http://lod.bco-dmo.org/id/dataset/858513 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 2021-08-13 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Metabolic potential for heterotrophic utilization of a large array of organics by coccolithophores determined through experiments at Bigelow Laboratory for Ocean Sciences using BioLog Eco-plates 2021-10-05 publication 2021-10-05 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2021-10-05 publication https://doi.org/10.26008/1912/bco-dmo.858513.1 William M. Balch Bigelow Laboratory for Ocean Sciences 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: Godrijan, J., Drapeau, D. T., Balch, W. M. (2021) Metabolic potential for heterotrophic utilization of a large array of organics by coccolithophores determined through experiments at Bigelow Laboratory for Ocean Sciences using BioLog Eco-plates. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2021-10-05 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.858513.2 [access date] BioLog Eco-plates experiment - Metabolic potential Dataset Description: Methods and Sampling: &lt;p&gt;BioLog Eco-plates contained 96-wells, prefilled with: (1) a colorless tetrazolium dye that reduces to a violet formazin if the substrate is oxidized, (2) triplicates of 31 different organic compounds in equimolar quantities, and (3) triplicate water blanks as a control for airborne bacterial contamination. We used a single coccolithophore strain in each plate. We started each experiment by inoculating a 96-well plate with 100 μL of log-phase cell suspension from each log phase culture. We carried out all inoculations under subdued light and all incubations in complete darkness.&amp;nbsp;At time-zero (T0), 24 h, 48 h, and 72 h, we measured the reduced violet tetrazolium dye absorption on a FilterMax F5 multimode plate reader (Molecular Devices, LLC, San Jose, CA, U.S.A.) for absorption at 595 nm. We interpreted the increasing optical density at 595 nm as heterotrophic metabolism of the organic compound by the coccolithophore cultures. (Note: For two strains, CCMP298 and CCMP 3337, T72 was not performed, but the measurement was instead taken at T120.)&lt;/p&gt; &lt;p&gt;Several limitations to the BioLog Eco-plates should be noted (Stefanowicz 2006). One limitation is that the technique assumes that the uptake of each substrate is independent from any other (i.e., two substrates are not used in a synergistic fashion). The technique also assumes the concentrations of the substrates in each well of the microtiter plate are optimal for the organism in question, rather than too high (i.e., inhibitory) or low (limiting) based on the organism's specific uptake kinetic parameters. Therefore, we could not make any inferences on the uptake kinetics of DOC utilization using the microtiter plates. Furthermore, ions in seawater (specifically Ca&lt;sup&gt;++&lt;/sup&gt;) can cause false positives in BioLog Eco-plates (Pierce et al. 2014). It is critical to lower the Ca&lt;sup&gt;++&lt;/sup&gt; concentration from 10 mmol L⁻¹ (normal concentration in seawater) to ~ 2.5 mmol L⁻¹ in order to eliminate false positives (Pierce et al. 2014). The BioLog Company suggests doing this with chelators. An alternative method was suggested by Tuchman et al. (2006) in which the cultures were centrifuged and pelleted to separate them from the nutrient-rich media, which might contain other growth-inducing substrates. Then the pellet should be resuspended in nutrient-free saline solution. We followed these latter recommendations and resuspended the coccolithophores in ASW with 2.5 mmol L⁻¹ calcium.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1635748 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1635748 completed William M. Balch Bigelow Laboratory for Ocean Sciences 207-315-2567 60 Bigelow Drive East Boothbay ME 04544 USA bbalch@bigelow.org pointOfContact asNeeded Dataset Version: 2 Unknown Strain_code Species Isolated_Date Deposit_Date Collection_Site_Lat Collection_Site_Long Collection_Site_Sea Substrate T0_AVG T0_SD T24_AVG T24_SD T48_AVG T48_SD T72_AVG T72_SD T120_AVG T120_SD FilterMax F5 multimode plate reader theme None, User defined taxon_code species date latitude longitude region treatment absorbance featureType BCO-DMO Standard Parameters plate reader instrument BCO-DMO Standard Instruments 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. Coccolithophore Mixotrophy