ERDDAP > info > bcodmo_dataset_659109

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	[Lophelia pertusa experiments: calcification and pH] - Net calcification of L. pertusa specimens exposed to different pH treatments collected on R/V Ronald Brown in Florida from October to November 2010 (Lophelia OA project) (Physiological and genetic responses of the deep-water coral, Lophelia pertusa, to ongoing ocean acidification in the Gulf of Mexico)		I   M	background			BCO-DMO	bcodmo_dataset_659109

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	All methods are fully described in: Lunden et al. 2014 Frontiers in Marine Science \u201cAcute survivorship of the deep-sea coral Lophelia pertusa from the Gulf of Mexico under acidification, warming, and deoxygenation\u201d From the Paper: Forty-one nubbins of L. pertusa used in the experiments were collected in November 2010 on the NOAA Ship Ronald H. Brown with ROV Jason II as part of the \u201cLophelia II\u201d project jointly sponsored by the Bureau of Ocean Energy Management and the NOAA Office of Ocean Exploration and Research in the Gulf of Mexico (GoM). Permits for the collection of corals were obtained from the U.S. Department of the Interior prior to any collection activities. Spatially discrete coral branches were collected with the ROV and placed in temperature-insulated bioboxes (volume = 20 l) at depth. Upon return to the surface, corals were kept alive in 20 l aquaria in the ship\u2019s constant- temperature room. Partial water changes were made regularly while at sea. Upon return to port, corals were immediately transported overnight to the laboratory on wet ice. In the laboratory, corals were maintained in one of two 570 liter recirculating aquaria systems at temperature 8 degrees celsius and salinity 35 ppt (Lunden et al., 2014). Regular partial water changes (15\u201320%) were performed with seawater made using Instant Ocean\u00a0sea salt. Submersible power heads were placed in each holding tank to ensure water movement and turbulence sufficient to cause swaying of coral polyps. Corals were fed three times weekly using a combination of MarineSnow\u00a0PlanktonDiet (Two Little Fishies, Miami Gardens, FL) and freshly hatched Artemia nauplii. Survivorship was assessed by daily observations of polyp tissue presence and behavior. Final survivorship counts were taken 3 to 4 days following the end of each treatment after transfer to the maintenance tank. Survivorship is reported as percent cumulative mortality. Net calcification was measured using the buoyant weight technique (Davies, 1989). Coral nubbins were buoyantly weighed at the start and end of each experimental period (days eight and fifteen) using a Denver Instruments SI-64 analytical balance (d = 0.1mg, Fisher Scientific, Waltham, MA). A weighing chamber was constructed using 1/2\u201d plexiglass to prevent disturbances from air movement during weighing. Each coral nubbin was transported individually from its respective aquarium to the weighing chamber in a four- liter Pyrex\u00a0beaker and suspended from the balance. The buoyant weight was recorded after the coral nubbin stabilized, typically 2 min. Each coral nubbin was weighed three times to determine measurement precision (2\u20133 mg). Seawater density was determined in each aquarium by buoyantly weighing a 2.5 cm^2 aluminum block with known density (2.7 g/cm^\u22123). Coral weight in air (i.e., dry weight) was calculated by the following equation:\u00a0 Wa = Ww / (1\u2212 (Dw/SD))\u00a0 Where Wa = coral weight in air (dry weight)\u00a0 Ww = coral weight in water (buoyant weight)\u00a0 Dw = density of seawater\u00a0 SD = coral skeletal density (= 2.82 g/cm^\u22123, Lunden et al., 2013).\u00a0 Coral growth rate is reported as percent growth per day (%/d\u22121), which was calculated by the equation: Gt = 100 \u00d7 (Mt2 \u2212 Mt1)/(Mt1(T2 \u2212T1)) Where Gt =growth rate as %/d^\u22121\u00a0 Mt2 = mass (mg, dry weight) at time 2 (end of experimental period, day 15)\u00a0 Mt1= mass (mg, dry weight) at time 1 (start of experimental period, day 8) T2 = time 2 (end of experimental period, day 15)\u00a0 T1= time 1 (start of experimental period, day 8)
attribute	NC_GLOBAL	awards_0_award_nid	String	54992
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1220478
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward?AWD_ID=1220478
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	pH data from Lophelia pertusa experiments Erik Cordes, PI Version 16 September 2016
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	2016-09-20T00:01:17Z
attribute	NC_GLOBAL	date_modified	String	2019-05-10T18:02:33Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.659109.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/659109
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Water Temp Sensor
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Indicates water temperature
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	659592
attribute	NC_GLOBAL	instruments_0_description	String	General term for an instrument that measures the temperature of the water with which it is in contact (thermometer).
