http://lod.bco-dmo.org/id/dataset/511526 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 2014-04-16 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Experimental results: Exopolymer and carbohydrate production by diatoms with growth; conducted at the Thornton lab, TAMU from 2007-2012 (Diatom EPS Production project) 2014-04-16 publication 2014-04-16 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2019-11-21 publication https://doi.org/10.1575/1912/bco-dmo.511526.1 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 and carbohydrate production by diatoms with growth; 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 2014-04-16 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.511526.1 [access date] Exopolymer and carbohydrate production by diatoms with growth. Dataset Description: &lt;p&gt;Data from laboratory experiment on exopolymer and carbohydrate production by the diatoms &lt;em&gt;Thalassiosira weissflogii&lt;/em&gt; (CCMP 1051),&lt;em&gt; Skeletonema marinoi&lt;/em&gt; (CCMP 1332), and &lt;em&gt;Cylindrotheca closterium&lt;/em&gt; (CCMP 339) during the growth to death phases of the cultures.&lt;/p&gt; &lt;p&gt;&lt;em&gt;Related references:&lt;/em&gt;&lt;br /&gt; Chen, J. 2014. Factors affecting carbohydrate production and the formation of transparent exopolymer particles (TEP) by diatoms. Ph.D. dissertation, Texas A&amp;amp;M University, College Station, TX.&lt;/p&gt; Methods and Sampling: &lt;p&gt;&lt;strong&gt;Growth of the diatoms&lt;/strong&gt;&lt;br /&gt; The diatoms &lt;em&gt;Thalassiosira weissflogii&lt;/em&gt; (CCMP 1051), &lt;em&gt;Skeletonema marinoi&lt;/em&gt; (CCMP 1332), and &lt;em&gt;Cylindrotheca closterium&lt;/em&gt; (CCMP 339) were grown in artificial seawater (Berges et al. 2001) in batch culture at 20 °C with 100 µM&amp;nbsp; NaNO&lt;sub&gt;3&lt;/sub&gt;, 200 µM of NaH&lt;sub&gt;2&lt;/sub&gt;PO&lt;sub&gt;4&lt;/sub&gt;·H&lt;sub&gt;2&lt;/sub&gt;O, and 200 µM of Na&lt;sub&gt;2&lt;/sub&gt;SiO&lt;sub&gt;3&lt;/sub&gt;·9H&lt;sub&gt;2&lt;/sub&gt;O. Illumination was on a 14 h:10 h light:dark cycle at a photon flux density of 160 µmol m&lt;sup&gt;-2&lt;/sup&gt; s&lt;sup&gt;-1&lt;/sup&gt;. There were three replicate cultures. Cultures were sampled during both the growth and death of the cultures over several weeks.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Measures of diatom abundance and biomass&lt;/strong&gt;&lt;br /&gt; 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). 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).&lt;br /&gt; &lt;br /&gt; 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 &lt;em&gt;T. wessiflogii&lt;/em&gt; and &lt;em&gt;S. marinoi&lt;/em&gt; were cylinders. The volume of &lt;em&gt;Cylindrotheca closterium&lt;/em&gt; was estimated assuming that its shape was equivalent to two cones.&lt;br /&gt; &lt;br /&gt; Chlorophyll &lt;em&gt;a&lt;/em&gt; concentration 90% acetone extractions from biomass retained on GF/C (Whatman) were measured using a Turner Designs 700 fluorometer, which was calibrated using chlorophyll &lt;em&gt;a&lt;/em&gt; standards (Sigma) (Arar and Collins 1997). The extract was diluted with 90% acetone if the chl &lt;em&gt;a&lt;/em&gt; concentration were too high.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Bacteria abundance&lt;/strong&gt;&lt;br /&gt; 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 µg ml&lt;sup&gt;-1&lt;/sup&gt;.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Carbohydrate analysis&lt;/strong&gt;&lt;br /&gt; 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.