Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | [Cultures isolated from A. bipinnata 2008-2016] - Symbiodinium cultures isolated from the octocoral Antillogorgia bipinnata in the Florida Keys and processed at Coffroth lab at the University at Buffalo in 2008, 2013 and 2016 (Host Symbiont Temp Response project) (RUI: Collaborative Research: Genetic variation as a driver of host and symbiont response to increased temperature on coral reefs) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_728215) |
| Information: | Summary
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| FGDC
| ISO 19115
| Metadata
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Attributes {
s {
Culture_ID {
String bcodmo_name "sample";
String description "Identification of sample; culture name (08-0689.4; 08-0689.6; 08-0690.1; 13-117; 13-143; etc.)";
String long_name "Culture ID";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
Incubation_Temperature {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 26, 30;
String bcodmo_name "temp_inc";
String description "Temperature at which the culture is maintained";
String long_name "Incubation Temperature";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TINCDTNX/";
String units "degree Celsius (C)";
}
Host {
String bcodmo_name "species";
String description "Octocoral from which the symbiont was isolated. Note - In the vast majority of cases; the culture is NOT representative of the host symbiont population (Santos et al 2001)";
String long_name "Host";
String units "unitless";
}
Putative_Species {
String bcodmo_name "species";
String description "Putative species based on sequence analysis of B7 SYM15 flanking region (LaJeunesse et al 2012; Parkinson et al 2015)";
String long_name "Putative Species";
String units "unitless";
}
Location {
String bcodmo_name "site_descrip";
String description "Location where adult colony was collected";
String long_name "Location";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 24.54955, 25.1326;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude of sample location; positive north.";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -81.75458, -80.26195;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude of sample location; positive east";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "degrees_east";
}
State_Country {
String bcodmo_name "region";
String description "State/Country where adult colony was collected";
String long_name "State Country";
String units "unitless";
}
Ocean {
String bcodmo_name "region";
String description "Ocean where adult colony was collected";
String long_name "Ocean";
String units "unitless";
}
Host_stage {
String bcodmo_name "stage";
String description "Developmental stage of host";
String long_name "Host Stage";
String units "unitless";
}
Axenic {
String bcodmo_name "unknown";
String description "Whether or not the culture is axenic";
String long_name "Axenic";
String units "unitless";
}
Isolated_by {
String bcodmo_name "person";
String description "Researcher who isolated the culture";
String long_name "Isolated By";
String units "unitless";
}
Year_isolated {
Int16 _FillValue 32767;
Int16 actual_range 2008, 2016;
String bcodmo_name "year";
String description "The year in which the culture was isolated in four digit year format";
String long_name "Year Isolated";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
String units "years";
}
Clade {
String bcodmo_name "taxon";
String description "Clade designation";
String long_name "Clade";
String units "unitless";
}
cp_type {
Int16 _FillValue 32767;
Int16 actual_range 184, 184;
String bcodmo_name "unknown";
String description "Fragment length of the hypervariable region of Domain V of symbiont 23S rDNA (Santos et al 2003) as base pairs";
String long_name "Cp Type";
String units "unitless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Symbionts were isolated from adult colonies of Antillogorgia bipinnata
following the protocol outline in Santos et al 2001. Briefly, a small piece
(1-2 cm) of the branch was ground in a glass tissue homogenizer with 2 ml of
filtered seawater (FSW) and poured through a series of meshes (250 \\u00b5m on
top, then 120 \\u00b5m, then 70 \\u00b5m mesh) into a 15 ml tube.\\u00a0 The mesh
was washed with 1 ml FSW several times for a final volume between 3 and
10\\u00a0ml. This slurry was spun for 5 min at 500-800 rpm on a Beckman J6-HC
centrifuge to pellet symbiont cells, the supernatant removed and resuspended
in 10 ml of FSW.\\u00a0 This step was repeated again and then the pellet was
resuspended in 1.0 ml of F/2 (Gulliard and Ryther 1962).\\u00a0 Cultures were
started by using 20-50 \\u00b5l of the resuspended pellets to inoculate 30ml of
F/2 and incubated at the appropriate temperature.\\u00a0 \\u00a0 \\u00a0
Clade identity and Cp-type were determined following the protocols outline in
