ERDDAP > info > bcodmo_dataset_732890

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
		data	graph		files	public	[Symbiodinium Fv/Fm over a temperature gradient] - Fv/Fm for cultured Clade A & B Symbiodinium with 2 treatments measured over a range of temperatures (Coevolution of scleractinian corals and their associated microorganisms)		I   M	background			BCO-DMO	bcodmo_dataset_732890

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	Symbiodinium culture preparation: Cultures were obtained from the LaJeunesse algal collection at Penn State University. Phylogenetic relationships of these strains are described in Parkinson et al., (2015). Symbiodinium cultures were grown and maintained in liquid media (ASPA-8A, Blank, 1987) at 26 \u02daC with fluorescent lights delivering 80-100 \u03bcmol quanta m-2 s-1 (measured using a DIVING-PAM equipped with a flat cosine-corrected Fiber Quantum Sensor, Walz, Germany) on a 12:12 hours Light:Dark photoperiod in Innovator 44 incubators (New Brunswick, USA). Symbiodinium cultures of equal starting concentration (3 x 104 cells 126 mL-1) for each strain were grown for 7.5 days at 26 \u02daC at logarithmic growth phase prior to experimentation. After 7.5 days of incubation at 26 \u02daC, one culture of each strain was subjected to a high temperature treatment of 31 \u02daC for two light cycles and one dark cycle (i.e., 1.5 d), whilst another was maintained at 26 \u02daC. Data collection:\u00a0100 \u03bcL aliquots (8.33 x 104 cells mL-1, calculated as the average of twelve independent hemocytometer measurements) of dark- adapted cultures were then subjected to 5 minutes of elevated temperatures in a thermocycler (Eppendorf Mastercycler Pro S). Chlorophyll fluorescence parameters were measured immediately after the 5 min temperature exposure using a Fluorometer (see below). Measurements were performed at 25 temperatures (i.e. 26, 30.3, 30.5, 31, 31.7, 32.6, 33.7, 34.8, 35.9, 36.8, 37.6, 38.1, 38.3, 38.8, 38.9, 39.4, 40.1, 41,42, 43, 44, 44.9, 45.6, 46.1, 46.2 \u02daC) and replicated three times per Symbiodinium strain per treatment. A modified protocol by D\u00edaz-Almeyda et al., 2011 was used. Fv/Fm was automatically calculated/determined by fitting each fluorescence transient to the bio-physical model of Kolber et al. (1998) using the FIREPRO software (Satlantic, Version 1.4.3) integrated with the FIRe system. Reference excitation profile used by FIReView to normalize the variable fluorescence profile: [EXCFOP.TXT](\\"https://datadocs.bco- dmo.org/docs/medina/Varadero_Reef/data_docs/732890/1/EXCFOP.TXT\\") Column 1: incremental sample counter Column 2: elapsed time measured in microSeconds (uS) Column 3: reference excitation profile Column 4: relative fluorescence profile normalized to the reference excitation, or the fluorescence yield Calibration date: 1/ 1/2002 Time (in seconds) of day reading was taken =\u00a079931 Methodology Reference: D\u00edaz-Almeyda, E., Thom\u00e9, P. E., Hafidi, M. El, and Iglesias- Prieto, R. (2011). Differential stability of photosynthetic membranes and fatty acid composition at elevated temperature in Symbiodinium. Coral Reefs, 30(1), 217\u2013225. [https://doi.org/10.1007/s00338-010-0691-5](\\"https://doi.org/10.1007/s00338-010-0691-5\\").