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Cell permeability&lt;/strong&gt;&lt;br /&gt; 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.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;TEP staining and analysis&lt;/strong&gt;&lt;br /&gt; 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).&lt;/p&gt; &lt;p&gt;&lt;strong&gt;CSP staining and analysis&lt;/strong&gt;&lt;br /&gt; 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).&lt;/p&gt; &lt;p&gt;&lt;strong&gt;References cited&lt;/strong&gt;&lt;br /&gt; Alldredge, A. L., Passow, U. &amp;amp; Logan B. E. 1993. The abundance and significance of a class of large, transparent organic particles in the ocean. &lt;em&gt;Deep-Sea Res&lt;/em&gt;.&lt;em&gt; Oceanogr&lt;/em&gt;.,&lt;em&gt; I. &lt;/em&gt;40: 1131-1140. doi:&lt;a href=&quot;http://dx.doi.org/10.1016/0967-0637%2893%2990129-Q&quot; target=&quot;_blank&quot;&gt;10.1016/0967-0637(93)90129-Q&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Arar, E. J. &amp;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.&lt;/p&gt; &lt;p&gt;Berges, J. A., Franklin D. J. &amp;amp; Harrison, P. J. 2001. Evolution of an artificial seawater medium: Improvements in enriched seawater, artificial water over the last two decades. &lt;em&gt;J. Phycol&lt;/em&gt;. 37:1138-1145. doi:&lt;a href=&quot;http://dx.doi.org/10.1046/j.1529-8817.2001.01052.x&quot; target=&quot;_blank&quot;&gt;10.1046/j.1529-8817.2001.01052.x&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Dubois, M., Gilles, K. A., Hamilton, J. K., Rebers, P. A. &amp;amp; Smith, F. 1956. Colorimetric method for determination of sugars and related substances. &lt;em&gt;Anal. Chem.&lt;/em&gt; 28: 350–356. doi:&lt;a href=&quot;http://dx.doi.org/10.1021/ac60111a017&quot; target=&quot;_blank&quot;&gt;10.1021/ac60111a017&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Engel, A. 2009. Determination of Marine Gel Particles. &lt;em&gt;In&lt;/em&gt; Wurl, O. [Ed.] &lt;em&gt;Practical Guidelines for the Analysis of Seawater&lt;/em&gt;. CRC Press, Taylor &amp;amp; Francis Group, Boca Raton, Florida, pp.125-142.&lt;/p&gt; &lt;p&gt;Franklin, D. J., Airs, R. L., Fernandes, M., Bell, T. G., Bongaerts, R. J., Berges, J. A. &amp;amp; Malin, G. 2012. Identification of senescence and death in &lt;em&gt;Emiliania huxleyi&lt;/em&gt; and &lt;em&gt;Thalassiosira pseudonana&lt;/em&gt;: Cell staining, chlorophyll alterations, and dimethylsulfoniopropionate (DMSP) metabolism. &lt;em&gt;Limnol. Oceanogr.&lt;/em&gt; 57: 305–317. doi:10.4319/lo.2012.57.1.0305&lt;/p&gt; &lt;p&gt;Guillard, R. R. L. &amp;amp; Sieracki, M. S. 2005. Counting cells in cultures with the light microscope. &lt;em&gt;In&lt;/em&gt; Andersen R. A. [Ed.] &lt;em&gt;Algal Culturing Techniques&lt;/em&gt;. Elsevier Academic Press, Burlington, MA, pp. 239-252.&lt;/p&gt; &lt;p&gt;Logan, B. E., Grossart, H. P. &amp;amp; Simon, M. 1994. Direct observation of phytoplankton, TEP and aggregates on polycarbonate filters using brightfield microscopy. &lt;em&gt;J. Plankton Res.&lt;/em&gt;16: 1811-1815.doi:&lt;a href=&quot;http://dx.doi.org/10.1093/plankt/16.12.1811&quot; target=&quot;_blank&quot;&gt;10.1093/plankt/16.12.1811&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Menden-Deuer S. &amp;amp; Lessard, E. J. 2000. Carbon to volume relationships for dinoflagellates, diatoms, and other protists plankton. &lt;em&gt;Limnol. Oceanogr.