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Dataset Title:  Photosynthetic efficiency data from light stress in phytoplankton and
dinoflagellate grazing response experiments from July of 2015 to September of
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_779033)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Experiment_ID {
    String bcodmo_name "exp_id";
    String description "Shows letter (A-I) corresponding to experiment ID system used in Strom et al. (submitted), followed by experiment ID used in Strom lab.";
    String long_name "Experiment ID";
    String units "unitless";
  Experiment_Date {
    String bcodmo_name "date";
    String description "Calendar date on which experiment was conducted (ISO 8601 format yyyy-mm-dd)";
    String long_name "Experiment Date";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
    String source_name "Experiment_Date";
    String time_precision "1970-01-01";
    String units "unitless";
  Phytoplankton_Species {
    String bcodmo_name "animal_group";
    String description "Shows species and strain number (CCMP), where available, for phytoplankton used in light stress experiments; see species list for definitions (H. rotundata strain number refers to SCCAP culture collection)";
    String long_name "Phytoplankton Species";
    String units "unitless";
  Bottle_Type {
    String bcodmo_name "bottle";
    String description "Composition of bottles used for outdoor light exposure; PC = polycarbonate; Tef = Teflon";
    String long_name "Bottle Type";
    String units "unitless";
  Num_Screens {
    Byte _FillValue 127;
    Byte actual_range 0, 7;
    String bcodmo_name "sample_descrip";
    String description "Number of neutral density screen layers used to wrap bottles during outdoor exposure period";
    String long_name "Num Screens";
    String units "unitless";
  Total_PAR {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0897, 9.18;
    String bcodmo_name "PAR";
    String description "Total (cumulative) dose of photosynthetically active radiation received by the sample during the outdoor incubation period";
    String long_name "Total PAR";
    String units "mol photons m-2";
  Time_interval {
    String bcodmo_name "sample_descrip";
    String description "Designates whether the reported data were collected during the outdoor light exposure period (‘exposure’), or during the indoor, low light recovery period (‘recovery’)";
    String long_name "Time Interval";
    String units "unitless";
  Sampling_Time {
    Int16 _FillValue 32767;
    Int16 actual_range 0, 1568;
    String bcodmo_name "time_elapsed";
    String description "Shows the time (min) after initiation of exposure period when Fv/Fm samples were collected from incubation bottles.";
    String long_name "Sampling Time";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/";
    String units "count";
  Replicate_Number {
    Byte _FillValue 127;
    Byte actual_range 1, 4;
    String bcodmo_name "replicate";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "Identifies an individual replicate bottle";
    String long_name "Replicate Number";
    String units "unitless";
  FvFm {
    Float32 _FillValue NaN;
    Float32 actual_range -0.035, 0.784;
    String bcodmo_name "Fv2Fm";
    String description "Photosynthetic efficiency Fv/Fm (= variable fluorescence/maximum fluorescence) as measured using a Walz Water PAM fluorometer after 20 min dark acclimation at 15°C";
    String long_name "FV FM";
    String units "dimensionless";
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Phytoplankton light stress \\u2013 dinoflagellate grazing experiments
General information
Emiliania huxleyi strains were grown in f/50 without added Si, except for
CCMP1516 which was grown in f/2 for experiments D and I and in f/50 otherwise.
All other phytoplankton were grown in f/2 medium without added Si. Most
strains (designated CCMP) were obtained from the National Center for Marine
Algae and Microbiota except Heterocapsa rotundata, which was from the
Norwegian Culture Collection of Algae (NORCCA). Heterotrophic dinoflagellates
Amphidinium longum and Oxyrrhis marina were isolated from marine waters of the
Salish Sea, grown in ciliate medium (Gifford 1985), and maintained on a
mixture of phytoflagellate species. All cultures of any type were grown at a
salinity of 30 and a temperature of 15\\u00b0C. Phytoplankton were grown at a
range of low to moderate irradiances, depending on experiment on a 12L:12D
cycle. Heterotrophic dinoflagellates were grown at 10-20 \\u00b5mol photons m-2
s-1 on a 12L:12D cycle. Before use in experiments, dinoflagellate predators
were fed only Rhodomonas sp. 755 (A. longum) or Dunaliella tertiolecta (O.
marina) and allowed to consume these prey until they were nearly gone from the
Cells were exposed to experimental light treatments outdoors in a shallow tank
filled with flowing seawater supplied from nearby coastal waters. Temperature
during experiments was monitored at regular intervals with a thermometer
mounted in an unscreened incubation bottle, and ranged from 14-15\\u00b0C
except for Exp. A, where it averaged 17\\u00b0C. Light (incident
photosynthetically active radiation, or PAR) was measured with a Li-Cor
2\\u03c0 sensor, and logged at 5-min intervals so that total experiment light
dose (mol photons m-2) could be computed for specific incubation periods.
