
String long_name "TEP";
String units "TEP per milliliter (TEP mL-1)";
}
TEP_mean_size {
Int16 _FillValue 32767;
Int16 actual_range 701, 2465;
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)";
}
TEP_sd {
Int16 _FillValue 32767;
Int16 actual_range 286, 1443;
String bcodmo_name "standard deviation";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Standard deviation of TEP_mean_size.";
String long_name "TEP Sd";
String units "square micrometers (um^2)";
}
TEP_n {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 25, 25;
String bcodmo_name "number";
String description "n used in determination of TEP_mean_size.";
String long_name "TEP N";
String units "dimensionless";
}
tot_TEP_area {
Int16 _FillValue 32767;
Int16 actual_range 231, 604;
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)";
}
TEP_prod_rate {
Int16 _FillValue 32767;
Int16 actual_range 64, 330;
String bcodmo_name "unknown";
String description "TEP production rate.";
String long_name "TEP Prod Rate";
String units "square millimeters per milliliter per day (mm^2 mL-1 day-1)";
}
vol_conc {
Int16 _FillValue 32767;
Int16 actual_range 49, 393;
String bcodmo_name "unknown";
String description "Particulate volume concentration. Volume concentration and aggegation were measured using Laser in situ sacattering and transmissometry (LISST) (Rzadkowolski & Thornton 2012).";
String long_name "Vol Conc";
String units "microliters per liter (uL L-1)";
}
vol_conc_sd {
Int16 _FillValue 32767;
Int16 actual_range 3, 193;
String bcodmo_name "standard deviation";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Standard deviation of vol_conc.";
String long_name "Vol Conc Sd";
String units "microliters per liter (uL L-1)";
}
vol_conc_n {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 100, 100;
String bcodmo_name "number";
String description "n used in determination of vol_conc.";
String long_name "Vol Conc N";
String units "dimensionless";
}
agg_vol_conc {
Int16 _FillValue 32767;
Int16 actual_range 15, 225;
String bcodmo_name "unknown";
String description "Aggregated volume concentration (particles > 63 um ESD). Particulate volume concentration and aggegation were measured using Laser in situ sacattering and transmissometry (LISST) (Rzadkowolski & Thornton 2012).";
String long_name "Agg Vol Conc";
String units "microliters per liter (uL L-1)";
}
agg_vol_conc_sd {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 3, 48;
String bcodmo_name "standard deviation";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Standard deviation of agg_vol_conc.";
String long_name "Agg Vol Conc Sd";
String units "microliters per liter (uL L-1)";
}
agg_vol_conc_n {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 100, 100;
String bcodmo_name "number";
String description "n used in determination of agg_vol_conc.";
String long_name "Agg Vol Conc N";
String units "dimensionless";
}
stained_cells {
Int16 _FillValue 32767;
Int16 actual_range 64, 4660;
String bcodmo_name "unknown";
String description "Number 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";
String units "cells per milliliter (cells mL-1)";
}
stained_cells_pcnt {
Float32 _FillValue NaN;
Float32 actual_range 0.2, 3.6;
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 {
Int32 _FillValue 2147483647;
Int32 actual_range 9284, 2668932;
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 (cells mL-1)";
}
bact_per_diatom {
Float32 _FillValue NaN;
Float32 actual_range 0.3, 21.1;
String bcodmo_name "unknown";
String description "Bacteria abundance per diatom.";
String long_name "Bact Per Diatom";
String units "dimensionless";
}
C_to_N {
Float32 _FillValue NaN;
Float32 actual_range 8.1, 18.8;
String bcodmo_name "C_to_N";
String description "Ratio of carbon to nitrogen. C:N ratio was measured using a Carlo Erba NA1500 Elemental Analyzer. Standards were acetanilide, methionine, graphite (USGS 24, USGS 40, and USGS 41) (Verardo, Froelich, & McIntyre 1990).";
String long_name "C To N";
String units "dimensionless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Growth of the diatom
Thalassiosira wessiflogii (CCMP 1051) was obtained from the National Center
for Culture of Marine Algae and Microbiota (NCMA). The diatom was grown in
artificial seawater (Berges et al. 2001) in nitrogen-limited 1000 ml semi-
continuous cultures at a sequence of dilution rates. The macronutrient
concentrations in the artificial seawater recipe were modified from Berges et
al. (2001) to affect nitrogen limitation; concentrations of nitrogen,
phosphorus and silicon were 60 \\u00b5M (as NaNO3), 100 \\u00b5M (NaH2PO4), and
100 \\u00b5M (Na2SiO3), respectively. Culture temperature was maintained at 20
\\u00b1 0.1 \\u00b0C throughout the experiment. Photon flux density on the
surface of the culture bottles was 150 \\u00b5mol m-2 s-1. The cultures were
stirred with 2.5 cm long stir bars using magnetic stirrers at 120 revolutions
per minute. The cultures were grown at a sequence of dilution rates (0.3, 0.5,
0.7, 0.9 and 0.3 day-1) affected by daily dilution at 10:00 am every day. To
induce a dilution rate of 0.3 day-1, 0.3 of the culture volume (300 ml) was
removed and replaced with 300 ml of fresh medium to maintain a constant total
culture volume (1000 ml).