&lt;/em&gt; 45: 569- 579. doi:&lt;a href=&quot;http://dx.doi.org/10.4319/lo.2000.45.3.0569&quot; target=&quot;_blank&quot;&gt;10.4319/lo.2000.45.3.0569&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Myklestad, S. M., Skanoy, E., Hestmann S. 1997. A sensitive and rapid method for analysis of dissolved mono- and polysaccharides in seawater. &lt;em&gt;Marine Chemistry&lt;/em&gt; 56: 279-286. doi:&lt;a href=&quot;http://dx.doi.org/10.1016/S0304-4203(96)00074-6&quot; target=&quot;_blank&quot;&gt;10.1016/S0304-4203(96)00074-6&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Parsons, T. R., Maita, Y. &amp;amp; Lalli, C. M. 1984. A Manual of Chemical and Biological Methods for Seawater Analysis. &lt;em&gt;Pergamon Press&lt;/em&gt;, Oxford, UK.&lt;/p&gt; &lt;p&gt;Passow, U. &amp;amp; Alldredge, A. L. 1995. A dye-binding assay for the spectrophotometric measurement of transparent exopolymer particles (TEP). &lt;em&gt;Limnol. Oceanogr.&lt;/em&gt; 40: 1326-1335. doi:&lt;a href=&quot;http://dx.doi.org/10.4319/lo.1995.40.7.1326&quot; target=&quot;_blank&quot;&gt;10.4319/lo.1995.40.7.1326&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Porter, K. G. &amp;amp; Feig, Y. S. 1980. The use of DAPI for identifying and counting aquatic microflora. &lt;em&gt;Limnol. Oceanogr.&lt;/em&gt; 25:943–948. doi:&lt;a href=&quot;http://dx.doi.org/10.4319/lo.1980.25.5.0943&quot; target=&quot;_blank&quot;&gt;10.4319/lo.1980.25.5.0943&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Underwood, G. J. C., Paterson D. M., Parkes R. J. 1995. The measurement of microbial carbohydrate exopolymers from intertidal sediments. &lt;em&gt;Limnol. Oceanogr.&lt;/em&gt; 40: 1243-1253. doi:&lt;a href=&quot;http://dx.doi.org/10.4319/lo.1995.40.7.1243&quot; target=&quot;_blank&quot;&gt;10.4319/lo.1995.40.7.1243&lt;/a&gt;&lt;/p&gt; &lt;p&gt;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. &lt;em&gt;J. Phycol.&lt;/em&gt; 40: 293-304. doi:&lt;a href=&quot;http://dx.doi.org/10.1111/j.1529-8817.2004.03076.x&quot; target=&quot;_blank&quot;&gt;10.1111/j.1529-8817.2004.03076.x&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Veldhuis, M. J. W., Kraay, G. W. &amp;amp; Timmermans, K. R. 2001. Cell death in phytoplankton: correlation between changes in membrane permeability, photosynthetic activity, pigmentation and growth. &lt;em&gt;Eur. J. Phycol. &lt;/em&gt;36: 167–177. doi:&lt;a href=&quot;http://dx.doi.org/10.1080/09670260110001735318&quot; target=&quot;_blank&quot;&gt;10.1080/09670260110001735318&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Zack, G. W., Rogers, W.E., Latt S. A. 1977. Automatic-measurement of sister chromatid exchange frequency, &lt;em&gt;J. Histochem. Cytochem.&lt;/em&gt;, &lt;em&gt;25&lt;/em&gt;(7), 741-753. doi:&lt;a href=&quot;http://dx.doi.org/10.1177/25.7.70454&quot; target=&quot;_blank&quot;&gt;10.1177/25.7.70454&lt;/a&gt;&lt;/p&gt; 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 growth_phase day culture cell_abundance cell_vol_mean chla chla_per_cell chla_per_cell_vol tot_carb tot_carb_per_cell tot_carb_per_cell_vol colloidal_carb collodial_per_cell colloidal_per_cell_vol EPS_carb EPS_carb_per_cell EPS_carb_per_cell_vol HW_carb HW_carb_per_cell HW_carb_per_cell_vol HB_carb HB_carb_per_cell HB_carb_per_cell_vol residual_carb residual_carb_per_cell residual_carb_per_cell_vol TPTZ_intracell_mono TPTZ_extracell_mono TPTZ_intracell_polysacc TPTZ_extracell_polysacc TEP_conc_mean TEP_mean_size tot_TEP_area CSP_conc_mean CSP_mean_size tot_CSP_area stained_cells_pcnt bacteria bact_per_diatom Epifluorescence Microscope Hemocytometer Light Microscope Turner Designs 700 Fluorometer UV-Mini 1240 Spectrophotometer theme None, User defined species scientific name (binomial) No BCO-DMO term replicate diatom abundance chlorophyll a bacterial abundance featureType BCO-DMO Standard Parameters Fluorescence Microscope 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 2014-04-16 O&amp;M Building, Texas A&amp;M University, College Station, TX 77840 0 BCO-DMO catalogue of parameters from Experimental results: Exopolymer and carbohydrate production by diatoms with growth; 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/511537.rdf Name: species Units: dimensionless Description: <p>Species name.