Control treatments were incubated in 60-ml polycarbonate bottles screened with
sufficient neutral density screening to approximate growth irradiances. Higher
light exposures were achieved using fewer (or no) layers of neutral density
screening, depending on experiment. Except for Exp. E, which used
polycarbonate bottles only, all high light treatments used 60-ml Teflon
bottles, which are transparent to UV wavelengths. In some experiments high
light treatments included both Teflon (UV-transparent) and polycarbonate (UV-
opaque) bottles, to isolate the effects of UV on protist responses. Bottles
were incubated at ~10 cm depth in the outdoor tank.
Experiments A-F exposed only the phytoplankton prey to the light stress
treatments (\\u2018Single_factor_grazing (prey-only)\\u2019 data set
dmo.org/dataset/779043\\\\\")). Cultures were divided into incubation bottles
(n=3-5 depending on experiment) and placed in the outdoor tank for 60-120 min.
Photosynthetic efficiency (Fv/Fm) was monitored before cells were taken
outside (t=0) and, after gentle mixing, at 30-min intervals during the
incubations (\\u2018FvFm\\u2019 data set [https://www.bco-
dmo.org/dataset/779033](\\\\\"https://www.bco-dmo.org/dataset/779033\\\\\")). After
outdoor exposure, phytoplankton were returned to the laboratory and a
subsample from each replicate was added to a corresponding 30-ml polycarbonate
bottle containing heterotrophic dinoflagellate predator A. longum to initiate
predation experiments. The remainder of the phytoplankton culture volume was
placed in an incubator at the culture growth irradiance level, and Fv/Fm
monitored at regular intervals during this recovery period.
Prey concentrations for predation experiments ranged from 5.0 x 103 cells ml-1
for dinoflagellate Heterocapsa rotundata to 5.0 x 104 cells ml-1 for the
various E. huxleyi strains. Prey biomass densities were equivalent for all
prey types, at ~500 \\u00b5g C liter-1. Carbon per cell for each phytoplankton
species was estimated from measured cell volumes and published C:volume
conversion factors (Menden-Deuer & Lessard 2000). A. longum concentrations
were ~1-2 x 103 cells ml-1, and O. marina concentration (Exp. I only, see
below) was 260 cells ml-1. For \\u2018prey only exposure\\u2019 experiments,
predation tests were conducted for 50 min in a laboratory incubator at
15\\u00b0C and ~50 \\u00b5mol photons m-2 s-1. For \\u2018prey and predator
exposure\\u2019 experiments, predation tests were conducted for 40-60 min under
either control or high light outdoor illumination conditions. Predation tests
were terminated by adding cells to cold 10% glutaraldehyde and DAPI stain
(final concentrations 0.5% and 0.1 \\u00b5g ml-1, respectively). After fixation
overnight in 4\\u00b0C and darkness, samples were filtered (3 or 5 \\u00b5m
pore-size polycarbonate filters), mounted on slides, and frozen for later
examination by epifluorescence microscopy. UV excitation was used to locate
and identify dinoflagellate predators from the DAPI-induced fluorescence of
their nuclei. Ingested prey were detected using blue light excitation, from
the orange (cryptophyte) or red (all other prey) autofluorescence of the prey
pigments inside the predator food vacuoles Because A. longum uses a peduncle
to feed on cryptophytes, rather than phagocytizing intact cells, the number of
ingested prey per predator cannot be quantified for this predator \\u2013 prey
combination. Therefore for all predator and prey types, each micrograzer cell
was scored as \\u2018feeding\\u2019 or \\u2018not feeding\\u2019. At least 250
micrograzers per slide were scored; predation intensity was calculated as
fraction of the population feeding (= # micrograzers with ingested prey /
total # micrograzers scored).
