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   set  data   graph     files  public Series 3A: Multiple stressor experiments on T. pseudonana (CCMP1014) \u2013 cell abundance by
flow cytometry
   ?     I   M   background (external link) RSS Subscribe BCO-DMO bcodmo_dataset_771421

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 Three CO2 concentrations were tested: 410 ppm, 750 ppm, and 1000 ppm
respectively. For each CO2 concentration, four temperatures were tested: 15
degrees-C, 20 degrees-C, 25 degrees-C, and 30 degrees-C. Within each
temperature, three light levels were tested: a sub-optimum light (SOL)
intensity of 60 umol photons \u00b7 m-2 \u00b7 s-1, an optimum light (OL)
intensity of 400 umol photons \u00b7 m-2 \u00b7 s-1 and an extreme light (EL)
intensity of 800 umol photons \u00b7 m-2 \u00b7 s-1. All lights were set at a
12 h day: 12 h dark cycle. For logistical reasons, experiments were partially
conducted in series, with all light treatments at two temperatures (either 15
degrees-C and 25 degrees-C or 20 degrees-C and 30 degrees-C) running
simultaneously. This was repeated for each CO2 concentration.

Experiments were conducted in Multicultivator MC-1000 OD units (Photon Systems
Instruments, Drasov, Czech Republic). Each unit consists of eight 85 ml test-
tubes immersed in a thermostated water bath, each independently illuminated by
an array of cool white LEDs set at specific intensity and timing. A 0.2um
filtered CO2-air mix (Praxair Distribution Inc.) was bubbled through sterile
artificial seawater, and the humidified gas mix was supplied to each tube via
gentle sparging through a 2um stainless steel diffuser. Flow rates were
gradually increased over the course of the incubation to compensate for the
DIC uptake of actively growing cells, and ranged from <0.04 Liters per minute
(LPM) at the start of the incubations to 0.08 LPM in each tube after 2 days.
For each CO2 and temperature level, replication was achieved by incubating
three tubes at sub-optimum light intensities, two tubes at optimum light
intensity, and three tubes at extreme light intensities. Each experiment was
split into two phases: An acclimation phase spanning 4 days, was used to
acclimate cultures to their new environment. Pre-acclimated, exponentially-
growing cultures were then inoculated into fresh media and incubated through a
3-day experimental phase during which assessments of growth, photophysiology,
and nutrient cycling were carried out daily. All sampling started 5 hours into
the daily light cycle to minimize the effects of diurnal cycles.

Experiments were conducted with artificial seawater (ASW) prepared using
previously described methods (Kester et. al 1967), and enriched with nitrate
(NO3), phosphate (PO4), silicic acid (Si[OH]4), at levels ensuring that the
cultures would remain nutrient-replete over the course of the experiment.
Trace metals and vitamins were added as in f/2 (Guillard 1975). The expected
DIC concentration and pH of the growth media was determined for the different
pCO2 and temperatures using the CO2SYS calculator (Pierrot et al. 2006), with
constants from Mehrbach et al. (1973, refit by Dickson & Millero 1987), and
inputs of temperature, salinity, total alkalinity (2376.5 umol \u00b7 kg-1),
pCO2, phosphate, and silicic acid. DIC levels in ASW at the start of each
phase of the experiments were manipulated by the addition of NaHCO3, and was
then maintained by bubbling a CO2-Air mix through the cultures over the course
of the experiments. The pH of the growth media was measured
spectrophometrically using the m-cresol purple method (Dickson 1993), and
adjusted using 0.1N HCl or 0.1M NaOH. The media was distributed into 75 ml
aliquots and each aliquot was inoculated with 5 ml of the T. pseudonana CCMP
1014 (TP1014) stock culture at the start of the experiments.