</p> http://lod.bco-dmo.org/id/dataset-parameter/511538.rdf Name: growth_phase Units: dimensionless Description: <p>Growth phase of the diatom (exponential, stationary, declining, death).</p> http://lod.bco-dmo.org/id/dataset-parameter/511539.rdf Name: day Units: dimensionless Description: <p>Day of the experiment.</p> http://lod.bco-dmo.org/id/dataset-parameter/511540.rdf Name: culture Units: dimensionless Description: <p>Identifier of the culture replicate.</p> http://lod.bco-dmo.org/id/dataset-parameter/511541.rdf Name: cell_abundance Units: cells per milliliter (mL-1) Description: <p>Cell count. Counts of 400 cells were made by transmitted light microscopy using a hemacytometer (Fuchs-Rosenthal ruling Hauser Scientific) (Guillard &amp; Sieracki 2005).</p> http://lod.bco-dmo.org/id/dataset-parameter/511542.rdf Name: cell_vol_mean Units: cubic micrometers (um^3) Description: <p>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.</p> http://lod.bco-dmo.org/id/dataset-parameter/511543.rdf Name: chla Units: micrograms per liter (ug L-1) Description: <p>Concentration of chlorophyll a measured by fluorescence (Arar &amp; Collins 1997; Method 445.0. EPA).</p> http://lod.bco-dmo.org/id/dataset-parameter/511544.rdf Name: chla_per_cell Units: picograms per cell (pg cell-1) Description: <p>Concentration of chlorophyll a per cell.</p> http://lod.bco-dmo.org/id/dataset-parameter/511545.rdf Name: chla_per_cell_vol Units: femtograms per cubic micrometer (fg um-3) Description: <p>Concentration of chlorophyll a per cell volume.</p> http://lod.bco-dmo.org/id/dataset-parameter/511546.rdf Name: tot_carb Units: micrograms per milliliter (ug mL-1) Description: <p>Total carbohydrate concentration measured using the PSA method (Dubois et al. 1956).</p> http://lod.bco-dmo.org/id/dataset-parameter/511547.rdf Name: tot_carb_per_cell Units: picograms per cell (pg cell-1) Description: <p>Total carbohydrate concentration per cell.</p> http://lod.bco-dmo.org/id/dataset-parameter/511548.rdf Name: tot_carb_per_cell_vol Units: femtograms per cubic micrometer (fg um-3) Description: <p>Total carbohydrate concentration per cell volume.</p> http://lod.bco-dmo.org/id/dataset-parameter/511549.rdf Name: colloidal_carb Units: micrograms per milliliter (ug mL-1) Description: <p>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).</p> http://lod.bco-dmo.org/id/dataset-parameter/511550.rdf Name: collodial_per_cell Units: picograms per cell (pg cell-1) Description: <p>Colloidal carbohydrate concentration per cell.</p> http://lod.bco-dmo.org/id/dataset-parameter/511551.rdf Name: colloidal_per_cell_vol Units: femtograms per cubic micrometer (fg um-3) Description: <p>Colloidal carbohydrate concentration per cell volume.</p> http://lod.bco-dmo.org/id/dataset-parameter/511552.rdf Name: EPS_carb Units: micrograms per milliliter (ug mL-1) Description: <p>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).</p> http://lod.bco-dmo.org/id/dataset-parameter/511553.rdf Name: EPS_carb_per_cell Units: picograms per cell (pg cell-1) Description: <p>Exopolymer (EPS) carbohydrate concentration per cell.