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/134/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Water Temperature Sensor
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	647
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Temperature sensor
attribute	NC_GLOBAL	instruments_1_acronym	String	Aquarium
attribute	NC_GLOBAL	instruments_1_dataset_instrument_description	String	20 L aquaria were used on the ship and 570 L recirculating aquaria systems were used in the lab
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	659590
attribute	NC_GLOBAL	instruments_1_description	String	Aquarium - a vivarium consisting of at least one transparent side in which water-dwelling plants or animals are kept
attribute	NC_GLOBAL	instruments_1_instrument_name	String	Aquarium
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	711
attribute	NC_GLOBAL	instruments_1_supplied_name	String	Aquarium
attribute	NC_GLOBAL	instruments_2_acronym	String	Scale
attribute	NC_GLOBAL	instruments_2_dataset_instrument_description	String	Used for buoyant weights; d = 0.1mg, Fisher Scientific
attribute	NC_GLOBAL	instruments_2_dataset_instrument_nid	String	659591
attribute	NC_GLOBAL	instruments_2_description	String	An instrument used to measure weight or mass.
attribute	NC_GLOBAL	instruments_2_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB13/
attribute	NC_GLOBAL	instruments_2_instrument_name	String	Scale
attribute	NC_GLOBAL	instruments_2_instrument_nid	String	714
attribute	NC_GLOBAL	instruments_2_supplied_name	String	Denver Instruments SI-64 Analytical Balance
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, biological, calcification, chemical, data, dataset, density, dmo, dry, dry_weight_end, dry_weight_start, earth, Earth Science > Oceans > Salinity/Density > Salinity, end, erddap, group, individual, management, net, net_calcification, ocean, oceanography, oceans, office, omega, omega_Ar, percent, percent_survivorship, pH_total, pH_treatment, practical, preliminary, salinity, science, sea, sea_water_practical_salinity, seawater, start, survivorship, temperature, total, treatment, water, weight
attribute	NC_GLOBAL	keywords_vocabulary	String	GCMD Science Keywords
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/659109/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/659109
attribute	NC_GLOBAL	param_mapping	String	{'659109': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/659109/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Temple University
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	Temple
attribute	NC_GLOBAL	people_0_person_name	String	Erik E Cordes
attribute	NC_GLOBAL	people_0_person_nid	String	51539
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	Temple University
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	Temple
attribute	NC_GLOBAL	people_1_person_name	String	Erik E Cordes
attribute	NC_GLOBAL	people_1_person_nid	String	51539
attribute	NC_GLOBAL	people_1_role	String	Contact
attribute	NC_GLOBAL	people_1_role_type	String	related
attribute	NC_GLOBAL	people_2_affiliation	String	Lock Haven University
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	LHU
attribute	NC_GLOBAL	people_2_person_name	String	Dr Jay Lunden
attribute	NC_GLOBAL	people_2_person_nid	String	659079
attribute	NC_GLOBAL	people_2_role	String	Contact
attribute	NC_GLOBAL	people_2_role_type	String	related
attribute	NC_GLOBAL	people_3_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_3_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_3_person_name	String	Hannah Ake
attribute	NC_GLOBAL	people_3_person_nid	String	650173
attribute	NC_GLOBAL	people_3_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_3_role_type	String	related
attribute	NC_GLOBAL	project	String	Lophelia OA
attribute	NC_GLOBAL	projects_0_acronym	String	Lophelia OA
