http://lod.bco-dmo.org/id/dataset/511217
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2014-04-15
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Experimental results: Exopolymer production by phytoplankton under oxidative stress; conducted at the Thornton lab, TAMU from 2007-2012 (Diatom EPS Production project)
2014-04-15
publication
2014-04-15
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-11-21
publication
https://doi.org/10.1575/1912/bco-dmo.511217.1
Daniel C.O. Thornton
Texas A&M University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Thornton, D. (2014) Experimental results: Exopolymer production by phytoplankton under oxidative stress; conducted at the Thornton lab, TAMU from 2007-2012 (Diatom EPS Production project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2014-04-15 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.511217.1 [access date]
Exopolymer production by phytoplankton under oxidative stress. Dataset Description: <p>Data from laboratory experiment on exopolymer production by the diatom <em>Thalassiosira wessiflogii</em> (CCMP 1051) and the cyanobacterium <em>Synechococcus elongates_cf</em> (CCMP 1379) under conditions of oxidative stress.</p>
<p><em>Related references:</em><br />
Chen, J. 2014. Factors affecting carbohydrate production and the formation of transparent exopolymer particles (TEP) by diatoms. Ph.D. dissertation, Texas A&amp;M University, College Station, TX.</p> Methods and Sampling: <p><strong>Growth of the phytoplankton</strong><br />
The diatom <em>Thalassiosira wessiflogii</em> (CCMP 1051) and the cyanobacterium <em>Synechococcus elongates_cf</em> (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 µM (as NaNO<sub>3</sub>), 25 µM (NaH<sub>2</sub>PO<sub>4</sub>), and 400 µM (Na<sub>2</sub>SiO<sub>3</sub>), respectively. Culture temperatures were maintained at 20 ± 1 °C. Photon flux density on the surface of the culture bottles was 40 to 45 µmol m<sup>-2</sup> s<sup>-1</sup> 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 µM H<sub>2</sub>O<sub>2</sub>. The treatments were sampled once a day over the next three days.</p>
<p><strong>Measures of phytoplankton abundance and biomass</strong><br />
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). 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).<br />
<br />
Chlorophyll <em>a</em> concentration 90% acetone extractions from biomass retained on GF/C (Whatman) were measured using a Turner Designs 700 fluorometer, which was calibrated using chlorophyll <em>a</em> standards (Sigma) (Arar and Collins 1997). The extract was diluted with 90% acetone if the chl<em> a</em> concentration were too high.</p>
<p><strong>Cell permeability</strong><br />
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.</p>
<p><strong>TEP staining and analysis</strong><br />
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).</p>
<p><strong>CSP staining and analysis</strong><br />
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).</p>
<p><strong>Quantum yield of photosystem II</strong><br />
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).</p>
<p><strong>Caspase-like activity</strong><br />
Caspase-like activity was measured based on the method of Bouchard &amp; 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).</p>
<p><strong>References cited</strong><br />
Alldredge, A. L., Passow, U. &amp; Logan B. E. 1993. The abundance and significance of a class of large, transparent organic particles in the ocean. <em>Deep-Sea Res</em>.<em> Oceanogr</em>.,<em> I. </em>40: 1131-1140. doi:<a href="http://dx.doi.org/10.1016/0967-0637%2893%2990129-Q" target="_blank">10.1016/0967-0637(93)90129-Q</a></p>
<p>Arar, E. J. &amp; 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.</p>
