http://lod.bco-dmo.org/id/dataset/674277
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
2017-01-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Synechococcus cell silica uptake from cultures with added nutrients from laboratory experiments at the Dauphin Island Sea Lab between 2013 and 2015 (Si_in_Syn project)
2017-12-04
publication
2017-12-04
revision
BCO-DMO Linked Data URI
2017-12-04
creation
http://lod.bco-dmo.org/id/dataset/674277
Jeffrey W. Krause
Dauphin Island Sea Lab
principalInvestigator
Mark A. Brzezinski
University of California-Santa Barbara
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: Krause, J. W., Brzezinski, M. A. (2017) Synechococcus cell silica uptake from cultures with added nutrients from laboratory experiments at the Dauphin Island Sea Lab between 2013 and 2015 (Si_in_Syn project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-12-04 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/674277 [access date]
Synechococcus cell silica uptake from cultures with added nutrients Dataset Description: <p>The effect of nutrients other than Si on the rate of Si accumulation was examined to better understand the factors controlling cellular Si content in&nbsp;<em>Synechococcus</em>. &nbsp;This dataset contains&nbsp;Synechococcus&nbsp;cyanobacteria&nbsp;silica uptake&nbsp;rates from cultures grown in Sargasso Sea water with no additions or&nbsp;additions of all f/2 media nutrients, f/2 media vitamins and trace metals, phosphate, nitrate, or silicic acid. &nbsp;Experiments took place at the Krause Lab at Dauphin Island Sea Laboratory (30.2501,-88.0788) between March 2013 to August&nbsp;2015.</p>
<p>These results are also presented in the following paper:</p>
<p>Brzezinski, M. A., Krause, J. W., Baines, S. B., Collier, J. L., Ohnemus, D. C. and Twining, B. S. (2017), Patterns and regulation of silicon accumulation in Synechococcus spp.. J. Phycol., 53: 746–761. doi:<a href="http://doi.org/10.1111/jpy.12545" target="_blank">10.1111/jpy.12545</a></p> Methods and Sampling: <p>Monocultures of Synechococcus clone 1333&nbsp;were used to examine variation and controls on Si quotas and rates of Si accumulation. &nbsp;The culture&nbsp;was procured from the National Center for Marine Algae and Microbiota (NCMA) at the Bigelow Laboratory for Ocean Sciences in Boothbay Harbor, Maine. &nbsp;This&nbsp;clone&nbsp;are also available in other culture collections and has various strain names. Here it is referred to by its NCMA strain number 1333 (a.k.a. CCMP number). &nbsp;</p>
<p>Cells were preconditioned in f/2 Sargasso seawater medium with 120 uM silicic acid.&nbsp; Inocula for experimental cultures were prepared by centrifuging and resuspending aliquots of culture into unamended surface Sargasso seawater (two centrifuge/resuspension cycles) to dilute the medium silicic acid.&nbsp; The carry-over of dissolved silicic acid with the cell inoculum was variable resulting in increases in [Si(OH)4] ranging from 1 - 3 uM when cells were added to experimental culture vessels.&nbsp; The specific centrifuging time and g-force were shown not to affect growth rate in cells relative to those added to fresh media without being concentrated (data not shown).&nbsp;</p>
<p>Cells were incubated at&nbsp;21C with low light 65 microeinsteins per second per square meter (uE/m2/s) without bubbling. A&nbsp;12 h&nbsp;light:12 h dark photocycle was used. &nbsp;Additions of individual components of the f/2 media were made: +NO<sub>3</sub>, +PO<sub>4</sub>, +vitamins &amp; trace metals, +Si, +All constituents, and a control consisting of only aged Sargasso Sea water with triplicate measurements per treatment. &nbsp;Cells were incubated for an additional four hours after incubation.</p>
<p>Each incubation was terminated by filtration and processed for measurement of 32Si activity following Krause et al. (2011).&nbsp; Briefly, Synechococcus cells were filtered onto 0.2 µm polycarbonate membrane filters, the filters mounted on nylon disc planchettes, air dried, covered with mylar film and secured to the planchettes with nylon rings.&nbsp; After aging for 120 days, secular equilibrium between 32Si and its daughter 32P was achieved and 32Si activity was determined using gas-flow proportional counting using GM 25-5 multicounters (Risø National Laboratory, Technical University of Denmark).&nbsp;&nbsp;</p>
<p>Full details of culturing and experimental methods are described in Brzezinski et al. (in review). (as of 05 Jan 2017)</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1335012 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1135012
completed
Jeffrey W. Krause
Dauphin Island Sea Lab
251-861-2141 x2289
101 Bienville Blvd
Dauphin Island
AL
36528
USA
jkrause@disl.edu
pointOfContact
Mark A. Brzezinski
University of California-Santa Barbara
805-893-7061
UCSB Marine Science Institute Bldg 520 Rm 4002 Fl 4L
Santa Barbara
CA
93106
USA
mark.brzezinski@lifesci.ucsb.edu
pointOfContact
asNeeded
Unknown
clone_id
clone_lat
clone_lon
treatment
treatment_descrip
uptake_rate
GM 25-5 multicounter
theme
None, User defined
sample identification
latitude
longitude
treatment
Silicon
featureType
BCO-DMO Standard Parameters
GM multicounter
instrument
BCO-DMO Standard Instruments
Krause_DISL_2013-2015
service
Deployment Activity
Dauphin Island Sea Lab
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.