</p> http://lod.bco-dmo.org/id/dataset-parameter/511554.rdf Name: EPS_carb_per_cell_vol Units: femtograms per cubic micrometer (fg um-3) Description: <p>Exopolymer (EPS) carbohydrate concentration per cell volume.</p> http://lod.bco-dmo.org/id/dataset-parameter/511555.rdf Name: HW_carb Units: micrograms per milliliter (ug mL-1) Description: <p>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).</p> http://lod.bco-dmo.org/id/dataset-parameter/511556.rdf Name: HW_carb_per_cell Units: picograms per cell (pg cell-1) Description: <p>Intracellular carbohydrate (hot water (HW) extraction) concentration per cell.</p> http://lod.bco-dmo.org/id/dataset-parameter/511557.rdf Name: HW_carb_per_cell_vol Units: femtograms per cubic micrometer (fg um-3) Description: <p>Intracellular carbohydrate (hot water (HW) extraction) concentration per cell volume.</p> http://lod.bco-dmo.org/id/dataset-parameter/511558.rdf Name: HB_carb Units: micrograms per milliliter (ug mL-1) Description: <p>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).</p> http://lod.bco-dmo.org/id/dataset-parameter/511559.rdf Name: HB_carb_per_cell Units: picograms per cell (pg cell-1) Description: <p>Cell-wall associated carbohydrate (hot bicarbonate (HB) extraction) concentration per cell.</p> http://lod.bco-dmo.org/id/dataset-parameter/511560.rdf Name: HB_carb_per_cell_vol Units: femtograms per cubic micrometer (fg um-3) Description: <p>Cell-wall associated carbohydrate (hot bicarbonate (HB) extraction) concentration per cell volume.</p> http://lod.bco-dmo.org/id/dataset-parameter/511561.rdf Name: residual_carb Units: micrograms per milliliter (ug mL-1) Description: <p>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).</p> http://lod.bco-dmo.org/id/dataset-parameter/511562.rdf Name: residual_carb_per_cell Units: picograms per cell (pg cell-1) Description: <p>Residual carbohydrate concentration per cell.</p> http://lod.bco-dmo.org/id/dataset-parameter/511563.rdf Name: residual_carb_per_cell_vol Units: femtograms per cubic micrometer (fg um-3) Description: <p>Residual carbohydrate concentration per cell volume.</p> http://lod.bco-dmo.org/id/dataset-parameter/511564.rdf Name: TPTZ_intracell_mono Units: micrograms per milliliter (ug mL-1) Description: <p>Intracellular monosaccharide concentration determined using the TPTZ method (Myklestad et al. 1997).</p> http://lod.bco-dmo.org/id/dataset-parameter/511565.rdf Name: TPTZ_extracell_mono Units: micrograms per milliliter (ug mL-1) Description: <p>Extracellular monosaccharide concentration determined using the TPTZ method (Myklestad et al. 1997).</p> http://lod.bco-dmo.org/id/dataset-parameter/511566.rdf Name: TPTZ_intracell_polysacc Units: micrograms per milliliter (ug mL-1) Description: <p>Intracellular polysaccharide concentration determined using the TPTZ method (Myklestad et al. 1997).</p> http://lod.bco-dmo.org/id/dataset-parameter/511567.rdf Name: TPTZ_extracell_polysacc Units: micrograms per milliliter (ug mL-1) Description: <p>Extracellular polysaccharide concentration determined using the TPTZ method (Myklestad et al. 1997).</p> http://lod.bco-dmo.org/id/dataset-parameter/511568.rdf Name: TEP_conc_mean Units: TEP per milliliter (TEP mL-1) Description: <p>Mean transparent exopolymer particle (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/511569.rdf Name: TEP_mean_size Units: square micrometers (um^2) Description: <p>Mean size of Transparent exopolymer particles (TEP).