<p>Berges, J. A., Franklin D. J. &amp; Harrison, P. J. 2001. Evolution of an artificial seawater medium: Improvements in enriched seawater, artificial water over the last two decades. <em>J. Phycol</em>. 37:1138-1145. doi:<a href="http://dx.doi.org/10.1046/j.1529-8817.2001.01052.x" target="_blank">10.1046/j.1529-8817.2001.01052.x</a></p>
<p>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 <em>Microcystis aeruginosa</em>. <em>J. Phycol.</em>, <em>47</em>(6), 1316-1325. doi:<a href="http://dx.doi.org/10.1111/j.1529-8817.2011.01074.x" target="_blank">10.1111/j.1529-8817.2011.01074.x</a></p>
<p>Engel, A. 2009. Determination of Marine Gel Particles. <em>In</em> Wurl, O. [Ed.] <em>Practical Guidelines for the Analysis of Seawater</em>. CRC Press, Taylor &amp; Francis Group, Boca Raton, Florida, pp.125-142.</p>
<p>Franklin, D. J., Airs, R. L., Fernandes, M., Bell, T. G., Bongaerts, R. J., Berges, J. A. &amp; Malin, G. 2012. Identification of senescence and death in <em>Emiliania huxleyi</em> and <em>Thalassiosira pseudonana</em>: Cell staining, chlorophyll alterations, and dimethylsulfoniopropionate (DMSP) metabolism. <em>Limnol. Oceanogr.</em> 57: 305–317. doi:10.4319/lo.2012.57.1.0305</p>
<p>Genty, B., Briantais, J. M., Baker N. R. 1989. The relationship between the quantum yield of photosynthetic electron-transport and quenching of chlorophyll fluorescence, <em>Biochimica et Biophysica Acta</em>, 990(1), 87-92. doi:<a href="http://dx.doi.org/10.1016/S0304-4165(89)80016-9" target="_blank">10.1016/S0304-4165(89)80016-9</a></p>
<p>Guillard, R. R. L. &amp; Sieracki, M. S. 2005. Counting cells in cultures with the light microscope. <em>In</em> Andersen R. A. [Ed.] <em>Algal Culturing Techniques</em>. Elsevier Academic Press, Burlington, MA, pp. 239-252.</p>
<p>Logan, B. E., Grossart, H. P. &amp; Simon, M. 1994. Direct observation of phytoplankton, TEP and aggregates on polycarbonate filters using brightfield microscopy. <em>J. Plankton Res.</em>16: 1811-1815.doi:<a href="http://dx.doi.org/10.1093/plankt/16.12.1811" target="_blank">10.1093/plankt/16.12.1811</a></p>
<p>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. <em>Ecotox Environ Safe</em> 44:322-327. doi:<a href="http://dx.doi.org/10.1006/eesa.1999.1840" target="_blank">10.1006/eesa.1999.1840</a></p>
<p>Parsons, T. R., Maita, Y. &amp; Lalli, C. M. 1984. A Manual of Chemical and Biological Methods for Seawater Analysis. <em>Pergamon Press</em>, Oxford, UK.</p>
<p>Passow, U. &amp; Alldredge, A. L. 1995. A dye-binding assay for the spectrophotometric measurement of transparent exopolymer particles (TEP). <em>Limnol. Oceanogr.</em> 40: 1326-1335. doi:<a href="http://dx.doi.org/10.4319/lo.1995.40.7.1326" target="_blank">10.4319/lo.1995.40.7.1326</a></p>
<p>Veldhuis, M. J. W., Kraay, G. W. &amp; Timmermans, K. R. 2001. Cell death in phytoplankton: correlation between changes in membrane permeability, photosynthetic activity, pigmentation and growth. <em>Eur. J. Phycol. </em>36: 167–177. doi:<a href="http://dx.doi.org/10.1080/09670260110001735318" target="_blank">10.1080/09670260110001735318</a></p>
<p>Zack, G. W., Rogers, W.E., Latt S. A. 1977. Automatic-measurement of sister chromatid exchange frequency, <em>J. Histochem. Cytochem.</em>, <em>25</em>(7), 741-753. doi:<a href="http://dx.doi.org/10.1177/25.7.70454" target="_blank">10.1177/25.7.70454</a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0726369 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0726369
completed
Daniel C.O. Thornton
Texas A&M University
979-845-4092
Department of Oceanography Texas A&M
College Station
TX
77840
USA
dthornton@ocean.tamu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