Santos et al (2003). Briefly, DNA was amplified using the primers HYPERUP and
HYPERDN on and MJ96 or BioRad thermocyclers. PCR products were visualized and
scored using size standards on a LI-COR 4200 NEN\\u00ae Global IR2 DNA
sequencing system as specified in Santos et al (2003). Putative species
identity was based on sequence analysis of B7SYM15 flanking region (LaJeunesse
et al. 2012, Parkinson et al. 2015).\\u00a0 Briefly, the B7SYM15 flanking
region was amplified and directly sequenced in 5\\u2019 and 3\\u2019 directions
on a 3730XL DNA Analyzer (High Throughput Genomics Center, University of
Washington). Sequences were compared to known species within the GenBank
database using BLAST- Basic Local Alignment Search Tool
([https://blast.ncbi.nlm.nih.gov/Blast.cgi](\\\\\"https://blast.ncbi.nlm.nih.gov/Blast.cgi\\\\\")).\\u00a0";
String awards_0_award_nid "658940";
String awards_0_award_number "OCE-1559286";
String awards_0_data_url "https://www.nsf.gov/awardsearch/showAward?AWD_ID=1559286";
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
"Symbiodinium cultures isolated from the octocoral Antillogorgia bipinnata from 2008-2016.
PI: Mary Alice Coffroth
Co-PI: Casey terHorst
Version: 20180216
*Host: In the vast majority of cases, the culture is NOT representative of the host symbiont population
**Putative_species: Putative species based on sequence analysis of B7 SYM15 flanking region (LaJeunesse et al 2012, Parkinson et al 2015)";
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 "2018-02-22T19:09:35Z";
String date_modified "2019-10-02T20:52:30Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.728215.1";
Float64 Easternmost_Easting -80.26195;
Float64 geospatial_lat_max 25.1326;
Float64 geospatial_lat_min 24.54955;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -80.26195;
Float64 geospatial_lon_min -81.75458;
String geospatial_lon_units "degrees_east";
String history
"2024-12-22T11:13:47Z (local files)
2024-12-22T11:13:47Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_728215.html";
String infoUrl "https://www.bco-dmo.org/dataset/728215";
String institution "BCO-DMO";
String instruments_0_acronym "Automated Sequencer";
String instruments_0_dataset_instrument_description "DNA was amplified using the primers HYPERUP and HYPERDN on and MJ96 thermocycler and PCR products were visualized and scored using size standards on the LI-COR 4200 NEN® Global IR2 DNA sequencing system as specified in Santos et al (2003).";
String instruments_0_dataset_instrument_nid "729037";
String instruments_0_description "General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.";
String instruments_0_instrument_name "Automated DNA Sequencer";
String instruments_0_instrument_nid "649";
String instruments_0_supplied_name "LI-COR 4200 NEN® Global IR2 DNA";
String instruments_1_acronym "Automated Sequencer";
String instruments_1_dataset_instrument_description "The B7SYM15 flanking region was amplified and directly sequenced in 5’ and 3’ directions on a 3730XL DNA Analyzer (High Throughput Genomics Center, University of Washington).";
String instruments_1_dataset_instrument_nid "729038";
String instruments_1_description "General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.";
String instruments_1_instrument_name "Automated DNA Sequencer";
String instruments_1_instrument_nid "649";
String instruments_1_supplied_name "3730XL DNA Analyzer";
String instruments_2_dataset_instrument_description "This slurry was spun for 5 min at 500-800 rpm on a Beckman J6-HC centrifuge to pellet symbiont cells, the supernatant removed and responded in 10 ml of FSW.";
String instruments_2_dataset_instrument_nid "729036";
String instruments_2_description "A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.";
String instruments_2_instrument_name "Centrifuge";
String instruments_2_instrument_nid "629890";
String instruments_2_supplied_name "Beckman J6-HC centrifuge";
String keywords "axenic, bco, bco-dmo, biological, chemical, clade, country, cp_type, culture, Culture_ID, data, dataset, dmo, erddap, host, Host_stage, incubation, Incubation_Temperature, isolated, Isolated_by, latitude, Location, longitude, management, ocean, oceanography, office, preliminary, putative, Putative_Species, species, stage, state, State_Country, temperature, type, year, Year_isolated";
String license "https://www.bco-dmo.org/dataset/728215/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/728215";
Float64 Northernmost_Northing 25.1326;
String param_mapping "{'728215': {'Latitude': 'flag - latitude', 'longitude': 'flag - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/728215/parameters";
String people_0_affiliation "State University of New York at Buffalo";
String people_0_affiliation_acronym "SUNY Buffalo";
String people_0_person_name "Mary Alice Coffroth";
