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     data   graph     files  public Flow cytometry measurements from HHQ experiments conducted during the MesoHux mesocosm
experiment, May 2017, Bergen, Norway
   ?     I   M   background (external link) RSS BCO-DMO bcodmo_dataset_753431

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 Triplicate 5 mL samples were preserved for flow cytometry with 0.5%
glutaraldehyde (final concentration), incubated at 4\u00b0C for 10 min and
frozen (-80\u00b0C) until analysis (within 2-3 weeks; Kemp et al. 1993). To
calculate phytoplankton group abundances, 200 \u00b5l aliquots of fixed sample
were added to a 96-well plate and run on a Guava flow cytometer (Millipore).
Filtered seawater (0.45 \u00b5m) was run as a blank\u00a0and instrument-
specific beads were used to calibrate the cytometer. Samples were analyzed at
low flow rate (0.24 \u00b5l s-1) for 3 min. Three major phytoplankton groups
were distinguishable based on plots of forward scatter vs. orange
(phycoerythrin-containing, Synechococcus spp.) or red (pico- and
nanoeukaryotes) fluorescence signals (Worden and Binder 2003).\u00a0

Samples for enumerating bacteria were stained prior to running on the Guava in
0.5% v/v SybrGreen I DNA stain for 1 hour at room temperature in the dark.

Mesocosm treatment for all HHQ experiments was as follows:
Redfield: N:P added in a 16:1 ratio during the first 3 days of the
experiment, no shading

HHQ treatments here are as follows:
High HHQ - 100 ng mL-1 (410 uM) added to triplicate 5L bottles.
DMSO control - equivalent (v:v) DMSO added to triplicate 5L bottles.

\u00a0All bottles were incubated for 24h in a flow-through tank, that was
shaded to mimic in situ conditions. Chlorophyll samples were taken at T0 and
T24 for all experiments.