species
day
H2O2
turbidity
cell_conc
chla
PSII
caspase_like_activity
stained_cells_pcnt
TEP_conc
TEP_abund
TEP_per_chla
CSP_conc
CSP_abund
CSP_per_chla
Epifluorescence Microscope
Pulse Amplitude Modulated Fluorometer
Hemocytometer
Light Microscope
Turner Designs 700 Fluorometer
UV-Mini 1240 Spectrophotometer
theme
None, User defined
species scientific name (binomial)
day of month
Hydrogen Peroxide
turbidity
No BCO-DMO term
chlorophyll a
featureType
BCO-DMO Standard Parameters
Fluorescence Microscope
Fluorometer
Hemocytometer
Microscope - Optical
Turner Designs 700 Laboratory Fluorometer
UV Spectrophotometer-Shimadzu
instrument
BCO-DMO Standard Instruments
lab_Thornton
service
Deployment Activity
College Station, Texas, 77843
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Effect of Temperature on Extracellular Polymeric Substance Production (EPS) by Diatoms
https://osprey.bco-dmo.org/project/2255
Effect of Temperature on Extracellular Polymeric Substance Production (EPS) by Diatoms
<p><strong>Description from NSF Propsoal:</strong><br />
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. <strong>The proposed research will test the central hypothesis: Temperature increase affects diatom release of EPS, which act as a glue, increasing aggregation</strong>. Previous work by the investigator showed that increased temperatures affected the aggregation of Skeletonema costatum. Four specific hypotheses will be tested:<br />
H1: Diatoms produce more EPS with increasing temperature.<br />
H2: Diatoms produce more transparent exopolymer particles (TEP) with increasing temperature.<br />
H3: The quantity or composition of cell-surface carbohydrates in diatoms changes with temperature.<br />
H4: Aggregation of diatom cultures and natural plankton increases with temperature.</p>
<p>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.</p>
<p>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.</p>
<p><strong>Related Publications:</strong><br />
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: <a href="http://dx.doi.org/10.1080/09670262.2011.646314" target="_blank">10.1080/09670262.2011.646314</a></p>
<p>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: <a href="http://dx.doi.org/10.1155/2009/105901" target="_blank">10.1155/2009/105901</a></p>
<p>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: <a href="http://dx.doi.org/10.1080/09670262.2013.875596" target="_blank">10.1080/09670262.2013.875596</a></p>
<p>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: <a href="http://dx.doi.org/10.3354/ame01265 " target="_blank">10.3354/ame01265</a></p>
Diatom EPS Production
largerWorkCitation
project
eng; USA
oceans
College Station, Texas, 77843
2014-04-15
O&M Building, Texas A&M University, College Station, TX 77840
0
BCO-DMO catalogue of parameters from Experimental results: Exopolymer production by phytoplankton under oxidative stress; conducted at the Thornton lab, TAMU from 2007-2012 (Diatom EPS Production project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/511339.rdf
Name: species
Units: dimensionless
Description: <p>Species name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/511340.rdf
Name: day
Units: dimensionless
Description: <p>Day of the experiment.</p>
http://lod.bco-dmo.org/id/dataset-parameter/511341.rdf
Name: H2O2
Units: micromolar (uM)
Description: <p>Hydrogen peroxide concentration.</p>
http://lod.bco-dmo.org/id/dataset-parameter/511342.rdf
Name: turbidity
Units: NTU
Description: <p>Turbidity of the cultures measured by absorbance at 750 nm in a 1 cm path cuvette using a spectrophotometer.</p>
http://lod.bco-dmo.org/id/dataset-parameter/511343.rdf
Name: cell_conc
Units: cells per milliliter (cells mL-1)