Experiments G, H, and I used a matrix design in which predators and prey were
exposed to experimental irradiances separately, then combined in various ways
and predation measured in outdoor irradiance conditions (\\u2018Prey and
predator exposure\\u2019 data set [https://www.bco-
Cultures of predators and prey were incubated in separate bottles for the
first 1-1.2 h of exposure time. After that, appropriate volumes of prey with
various exposure histories were introduced into predator bottles with various
exposure histories, and those predation tests incubated for an additional
40-60 min at the original predator irradiance level. Fv/Fm was monitored
throughout (\\u2018Photosynthetic efficiency\\u2019 data set [https://www.bco-
dmo.org/dataset/779033](\\\\\"https://www.bco-dmo.org/dataset/779033\\\\\")), first
in the original phytoplankton-only bottles and then in the remaining
phytoplankton volume after predation tests were initiated, and finally through
a recovery period in the laboratory as described above. At the end of the
predation test period, samples were fixed and slides prepared as described
For more information see Strom et al. (2020).";
    String awards_0_award_nid "614837";
    String awards_0_award_number "OCE-1434842";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1434842";
    String awards_0_funder_name "NSF Division of Ocean Sciences";
    String awards_0_funding_acronym "NSF OCE";
    String awards_0_funding_source_nid "355";
    String awards_0_program_manager "David L. Garrison";
    String awards_0_program_manager_nid "50534";
    String cdm_data_type "Other";
    String comment 
"Photosynthetic efficiency data from light stress 
  PI: Suzanne Strom 
  Data Version 1: 2019-10-15";
    String Conventions "COARDS, CF-1.6, ACDD-1.3";
    String creator_email "info@bco-dmo.org";
    String creator_name "BCO-DMO";
    String creator_type "institution";
    String creator_url "https://www.bco-dmo.org/";
    String data_source "extract_data_as_tsv version 2.3  19 Dec 2019";
    String date_created "2019-10-11T15:23:55Z";
    String date_modified "2020-03-19T20:25:59Z";
    String defaultDataQuery "&time<now";
    String doi "10.26008/1912/bco-dmo.779033.1";
    String history 
"2023-06-01T05:11:15Z (local files)
2023-06-01T05:11:15Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_779033.das";
    String infoUrl "https://www.bco-dmo.org/dataset/779033";
    String institution "BCO-DMO";
    String instruments_0_acronym "LI-COR Biospherical PAR";
    String instruments_0_dataset_instrument_description "Irradiance measurements: Li-Cor 1400 data logger with 2-pi (cosine) photosynthetically active radiation (PAR) sensor";
    String instruments_0_dataset_instrument_nid "779036";
    String instruments_0_description "The LI-COR Biospherical PAR Sensor is used to measure Photosynthetically Available Radiation (PAR) in the water column.  This instrument designation is used when specific make and model are not known.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0074/";
    String instruments_0_instrument_name "LI-COR Biospherical PAR Sensor";
    String instruments_0_instrument_nid "480";
    String instruments_0_supplied_name "Li-Cor 1400 data logger with 2-pi (cosine) photosynthetically active radiation (PAR) sensor";
    String instruments_1_acronym "Fluorometer";
    String instruments_1_dataset_instrument_description "Photosynthetic efficiency measurements: Pulse-Amplitude Modulated Fluorometer: Walz Water PAM";
    String instruments_1_dataset_instrument_nid "779035";
    String instruments_1_description "A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.";
    String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/113/";
    String instruments_1_instrument_name "Fluorometer";
    String instruments_1_instrument_nid "484";
    String instruments_1_supplied_name "Pulse-Amplitude Modulated Fluorometer: Walz Water PAM";
    String keywords "available, bco, bco-dmo, biological, bottle, Bottle_Type, chemical, data, dataset, date, dmo, erddap, experiment, Experiment_ID, FvFm, interval, management, num, Num_Screens, number, oceanography, office, par, photosynthetically, phytoplankton, Phytoplankton_Species, preliminary, radiation, replicate, Replicate_Number, sampling, Sampling_Time, screens, species, time, Time_interval, total, Total_PAR, type";
    String license "https://www.bco-dmo.org/dataset/779033/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/779033";
    String param_mapping "{'779033': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/779033/parameters";
    String people_0_affiliation "University of Washington";
    String people_0_affiliation_acronym "UW";
    String people_0_person_name "Suzanne Strom";
    String people_0_person_nid "50471";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Woods Hole Oceanographic Institution";
    String people_1_affiliation_acronym "WHOI BCO-DMO";
    String people_1_person_name "Amber York";
    String people_1_person_nid "643627";
    String people_1_role "BCO-DMO Data Manager";
    String people_1_role_type "related";
    String project "Protist signaling";