Data were processed in Excel with statistics run in Excel, R, or Matlab.
attribute NC_GLOBAL awards_0_award_nid String 709952
attribute NC_GLOBAL awards_0_award_number String OCE-1657898
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1657898 (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 David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String HHQ Flow Cytometry
from MesoHux mesocosm experiment, May 2017, Bergen, Norway
PI: E. Harvey (SkIO)
version: 2019-01-23
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 version 2.2d 13 Jun 2019
attribute NC_GLOBAL date_created String 2019-01-23T17:23:32Z
attribute NC_GLOBAL date_modified String 2019-03-14T19:39:56Z
attribute NC_GLOBAL defaultDataQuery String &time
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.753431.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/753431 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Niskin bottle
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Used to collect water samples.
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 753438
attribute NC_GLOBAL instruments_0_description String A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24 or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Niskin bottle
attribute NC_GLOBAL instruments_0_instrument_nid String 413
attribute NC_GLOBAL instruments_0_supplied_name String 5 L Niskin
attribute NC_GLOBAL instruments_1_acronym String Flow Cytometer
attribute NC_GLOBAL instruments_1_dataset_instrument_description String Used for cell counts
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 753444
attribute NC_GLOBAL instruments_1_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_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB37/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Flow Cytometer
attribute NC_GLOBAL instruments_1_instrument_nid String 660
attribute NC_GLOBAL instruments_1_supplied_name String Millipore Guava inCyte BG HT flow cytometer
attribute NC_GLOBAL keywords String 15um, bacteria, bco, bco-dmo, biological, chemical, data, dataset, date, dmo, erddap, experiment, Experiment_num, management, nanoeukaryotes, num, oceanography, office, phytoplankton, phytoplankton species, picoeukaryotes, preliminary, replication, sample, species, synechococcus, time, time2, total, Total_Phytoplankton_lt_15um
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/753431 (external link)
attribute NC_GLOBAL param_mapping String {'753431': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/753431/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Skidaway Institute of Oceanography
attribute NC_GLOBAL people_0_affiliation_acronym String SkIO
attribute NC_GLOBAL people_0_person_name String Dr Elizabeth Harvey
attribute NC_GLOBAL people_0_person_nid String 645518
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 University of Rhode Island
attribute NC_GLOBAL people_1_affiliation_acronym String URI
attribute NC_GLOBAL people_1_person_name String Dr David Rowley
attribute NC_GLOBAL people_1_person_nid String 709954
attribute NC_GLOBAL people_1_role String Co-Principal Investigator
attribute NC_GLOBAL people_1_role_type String originator
attribute NC_GLOBAL people_2_affiliation String Haverford College
attribute NC_GLOBAL people_2_affiliation_acronym String Haveford
attribute NC_GLOBAL people_2_person_name String Dr Kristen E. Whalen
attribute NC_GLOBAL people_2_person_nid String 709960
attribute NC_GLOBAL people_2_role String Co-Principal Investigator
attribute NC_GLOBAL people_2_role_type String originator
attribute NC_GLOBAL people_3_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_3_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_3_person_name String Nancy Copley
attribute NC_GLOBAL people_3_person_nid String 50396
attribute NC_GLOBAL people_3_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_3_role_type String related
attribute NC_GLOBAL project String Collaborative Research: Building a framework for the role of bacterial-derived chemical signals in mediating phytoplankton population dynamics
attribute NC_GLOBAL projects_0_acronym String HHQSignals
attribute NC_GLOBAL projects_0_description String NSF Abstract:
Bacteria and phytoplankton play a central role in the modification and flow of materials and nutrients through the marine environment. While it has been established that interactions between these two domains are complex, the mechanisms that underpin these interactions remain largely unknown. There is increasing recognition, however, that dissolved chemical cues govern these microbial interactions. This project focuses on establishing a mechanistic framework for how bacterially derived signaling molecules influence interactions between phytoplankton and bacteria. The quorum-sensing (QS) molecule, 2-heptyl-4-quinolone (HHQ) will be used as a model compound for these investigations. Previously published work suggests that exposure to very low levels of HHQ results in phytoplankton mortality. Gaining a mechanistic understanding of these ecologically important interactions will help to inform mathematical models for the accurate prediction of the cycling of material through the marine microbial loop. This work initiates a new, hybrid workshop-internship undergraduate research program in chemical ecology, with a focus
Bacteria and phytoplankton play a central role in the modification and flow of materials and nutrients through the marine environment. While it has been established that interactions between these two domains are complex, the mechanisms that underpin these interactions remain largely unknown. There is increasing recognition, however, that dissolved chemical cues govern these microbial interactions. This project focuses on establishing a mechanistic framework for how bacterially derived signaling molecules influence interactions between phytoplankton and bacteria. The quorum-sensing (QS) molecule, 2-heptyl-4-quinolone (HHQ) will be used as a model compound for these investigations. Previously published work suggests that exposure to very low levels of HHQ results in phytoplankton mortality. Gaining a mechanistic understanding of these ecologically important interactions will help to inform mathematical models for the accurate prediction of the cycling of material through the marine microbial loop. This work initiates a new, hybrid workshop-internship undergraduate research program in chemical ecology, with a focus into bacteria-phytoplankton interactions. Undergraduate students participate in an intense summer learning experience where research and field-based exercises are supplemented with short-lecture based modules. Students return to their home institutions and work closely with the PIs to conduct interdisciplinary research relating to the aims and scope of the summer research. This research also provides training and career development to two graduate students and a postdoctoral scientist.
Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and microbial trophic structure in the ocean. The intricate relationships between these two domains of life are mediated via excreted molecules that facilitate communication and determine competitive outcomes. Despite their predicted importance, identifying these released compounds has remained a challenge. The PIs recently identified a bacterial QS molecule, HHQ, produced by globally distributed marine gamma-proteobacteria, which induces phytoplankton mortality. The PIs therefore hypothesize that bacteria QS signals are critical drivers of phytoplankton population dynamics and, ultimately, biogeochemical fluxes. This project investigates the timing and magnitude of HHQ production, and the physiological and transcriptomic responses of susceptible phytoplankton species to HHQ exposure, and quantifies the influence of HHQ on natural algal and bacterial assemblages. The work connects laboratory and field-based experiments to understand the governance of chemical signaling on marine microbial interactions, and has the potential to yield broadly applicable insights into how microbial interactions influence biogeochemical fluxes in the marine environment.
attribute NC_GLOBAL projects_0_end_date String 2020-03
attribute NC_GLOBAL projects_0_geolocation String Bergen, Norway
attribute NC_GLOBAL projects_0_name String Collaborative Research: Building a framework for the role of bacterial-derived chemical signals in mediating phytoplankton population dynamics
attribute NC_GLOBAL projects_0_project_nid String 709948
attribute NC_GLOBAL projects_0_start_date String 2017-04
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 includes flow cytometry measurements from HHQ experiments conducted during the MesoHux mesocosm experiment, May 2017, Bergen, Norway. Microbial mesocosms were spiked with 2-heptyl-4-quinolone (HHQ).
attribute NC_GLOBAL title String Flow cytometry measurements from HHQ experiments conducted during the MesoHux mesocosm experiment, May 2017, Bergen, Norway
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5-beta
variable Date   String  
attribute Date description String sampling date formatted as Mon dd yyyy
attribute Date ioos_category String Time
attribute Date long_name String Date
attribute Date units String unitless
variable Sample   String  
attribute Sample description String sample identifier
attribute Sample ioos_category String Unknown
attribute Sample long_name String Sample
attribute Sample units String unitless
variable Experiment_num   byte  
attribute Experiment_num _FillValue byte 127
attribute Experiment_num actual_range byte 1, 8
attribute Experiment_num description String experiment number
attribute Experiment_num ioos_category String Unknown
attribute Experiment_num long_name String Experiment Num
attribute Experiment_num units String unitless
variable time2   byte  
attribute time2 _FillValue byte 127
attribute time2 actual_range byte 0, 24
attribute time2 description String time since start of experiment
attribute time2 ioos_category String Time
attribute time2 long_name String Time
attribute time2 units String hours
variable Replication   byte  
attribute Replication _FillValue byte 127
attribute Replication actual_range byte 1, 3
attribute Replication description String replicate number
attribute Replication ioos_category String Unknown
attribute Replication long_name String Replication
attribute Replication units String unitless
variable Bacteria   int  
attribute Bacteria _FillValue int 2147483647
attribute Bacteria actual_range int 517817, 2152006
attribute Bacteria description String number of bacterial cells
attribute Bacteria ioos_category String Unknown
attribute Bacteria long_name String Bacteria
attribute Bacteria units String cells/milliliter
variable Synechococcus   short  
attribute Synechococcus _FillValue short 32767
attribute Synechococcus actual_range short 420, 25704
attribute Synechococcus description String number of Synechococcus cells
attribute Synechococcus ioos_category String Unknown
attribute Synechococcus long_name String Synechococcus
attribute Synechococcus units String cells/milliliter
variable Picoeukaryotes   int  
attribute Picoeukaryotes _FillValue int 2147483647
attribute Picoeukaryotes actual_range int 551, 40121
attribute Picoeukaryotes description String number of Picoeukaryotes cells
attribute Picoeukaryotes ioos_category String Unknown
attribute Picoeukaryotes long_name String Picoeukaryotes
attribute Picoeukaryotes units String cells/milliliter
variable Nanoeukaryotes   short  
attribute Nanoeukaryotes _FillValue short 32767
attribute Nanoeukaryotes actual_range short 374, 32076
attribute Nanoeukaryotes description String number of Nanoeukaryotes cells
attribute Nanoeukaryotes ioos_category String Unknown
attribute Nanoeukaryotes long_name String Nanoeukaryotes
attribute Nanoeukaryotes units String cells/milliliter
variable Total_Phytoplankton_lt_15um   int  
attribute Total_Phytoplankton_lt_15um _FillValue int 2147483647
attribute Total_Phytoplankton_lt_15um actual_range int 2592, 73204
attribute Total_Phytoplankton_lt_15um description String total number of phytoplankton cells less than 15 microns in diameter
attribute Total_Phytoplankton_lt_15um ioos_category String Phytoplankton Species
attribute Total_Phytoplankton_lt_15um long_name String Total Phytoplankton Lt 15um
attribute Total_Phytoplankton_lt_15um 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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