</p> http://lod.bco-dmo.org/id/dataset-parameter/511570.rdf Name: tot_TEP_area Units: square millimeters per milliliter (mm^2 mL-1) Description: <p>Total TEP area.</p> http://lod.bco-dmo.org/id/dataset-parameter/511571.rdf Name: CSP_conc_mean Units: CSP per milliliter (mL-1) Description: <p>Mean coomassie staining particle (CSP) concentration. CSP retained on 0.4 polycarbonate filters and stained with Coomassie briliant blue blue (Long &amp; Azam 1996).</p> http://lod.bco-dmo.org/id/dataset-parameter/511572.rdf Name: CSP_mean_size Units: square micrometers (um^2) Description: <p>Mean size of coomassie staining particle (CSP).</p> http://lod.bco-dmo.org/id/dataset-parameter/511573.rdf Name: tot_CSP_area Units: square millimeters per milliliter (mm^2 mL-1) Description: <p>Total CSP area.</p> http://lod.bco-dmo.org/id/dataset-parameter/511574.rdf Name: stained_cells_pcnt Units: percent (%) Description: <p>% 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.</p> http://lod.bco-dmo.org/id/dataset-parameter/511575.rdf Name: bacteria Units: cells per milliliter (mL-1) Description: <p>Bacteria abundance determined by DAPI staining and counts using an epifluorescence microscope (Porter &amp; Feig 1980).</p> http://lod.bco-dmo.org/id/dataset-parameter/511576.rdf Name: bact_per_diatom Units: dimensionless Description: <p>Bacteria abundance per diatom.</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 19390 https://darchive.mblwhoilibrary.org/bitstream/1912/24876/1/dataset-511526_growth-phase-exopolymers__v1.tsv download https://doi.org/10.1575/1912/bco-dmo.511526.1 download onLine dataset &lt;p&gt;&lt;strong&gt;Growth of the diatoms&lt;/strong&gt;&lt;br /&gt; The diatoms &lt;em&gt;Thalassiosira weissflogii&lt;/em&gt; (CCMP 1051), &lt;em&gt;Skeletonema marinoi&lt;/em&gt; (CCMP 1332), and &lt;em&gt;Cylindrotheca closterium&lt;/em&gt; (CCMP 339) were grown in artificial seawater (Berges et al. 2001) in batch culture at 20 °C with 100 µM&amp;nbsp; NaNO&lt;sub&gt;3&lt;/sub&gt;, 200 µM of NaH&lt;sub&gt;2&lt;/sub&gt;PO&lt;sub&gt;4&lt;/sub&gt;·H&lt;sub&gt;2&lt;/sub&gt;O, and 200 µM of Na&lt;sub&gt;2&lt;/sub&gt;SiO&lt;sub&gt;3&lt;/sub&gt;·9H&lt;sub&gt;2&lt;/sub&gt;O. Illumination was on a 14 h:10 h light:dark cycle at a photon flux density of 160 µmol m&lt;sup&gt;-2&lt;/sup&gt; s&lt;sup&gt;-1&lt;/sup&gt;. There were three replicate cultures. Cultures were sampled during both the growth and death of the cultures over several weeks.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Measures of diatom abundance and biomass&lt;/strong&gt;&lt;br /&gt; 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). 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).&lt;br /&gt; &lt;br /&gt; 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 &lt;em&gt;T. wessiflogii&lt;/em&gt; and &lt;em&gt;S. marinoi&lt;/em&gt; were cylinders. The volume of &lt;em&gt;Cylindrotheca closterium&lt;/em&gt; was estimated assuming that its shape was equivalent to two cones.&lt;br /&gt; &lt;br /&gt; Chlorophyll &lt;em&gt;a&lt;/em&gt; concentration 90% acetone extractions from biomass retained on GF/C (Whatman) were measured using a Turner Designs 700 fluorometer, which was calibrated using chlorophyll &lt;em&gt;a&lt;/em&gt; standards (Sigma) (Arar and Collins 1997). The extract was diluted with 90% acetone if the chl &lt;em&gt;a&lt;/em&gt; concentration were too high.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Bacteria abundance&lt;/strong&gt;&lt;br /&gt; 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 µg ml&lt;sup&gt;-1&lt;/sup&gt;.