attribute	NC_GLOBAL	projects_0_description	String	The Gulf of Mexico deep water ecosystems are threatened by the persistent threat of ocean acidification. Deep-water corals will be among the first to feel the effects of this process, in particular the deep-water scleractinians that form their skeleton from aragonite. The continued shoaling of the aragonite saturation horizon (the depth below which aragonite is undersaturated) will place many of the known, and as yet undiscovered, deep-water corals at risk in the very near future. The most common deep-water framework-forming scleractinian in the world's oceans is Lophelia pertusa. This coral is most abundant in the North Atlantic, where aragonite saturation states are relatively high, but it also creates extensive reef structures between 300 and 600 m depth in the Gulf of Mexico where aragonite saturation states were previously unknown. Preliminary data indicate that pH at this depth range is between 7.85 and 8.03, and the aragonite saturation state is typically between 1.28 and 1.69. These are the first measurements of aragonite saturation state for the deep Gulf of Mexico, and are among the lowest Aragonite saturation state yet recorded for framework-forming corals in any body of water, at any depth. This project will examine the effects of ocean acidification on L. pertusa, combining laboratory experiments, rigorous oceanographic measurements, the latest genome and transcriptome sequencing platforms, and quantitative PCR and enzyme assays to examine changes in coral gene expression and enzyme activity related to differences in carbonate chemistry. Short-term and long-term laboratory experiments will be performed at Aragonite saturation state of 1.45 and 0.75 and the organismal (e.g., survivorship and calcification rate) and genetic (e.g., transcript abundance) responses of the coral will be monitored. Genomic DNA and RNA will be extracted, total mRNA purified, and comprehensive and quantitative profiles of the transcriptome generated using a combination of 454 and Illumina sequencing technologies. Key genes in the calcification pathways as well as other differentially expressed genes will be targeted for specific qPCR assays to verify the Illumina sequencing results. On a research cruise, L. pertusa will be sampled (preserved at depth) along a natural gradient in carbonate chemistry, and included in the Illumina sequencing and qPCR assays. Water samples will be obtained by submersible-deployed niskin bottles adjacent to the coral collections as well as CTD casts of the water column overlying the sites. Water samples will be analyzed for pH, alkalinity, nitrates and soluble reactive phosphorus. These will be used in combination with historical data in a model to hindcast Aragonite saturation state. This project will provide new physiological and genetic data on an ecologically-significant and anthropogenically-threatened deepwater coral in the Gulf of Mexico. An experimental system, already developed by the PIs, offers controlled conditions to test the effect of Aragonite saturation state on calcification rates in scleractinians and, subsequently, to identify candidate genes and pathways involved in the response to reduced pH and Aragonite saturation state. Both long-term and population sampling experiments will provide additional transcriptomic data and specifically investigate the expression of the candidate genes. These results will contribute to our understanding of the means by which scleractinians may acclimate and acclimatize to low pH, alkalinity, and Aragonite saturation state. Furthermore, the investigators will continue a time series of oceanographic measurements of the carbonate system in the Gulf of Mexico, which will allow the inclusion of this significant body of water in models of past and future ocean acidification scenarios.
attribute	NC_GLOBAL	projects_0_end_date	String	2015-08
attribute	NC_GLOBAL	projects_0_geolocation	String	Northern Gulf of Mexico
attribute	NC_GLOBAL	projects_0_name	String	Physiological and genetic responses of the deep-water coral, Lophelia pertusa, to ongoing ocean acidification in the Gulf of Mexico
attribute	NC_GLOBAL	projects_0_project_nid	String	2224
attribute	NC_GLOBAL	projects_0_start_date	String	2012-09
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	percent_survivorship
attribute	NC_GLOBAL	summary	String	Net calcification of L. pertusa specimens exposed to different pH treatments collected on R/V Ronald Brown in Florida from October to November 2010 (Lophelia OA project)
attribute	NC_GLOBAL	title	String	[Lophelia pertusa experiments: calcification and pH] - Net calcification of L. pertusa specimens exposed to different pH treatments collected on R/V Ronald Brown in Florida from October to November 2010 (Lophelia OA project) (Physiological and genetic responses of the deep-water coral, Lophelia pertusa, to ongoing ocean acidification in the Gulf of Mexico)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	pH_treatment		String
attribute	pH_treatment	bcodmo_name	String	treatment