https://osprey.bco-dmo.org/project/648016 Coccolithophore Mixotrophy <p><strong>NSF Award Abstract</strong><br /> Coccolithophores are single-cell algae that are covered with limestone (calcite) plates called coccoliths. They may make up most of the phytoplankton biomass in the oceans. Coccolithophores are generally considered to be autotrophs, meaning that they use photosynthesis to fix carbon into both soft plant tissue and hard minerogenic calcite, using sunlight as an energy source ("autotrophic"). However, there is an increasing body of evidence that coccolithophores are "mixotrophic", meaning that they can fix carbon from photosynthesis as well as grow in darkness by engulfing small organic particles plus taking up other simple carbon molecules from seawater. The extent to which Coccolithophores engage in mixotrophy can influence the transfer of carbon into the deep sea. This work is fundamentally directed at quantifying coccolithophore mixotrophy -- the ability to use dissolved and reduce carbon compounds for energy -- using lab and field experiments plus clarifying its relevance to ocean biology and chemistry. This work will generate broader impacts in three areas: 1) Undergraduate training: Two REU undergraduates will be trained during the project. The student in the second year will participate in the research cruise. 2) Café Scientifique program: This work will be presented in Bigelow Laboratory’s Café Scientifique program. These are free public gatherings where the public is invited to join in a conversation about the latest ideas and issues in ocean science and technology. 3) Digital E-Book: We propose to make a digital E-book to specifically highlight and explain mixotrophy within coccolithophores. Images of mixotrophic coccolithophores would be the primary visual elements of the book. The E-book will be publicly available and distributed to our educational affiliate, Colby College. The goal of the book is to further communicate the intricacies of the microbial world, food web dynamics, plus their relationship to the global carbon cycle, to inspire interest, education, and curiosity about these amazing life forms.</p> <p>Coccolithophores can significantly affect the draw-down of atmospheric CO2 and they can transfer CO2 from the surface ocean and sequester it in the deep sea via two carbon pump mechanisms: (1) The "alkalinity pump" (also known as the calcium carbonate pump), where coccolithophores in the surface ocean take up dissolved inorganic carbon (DIC; primarily a form called bicarbonate, a major constituent of ocean alkalinity). They convert half to CO2, which is either fixed as plant biomass or released as the gas, and half is synthesized into their mineral coccoliths. Thus, coccolithophore calcification can actually increase surface CO2 on short time scales (i.e. weeks). However, over months to years, coccoliths sink below thousands of meters, where they dissolve and release bicarbonate back into deep water. Thus, sinking coccoliths essentially "pump" bicarbonate alkalinity from surface to deep waters, where that carbon remains isolated in the abyssal depths for thousands of years. (2) The "biological pump", where the ballasting effect of the dense limestone coccoliths speeds the sinking of organic, soft-tissue debris (particulate organic carbon or POC), essentially "pumping" this soft carbon tissue to depth. The biological pump ultimately decreases surface CO₂. The soft-tissue and alkalinity pumps reinforce each other in maintaining a vertical gradient in DIC (more down deep than at the surface) but they oppose each other in terms of the air-sea exchange of CO₂. Thus, the net effect of coccolithophores on atmospheric CO2 depends on the balance of their CO₂-raising effect associated with the alkalinity pump and their CO2-lowering effect associated with the soft-tissue biological pump. It is virtually always assumed that coccolith particulate inorganic carbon (PIC) originates exclusively from dissolved inorganic carbon (DIC, as bicarbonate), not dissolved organic carbon (DOC). The goal of this proposal is to describe a) the potential uptake and assimilation of an array of DOC compounds by coccolithophores, b) the rates of uptake, and potential incorporation of DOC by coccolithophores into PIC coccoliths, which, if true, would represent a major shift in the alkalinity pump paradigm. This work is fundamentally directed at quantifying coccolithophore mixotrophy using