Measures of phytoplankton abundance and biomass
Counts of 400 cells from each replicate culture were made by light
microscopy using a hemocytometer (Fuchs-Rosenthal ruling, Hauser Scientific)
(Guillard and Sieracki 2005) from samples preserved in Lugol\\u2019s iodine
(Parsons et al. 1984). Cell volume was determined using live cells (Menden-
Deuer and Lessard 2000). The volume of 100 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 T.
wessiflogii is a cylinder.
Chlorophyll a concentrations in the cultures was determined by fluorescence
(Arar and Collins 1997). 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.
The carbon and nitrogen content of particulate organic matter in the cultures
was determined by elemental analysis using a Carlo Erba NA1500 Elemental
Analyzer. Standards were acetanilide, methionine, graphite (USGS 24, USGS 40,
and USGS 41) (Verardo et al. 1990).\\u00a0
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.
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 and the number of
cells that stained with SYTOX Green was enumerated.
Total carbohydrate
Total carbohydrate concentrations were determined in unfiltered liquid
samples from the cultures using the phenol-sulfuric acid (PSA) method (Dubois
et al. 1956) calibrated with d-glucose. The concentration of total
carbohydrate was expressed as glucose equivalents.
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 and the area
of 100 TEP particles from each replicate culture was determined after manually
drawing around each particle using Axio Vision 4.8 (Carl Zeiss MicroImaging )
image analysis software.\\u00a0
Particle size distribution and aggregation
The particle size distribution (PSD) and volume concentration of particles
in the T. weissiflogii cultures was measured using laser scattering following
the method of Rzadkowolski and Thornton (2012) using a Laser In Situ
Scattering and Transmissometry instrument (LISST-100X, Type C; Sequoia
Scientific). Sample (150 ml) from each replicate culture was placed into a
chamber attached to the LISST and the PSD was measured 100 times at a rate of
1 Hz. The PSD of the culture was blank corrected by subtracting the PSD of 0.2
\\u00b5m filtered artificial seawater.
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\\(93\\)90129-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\\\\\")
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\\\\\")
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\\\\\")
Rzadkowlski, C. E. & Thornton, D. C. O. 2012. Using laser scattering to
identify diatoms and conduct aggregation experiments. Eur. J. Phycol.47:30-41.
doi:[10.1080/09670262.2011.646314](\\\\\"https://dx.doi.org/10.1080/09670262.2011.646314\\\\\")
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\\\\\")
Verardo, D. J., Froelich, P. N. & McIntyre, A. 1990. Determination of organic
carbon and nitrogen in marine sediments using the Carlo Erba NA-1500 analyzer.
Deep-Sea Res.A 37:157-165.
doi:[10.1016/0198-0149(90)90034-S](\\\\\"https://dx.doi.org/10.1016/0198-0149\\(90\\)90034-S\\\\\")";
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
"Thalassiosira wessiflogii growth rate and TEP
PI: Daniel C.O. Thornton (Texas A&M)
Version: 07 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 "2014-04-07T16:01:42Z";
String date_modified "2019-11-21T17:48:58Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.506135.1";
String history
"2024-12-22T03:22:26Z (local files)
2024-12-22T03:22:26Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_506135.html";
String infoUrl "https://www.bco-dmo.org/dataset/506135";
String institution "BCO-DMO";
String instruments_0_acronym "TD-700";
String instruments_0_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_0_dataset_instrument_nid "506238";
String instruments_0_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_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0510/";
String instruments_0_instrument_name "Turner Designs 700 Laboratory Fluorometer";
String instruments_0_instrument_nid "694";
String instruments_0_supplied_name "Turner Designs 700 Fluorometer";
String instruments_1_dataset_instrument_description "Bacterial abunance and cell permeability were determined using an epifluorescence microscope (Axioplan 2, Carl Zeiss MicroImaging).";
String instruments_1_dataset_instrument_nid "506241";
String instruments_1_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_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB06/";
String instruments_1_instrument_name "Microscope-Fluorescence";
String instruments_1_instrument_nid "695";
String instruments_1_supplied_name "Epifluorescence Microscope";
String instruments_2_acronym "Hemocytometer";
String instruments_2_dataset_instrument_description "Counts of 400 cells from each replicate culture were made by light microscopy using a hemocytometer (Fuchs-Rosenthal ruling, Hauser Scientific).";
String instruments_2_dataset_instrument_nid "506236";
String instruments_2_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_2_instrument_name "Hemocytometer";
String instruments_2_instrument_nid "704";