attribute	NC_GLOBAL	awards_0_award_nid	String	551036
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1442206
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1442206
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	Michael E. Sieracki
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	50446
attribute	NC_GLOBAL	awards_1_award_nid	String	717027
attribute	NC_GLOBAL	awards_1_award_number	String	OCE-1642311
attribute	NC_GLOBAL	awards_1_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1642311
attribute	NC_GLOBAL	awards_1_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_1_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_1_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_1_program_manager	String	Michael E. Sieracki
attribute	NC_GLOBAL	awards_1_program_manager_nid	String	50446
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Symbiodinium Fv/Fm over a temperature gradient Fv/Fm for Clade A & B Symbiodinium with 2 temperature treatments measured over a range of temperatures PI: M. Medina (PSU) version: 2018-03-26
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	2018-04-04T19:41:57Z
attribute	NC_GLOBAL	date_modified	String	2019-12-11T16:16:16Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.732890.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/732890
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Fluorometer
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Used to measure fluorescence. Settings: default settings of the manufacturer with the following changes: Gain: 800; # of samples: 4; STF: 60 μs. See Exc profile,the reference excitation profile used by FIReView to normalize the variable fluorescence profile. See also: http://www.seabird.com/FIRe-System
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	732902
attribute	NC_GLOBAL	instruments_0_description	String	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.
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/113/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Fluorometer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	484
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Fluorescence Induction and Relaxation (FIRe) Fluorometer system and fibre optic probe (Satlantic, Halifax, Nova Scotia, Canada)
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, biological, chemical, data, dataset, dmo, erddap, Fv_Fm, management, oceanography, office, preliminary, replicate, species, strain, temperature, treatment
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/732890/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/732890
attribute	NC_GLOBAL	param_mapping	String	{'732890': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/732890/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Pennsylvania State University
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	PSU
attribute	NC_GLOBAL	people_0_person_name	String	Mónica Medina
attribute	NC_GLOBAL	people_0_person_nid	String	472486
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	Pennsylvania State University
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	PSU
attribute	NC_GLOBAL	people_1_person_name	String	Roberto Iglesias-Prieto
attribute	NC_GLOBAL	people_1_person_nid	String	717031
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	Emory University
attribute	NC_GLOBAL	people_2_person_name	String	Erika Díaz-Almeyda
attribute	NC_GLOBAL	people_2_person_nid	String	733106
attribute	NC_GLOBAL	people_2_role	String	Scientist
attribute	NC_GLOBAL	people_2_role_type	String	originator
attribute	NC_GLOBAL	people_3_affiliation	String	Pennsylvania State University
attribute	NC_GLOBAL	people_3_affiliation_acronym	String	PSU
attribute	NC_GLOBAL	people_3_person_name	String	Frederic Joseph Pollock
attribute	NC_GLOBAL	people_3_person_nid	String	733104
attribute	NC_GLOBAL	people_3_role	String	Scientist
attribute	NC_GLOBAL	people_3_role_type	String	originator
attribute	NC_GLOBAL	people_4_affiliation	String	Pennsylvania State University
attribute	NC_GLOBAL	people_4_affiliation_acronym	String	PSU
attribute	NC_GLOBAL	people_4_person_name	String	Joost Samir Mansour
attribute	NC_GLOBAL	people_4_person_nid	String	733100
attribute	NC_GLOBAL	people_4_role	String	Contact
attribute	NC_GLOBAL	people_4_role_type	String	related
attribute	NC_GLOBAL	people_5_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_5_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_5_person_name	String	Nancy Copley
attribute	NC_GLOBAL	people_5_person_nid	String	50396
attribute	NC_GLOBAL	people_5_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_5_role_type	String	related
attribute	NC_GLOBAL	project	String	GCMB,Varadero Reef
attribute	NC_GLOBAL	projects_0_acronym	String	GCMB
attribute	NC_GLOBAL	projects_0_description	String	Description from NSF award abstract: Coral reefs are among the most biologically diverse marine ecosystems on the planet, and provide substantial economic and ecological benefits to coastal communities. Corals are composed of both the Cnidarian animal host and complex communities of unique and underexplored microbial organisms. Today these natural wonders are in global decline, threatened by the intersecting effects of multiple stressors including overfishing, pollution, and climate change. These stressors can alter coral microbial communities in ways that may contribute to the susceptibility of corals to disease or overgrowth by algae. Therefore, understanding the relationships between corals and their microbiota may be useful for efforts to understand coral disease and preserve reef ecosystems. The microbial diversity of coral species in many diverse and ancient groups of corals remains unexplored, but understanding these communities will help to extend the knowledge gained in well-studied corals to diverse reefs worldwide. This project aims to describe microbial diversity across all major groups of reef-building corals in each of several distinct ecosystems across the globe, to determine the genome sequences and metabolic capabilities of key coral bacteria, and to test whether the composition of coral microbial communities helps to explain the overall vulnerability or resistance of different coral species to stress or disease.  Coral species differ in their susceptibility to bleaching and disease, but these differences are only partially explained by coral phylogeny. Therefore this project will test the extent to which incorporating the microbiota (or their contributed genes) better predicts these and other traits. Recent technological advances have broadened understanding of how complex microbiomes shape the life history, physiology, and evolution of their multicellular hosts (e.g., the human microbiome). The use of newly developed DNA sequencing techniques will allow a more complete exploration of microbial diversity in corals than has previously been feasible, while advanced computational methods will help to maximize the value of sequenced bacterial genomes. Improved predictive models that incorporate both coral phylogeny and microbial function will help inform conservation strategies and yield predictive biomarkers for coral vulnerability to disease or bleaching. Relating the diversity of corals to the diversity of their microbes will also provide important insights into how intimate symbiotic associations with microorganisms arose and are maintained in diverse animals.