Description: <p>Cell concentration. Counts of 400 cells were made by transmitted light microscopy using a hemacytometer (Fuchs-Rosenthal ruling Hauser Scientific) (Guillard & Sieracki 2005).</p>
http://lod.bco-dmo.org/id/dataset-parameter/511344.rdf
Name: chla
Units: micrograms per liter (ug L-1)
Description: <p>Chlorophyll a measured by fluorescence (Arar & Collins 1997; Method 445.0. EPA).</p>
http://lod.bco-dmo.org/id/dataset-parameter/511345.rdf
Name: PSII
Units: quantum yield of photosystem II
Description: <p>Quantum yield of photosystem II measured after Marwood et al. (1999) using pulse amplitude modulated chlorophyll fluorometer.</p>
http://lod.bco-dmo.org/id/dataset-parameter/511346.rdf
Name: caspase_like_activity
Units: relative fluorescence units per milligrams protein per hour (RFU mg protein-1 h-1)
Description: <p>Caspase-like activity was measured after Bouchard & Purdie (2011).</p>
http://lod.bco-dmo.org/id/dataset-parameter/511347.rdf
Name: stained_cells_pcnt
Units: percent (%)
Description: <p>% 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.</p>
http://lod.bco-dmo.org/id/dataset-parameter/511348.rdf
Name: TEP_conc
Units: micrometers TEP per milliliter (um2 mL-1)
Description: <p>Transparent exopolymer particles (TEP) concentration. TEP retained on 0.4 polycarbonate filters and stained with Alcian blue (Alldredge et al. 1993).</p>
http://lod.bco-dmo.org/id/dataset-parameter/511349.rdf
Name: TEP_abund
Units: TEP per milliliter (mL-1)
Description: <p>Transparent exopolymer particles (TEP) abundance. TEP retained on 0.4 polycarbonate filters and stained with Alcian blue (Alldredge et al. 1993).</p>
http://lod.bco-dmo.org/id/dataset-parameter/511350.rdf
Name: TEP_per_chla
Units: square millimeters of TEP per nanogram of chla (mm2 (ng chl. a)-1)
Description: <p>Transparent exopolymer particles (TEP) per chlorophyll a.</p>
http://lod.bco-dmo.org/id/dataset-parameter/511351.rdf
Name: CSP_conc
Units: micrometers CSP per milliliter (um2 mL-1)
Description: <p>Coomassie staining particles (CSP) concentration. CSP retained on 0.4 polycarbonate filters and stained with Coomassie briliant blue blue (Long & Azam 1996).</p>
http://lod.bco-dmo.org/id/dataset-parameter/511352.rdf
Name: CSP_abund
Units: CSP per milliliter (mL-1)
Description: <p>Coomassie staining particles (CSP) abundance. CSP retained on 0.4 polycarbonate filters and stained with Coomassie briliant blue blue (Long & Azam 1996).</p>
http://lod.bco-dmo.org/id/dataset-parameter/511353.rdf
Name: CSP_per_chla
Units: square millimeters of CSP per nanogram of chlorophyll a (mm2 (ng chl. a)-1)
Description: <p>Coomassie staining particles (CSP) per chlorophyll a.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
9391
https://darchive.mblwhoilibrary.org/bitstream/1912/24875/1/dataset-511217_oxidative-stress-tep__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.511217.1
download
onLine
dataset
<p><strong>Growth of the phytoplankton</strong><br />
The diatom <em>Thalassiosira wessiflogii</em> (CCMP 1051) and the cyanobacterium <em>Synechococcus elongates_cf</em> (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 µM (as NaNO<sub>3</sub>), 25 µM (NaH<sub>2</sub>PO<sub>4</sub>), and 400 µM (Na<sub>2</sub>SiO<sub>3</sub>), respectively. Culture temperatures were maintained at 20 ± 1 °C. Photon flux density on the surface of the culture bottles was 40 to 45 µmol m<sup>-2</sup> s<sup>-1</sup> 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 µM H<sub>2</sub>O<sub>2</sub>. The treatments were sampled once a day over the next three days.</p>
<p><strong>Measures of phytoplankton abundance and biomass</strong><br />
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). 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).<br />