Understanding the Role of Picocyanobacteria in the Marine Silicate Cycle
https://osprey.bco-dmo.org/project/544555
Understanding the Role of Picocyanobacteria in the Marine Silicate Cycle
<p><em>Extracted from the NSF award abstract:</em></p>
<p>INTELECTUAL MERIT: The investigators will follow-up on their discovery of significant accumulation of silicon by marine picocyanobacteria of the genus Synechococcus to assess the contribution of these organisms to the cycling of biogenic silica in the ocean. Oceanographers have long assumed that diatoms are the dominant marine organisms controlling the cycling of silica in the ocean. Recently, however, single-cell analyses of picocyanobacterial cells from field samples surprisingly revealed the presence of substantial amounts of silicon within Synechococcus. The contribution of Synechococcus to biogenic silica often rivaled that of living diatoms in the two systems examined. Moreover, size fractionation of biogenic silica indicates that up to 25% of biogenic silica can exist in the picoplanktonic size fraction. Given that picocyanobacteria dominate phytoplankton biomass and primary production over much of the world's ocean, these findings raise significant questions about the factors controlling the marine silica cycle globally, as well as the proper interpretation of biogenic silica measurements, Si:N ratios in particulate matter, and ratios of silicate and nitrate depletion. It also suggests that picocyanobacterial populations may be subject to previously unknown constraints on their productivity.</p>
<p>The project will have both laboratory and field components. Because cellular Si varies substantially among the field-collected samples and laboratory strains so far analyzed, the laboratory component will document variability in Si uptake and cellular Si concentrations, while determining what role physiological and phylogenetic factors play in this variability. The investigators will use strains of Synechococcus for which there are already genome sequences. Laboratory experiments will 1) use 32Si radiotracer uptake experiments to assess the degree of variability in Si content and Si uptake kinetics among strains of Synechococcus acclimated to different levels of silicate, 2) characterize the intracellular distribution and chemistry of silicon within cells using fractionation techniques, density centrifugation, electron microscopy and x-ray absorption spectroscopy, and 3) use bioinformatic analyses of published genomes to determine whether uptake of Si can be predicted based on phylogenetic relationships, to identify candidate genes involved in cyanobacterial Si metabolism, and to develop probes for community structure that can be related to cellular Si content. Field work at the Bermuda Atlantic Time Series (BATS) site will assess the contribution of Synechococcus and diatoms to total biogenic silica in surface waters at times of the year when the former are typically dominant. Field measurements will include size fractionation of biogenic silica biomass and Si uptake, and synchrotron-based x-ray fluorescence microscopy, and the phylogenetic composition of the Synechococcus assemblage.</p>
<p>BROADER IMPACTS: This project has the potential to drive a major paradigm shift in our understanding of the marine silicon cycle. In addition, one PhD student will be trained at Stony Brook. Each PI will provide research experience to a number of undergraduates working on original research projects for credit, as a part of an REU program or as the basis for undergraduate theses. Stony Brook research programs for undergraduates are supported with summer research money from the Undergraduate Research and Creative Activities (URECA) program, and draw on its very diverse student body. The investigators will also engage promising high school level students through several residential programs that the PIs have been a part of in the past. These include the BLOOM program at Bigelow and the Simons Summer Research Fellowship Program at Stony Brook. The PI has continuing relationship with a regional high school (Brentwood) with a high proportion of underrepresented minorities. PI Twining is involved in the Café Scientifique program at Bigelow. Baines will engage in similar outreach through the Center for Science and Mathematics Education (CESAME) sponsored Open Science Nights. Finally, PI Baines will cooperate with CESAMEs teacher education programs, with the aim of incorporating biological oceanography into K-12 curricula. PIs Krause and Brzezinski will incorporate aspects of phytoplankton ecology into UCSB's Oceans to Classroom Program that brings marine research at UCSB to life for over 18,000 K-12 students each year.</p>
Si_in_Syn
largerWorkCitation
project
eng; USA
oceans
Dauphin Island Sea Lab
-73.06
-73.06
41.19
41.19
2017-12-04
Samples collected in western North Atlantic Ocean between Puerto Rico, Bermuda, and Gulf of Maine.