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Carbohydrate analysis&lt;/strong&gt;&lt;br /&gt; 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.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Cell permeability&lt;/strong&gt;&lt;br /&gt; 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.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;TEP staining and analysis&lt;/strong&gt;&lt;br /&gt; 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).&lt;/p&gt; &lt;p&gt;&lt;strong&gt;CSP staining and analysis&lt;/strong&gt;&lt;br /&gt; 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).&lt;/p&gt; &lt;p&gt;&lt;strong&gt;References cited&lt;/strong&gt;&lt;br /&gt; Alldredge, A. L., Passow, U. &amp;amp; Logan B. E. 1993. The abundance and significance of a class of large, transparent organic particles in the ocean. &lt;em&gt;Deep-Sea Res&lt;/em&gt;.&lt;em&gt; Oceanogr&lt;/em&gt;.,&lt;em&gt; I. &lt;/em&gt;40: 1131-1140. doi:&lt;a href=&quot;http://dx.doi.org/10.1016/0967-0637%2893%2990129-Q&quot; target=&quot;_blank&quot;&gt;10.1016/0967-0637(93)90129-Q&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Arar, E. J. &amp;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.&lt;/p&gt; &lt;p&gt;Berges, J. A., Franklin D. J. &amp;amp; Harrison, P. J. 2001. Evolution of an artificial seawater medium: Improvements in enriched seawater, artificial water over the last two decades. &lt;em&gt;J. Phycol&lt;/em&gt;. 37:1138-1145. doi:&lt;a href=&quot;http://dx.doi.org/10.1046/j.1529-8817.2001.01052.x&quot; target=&quot;_blank&quot;&gt;10.1046/j.1529-8817.2001.01052.x&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Dubois, M., Gilles, K. A., Hamilton, J. K., Rebers, P. A. &amp;amp; Smith, F. 1956. Colorimetric method for determination of sugars and related substances. &lt;em&gt;Anal. Chem.&lt;/em&gt; 28: 350–356. doi:&lt;a href=&quot;http://dx.doi.org/10.1021/ac60111a017&quot; target=&quot;_blank&quot;&gt;10.1021/ac60111a017&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Engel, A. 2009. Determination of Marine Gel Particles. &lt;em&gt;In&lt;/em&gt; Wurl, O. [Ed.] &lt;em&gt;Practical Guidelines for the Analysis of Seawater&lt;/em&gt;. CRC Press, Taylor &amp;amp; Francis Group, Boca Raton, Florida, pp.125-142.&lt;/p&gt; &lt;p&gt;Franklin, D. J., Airs, R. L., Fernandes, M., Bell, T. G., Bongaerts, R. J., Berges, J. A. &amp;amp; Malin, G. 2012. Identification of senescence and death in &lt;em&gt;Emiliania huxleyi&lt;/em&gt; and &lt;em&gt;Thalassiosira pseudonana&lt;/em&gt;: Cell staining, chlorophyll alterations, and dimethylsulfoniopropionate (DMSP) metabolism. &lt;em&gt;Limnol. Oceanogr.&lt;/em&gt; 57: 305–317. doi:10.4319/lo.2012.57.1.0305&lt;/p&gt; &lt;p&gt;Guillard, R. R. L. &amp;amp; Sieracki, M. S. 2005. Counting cells in cultures with the light microscope. &lt;em&gt;In&lt;/em&gt; Andersen R. A. [Ed.] &lt;em&gt;Algal Culturing Techniques&lt;/em&gt;. Elsevier Academic Press, Burlington, MA, pp. 239-252.&lt;/p&gt; &lt;p&gt;Logan, B. E., Grossart, H. P. &amp;amp; Simon, M. 1994. Direct observation of phytoplankton, TEP and aggregates on polycarbonate filters using brightfield microscopy. &lt;em&gt;J. Plankton Res.&lt;/em&gt;16: 1811-1815.doi:&lt;a href=&quot;http://dx.doi.org/10.1093/plankt/16.12.1811&quot; target=&quot;_blank&quot;&gt;10.1093/plankt/16.12.1811&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Menden-Deuer S. &amp;amp; Lessard, E. J. 2000. Carbon to volume relationships for dinoflagellates, diatoms, and other protists plankton. &lt;em&gt;Limnol. Oceanogr.