attribute	NC_GLOBAL	projects_0_end_date	String	2018-08
attribute	NC_GLOBAL	projects_0_geolocation	String	Circumtropical
attribute	NC_GLOBAL	projects_0_name	String	Coevolution of scleractinian corals and their associated microorganisms
attribute	NC_GLOBAL	projects_0_project_nid	String	551037
attribute	NC_GLOBAL	projects_0_project_website	String	http://oregonstate.edu/microbiology/vegathurberlab/global-coral-microbiome-project
attribute	NC_GLOBAL	projects_0_start_date	String	2014-09
attribute	NC_GLOBAL	projects_1_acronym	String	Varadero Reef
attribute	NC_GLOBAL	projects_1_description	String	NSF Award Abstract: Coral reefs provide invaluable services to coastal communities, but coral populations worldwide are in a state of unprecedented decline. Studying resilient reefs is of primary importance for coral conservation and restoration efforts. A unique natural experiment in coral resilience to stress has been playing out in Cartagena Bay, Colombia since the Spanish conquistadors diverted the Magadalena River into the Bay in 1582. Varadero Reef at the southern mouth of the Bay has survived centuries of environmental insults and changing conditions with up to 80% coral cover. This reef provides an ideal system to test biological robustness theory. Given that Varadero is a highly perturbed system, we hypothesize that while likely more robust to perturbation than nearby pristine reefs, it will be less physiologically efficient. Some of the large star coral colonies (Orbicella faveolata) at this site have existed since before the construction of the Canal del Dique. These coral specimens contain invaluable information regarding the conditions of the Magdalena River wathershed and its construction in the XIV century. Changes in turbidity of the plume associated with the urban industrial and agricultural development of Colombia can be documented as variations in calcification rates and changes in the microstructure of the skeleton. The Colombian government has announced the approval for the construction of a shipping channel that will go right over this reef, with the goal to start dredging as early as Fall 2016 or early 2017. The RAPID funding mechanism would enable immediate collection of data and information of why this reef has survived centuries of environmental stress that can shed light on what genotype combinations of coral and its microbial constituents will fare better in similar conditions at other reef locations around the world. Coral reef conservation biology will benefit from this study by generating data for the development of stress diagnostic tools to identify resilient corals. This project will help broaden participation in science by training a diverse cohort of students to work effectively in the global arena while fostering productive collaborations with several Colombian researchers and educational institutions. Students will also gain cultural empathy and sensitivity through direct engagement with the members of society who are most directly impacted by coral reef degradation (e.g. fishermen). Student researchers from Penn State University will work alongside their Colombian counterparts to develop a series of bilingual blog posts to record the cultural and scientific aspects of this project's research expeditions. The blog postings will be submitted for wide dissemination to the Smithsonian's Ocean Portal where Penn State students have published in the past. An educational coral kit developed by the Medina Lab and extensively tested in schools in the US has been translated into Spanish and will be used in local schools in Cartagena and vicinities. All expedition data and metadata will be incorporated into the Global Coral Microbiome Project's interactive web portal, a responsive outreach tool allows researchers, students and/or teachers to access a wealth of information about every coral colony we sample and to virtually explore coral reefs around the world from any internet-enabled device. This research will generate information to understand functional traits related to symbioses stability under different perturbation regimes. Comparative analyses of microbiome modifications generated during the reciprocal transplantation will allow us to document possible differential responses of the holobionts to acute and chronic stressors relative to corals not exposed to significant levels of perturbation. The development of local bio-optical models of coral calcification and the characterization of the coral holobiont will permit the distinction between the effects in calcification attributed to local turbidity from those that can be ;attributed to differences in host genotype and/or microbial community composition and function. The information recorded in coral skeletons can be used to reconstruct the rates of agricultural, industrial and urban development of Colombia through the last 5 centuries as changes in the turbidity of the effluent of the Magdalena River.