<br />
Chlorophyll <em>a</em> concentration 90% acetone extractions from biomass retained on GF/C (Whatman) were measured using a Turner Designs 700 fluorometer, which was calibrated using chlorophyll <em>a</em> standards (Sigma) (Arar and Collins 1997). The extract was diluted with 90% acetone if the chl<em> a</em> concentration were too high.</p>
<p><strong>Cell permeability</strong><br />
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.</p>
<p><strong>TEP staining and analysis</strong><br />
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).</p>
<p><strong>CSP staining and analysis</strong><br />
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).</p>
<p><strong>Quantum yield of photosystem II</strong><br />
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).</p>
<p><strong>Caspase-like activity</strong><br />
Caspase-like activity was measured based on the method of Bouchard &amp; 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).</p>
<p><strong>References cited</strong><br />
Alldredge, A. L., Passow, U. &amp; Logan B. E. 1993. The abundance and significance of a class of large, transparent organic particles in the ocean. <em>Deep-Sea Res</em>.<em> Oceanogr</em>.,<em> I. </em>40: 1131-1140. doi:<a href="http://dx.doi.org/10.1016/0967-0637%2893%2990129-Q" target="_blank">10.1016/0967-0637(93)90129-Q</a></p>
<p>Arar, E. J. &amp; 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.</p>
<p>Berges, J. A., Franklin D. J. &amp; Harrison, P. J. 2001. Evolution of an artificial seawater medium: Improvements in enriched seawater, artificial water over the last two decades. <em>J. Phycol</em>. 37:1138-1145. doi:<a href="http://dx.doi.org/10.1046/j.1529-8817.2001.01052.x" target="_blank">10.1046/j.1529-8817.2001.01052.x</a></p>
<p>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 <em>Microcystis aeruginosa</em>. <em>J. Phycol.</em>, <em>47</em>(6), 1316-1325. doi:<a href="http://dx.doi.org/10.1111/j.1529-8817.2011.01074.x" target="_blank">10.1111/j.1529-8817.2011.01074.x</a></p>
<p>Engel, A. 2009. Determination of Marine Gel Particles. <em>In</em> Wurl, O. [Ed.] <em>Practical Guidelines for the Analysis of Seawater</em>. CRC Press, Taylor &amp; Francis Group, Boca Raton, Florida, pp.125-142.</p>
<p>Franklin, D. J., Airs, R. L., Fernandes, M., Bell, T. G., Bongaerts, R. J., Berges, J. A. &amp; Malin, G. 2012. Identification of senescence and death in <em>Emiliania huxleyi</em> and <em>Thalassiosira pseudonana</em>: Cell staining, chlorophyll alterations, and dimethylsulfoniopropionate (DMSP) metabolism. <em>Limnol. Oceanogr.</em> 57: 305–317. doi:10.4319/lo.2012.57.1.0305</p>
<p>Genty, B., Briantais, J. M., Baker N. R. 1989. The relationship between the quantum yield of photosynthetic electron-transport and quenching of chlorophyll fluorescence, <em>Biochimica et Biophysica Acta</em>, 990(1), 87-92. doi:<a href="http://dx.doi.org/10.1016/S0304-4165(89)80016-9" target="_blank">10.1016/S0304-4165(89)80016-9</a></p>
<p>Guillard, R. R. L. &amp; Sieracki, M. S. 2005. Counting cells in cultures with the light microscope. <em>In</em> Andersen R. A. [Ed.] <em>Algal Culturing Techniques</em>. Elsevier Academic Press, Burlington, MA, pp. 239-252.</p>
<p>Logan, B. E., Grossart, H. P. &amp; Simon, M. 1994. Direct observation of phytoplankton, TEP and aggregates on polycarbonate filters using brightfield microscopy. <em>J. Plankton Res.</em>16: 1811-1815.doi:<a href="http://dx.doi.org/10.1093/plankt/16.12.1811" target="_blank">10.1093/plankt/16.12.1811</a></p>
<p>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. <em>Ecotox Environ Safe</em> 44:322-327. doi:<a href="http://dx.doi.org/10.1006/eesa.1999.1840" target="_blank">10.1006/eesa.1999.1840</a></p>