Flow cytometry:
Samples were fixed in Hexamethylenetetramine-buffered formaldehyde (final
concentration 1% v/v) and stored at 4 degrees C in the dark for a maximum of 4
days. Cell counts were confirmed to be unaffected over storage for up to a
week. Samples were analyzed on a Guava easyCyte HT Benchtop Flow Cytometer
(Millipore-Sigma, USA). All data acquisitions were done with logarithmic
signal amplification. Cytometer sample flow rates were kept low (0.24 uL
\u00b7 s-1) to accommodate high cell concentrations. Diatoms were identified
based on size and chlorophyll autofluorescence using the forward scatter
channel (FSC) and Red-FL (695/50 nm) channel respectively. Growth rates were
derived by fitting an exponential curve to cell concentrations vs. time for a
48-hour period during which cells exhibited exponential growth in the
experimental phase. Growth rates in treatments where cells did not grow, or
declined in abundance were listed as 0. Particle sizes (equivalent spherical
diameter in \u00b5m, ESD) were derived from FSC using size-calibration beads
of known diameters ranging from 2 \u00b5m to 10 um (Particle Size standard
kit, Spherotech Inc.).
attribute NC_GLOBAL awards_0_award_nid String 654346
attribute NC_GLOBAL awards_0_award_number String OCE-1538602
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1538602 (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 Michael E. Sieracki
attribute NC_GLOBAL awards_0_program_manager_nid String 50446
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Series 3A-2: Multiple stressor experiments on T. pseudonana (CCMP1014): cell abundance
PI: U. Passow, N. D'Souza (UCSB), E. Laws (LSU)
version date: 2019-06-17
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 2.3 19 Dec 2019
attribute NC_GLOBAL dataset_current_state String Final and no updates
attribute NC_GLOBAL date_created String 2019-06-19T20:45:04Z
attribute NC_GLOBAL date_modified String 2020-06-29T12:53:35Z
attribute NC_GLOBAL defaultDataQuery String &amp;time&lt;now
attribute NC_GLOBAL doi String 10.26008/1912/bco-dmo.771421.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/771421 (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 measure abundance and forward scatter (proxy for cell size).
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 771433
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 Guava easyCyte HT Benchtop Flow Cytometer (Millipore-Sigma, USA)
attribute NC_GLOBAL instruments_1_acronym String Spectrophotometer
attribute NC_GLOBAL instruments_1_dataset_instrument_description String Used to measure pH.
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 771432
attribute NC_GLOBAL instruments_1_description String An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples.
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB20/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Spectrophotometer
attribute NC_GLOBAL instruments_1_instrument_nid String 707
attribute NC_GLOBAL instruments_1_supplied_name String Genesys 10SVIS spectrophotometer
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Used for incubation of TP1014 cultures.
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 771429
attribute NC_GLOBAL instruments_2_description String An instrument used for the purpose of culturing small cells such as algae or bacteria. May provide temperature and light control and bubbled gas introduction.
attribute NC_GLOBAL instruments_2_instrument_name String Cell Cultivator
attribute NC_GLOBAL instruments_2_instrument_nid String 714540
attribute NC_GLOBAL instruments_2_supplied_name String Multicultivator MC-1000 OD (Qubit Systems)
attribute NC_GLOBAL keywords String abund, bco, bco-dmo, biological, carbon, carbon dioxide, chemical, co2, data, dataset, day, dioxide, dmo, EL_A_abund, EL_B_abund, EL_C_abund, erddap, management, oceanography, office, OL_A_abund, OL_B_abund, phase, preliminary, replicate, sol, SOL_A_abund, SOL_B_abund, SOL_C_abund, temperature
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/771421/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/771421 (external link)
attribute NC_GLOBAL param_mapping String {'771421': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/771421/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of California-Santa Barbara
attribute NC_GLOBAL people_0_affiliation_acronym String UCSB-MSI
attribute NC_GLOBAL people_0_person_name String Uta Passow
attribute NC_GLOBAL people_0_person_nid String 51317
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 Louisiana State University
attribute NC_GLOBAL people_1_affiliation_acronym String LSU-SC&E
attribute NC_GLOBAL people_1_person_name String Dr Edward Laws
attribute NC_GLOBAL people_1_person_nid String 50767
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 University of California-Santa Barbara
attribute NC_GLOBAL people_2_affiliation_acronym String UCSB-MSI
attribute NC_GLOBAL people_2_person_name String Nigel D'Souza
attribute NC_GLOBAL people_2_person_nid String 748936
attribute NC_GLOBAL people_2_role String Scientist
attribute NC_GLOBAL people_2_role_type String originator
attribute NC_GLOBAL people_3_affiliation String University of California-Santa Barbara
attribute NC_GLOBAL people_3_affiliation_acronym String UCSB-MSI
attribute NC_GLOBAL people_3_person_name String Nigel D'Souza
attribute NC_GLOBAL people_3_person_nid String 748936
attribute NC_GLOBAL people_3_role String Contact
attribute NC_GLOBAL people_3_role_type String related