String people_0_person_nid "472488";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "California State University Northridge";
String people_1_affiliation_acronym "CSU-Northridge";
String people_1_person_name "Casey terHorst";
String people_1_person_nid "632541";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Woods Hole Oceanographic Institution";
String people_2_affiliation_acronym "WHOI BCO-DMO";
String people_2_person_name "Mathew Biddle";
String people_2_person_nid "708682";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "Host Symbiont Temp Response";
String projects_0_acronym "Host Symbiont Temp Response";
String projects_0_description
"Description from NSF award abstract:
On coral reefs, mutualisms with single celled algae (Symbiodinium) and reef species literally and figuratively form the foundation of reef ecosystems. Coral reefs are among the most threatened ecosystems under a changing climate and are rapidly declining due to increasing levels of environmental stress, namely increased temperatures. Climate change is resulting in even warmer ocean temperatures that threaten associations between Symbiodinium and their hosts. In this project the investigators examine the genetic diversity of Symbiodinium and the potential for this important species to evolve in response to temperature. The project will also address whether the ecological and evolutionary dynamics of the Symbiodinium population affect the performance of their host. If so, this suggests that the evolution of microscopic organisms with short generation times could confer adaptation to longer-lived host species on ecologically and economically vital coral reefs. Given that diversity is already being lost on many reefs, considering how evolutionary changes in Symbiodinium will affect reef species is crucial for predicting the responses of reefs to future climate change. This project provides training for two graduate students and several undergraduates at a Hispanic-serving institution. This work includes outreach to the students and the general public through the Aquarium of Niagara, local K-12 schools, and web-based education modules.
The effects of evolution on contemporary ecological processes are at the forefront of research in evolutionary ecology. This project will answer the call for experiments elucidating the effects of genetic variation in Symbiodinium performance and the effect on the response of the holobiont (host and symbiont) to increased temperature. These experiments examine the effects of temperature through both ecological and evolutionary mechanisms and will determine the relative importance of adaptation and acclimatization in replicated experimental populations. The investigators will examine how genetic variation within a species (Symbiodinium antillogorgium) affects symbiont performance in culture and in the host and how this affects the response of the holobiont to increased temperature. Further, the project examines whether holobiont response to increased temperature associated with climate change depends on particular GxG host-symbiont combinations. Moreover, the investigators will examine the effects of symbiont history on mutualist hosts, which have been largely ignored in eco-evolutionary studies. These experiments provide a first step in predicting whether invertebrate hosts on coral reefs will respond to global change via adaptation of their symbionts.";
String projects_0_end_date "2020-03";
String projects_0_geolocation "Florida Keys, Caribbean";
String projects_0_name "RUI: Collaborative Research: Genetic variation as a driver of host and symbiont response to increased temperature on coral reefs";
String projects_0_project_nid "632538";
String projects_0_start_date "2016-04";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 24.54955;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "Host,Location,State_Country,Ocean,Host_stage,Axenic,Isolated_by,Clade,cp_type";
String summary "Symbiodinium cultures isolated from the octocoral Antillogorgia bipinnata in the Florida Keys and processed at Coffroth lab at the University at Buffalo in 2008, 2013 and 2016.";
String title "[Cultures isolated from A. bipinnata 2008-2016] - Symbiodinium cultures isolated from the octocoral Antillogorgia bipinnata in the Florida Keys and processed at Coffroth lab at the University at Buffalo in 2008, 2013 and 2016 (Host Symbiont Temp Response project) (RUI: Collaborative Research: Genetic variation as a driver of host and symbiont response to increased temperature on coral reefs)";
String version "1";
Float64 Westernmost_Easting -81.75458;
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
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
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
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.