String instruments_2_supplied_name "Hemocytometer";
String instruments_3_dataset_instrument_description "The volume of 100 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).";
String instruments_3_dataset_instrument_nid "506237";
String instruments_3_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_3_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB05/";
String instruments_3_instrument_name "Microscope-Optical";
String instruments_3_instrument_nid "708";
String instruments_3_supplied_name "Light microscope";
String instruments_4_acronym "Carlo-Erba NA-1500";
String instruments_4_dataset_instrument_description "The carbon and nitrogen content of particulate organic matter in the cultures was determined by elemental analysis using a Carlo Erba NA1500 Elemental Analyzer.";
String instruments_4_dataset_instrument_nid "506240";
String instruments_4_description "A laboratory instrument that simultaneously determines total nitrogen and total carbon from a wide range of organic and inorganic sediment samples. The sample is completely and instantaneously oxidised by flash combustion, which converts all organic and inorganic substances into combustion products. The resulting combustion gases pass through a reduction furnace and are swept into the chromatographic column by the carrier gas which is helium. The gases are separated in the column and detected by the thermal conductivity detector which gives an output signal proportional to the concentration of the individual components of the mixture. The instrument was originally manufactured by Carlo-Erba, which has since been replaced by Thermo Scientific (part of Thermo Fisher Scientific). This model is no longer in production.";
String instruments_4_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0470/";
String instruments_4_instrument_name "Carlo-Erba NA-1500 Elemental Analyzer";
String instruments_4_instrument_nid "506239";
String instruments_4_supplied_name "Carlo Erba NA1500 Elemental Analyzer";
String instruments_5_acronym "Sequoia LISST";
String instruments_5_dataset_instrument_description "The particle size distribution (PSD) and volume concentration of particles in the T. weissiflogii cultures was measured using laser scattering following the method of Rzadkowolski and Thornton (2012) using a Laser In Situ Scattering and Transmissometry instrument (LISST-100X, Type C; Sequoia Scientific).";
String instruments_5_dataset_instrument_nid "506244";
String instruments_5_description
"A self-contained unit which measures the scattering of LASER light at a number of angles. This primary measurement is mathematically inverted to give a grain size distribution, and also scaled to obtain the volume scattering function. The size distribution is presented as concentration in each of the grain-size class bins. Optical transmission, water depth and temperature are recorded as supporting measurements.
The Sequoia LISST 100-X series instruments are available in two range sizes: 1.25-250 microns (Type B) and 2.5-500 microns (Type C).";
String instruments_5_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0044/";
String instruments_5_instrument_name "Sequoia Scientific Laser In-Situ Sediment Size Transmissometer";
String instruments_5_instrument_nid "506243";
String instruments_5_supplied_name "LISST-100X Type C Sequoia Scientific";
String keywords "abundance, agg, agg_vol_conc, agg_vol_conc_n, agg_vol_conc_sd, area, bact, bact_per_diatom, bacteria, bco, bco-dmo, biological, C_to_N, carb, cell, cell_abundance, cell_vol_mean, cell_vol_n, cell_vol_sd, cells, chemical, chemistry, chla, chla_per_cell, chla_per_cell_vol, chlorophyll, chlorophyll-a, conc, concentration, concentration_of_chlorophyll_in_sea_water, culture, data, dataset, day, diatom, dilution, dilution_rate, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Chlorophyll, erddap, management, mean, ocean, oceanography, oceans, office, pcnt, per, preliminary, prod, rate, science, sea, seawater, size, stained, stained_cells, stained_cells_pcnt, tep, TEP_mean_size, TEP_n, TEP_prod_rate, TEP_sd, tot, tot_carb, tot_carb_per_cell, tot_carb_per_cell_vol, tot_TEP_area, vol, vol_conc, vol_conc_n, vol_conc_sd, water";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/506135/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/506135";
String param_mapping "{'506135': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/506135/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 subsetVariables "cell_vol_n,TEP_n,vol_conc_n,agg_vol_conc_n";
String summary "Data from laboratory experiment on growth rate and transparent exopolymer particles (TEP) in the diatom Thalassiosira wessiflogii (CCMP 1051) in a semi-continuous culture (four replicate cultures).";
String title "[Thalassiosira wessiflogii growth rate and TEP] - Results from growth rate experiment with the diatom Thalassiosira wessiflogii in semi-continuous culture; conducted at the Thornton lab, TAMU from 2007-2012 (Diatom EPS Production project) (Effect of Temperature on Extracellular Polymeric Substance Production (EPS) by Diatoms)";
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.