BCO-DMO ERDDAP
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Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson
attribute NC_GLOBAL acquisition_description String Symbionts were isolated from adult colonies of Antillogorgia bipinnata\nfollowing the protocol outline in Santos et al 2001. Briefly, a small piece\n(1-2 cm) of the branch was ground in a glass tissue homogenizer with 2 ml of\nfiltered seawater (FSW) and poured through a series of meshes (250 \\u00b5m on\ntop, then 120 \\u00b5m, then 70 \\u00b5m mesh) into a 15 ml tube.\\u00a0 The mesh\nwas washed with 1 ml FSW several times for a final volume between 3 and\n10\\u00a0ml. This slurry was spun for 5 min at 500-800 rpm on a Beckman J6-HC\ncentrifuge to pellet symbiont cells, the supernatant removed and resuspended\nin 10 ml of FSW.\\u00a0 This step was repeated again and then the pellet was\nresuspended in 1.0 ml of F/2 (Gulliard and Ryther 1962).\\u00a0 Cultures were\nstarted by using 20-50 \\u00b5l of the resuspended pellets to inoculate 30ml of\nF/2 and incubated at the appropriate temperature.\\u00a0 \\u00a0 \\u00a0\n \nClade identity and Cp-type were determined following the protocols outline in\nSantos et al (2003). Briefly, DNA was amplified using the primers HYPERUP and\nHYPERDN on and MJ96 or BioRad thermocyclers. PCR products were visualized and\nscored using size standards on a LI-COR 4200 NEN\\u00ae Global IR2 DNA\nsequencing system as specified in Santos et al (2003). Putative species\nidentity was based on sequence analysis of B7SYM15 flanking region (LaJeunesse\net al. 2012, Parkinson et al. 2015).\\u00a0 Briefly, the B7SYM15 flanking\nregion was amplified and directly sequenced in 5\\u2019 and 3\\u2019 directions\non a 3730XL DNA Analyzer (High Throughput Genomics Center, University of\nWashington). Sequences were compared to known species within the GenBank\ndatabase using BLAST- Basic Local Alignment Search Tool\n([https://blast.ncbi.nlm.nih.gov/Blast.cgi](\\\\\"https://blast.ncbi.nlm.nih.gov/Blast.cgi\\\\\")).\\u00a0
attribute NC_GLOBAL awards_0_award_nid String 658940
attribute NC_GLOBAL awards_0_award_number String OCE-1559286
attribute NC_GLOBAL awards_0_data_url String https://www.nsf.gov/awardsearch/showAward?AWD_ID=1559286 (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 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 Symbiodinium cultures isolated from the octocoral Antillogorgia bipinnata from 2008-2016.  \n PI: Mary Alice Coffroth \n Co-PI: Casey terHorst \n Version: 20180216 \n  *Host: In the vast majority of cases, the culture is NOT representative of the host symbiont population                                                                   \n  **Putative_species: Putative species based on sequence analysis of B7 SYM15 flanking region (LaJeunesse et al 2012, Parkinson et al 2015)
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 date_created String 2018-02-22T19:09:35Z
attribute NC_GLOBAL date_modified String 2019-10-02T20:52:30Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.728215.1
attribute NC_GLOBAL Easternmost_Easting double -80.26195
attribute NC_GLOBAL geospatial_lat_max double 25.1326
attribute NC_GLOBAL geospatial_lat_min double 24.54955
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -80.26195
attribute NC_GLOBAL geospatial_lon_min double -81.75458
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/728215 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Automated Sequencer
attribute NC_GLOBAL instruments_0_dataset_instrument_description String 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).
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 729037
attribute NC_GLOBAL instruments_0_description String 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.
attribute NC_GLOBAL instruments_0_instrument_name String Automated DNA Sequencer
attribute NC_GLOBAL instruments_0_instrument_nid String 649
attribute NC_GLOBAL instruments_0_supplied_name String LI-COR 4200 NEN® Global IR2 DNA
attribute NC_GLOBAL instruments_1_acronym String Automated Sequencer
attribute NC_GLOBAL instruments_1_dataset_instrument_description String 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).
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 729038
attribute NC_GLOBAL instruments_1_description String 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.
attribute NC_GLOBAL instruments_1_instrument_name String Automated DNA Sequencer
attribute NC_GLOBAL instruments_1_instrument_nid String 649
attribute NC_GLOBAL instruments_1_supplied_name String 3730XL DNA Analyzer
attribute NC_GLOBAL instruments_2_dataset_instrument_description String 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.
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 729036
attribute NC_GLOBAL instruments_2_description String 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.
attribute NC_GLOBAL instruments_2_instrument_name String Centrifuge
attribute NC_GLOBAL instruments_2_instrument_nid String 629890
attribute NC_GLOBAL instruments_2_supplied_name String Beckman J6-HC centrifuge
attribute NC_GLOBAL keywords String 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
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/728215/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/728215 (external link)
attribute NC_GLOBAL Northernmost_Northing double 25.1326
attribute NC_GLOBAL param_mapping String {'728215': {'Latitude': 'flag - latitude', 'longitude': 'flag - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/728215/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String State University of New York at Buffalo
attribute NC_GLOBAL people_0_affiliation_acronym String SUNY Buffalo
attribute NC_GLOBAL people_0_person_name String Mary Alice Coffroth
attribute NC_GLOBAL people_0_person_nid String 472488
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 California State University Northridge
attribute NC_GLOBAL people_1_affiliation_acronym String CSU-Northridge
attribute NC_GLOBAL people_1_person_name String Casey terHorst
attribute NC_GLOBAL people_1_person_nid String 632541
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 Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_2_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_2_person_name String Mathew Biddle
attribute NC_GLOBAL people_2_person_nid String 708682
attribute NC_GLOBAL people_2_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL project String Host Symbiont Temp Response
attribute NC_GLOBAL projects_0_acronym String Host Symbiont Temp Response
attribute NC_GLOBAL projects_0_description String Description from NSF award abstract:\nOn 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.\nThe 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.