attribute NC_GLOBAL people_4_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_4_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_4_person_name String Nancy Copley
attribute NC_GLOBAL people_4_person_nid String 50396
attribute NC_GLOBAL people_4_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_4_role_type String related
attribute NC_GLOBAL project String Stressors on Marine Phytoplankton
attribute NC_GLOBAL projects_0_acronym String Stressors on Marine Phytoplankton
attribute NC_GLOBAL projects_0_description String The overarching goal of this project is to develop a framework for understanding the response of phytoplankton to multiple environmental stresses. Marine phytoplankton, which are tiny algae, produce as much oxygen as terrestrial plants and provide food, directly or indirectly, to all marine animals. Their productivity is thus important both for global elemental cycles of oxygen and carbon, as well as for the productivity of the ocean. Globally the productivity of marine phytoplankton appears to be changing, but while we have some understanding of the response of phytoplankton to shifts in one environmental parameter at a time, like temperature, there is very little knowledge of their response to simultaneous changes in several parameters. Increased atmospheric carbon dioxide concentrations result in both ocean acidification and increased surface water temperatures. The latter in turn leads to greater ocean stratification and associated changes in light exposure and nutrient availability for the plankton. Recently it has become apparent that the response of phytoplankton to simultaneous changes in these growth parameters is not additive. For example, the effect of ocean acidification may be severe at one temperature-light combination and negligible at another. The researchers of this project will carry out experiments that will provide a theoretical understanding of the relevant interactions so that the impact of climate change on marine phytoplankton can be predicted in an informed way. This project will engage high schools students through training of a teacher and the development of a teaching unit. Undergraduate and graduate students will work directly on the research. A cartoon journalist will create a cartoon story on the research results to translate the findings to a broader general public audience.
Each phytoplankton species has the capability to acclimatize to changes in temperature, light, pCO2, and nutrient availability - at least within a finite range. However, the response of phytoplankton to multiple simultaneous stressors is frequently complex, because the effects on physiological responses are interactive. To date, no datasets exist for even a single species that could fully test the assumptions and implications of existing models of phytoplankton acclimation to multiple environmental stressors. The investigators will combine modeling analysis with laboratory experiments to investigate the combined influences of changes in pCO2, temperature, light, and nitrate availability on phytoplankton growth using cultures of open ocean and coastal diatom strains (Thalassiosira pseudonana) and an open ocean cyanobacteria species (Synechococcus sp.). The planned experiments represent ideal case studies of the complex and interactive effects of environmental conditions on organisms, and results will provide the basis for predictive modeling of the response of phytoplankton taxa to multiple environmental stresses.
attribute NC_GLOBAL projects_0_end_date String 2018-09
attribute NC_GLOBAL projects_0_name String Collaborative Research: Effects of multiple stressors on Marine Phytoplankton
attribute NC_GLOBAL projects_0_project_nid String 654347
attribute NC_GLOBAL projects_0_start_date String 2015-10
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String Phase,Replicate
attribute NC_GLOBAL summary String The experiments were designed to test the combined effects of three CO2 concentrations, four temperatures, and three light intensities on growth of the diatom T. pseudonana CCMP1014 in a multifactorial design. This dataset contains measurements of cell abundances measured by forward scatter.
attribute NC_GLOBAL title String Series 3A: Multiple stressor experiments on T. pseudonana (CCMP1014) \u2013 cell abundance by flow cytometry
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5
variable Phase   String  
attribute Phase bcodmo_name String sample_descrip
attribute Phase description String Indicates whether the sample was collected during the acclimation phase or the experiment phase of the experiment.
attribute Phase long_name String Phase
attribute Phase units String unitless
variable CO2   short  
attribute CO2 _FillValue short 32767
attribute CO2 actual_range short 410, 1000
attribute CO2 bcodmo_name String pCO2
attribute CO2 description String Indicates the concentration of CO2 in the CO2-Air mix that was bubbled through the samples over the course of the experiment
attribute CO2 long_name String CO2
attribute CO2 nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/PCO2C101/ (external link)
attribute CO2 units String parts per million (ppm)
variable Temperature   byte  
attribute Temperature _FillValue byte 127
attribute Temperature actual_range byte 15, 30
attribute Temperature bcodmo_name String temperature
attribute Temperature description String Indicates the temperature at which the samples were incubated.