lab and field experiments plus clarifying its relevance to ocean biology and chemistry. There have been a number of technological advances to address this issue, all of which will be applied in this work. The investigators will: (a) screen coccolithophore cultures for the uptake and assimilation of a large array of DOC molecules, (b) perform tracer experiments with specific DOC molecules in order to examine uptake at environmentally-realistic concentrations, (c) measure fixation of DOC into organic tissue, separately from that fixed into PIC coccoliths, (d) separate coccolithophores from other phytoplankton and bacteria using flow cytometry and e) distinguish the modes of nutrition in these sorted coccolithophore cells. This work will fundamentally advance the state of knowledge of coccolithophore mixotrophy in the sea and address the balance of carbon that coccolithophores derived from autotrophic versus heterotrophic sources.</p> Cocco-Mix largerWorkCitation project eng; USA oceans -113.56 47.8333 -13.5833 59.5 1951-01-01 2013-11-20 Partially lab-based, with field sites in Gulf of Maine and NW Atlantic between the Gulf of Maine and Bermuda 0 BCO-DMO catalogue of parameters from Metabolic potential for heterotrophic utilization of a large array of organics by coccolithophores determined through experiments at Bigelow Laboratory for Ocean Sciences using BioLog Eco-plates 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/858749.rdf Name: Strain_code Units: unitless Description: <p>Strain code (CCMP) from the National Center for Marine Algae and Microbiota (NCMA)</p> http://lod.bco-dmo.org/id/dataset-parameter/858750.rdf Name: Species Units: unitless Description: <p>Species name</p> http://lod.bco-dmo.org/id/dataset-parameter/858751.rdf Name: Isolated_Date Units: unitless Description: <p>Strain isolation date; format: YYYY-MM-DD</p> http://lod.bco-dmo.org/id/dataset-parameter/858752.rdf Name: Deposit_Date Units: unitless Description: <p>Strain deposit date; format: YYYY-MM-DD</p> http://lod.bco-dmo.org/id/dataset-parameter/858753.rdf Name: Collection_Site_Lat Units: decimal degrees North Description: <p>Latitude of strain collection site; positive values = North</p> http://lod.bco-dmo.org/id/dataset-parameter/858754.rdf Name: Collection_Site_Long Units: decimal degrees East Description: <p>Longitude of strain collection site; positive values = East</p> http://lod.bco-dmo.org/id/dataset-parameter/858755.rdf Name: Collection_Site_Sea Units: unitless Description: <p>Body of water where strain was collected</p> http://lod.bco-dmo.org/id/dataset-parameter/858756.rdf Name: Substrate Units: unitless Description: <p>Substrate</p> http://lod.bco-dmo.org/id/dataset-parameter/858757.rdf Name: T0_AVG Units: unitless Description: <p>Average absorption at time-zero (T0)</p> http://lod.bco-dmo.org/id/dataset-parameter/858758.rdf Name: T0_SD Units: unitless Description: <p>Standard deviation of absorption at time-zero (T0)</p> http://lod.bco-dmo.org/id/dataset-parameter/858759.rdf Name: T24_AVG Units: unitless Description: <p>Average absorption at 24 hours</p> http://lod.bco-dmo.org/id/dataset-parameter/858760.rdf Name: T24_SD Units: unitless Description: <p>Standard deviation of absorption at 24 hours</p> http://lod.bco-dmo.org/id/dataset-parameter/858761.rdf Name: T48_AVG Units: unitless Description: <p>Average absorption at 48 hours</p> http://lod.bco-dmo.org/id/dataset-parameter/858762.rdf Name: T48_SD Units: unitless Description: <p>Standard deviation of absorption at 48 hours</p> http://lod.bco-dmo.org/id/dataset-parameter/858763.rdf Name: T72_AVG Units: unitless Description: <p>Average absorption at 72 hours</p> http://lod.bco-dmo.org/id/dataset-parameter/858764.rdf Name: T72_SD Units: unitless Description: <p>Standard deviation of absorption at 72 hours</p> http://lod.bco-dmo.org/id/dataset-parameter/858765.rdf Name: T120_AVG Units: unitless Description: <p>Average absorption at 120 hours</p> http://lod.bco-dmo.org/id/dataset-parameter/858766.rdf Name: T120_SD Units: unitless Description: <p>Standard deviation of absorption at 120 hours</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 115731 https://darchive.mblwhoilibrary.org/bitstream/1912/27608/1/dataset-858513_biolog-eco-plates-experiment-metabolic-potential__v2.tsv download 115731 https://darchive.mblwhoilibrary.org/bitstream/1912/27606/1/dataset-858513_biolog-eco-plates-experiment-metabolic-potential__v1.tsv