ERDDAP > info > bcodmo_dataset_728215

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
	set	data	graph		files	public	[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)		F   I   M	background			BCO-DMO	bcodmo_dataset_728215

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,.esriCsv,.geoJson
attribute	NC_GLOBAL	acquisition_description	String	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
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
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. 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)
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/
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
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
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/728215
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
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: 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.
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/
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/
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/
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/
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/
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

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.