0
BCO-DMO catalogue of parameters from Synechococcus cell silica uptake from cultures with added nutrients from laboratory experiments at the Dauphin Island Sea Lab between 2013 and 2015 (Si_in_Syn 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/675589.rdf
Name: clone_id
Units: unitless
Description: <p>Synechococcus clone identifier (NCMA strain and CCMP number)</p>
http://lod.bco-dmo.org/id/dataset-parameter/675590.rdf
Name: clone_lat
Units: decimal degrees
Description: <p>Latitude of the clone collection site</p>
http://lod.bco-dmo.org/id/dataset-parameter/675591.rdf
Name: clone_lon
Units: decimal degrees
Description: <p>Longitude of the clone collection site</p>
http://lod.bco-dmo.org/id/dataset-parameter/675592.rdf
Name: treatment
Units: unitless
Description: <p>Shorthand code for additions to culture medium (e.g. N means added nitrate)</p>
http://lod.bco-dmo.org/id/dataset-parameter/675593.rdf
Name: treatment_descrip
Units: untiless
Description: <p>Description of what additions were made to culture medium</p>
http://lod.bco-dmo.org/id/dataset-parameter/675644.rdf
Name: uptake_rate
Units: reciprocal hours (h-1)
Description: <p>Silica uptake rate</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
885
https://datadocs.bco-dmo.org/file/m77kmwRtPxKKBw/Culture_Media_Composition.csv
Culture_Media_Composition.csv
Primary data file for dataset ID 674277
download
https://osprey.bco-dmo.org/dataset/674277/data/download
download
onLine
dataset
<p>Monocultures of Synechococcus clone 1333&nbsp;were used to examine variation and controls on Si quotas and rates of Si accumulation. &nbsp;The culture&nbsp;was procured from the National Center for Marine Algae and Microbiota (NCMA) at the Bigelow Laboratory for Ocean Sciences in Boothbay Harbor, Maine. &nbsp;This&nbsp;clone&nbsp;are also available in other culture collections and has various strain names. Here it is referred to by its NCMA strain number 1333 (a.k.a. CCMP number). &nbsp;</p>
<p>Cells were preconditioned in f/2 Sargasso seawater medium with 120 uM silicic acid.&nbsp; Inocula for experimental cultures were prepared by centrifuging and resuspending aliquots of culture into unamended surface Sargasso seawater (two centrifuge/resuspension cycles) to dilute the medium silicic acid.&nbsp; The carry-over of dissolved silicic acid with the cell inoculum was variable resulting in increases in [Si(OH)4] ranging from 1 - 3 uM when cells were added to experimental culture vessels.&nbsp; The specific centrifuging time and g-force were shown not to affect growth rate in cells relative to those added to fresh media without being concentrated (data not shown).&nbsp;</p>
<p>Cells were incubated at&nbsp;21C with low light 65 microeinsteins per second per square meter (uE/m2/s) without bubbling. A&nbsp;12 h&nbsp;light:12 h dark photocycle was used. &nbsp;Additions of individual components of the f/2 media were made: +NO<sub>3</sub>, +PO<sub>4</sub>, +vitamins &amp; trace metals, +Si, +All constituents, and a control consisting of only aged Sargasso Sea water with triplicate measurements per treatment. &nbsp;Cells were incubated for an additional four hours after incubation.</p>
<p>Each incubation was terminated by filtration and processed for measurement of 32Si activity following Krause et al. (2011).&nbsp; Briefly, Synechococcus cells were filtered onto 0.2 µm polycarbonate membrane filters, the filters mounted on nylon disc planchettes, air dried, covered with mylar film and secured to the planchettes with nylon rings.&nbsp; After aging for 120 days, secular equilibrium between 32Si and its daughter 32P was achieved and 32Si activity was determined using gas-flow proportional counting using GM 25-5 multicounters (Risø National Laboratory, Technical University of Denmark).&nbsp;&nbsp;</p>
<p>Full details of culturing and experimental methods are described in Brzezinski et al. (in review). (as of 05 Jan 2017)</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Data Manager Processing Notes:</strong><br />
* added a conventional header with dataset name, PI name, version date<br />
* modified parameter names to conform with BCO-DMO naming conventions<br />
* blank values replaced with no data value 'nd'<br />
* latitude and longitude of Dauphin Island Sea Lab added to dataset<br />
* uptake rate limited to five decimal places</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
GM 25-5 multicounter
GM 25-5 multicounter
PI Supplied Instrument Name: GM 25-5 multicounter PI Supplied Instrument Description:GM 25-5 multicounters (Risø National Laboratory, Technical University of Denmark). Instrument Name: GM multicounter Instrument Short Name: Instrument Description: A gas flow multicounter (GM multicounter) is used for counting low-level beta doses. GM multicounters can be used for gas proportional counting of 32Si to 32P. For more information about GM multicounter usage see Krause et. al. 2011.
Deployment: Krause_DISL_2013-2015
Krause_DISL_2013-2015
lab Dauphin_Island_Sea_Lab
lab Dauphin_Island_Sea_Lab
laboratory
lab Dauphin_Island_Sea_Lab
lab Dauphin_Island_Sea_Lab
laboratory