attribute Temperature long_name String Temperature
attribute Temperature nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/ (external link)
attribute Temperature units String degrees Celsius
variable Day   String  
attribute Day bcodmo_name String days
attribute Day description String Indicates the timepoint (day) of sampling. D0 = day 0; D1 = day 1; etc.
attribute Day long_name String Day
attribute Day units String unitless
variable Replicate   String  
attribute Replicate bcodmo_name String replicate
attribute Replicate description String Indicates replication within a treatment. "NA" indicates "not applicable"
attribute Replicate long_name String Replicate
attribute Replicate units String unitless
variable SOL_A_abund   int  
attribute SOL_A_abund _FillValue int 2147483647
attribute SOL_A_abund actual_range int 3070, 308037
attribute SOL_A_abund bcodmo_name String abundance
attribute SOL_A_abund description String Cell abundance in replicate A incubated at sub optimum light (SOL)
attribute SOL_A_abund long_name String SOL A Abund
attribute SOL_A_abund nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute SOL_A_abund units String cells/milliliter
variable SOL_B_abund   int  
attribute SOL_B_abund _FillValue int 2147483647
attribute SOL_B_abund actual_range int 4978, 231584
attribute SOL_B_abund bcodmo_name String abundance
attribute SOL_B_abund description String Cell abundance in replicate B incubated at sub optimum light (SOL)
attribute SOL_B_abund long_name String SOL B Abund
attribute SOL_B_abund nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute SOL_B_abund units String cells/milliliter
variable SOL_C_abund   int  
attribute SOL_C_abund _FillValue int 2147483647
attribute SOL_C_abund actual_range int 4719, 267549
attribute SOL_C_abund bcodmo_name String abundance
attribute SOL_C_abund description String Cell abundance in replicate C incubated at sub optimum light (SOL)
attribute SOL_C_abund long_name String SOL C Abund
attribute SOL_C_abund nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute SOL_C_abund units String cells/milliliter
variable OL_A_abund   int  
attribute OL_A_abund _FillValue int 2147483647
attribute OL_A_abund actual_range int 24014, 2907077
attribute OL_A_abund bcodmo_name String abundance
attribute OL_A_abund description String Cell abundance in replicate A incubated at optimum light (OL)
attribute OL_A_abund long_name String OL A Abund
attribute OL_A_abund nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute OL_A_abund units String cells/milliliter
variable OL_B_abund   int  
attribute OL_B_abund _FillValue int 2147483647
attribute OL_B_abund actual_range int 26149, 2645518
attribute OL_B_abund bcodmo_name String abundance
attribute OL_B_abund description String Cell abundance in replicate B incubated at optimum light (OL)
attribute OL_B_abund long_name String OL B Abund
attribute OL_B_abund nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute OL_B_abund units String cells/milliliter
variable EL_A_abund   int  
attribute EL_A_abund _FillValue int 2147483647
attribute EL_A_abund actual_range int 34603, 2728738
attribute EL_A_abund bcodmo_name String abundance
attribute EL_A_abund description String Cell abundance in replicate A incubated at extreme light (EL)
attribute EL_A_abund long_name String EL A Abund
attribute EL_A_abund nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute EL_A_abund units String cells/milliliter
variable EL_B_abund   int  
attribute EL_B_abund _FillValue int 2147483647
attribute EL_B_abund actual_range int 33857, 2643524
attribute EL_B_abund bcodmo_name String abundance
attribute EL_B_abund description String Cell abundance in replicate B incubated at extreme light (EL)
attribute EL_B_abund long_name String EL B Abund
attribute EL_B_abund nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute EL_B_abund units String cells/milliliter
variable EL_C_abund   String  
attribute EL_C_abund bcodmo_name String abundance
attribute EL_C_abund description String Cell abundance in replicate C incubated at extreme light (EL)
attribute EL_C_abund long_name String EL C Abund
attribute EL_C_abund nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute EL_C_abund units String cells/milliliter

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.


 
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