attribute	NC_GLOBAL	projects_1_end_date	String	2018-06
attribute	NC_GLOBAL	projects_1_geolocation	String	Caribbean Sea (10°18’10”N, 75°34’ 55”W)
attribute	NC_GLOBAL	projects_1_name	String	RAPID: Coral robustness: lessons from an "improbable" reef
attribute	NC_GLOBAL	projects_1_project_nid	String	717028
attribute	NC_GLOBAL	projects_1_start_date	String	2016-07
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	summary	String	Coral photosynthetic endosymbionts (Symbiodinium) are phylogenetically very diverse, yet the extent of inter- and intraspecific functional variation within clades remains largely underexplored. Understanding this variability will be critical for future research on climate change mediated responses. A properly functioning thylakoid membrane is essential for optimal photosynthetic performance both in free-living and in hospite conditions. Here we analyze the thylakoid membrane melting points of 13 Symbiodinium strains from species in Clades B and A, grown at both control (26 \u00b0C) and high temperature (31 \u00b0C). We observed a broad range of responses to thermal stress regardless of taxonomic rank. Our results support and augment a growing body of literature demonstrating that functional differences among Symbiodinium spp. are as distinct at lower taxonomic levels (i.e. interspecific) as they are among major clades. These findings highlight the importance of assessing the variability of plastid traits across the Symbiodinium tree.
attribute	NC_GLOBAL	title	String	[Symbiodinium Fv/Fm over a temperature gradient] - Fv/Fm for cultured Clade A & B Symbiodinium with 2 treatments measured over a range of temperatures (Coevolution of scleractinian corals and their associated microorganisms)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	Strain		String
attribute	Strain	bcodmo_name	String	taxon
attribute	Strain	description	String	Symbiodinium strain
attribute	Strain	long_name	String	Strain
attribute	Strain	units	String	unitless
variable	Species		String
attribute	Species	bcodmo_name	String	species
attribute	Species	description	String	Symbiodinium species
attribute	Species	long_name	String	Species
attribute	Species	units	String	unitless
variable	Treatment		byte
attribute	Treatment	_FillValue	byte	127
attribute	Treatment	actual_range	byte	26, 31
attribute	Treatment	bcodmo_name	String	treatment
attribute	Treatment	description	String	relevant treatment (see methods): 26 = control temperature; 31 = high temperature treatment
attribute	Treatment	long_name	String	Treatment
attribute	Treatment	units	String	unitless
variable	Replicate		String
attribute	Replicate	bcodmo_name	String	replicate
attribute	Replicate	description	String	experimental repetition identifier
attribute	Replicate	long_name	String	Replicate
attribute	Replicate	units	String	unitless
variable	Temperature		float
attribute	Temperature	_FillValue	float	NaN
attribute	Temperature	actual_range	float	26.0, 46.2
attribute	Temperature	bcodmo_name	String	temperature
attribute	Temperature	description	String	measurement temperature
attribute	Temperature	long_name	String	Temperature
attribute	Temperature	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/
attribute	Temperature	units	String	degrees Celsius
variable	Fv_Fm		float
attribute	Fv_Fm	_FillValue	float	NaN
attribute	Fv_Fm	actual_range	float	-0.9, 0.397
attribute	Fv_Fm	bcodmo_name	String	Fv2Fm
attribute	Fv_Fm	description	String	Max photochemical quantum efficiency
attribute	Fv_Fm	long_name	String	FV FM
attribute	Fv_Fm	units	String	dimensionless

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.