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     data   graph     files  public Bacterial cell counts during CDOM monoculture experiment    ?     I   M   background (external link) RSS BCO-DMO bcodmo_dataset_748415

The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String 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 \u00b0C. Prior to analysis, thawed samples were pipetted through a cell
strainer (Flowmi, 70 \u00b5m 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 \u00b5m 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.
attribute NC_GLOBAL awards_0_award_nid String 734588
attribute NC_GLOBAL awards_0_award_number String OCE-1459406
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1459406 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Dr Henrietta N Edmonds
attribute NC_GLOBAL awards_0_program_manager_nid String 51517
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Bacterial cell counts during CDOM monoculture experiment, 2016
PI: K. Ziervogel (UNH)
version: 2018-10-16
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv.pl v1.0
attribute NC_GLOBAL date_created String 2018-10-17T19:59:29Z
attribute NC_GLOBAL date_modified String 2019-03-18T15:43:05Z
attribute NC_GLOBAL defaultDataQuery String &time
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.748415.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/748415 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Flow Cytometer
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Used to make cell counts.
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 748421
attribute NC_GLOBAL instruments_0_description String 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)
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB37/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Flow Cytometer
attribute NC_GLOBAL instruments_0_instrument_nid String 660
attribute NC_GLOBAL instruments_0_supplied_name String FACSCalibur flow cytometer (Becton-Dickson)
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, cell, cell_count, chemical, concentration, concentration_mL, concentration_uL, count, data, dataset, day, dmo, elapsed, end, erddap, flow, flow_rate, management, min, oceanography, office, point, preliminary, rate, start, statistics, taxon, taxonomy, time, time_elapsed_min, time_end, time_point_day, time_start, u, volume
attribute NC_GLOBAL license String The data may be used and redistributed for free but is not intended
for legal use, since it may contain inaccuracies. Neither the data
Contributor, ERD, NOAA, nor the United States Government, nor any
of their employees or contractors, makes any warranty, express or
implied, including warranties of merchantability and fitness for a
particular purpose, or assumes any legal liability for the accuracy,
completeness, or usefulness, of this information.
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/748415 (external link)
attribute NC_GLOBAL param_mapping String {'748415': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/748415/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of New Hampshire
attribute NC_GLOBAL people_0_affiliation_acronym String UNH
attribute NC_GLOBAL people_0_person_name String Kai Ziervogel
attribute NC_GLOBAL people_0_person_nid String 734583
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_1_person_name String Nancy Copley
attribute NC_GLOBAL people_1_person_nid String 50396
attribute NC_GLOBAL people_1_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL project String Collaborative Research: Planktonic Sources of Chromophoric Dissolved Organic Matter in Seawater
attribute NC_GLOBAL projects_0_acronym String PlankDOM
attribute NC_GLOBAL projects_0_description String NSF abstract:
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.
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.
attribute NC_GLOBAL projects_0_end_date String 2019-04
attribute NC_GLOBAL projects_0_geolocation String Northern Atlantic Ocean, 34.65 N, 69.63 W
attribute NC_GLOBAL projects_0_name String Collaborative Research: Planktonic Sources of Chromophoric Dissolved Organic Matter in Seawater
attribute NC_GLOBAL projects_0_project_nid String 734581
attribute NC_GLOBAL projects_0_start_date String 2015-05
attribute NC_GLOBAL publisher_name String Nancy Copley
attribute NC_GLOBAL publisher_role String BCO-DMO Data Manager(s)
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v29
attribute NC_GLOBAL summary String 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).\r\n\r\nThe data include bacterial cell counts during CDOM monoculture experiment. The phytoplankton cultures were Skeletonema sp., Leptocylindrus sp., Phaeocystis sp. and Coscinodiscus sp. Growth stages were initial, exponential, stationary, and degradation.
attribute NC_GLOBAL title String Bacterial cell counts during CDOM monoculture experiment
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.0-alpha
variable taxon   String  
attribute taxon description String phytoplankton
attribute taxon ioos_category String Taxonomy
attribute taxon long_name String Taxon
attribute taxon units String unitless
variable time_point_day   String  
attribute time_point_day description String growth phase (initial/exponential/stationary/degradation) and the number of days since the start of the experiment
attribute time_point_day ioos_category String Time
attribute time_point_day long_name String Time Point Day
attribute time_point_day units String days
variable time_start   String  
attribute time_start description String time at start of experiment
attribute time_start ioos_category String Time
attribute time_start long_name String Time Start
attribute time_start units String unitless
variable time_end   String  
attribute time_end description String time at end of experiment
attribute time_end ioos_category String Time
attribute time_end long_name String Time End
attribute time_end units String unitless
variable cell_count   int  
attribute cell_count _FillValue int 2147483647
attribute cell_count actual_range int 1526, 99900
attribute cell_count colorBarMaximum double 100.0
attribute cell_count colorBarMinimum double 0.0
attribute cell_count description String bacterial cell count as determined by flow cytometry
attribute cell_count ioos_category String Statistics
attribute cell_count long_name String Cell Count
attribute cell_count units String cells
variable flow_rate   byte  
attribute flow_rate _FillValue byte 127
attribute flow_rate actual_range byte 12, 60
attribute flow_rate description String flow rate of the sample
attribute flow_rate ioos_category String Unknown
attribute flow_rate long_name String Flow Rate
attribute flow_rate units String microliters/minute
variable time_elapsed_min   float  
attribute time_elapsed_min _FillValue float NaN
attribute time_elapsed_min actual_range float 1.0, 10.5
attribute time_elapsed_min description String flow count duration
attribute time_elapsed_min ioos_category String Time
attribute time_elapsed_min long_name String Time Elapsed Min
attribute time_elapsed_min units String minutes
variable volume   float  
attribute volume _FillValue float NaN
attribute volume actual_range float 12.6, 368.7
attribute volume description String volume of sample
attribute volume ioos_category String Unknown
attribute volume long_name String Volume
attribute volume units String microliters
variable concentration_uL   float  
attribute concentration_uL _FillValue float NaN
attribute concentration_uL actual_range float 17.3, 7928.6
attribute concentration_uL description String bacterial cell concentration
attribute concentration_uL ioos_category String Unknown
attribute concentration_uL long_name String Concentration U L
attribute concentration_uL units String cells/microliter
variable concentration_mL   float  
attribute concentration_mL _FillValue float NaN
attribute concentration_mL actual_range float 17000.0, 7900000.0
attribute concentration_mL description String bacterial cell concentration
attribute concentration_mL ioos_category String Unknown
attribute concentration_mL long_name String Concentration M L
attribute concentration_mL units String cells/milliliter

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.


 
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