&lt;/em&gt; 45: 569- 579. doi:&lt;a href=&quot;http://dx.doi.org/10.4319/lo.2000.45.3.0569&quot; target=&quot;_blank&quot;&gt;10.4319/lo.2000.45.3.0569&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Myklestad, S. M., Skanoy, E., Hestmann S. 1997. A sensitive and rapid method for analysis of dissolved mono- and polysaccharides in seawater. &lt;em&gt;Marine Chemistry&lt;/em&gt; 56: 279-286. doi:&lt;a href=&quot;http://dx.doi.org/10.1016/S0304-4203(96)00074-6&quot; target=&quot;_blank&quot;&gt;10.1016/S0304-4203(96)00074-6&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Parsons, T. R., Maita, Y. &amp;amp; Lalli, C. M. 1984. A Manual of Chemical and Biological Methods for Seawater Analysis. &lt;em&gt;Pergamon Press&lt;/em&gt;, Oxford, UK.&lt;/p&gt; &lt;p&gt;Passow, U. &amp;amp; Alldredge, A. L. 1995. A dye-binding assay for the spectrophotometric measurement of transparent exopolymer particles (TEP). &lt;em&gt;Limnol. Oceanogr.&lt;/em&gt; 40: 1326-1335. doi:&lt;a href=&quot;http://dx.doi.org/10.4319/lo.1995.40.7.1326&quot; target=&quot;_blank&quot;&gt;10.4319/lo.1995.40.7.1326&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Porter, K. G. &amp;amp; Feig, Y. S. 1980. The use of DAPI for identifying and counting aquatic microflora. &lt;em&gt;Limnol. Oceanogr.&lt;/em&gt; 25:943–948. doi:&lt;a href=&quot;http://dx.doi.org/10.4319/lo.1980.25.5.0943&quot; target=&quot;_blank&quot;&gt;10.4319/lo.1980.25.5.0943&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Underwood, G. J. C., Paterson D. M., Parkes R. J. 1995. The measurement of microbial carbohydrate exopolymers from intertidal sediments. &lt;em&gt;Limnol. Oceanogr.&lt;/em&gt; 40: 1243-1253. doi:&lt;a href=&quot;http://dx.doi.org/10.4319/lo.1995.40.7.1243&quot; target=&quot;_blank&quot;&gt;10.4319/lo.1995.40.7.1243&lt;/a&gt;&lt;/p&gt; &lt;p&gt;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. &lt;em&gt;J. Phycol.&lt;/em&gt; 40: 293-304. doi:&lt;a href=&quot;http://dx.doi.org/10.1111/j.1529-8817.2004.03076.x&quot; target=&quot;_blank&quot;&gt;10.1111/j.1529-8817.2004.03076.x&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Veldhuis, M. J. W., Kraay, G. W. &amp;amp; Timmermans, K. R. 2001. Cell death in phytoplankton: correlation between changes in membrane permeability, photosynthetic activity, pigmentation and growth. &lt;em&gt;Eur. J. Phycol. &lt;/em&gt;36: 167–177. doi:&lt;a href=&quot;http://dx.doi.org/10.1080/09670260110001735318&quot; target=&quot;_blank&quot;&gt;10.1080/09670260110001735318&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Zack, G. W., Rogers, W.E., Latt S. A. 1977. Automatic-measurement of sister chromatid exchange frequency, &lt;em&gt;J. Histochem. Cytochem.&lt;/em&gt;, &lt;em&gt;25&lt;/em&gt;(7), 741-753. doi:&lt;a href=&quot;http://dx.doi.org/10.1177/25.7.70454&quot; target=&quot;_blank&quot;&gt;10.1177/25.7.70454&lt;/a&gt;&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;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 we 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.&lt;/p&gt; 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:Bacteria were counted and 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/ Hemocytometer Hemocytometer PI Supplied Instrument Name: Hemocytometer PI Supplied 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. 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 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. 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). 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). 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