<p>Parsons, T. R., Maita, Y. &amp; Lalli, C. M. 1984. A Manual of Chemical and Biological Methods for Seawater Analysis. <em>Pergamon Press</em>, Oxford, UK.</p>
<p>Passow, U. &amp; Alldredge, A. L. 1995. A dye-binding assay for the spectrophotometric measurement of transparent exopolymer particles (TEP). <em>Limnol. Oceanogr.</em> 40: 1326-1335. doi:<a href="http://dx.doi.org/10.4319/lo.1995.40.7.1326" target="_blank">10.4319/lo.1995.40.7.1326</a></p>
<p>Veldhuis, M. J. W., Kraay, G. W. &amp; Timmermans, K. R. 2001. Cell death in phytoplankton: correlation between changes in membrane permeability, photosynthetic activity, pigmentation and growth. <em>Eur. J. Phycol. </em>36: 167–177. doi:<a href="http://dx.doi.org/10.1080/09670260110001735318" target="_blank">10.1080/09670260110001735318</a></p>
<p>Zack, G. W., Rogers, W.E., Latt S. A. 1977. Automatic-measurement of sister chromatid exchange frequency, <em>J. Histochem. Cytochem.</em>, <em>25</em>(7), 741-753. doi:<a href="http://dx.doi.org/10.1177/25.7.70454" target="_blank">10.1177/25.7.70454</a></p>
Specified by the Principal Investigator(s)
<p>Limited processing was necessary with this dataset. As this was a laboratory experiment it was designed in such a way to ensure that the parameters measured were likely to be within a measurable range and therefore there were no measurements below detection limits. Chlorophyll concentrations were frequently too high; this was resolved by diluting the sample into the measurable range. Measured parameters were normalized to volume as most of the parameters were expressed as concentrations.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Epifluorescence Microscope
Epifluorescence Microscope
PI Supplied Instrument Name: Epifluorescence Microscope PI Supplied Instrument Description:Cell permeability was determined using an epifluorescence microscope (Axioplan 2, Carl Zeiss MicroImaging). Instrument Name: Fluorescence Microscope Instrument Short Name: Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/
Pulse Amplitude Modulated Fluorometer
Pulse Amplitude Modulated Fluorometer
PI Supplied Instrument Name: Pulse Amplitude Modulated Fluorometer PI Supplied 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). Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
Hemocytometer
Hemocytometer
PI Supplied Instrument Name: Hemocytometer PI Supplied 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. Instrument Name: Hemocytometer Instrument Short Name:Hemocytometer Instrument 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.
Light Microscope
Light Microscope
PI Supplied Instrument Name: Light Microscope PI Supplied 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. Instrument Name: Microscope - Optical Instrument Short Name: Instrument 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". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Turner Designs 700 Fluorometer
Turner Designs 700 Fluorometer
PI Supplied Instrument Name: Turner Designs 700 Fluorometer PI Supplied 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). Instrument Name: Turner Designs 700 Laboratory Fluorometer Instrument Short Name:TD-700 Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0510/
UV-Mini 1240 Spectrophotometer
UV-Mini 1240 Spectrophotometer
PI Supplied Instrument Name: UV-Mini 1240 Spectrophotometer PI Supplied 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). Instrument Name: UV Spectrophotometer-Shimadzu Instrument Short Name:UV Spectrophotometer-Shimadzu Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/
Deployment: lab_Thornton
lab_Thornton
TAMU
laboratory
lab_Thornton
Daniel C.O. Thornton
Texas A&M University
TAMU
laboratory