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
attribute NC_GLOBAL acquisition_description String Symbiodinium culture preparation: Cultures were obtained from the LaJeunesse\nalgal collection at Penn State University. Phylogenetic relationships of these\nstrains are described in Parkinson et al., (2015). Symbiodinium cultures were\ngrown and maintained in liquid media (ASPA-8A, Blank, 1987) at 26 \\u02daC with\nfluorescent lights delivering 80-100 \\u03bcmol quanta m-2 s-1 (measured using\na DIVING-PAM equipped with a flat cosine-corrected Fiber Quantum Sensor, Walz,\nGermany) on a 12:12 hours Light:Dark photoperiod in Innovator 44 incubators\n(New Brunswick, USA). Symbiodinium cultures of equal starting concentration (3\nx 104 cells 126 mL-1) for each strain were grown for 7.5 days at 26 \\u02daC at\nlogarithmic growth phase prior to experimentation. After 7.5 days of\nincubation at 26 \\u02daC, one culture of each strain was subjected to a high\ntemperature treatment of 31 \\u02daC for two light cycles and one dark cycle\n(i.e., 1.5 d), whilst another was maintained at 26 \\u02daC.\n \nData collection:\\u00a0100 \\u03bcL aliquots (8.33 x 104 cells mL-1, calculated\nas the average of twelve independent hemocytometer measurements) of dark-\nadapted cultures were then subjected to 5 minutes of elevated temperatures in\na thermocycler (Eppendorf Mastercycler Pro S).\n \nChlorophyll fluorescence parameters were measured immediately after the 5 min\ntemperature exposure using a Fluorometer (see below). Measurements were\nperformed at 25 temperatures (i.e. 26, 30.3, 30.5, 31, 31.7, 32.6, 33.7, 34.8,\n35.9, 36.8, 37.6, 38.1, 38.3, 38.8, 38.9, 39.4, 40.1, 41,42, 43, 44, 44.9,\n45.6, 46.1, 46.2 \\u02daC) and replicated three times per Symbiodinium strain\nper treatment. A modified protocol by D\\u00edaz-Almeyda et al., 2011 was used.\n \nFv/Fm was automatically calculated/determined by fitting each fluorescence\ntransient to the bio-physical model of Kolber et al. (1998) using the FIREPRO\nsoftware (Satlantic, Version 1.4.3) integrated with the FIRe system.\n \nReference excitation profile used by FIReView to normalize the variable\nfluorescence profile: [EXCFOP.TXT](\\\\\"https://datadocs.bco-\ndmo.org/docs/medina/Varadero_Reef/data_docs/732890/1/EXCFOP.TXT\\\\\")  \n Column 1: incremental sample counter  \n Column 2: elapsed time measured in microSeconds (uS)  \n Column 3: reference excitation profile  \n Column 4: relative fluorescence profile normalized to the reference\nexcitation, or the fluorescence yield  \n Calibration date: 1/ 1/2002  \n Time (in seconds) of day reading was taken =\\u00a079931\n \nMethodology Reference:  \n D\\u00edaz-Almeyda, E., Thom\\u00e9, P. E., Hafidi, M. El, and Iglesias-\nPrieto, R. (2011). Differential stability of photosynthetic membranes and\nfatty acid composition at elevated temperature in Symbiodinium. Coral Reefs,\n30(1), 217\\u2013225.\n[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 (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 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 (external link)
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 \n     Fv/Fm for Clade A & B Symbiodinium with 2 temperature treatments measured over a range of temperatures \n   PI: M. Medina (PSU) \n   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/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3  19 Dec 2019
attribute NC_GLOBAL date_created String 2018-04-04T19:41:57Z
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 (external link)
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.\nSee 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/ (external link)
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 (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/732890 (external link)
attribute NC_GLOBAL param_mapping String {'732890': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/732890/parameters (external link)
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:\nCoral 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. \nCoral 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 (external link)
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:\nCoral 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.\nThis 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/ (external link)
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

 
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