    String projects_0_acronym "Protist signaling";
    String projects_0_description 
"Description from NSF proposal:
This proposal arises from the central premise that the oxidative stress response is an emergent property of phototrophic cellular systems, with implications for nearly every aspect of a phytoplankton cell’s life in the upper ocean. Oxidative stress (OS) arises from the uncompensated production of reactive oxygen species (ROS) within a cell, which can occur in response to a myriad of environmental stressors (e.g. nutrient limitation, temperature extremes, toxins, variable light exposure). In addition to the biochemical damage and physiological impairment that OS can cause, the phytoplankton OS response also includes increased net production and extracellular release of ROS, osmolytes, and other compounds that are known or suspected to be potent signals regulating protist behavior. We hypothesize that, through chemical signaling, oxidative stress acts to govern relationships among environmental variability, phytoplankton condition, and protist predation. Our proposed study of these integrated signaling and response processes has three overarching objectives: 1) Create and characterize oxidatively stressed phytoplankton. We will use light stress (variable exposure to visible light and UV) to create oxidatively stressed phytoplankton in the laboratory. Common coastal taxa with contrasting stress responses will be characterized using an array of fluorescent probes, biochemical measurements, and physiological assays. In addition, intracellular production and extracellular release of ROS and the associated chemical signal DMSP will be quantified. Use of Phaeodactylum tricornutum light stress mutants will add an independent means of connecting OS to signal production and predation response. 2) Examine protist predator responses to oxidatively stressed phytoplankton and associated chemical signals. Responses will be investigated by means of manipulation experiments and thorough characterization of associated signal chemistry. Assessment of predator response will be via predation rate measurements and population aggregation/dispersal behaviors in structured columns. 3) Investigate the prevalence of OS, its environmental correlates, and the microzooplankton predation response in the natural waters of a well-characterized local embayment. Application of ROS probes and OS assays to the natural environment and the design of OS manipulation experiments will be informed by the laboratory experiments using local protist species.
Our work will help to elucidate some of the multiple ways in which the OS response can affect phytoplankton fitness, contributing information that can be used to characterize the position of key coastal species along an OS response spectrum. Ultimately such information could be used in trait-based conceptual and numerical models in a manner analogous to cell size and other 'master traits'. Our research will also inform the relatively new and exciting field of chemical signaling in planktonic communities, exploring DMSP- and ROS-based signaling between two of the most significant groups in the plankton, the eukaryotic phytoplankton and their protist predators. Finally, findings will help elucidate the links between environmental stress, phytoplankton response, and predation in planktonic ecosystems. These links relate to central issues in biological oceanography, including the predator-prey interactions that influence bloom demise, and the mechanisms by which protists feed selectively and thereby structure prey communities. The proposed research is a cross-cutting endeavor that unites subjects usually studied in isolation through a novel conceptual framework. Thus the findings have the potential to generate broadly applicable new insights into the ecological and evolutionary regulation of this key trophic link in planktonic food webs.";
    String projects_0_end_date "2017-08";
    String projects_0_geolocation "Salish Sea: 48.5, -122.75";
    String projects_0_name "Environmental stress and signaling based on reactive oxygen species among planktonic protists";
    String projects_0_project_nid "614838";
    String projects_0_start_date "2014-09";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary "Fv/Fm (photosynthetic efficiency) data from light stress in phytoplankton and dinoflagellate grazing response experiments from July of 2015 to September of 2018. These data were published in Strom et al. (2020).";
    String title "Photosynthetic efficiency data from light stress in phytoplankton and dinoflagellate grazing response experiments from July of 2015 to September of 2018";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";


Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.

Tabledap request URLs must be in the form
For example,
Thus, the query is often a comma-separated list of desired variable names, followed by a collection of constraints (e.g., variable<value), each preceded by '&' (which is interpreted as "AND").

For details, see the tabledap Documentation.

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