attribute	pH_treatment	description	String	pH treatment; ambient, low, or very low
attribute	pH_treatment	long_name	String	P H Treatment
attribute	pH_treatment	units	String	unitless
variable	group		byte
attribute	group	_FillValue	byte	127
attribute	group	actual_range	byte	1, 2
attribute	group	bcodmo_name	String	sample
attribute	group	description	String	Specimen group
attribute	group	long_name	String	Group
attribute	group	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	group	units	String	unitless
variable	individual		byte
attribute	individual	_FillValue	byte	127
attribute	individual	actual_range	byte	2, 34
attribute	individual	bcodmo_name	String	individual
attribute	individual	description	String	Specimen ID number
attribute	individual	long_name	String	Individual
attribute	individual	units	String	unitless
variable	temperature		float
attribute	temperature	_FillValue	float	NaN
attribute	temperature	actual_range	float	7.0833, 9.0
attribute	temperature	bcodmo_name	String	temperature
attribute	temperature	description	String	Water temperature
attribute	temperature	long_name	String	Temperature
attribute	temperature	units	String	celsius
variable	salinity		float
attribute	salinity	_FillValue	float	NaN
attribute	salinity	actual_range	float	35.0833, 35.7
attribute	salinity	bcodmo_name	String	sal
attribute	salinity	colorBarMaximum	double	37.0
attribute	salinity	colorBarMinimum	double	32.0
attribute	salinity	description	String	Salinity of water
attribute	salinity	long_name	String	Sea Water Practical Salinity
attribute	salinity	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/
attribute	salinity	units	String	PPT
variable	TA		double
attribute	TA	_FillValue	double	NaN
attribute	TA	actual_range	double	2204.8003, 2428.5232
attribute	TA	bcodmo_name	String	TALK
attribute	TA	description	String	Total alkalinity of water
attribute	TA	long_name	String	TA
attribute	TA	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/MDMAP014/
attribute	TA	units	String	micromoles per kilogram (umol/kg -1)
variable	pH_total		float
attribute	pH_total	_FillValue	float	NaN
attribute	pH_total	actual_range	float	7.5933, 7.9183
attribute	pH_total	bcodmo_name	String	pH
attribute	pH_total	description	String	pH measured on the total hydrogen scale
attribute	pH_total	long_name	String	P H Total
attribute	pH_total	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/PHXXZZXX/
attribute	pH_total	units	String	unitless
variable	omega_Ar		float
attribute	omega_Ar	_FillValue	float	NaN
attribute	omega_Ar	actual_range	float	0.7586, 1.5305
attribute	omega_Ar	bcodmo_name	String	OM_ar
attribute	omega_Ar	description	String	Saturation state of aragonite
attribute	omega_Ar	long_name	String	Omega Ar
attribute	omega_Ar	units	String	unitless
variable	dry_weight_start		float
attribute	dry_weight_start	_FillValue	float	NaN
attribute	dry_weight_start	actual_range	float	4.1395, 48.7222
attribute	dry_weight_start	bcodmo_name	String	dry_wgt
attribute	dry_weight_start	description	String	Dry weight at start of experiment
attribute	dry_weight_start	long_name	String	Dry Weight Start
attribute	dry_weight_start	units	String	grams
variable	dry_weight_end		float
attribute	dry_weight_end	_FillValue	float	NaN
attribute	dry_weight_end	actual_range	float	4.1492, 48.7121
attribute	dry_weight_end	bcodmo_name	String	dry_wgt
attribute	dry_weight_end	description	String	Dry weight at end of experiment
attribute	dry_weight_end	long_name	String	Dry Weight End
attribute	dry_weight_end	units	String	grams
variable	net_calcification		float
attribute	net_calcification	_FillValue	float	NaN
attribute	net_calcification	actual_range	float	-0.0387, 0.0917
attribute	net_calcification	bcodmo_name	String	growth
attribute	net_calcification	description	String	Percent growth of coral colony per day
attribute	net_calcification	long_name	String	Net Calcification
attribute	net_calcification	units	String	percent per day (%/d -1)
variable	percent_survivorship		byte
attribute	percent_survivorship	_FillValue	byte	127
attribute	percent_survivorship	actual_range	byte	100, 100
attribute	percent_survivorship	bcodmo_name	String	unknown
attribute	percent_survivorship	colorBarMaximum	double	100.0
attribute	percent_survivorship	colorBarMinimum	double	0.0
attribute	percent_survivorship	description	String	Percent survivorship
attribute	percent_survivorship	long_name	String	Percent Survivorship
attribute	percent_survivorship	units	String	percent

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.