http://lod.bco-dmo.org/id/dataset/748415
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
2018-10-17
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacterial cell counts during CDOM monoculture experiment
2018-10-17
publication
2018-10-17
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-04-01
publication
https://doi.org/10.1575/1912/bco-dmo.748415.1
Kai Ziervogel
University of New Hampshire
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: Ziervogel, K. (2018) Bacterial cell counts during CDOM monoculture experiment. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-10-17 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.748415.1 [access date]
Bacterial cell counts during CDOM monoculture experiment Dataset Description: <p>This dataset is from a laboratory experiment. Four phytoplankton cultures and their associated bacterial communities were incubated in replicate roller bottles (1.9 L) over 3-6 weeks under laboratory conditions. Bacterial dynamics in the culture bottles were measured and correlated with geochemical parameters to determine the role of bacterial activities on the formation of CDOM in the cultures (Kinsey et al., 2018, see below).</p>
<p>The data include&nbsp;bacterial cell counts during CDOM monoculture experiment. The phytoplankton cultures were Skeletonema sp., Leptocylindrus sp., Phaeocystis sp. and&nbsp;Coscinodiscus sp. Growth stages were initial, exponential, stationary, and degradation.</p> Methods and Sampling: <p>Bacterial cells were enumerated by flow cytometry. At each sampling point 1 mL of experimental or control water was fixed with 0.1% glutaraldehyde (final concentration) for 10 min at room temperature in the dark, and stored frozen at -80 °C. Prior to analysis, thawed samples were pipetted through a cell strainer (Flowmi, 70 µm porosity) and stained with SYBR Green I for 15 min on ice in the dark. Counts were performed with a FACSCalibur flow cytometer (Becton-Dickson) using fluorescent microspheres (Molecular Probes) of 1 µm in diameter as internal size standard. Cells were enumerated according to their right angle scatter and green fluorescence using the FloJo 7.6.1 software.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1459406 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1459406
completed
Kai Ziervogel
University of New Hampshire
6038625478
kai.ziervogel@unh.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
taxon
time_point_day
time_start
time_end
cell_count
flow_rate
time_elapsed_min
volume
concentration_uL
concentration_mL
FACSCalibur flow cytometer (Becton-Dickson)
theme
None, User defined
taxon
time_point
time_start
time_end
count
flow rate
duration
volume
cell_concentration
featureType
BCO-DMO Standard Parameters
Flow Cytometer
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.
Collaborative Research: Planktonic Sources of Chromophoric Dissolved Organic Matter in Seawater
https://osprey.bco-dmo.org/project/734581
Collaborative Research: Planktonic Sources of Chromophoric Dissolved Organic Matter in Seawater
<p>NSF abstract:</p>
<p>Chromophoric dissolved organic matter (CDOM) is a small but important fraction of the marine carbon pool that interacts with solar radiation and thus affects many photochemical and biological processes in the ocean. Despite its importance, the chemical basis for the formation of oceanic CDOM remains unclear. CDOM may be formed from two possible sources: 1) heterotrophic bacterial transformations of primary productivity (plankton-derived), or 2) terrestrially-derived. This project will examine the role of phytoplankton as a source of CDOM in the ocean by utilizing a powerful, new technique to measure particulate organic matter absorbance and fluorescence, discrete chemical measurements of probable precursors to planktonic CDOM, and enzymatic assays. Results of this research will provide new insights into the origin and production of planktonic CDOM and its transformation by heterotrophic bacteria. This research on CDOM will be shared broadly through a module at a North Carolina Aquarium, and streaming live feeds of shipboard activities to elementary school classrooms.</p>
<p>Terrestrial and oceanic dissolved organic matter (DOM) differ in their chemical composition. Laboratory and open-ocean observations suggest that bacterial transformation of phytoplankton DOM produces humic-like CDOM signals that are visually similar to those in terrestrial CDOM. However, prior studies of oceanic CDOM using absorbance and fluorescence fit an electronic interaction (EI) model of intramolecular charge transfer (CT) reactions between donor and acceptor molecules common to partially-oxidized terrestrial molecules found in humic substances. This project will test the hypothesis that phytoplankton and bacteria provide a source of donors and acceptors that are microbially-transformed and linked, enabling CT contacts between them and creating oceanic CDOM. To address this, researchers will systematically study phytoplankton growth, including marine snow formation. A new technique for measuring base-extracted POM (BEPOM) absorbance and fluorescence will be used to incorporate planktonic CDOM results into the EI model, and supplemented with measurements of its probable chemical precursors. These experiments will improve understanding of how the production of CDOM in the ocean is linked to the optics and chemistry of planktonic CDOM formation. Determining the time course and extent of phytoplankton POM and DOM transformation by heterotrophic bacteria during the same phytoplankton growth experiments will provide an in-depth understanding as to how bacterial transformation of marine snow-associated planktonic organic matter drives CDOM production throughout the ocean.</p>
PlankDOM
largerWorkCitation
project
eng; USA
biota
oceans
2016-08-01
2017-03-31
Northern Atlantic Ocean, 34.65 N, 69.63 W
0
BCO-DMO catalogue of parameters from Bacterial cell counts during CDOM monoculture experiment
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/748435.rdf
Name: taxon
Units: unitless
Description: <p>phytoplankton</p>
http://lod.bco-dmo.org/id/dataset-parameter/748436.rdf
Name: time_point_day
Units: days
Description: <p>growth phase (initial/exponential/stationary/degradation) and the number of days since the start of the experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/748437.rdf
Name: time_start
Units: unitless
Description: <p>time at start of experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/748438.rdf
Name: time_end
Units: unitless
Description: <p>time at end of experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/748439.rdf
Name: cell_count
Units: cells
Description: <p>bacterial cell count as determined by flow cytometry</p>
http://lod.bco-dmo.org/id/dataset-parameter/748440.rdf
Name: flow_rate
Units: microliters/minute
Description: <p>flow rate of the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/748441.rdf
Name: time_elapsed_min
Units: minutes
Description: <p>flow count duration</p>
http://lod.bco-dmo.org/id/dataset-parameter/748442.rdf
Name: volume
Units: microliters
Description: <p>volume of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/748443.rdf
Name: concentration_uL
Units: cells/microliter
Description: <p>bacterial cell concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/748444.rdf
Name: concentration_mL
Units: cells/milliliter
Description: <p>bacterial cell concentration</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
5428
https://darchive.mblwhoilibrary.org/bitstream/1912/23945/1/dataset-748415_bacterial-cell-counts__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.748415.1
download
onLine
dataset
<p>Bacterial cells were enumerated by flow cytometry. At each sampling point 1 mL of experimental or control water was fixed with 0.1% glutaraldehyde (final concentration) for 10 min at room temperature in the dark, and stored frozen at -80 °C. Prior to analysis, thawed samples were pipetted through a cell strainer (Flowmi, 70 µm porosity) and stained with SYBR Green I for 15 min on ice in the dark. Counts were performed with a FACSCalibur flow cytometer (Becton-Dickson) using fluorescent microspheres (Molecular Probes) of 1 µm in diameter as internal size standard. Cells were enumerated according to their right angle scatter and green fluorescence using the FloJo 7.6.1 software.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing Notes:<br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- repeated data in 'taxa' and 'time_point_day' columns&nbsp;to create a flat file</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
FACSCalibur flow cytometer (Becton-Dickson)
FACSCalibur flow cytometer (Becton-Dickson)
PI Supplied Instrument Name: FACSCalibur flow cytometer (Becton-Dickson) PI Supplied Instrument Description:Used to make cell counts. Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/