attribute NC_GLOBAL projects_0_end_date String 2020-03
attribute NC_GLOBAL projects_0_geolocation String Florida Keys, Caribbean
attribute NC_GLOBAL projects_0_name String RUI: Collaborative Research: Genetic variation as a driver of host and symbiont response to increased temperature on coral reefs
attribute NC_GLOBAL projects_0_project_nid String 632538
attribute NC_GLOBAL projects_0_start_date String 2016-04
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 Southernmost_Northing double 24.54955
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String Host,Location,State_Country,Ocean,Host_stage,Axenic,Isolated_by,Clade,cp_type
attribute NC_GLOBAL summary String 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.
attribute NC_GLOBAL title String [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)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -81.75458
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable Culture_ID String
attribute Culture_ID bcodmo_name String sample
attribute Culture_ID description String Identification of sample; culture name (08-0689.4; 08-0689.6; 08-0690.1; 13-117; 13-143; etc.)
attribute Culture_ID long_name String Culture ID
attribute Culture_ID nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Culture_ID units String unitless
variable Incubation_Temperature byte
attribute Incubation_Temperature _FillValue byte 127
attribute Incubation_Temperature actual_range byte 26, 30
attribute Incubation_Temperature bcodmo_name String temp_inc
attribute Incubation_Temperature description String Temperature at which the culture is maintained
attribute Incubation_Temperature long_name String Incubation Temperature
attribute Incubation_Temperature nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/TINCDTNX/ (external link)
attribute Incubation_Temperature units String degree Celsius (C)
variable Host String
attribute Host bcodmo_name String species
attribute Host description String 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)
attribute Host long_name String Host
attribute Host units String unitless
variable Putative_Species String
attribute Putative_Species bcodmo_name String species
attribute Putative_Species description String Putative species based on sequence analysis of B7 SYM15 flanking region (LaJeunesse et al 2012; Parkinson et al 2015)
attribute Putative_Species long_name String Putative Species
attribute Putative_Species units String unitless
variable Location String
attribute Location bcodmo_name String site_descrip
attribute Location description String Location where adult colony was collected
attribute Location long_name String Location
attribute Location units String unitless
variable latitude double
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 24.54955, 25.1326
attribute latitude axis String Y
attribute latitude bcodmo_name String latitude
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String Latitude of sample location; positive north.
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
attribute latitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LATX/ (external link)
attribute latitude standard_name String latitude
attribute latitude units String degrees_north
variable longitude double
attribute longitude _CoordinateAxisType String Lon
attribute longitude _FillValue double NaN
attribute longitude actual_range double -81.75458, -80.26195
attribute longitude axis String X
attribute longitude bcodmo_name String longitude
attribute longitude colorBarMaximum double 180.0
attribute longitude colorBarMinimum double -180.0
attribute longitude description String Longitude of sample location; positive east
attribute longitude ioos_category String Location
attribute longitude long_name String Longitude
attribute longitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LONX/ (external link)
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable State_Country String
attribute State_Country bcodmo_name String region
attribute State_Country description String State/Country where adult colony was collected
attribute State_Country long_name String State Country
attribute State_Country units String unitless
variable Ocean String
attribute Ocean bcodmo_name String region
attribute Ocean description String Ocean where adult colony was collected
attribute Ocean long_name String Ocean
attribute Ocean units String unitless
variable Host_stage String
attribute Host_stage bcodmo_name String stage
attribute Host_stage description String Developmental stage of host
attribute Host_stage long_name String Host Stage
attribute Host_stage units String unitless
variable Axenic String
attribute Axenic bcodmo_name String unknown
attribute Axenic description String Whether or not the culture is axenic
attribute Axenic long_name String Axenic
attribute Axenic units String unitless
variable Isolated_by String
attribute Isolated_by bcodmo_name String person
attribute Isolated_by description String Researcher who isolated the culture
attribute Isolated_by long_name String Isolated By
attribute Isolated_by units String unitless
variable Year_isolated short
attribute Year_isolated _FillValue short 32767
attribute Year_isolated actual_range short 2008, 2016
attribute Year_isolated bcodmo_name String year
attribute Year_isolated description String The year in which the culture was isolated in four digit year format
attribute Year_isolated long_name String Year Isolated
attribute Year_isolated nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/ (external link)
attribute Year_isolated units String years
variable Clade String
attribute Clade bcodmo_name String taxon
attribute Clade description String Clade designation
attribute Clade long_name String Clade
attribute Clade units String unitless
variable cp_type short
attribute cp_type _FillValue short 32767
attribute cp_type actual_range short 184, 184
attribute cp_type bcodmo_name String unknown
attribute cp_type description String Fragment length of the hypervariable region of Domain V of symbiont 23S rDNA (Santos et al 2003) as base pairs
attribute cp_type long_name String Cp Type
attribute cp_type units String unitless

 
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