download https://doi.org/10.26008/1912/bco-dmo.858513.1 download onLine dataset &lt;p&gt;BioLog Eco-plates contained 96-wells, prefilled with: (1) a colorless tetrazolium dye that reduces to a violet formazin if the substrate is oxidized, (2) triplicates of 31 different organic compounds in equimolar quantities, and (3) triplicate water blanks as a control for airborne bacterial contamination. We used a single coccolithophore strain in each plate. We started each experiment by inoculating a 96-well plate with 100 μL of log-phase cell suspension from each log phase culture. We carried out all inoculations under subdued light and all incubations in complete darkness.&amp;nbsp;At time-zero (T0), 24 h, 48 h, and 72 h, we measured the reduced violet tetrazolium dye absorption on a FilterMax F5 multimode plate reader (Molecular Devices, LLC, San Jose, CA, U.S.A.) for absorption at 595 nm. We interpreted the increasing optical density at 595 nm as heterotrophic metabolism of the organic compound by the coccolithophore cultures. (Note: For two strains, CCMP298 and CCMP 3337, T72 was not performed, but the measurement was instead taken at T120.)&lt;/p&gt; &lt;p&gt;Several limitations to the BioLog Eco-plates should be noted (Stefanowicz 2006). One limitation is that the technique assumes that the uptake of each substrate is independent from any other (i.e., two substrates are not used in a synergistic fashion). The technique also assumes the concentrations of the substrates in each well of the microtiter plate are optimal for the organism in question, rather than too high (i.e., inhibitory) or low (limiting) based on the organism's specific uptake kinetic parameters. Therefore, we could not make any inferences on the uptake kinetics of DOC utilization using the microtiter plates. Furthermore, ions in seawater (specifically Ca&lt;sup&gt;++&lt;/sup&gt;) can cause false positives in BioLog Eco-plates (Pierce et al. 2014). It is critical to lower the Ca&lt;sup&gt;++&lt;/sup&gt; concentration from 10 mmol L⁻¹ (normal concentration in seawater) to ~ 2.5 mmol L⁻¹ in order to eliminate false positives (Pierce et al. 2014). The BioLog Company suggests doing this with chelators. An alternative method was suggested by Tuchman et al. (2006) in which the cultures were centrifuged and pelleted to separate them from the nutrient-rich media, which might contain other growth-inducing substrates. Then the pellet should be resuspended in nutrient-free saline solution. We followed these latter recommendations and resuspended the coccolithophores in ASW with 2.5 mmol L⁻¹ calcium.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;&lt;strong&gt;Data Processing:&lt;/strong&gt;&lt;br /&gt; The potential utilization of each organic compound was expressed as the average compound color development (ACCD). We averaged the absorption observed at five points across the center of each well at each time point and subtracted the average water control well. We then calculated the mean absorbance of replicate wells for each compound. The ACCD was computed as the percentage of the absorbance of each compound over the sum of absorbance of all compounds on a plate.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;BCO-DMO Processing:&lt;/strong&gt;&lt;br /&gt; - concatenated data from separate Excel sheets into one dataset;&lt;br /&gt; - joined the strain information from original file &quot;CCMP_cocco_strains.xlsx&quot; to the rest of the dataset, matching on the Strain_code field;&lt;br /&gt; - renamed fields to conform with BCO-DMO naming conventions;&lt;br /&gt; - replaced 'n.d.' with 'nd' (no data);&lt;br /&gt; - converted dates to YYYY-MM-DD format;&lt;br /&gt; - removed directionals from latitude and longitude column to allow for column to be typed as numeric;&lt;br /&gt; - removed comma in D,L-α-Glycerol-Phosphate in Substrate column to allow for download as a .csv;&lt;br /&gt; - replaced spaces in Species column and Collection_Site_Sea column with underscores to allow for sorting;&lt;br /&gt; &amp;nbsp;- rounded data as requested by data provider.&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 FilterMax F5 multimode plate reader FilterMax F5 multimode plate reader PI Supplied Instrument Name: FilterMax F5 multimode plate reader PI Supplied Instrument Description:FilterMax F5 multimode plate reader (Molecular Devices, LLC, San Jose, CA, U.S.A.). Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.